^DATABASE = GeoMiame
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
!Database_email = geo@ncbi.nlm.nih.gov
^SERIES = GSE99001
!Series_title = MBD1 activates neuronal developmental genes through modulating chromatin structure during neuronal maturation
!Series_geo_accession = GSE99001
!Series_status = Public on May 15 2018
!Series_submission_date = May 17 2017
!Series_last_update_date = May 15 2019
!Series_summary = This SuperSeries is composed of the SubSeries listed below.
!Series_overall_design = Refer to individual Series
!Series_type = Expression profiling by high throughput sequencing
!Series_type = Genome binding/occupancy profiling by high throughput sequencing
!Series_sample_id = GSM2629483
!Series_sample_id = GSM2629484
!Series_sample_id = GSM2629485
!Series_sample_id = GSM2629486
!Series_sample_id = GSM2629854
!Series_sample_id = GSM2629855
!Series_sample_id = GSM2629856
!Series_sample_id = GSM2629857
!Series_contact_name = Xinyu,,Zhao
!Series_contact_email = xinyu.zhao@wisc.edu
!Series_contact_department = Department of Neuroscience
!Series_contact_institute = University of Wisconsin-Madison
!Series_contact_address = 1500 HIGHLAND AVE, T513 Waisman Center
!Series_contact_city = Madison
!Series_contact_state = WI
!Series_contact_zip/postal_code = 53705
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE99nnn/GSE99001/suppl/GSE99001_RAW.tar
!Series_platform_id = GPL13112
!Series_platform_taxid = 10090
!Series_sample_taxid = 10090
!Series_relation = SuperSeries of: GSE98975
!Series_relation = SuperSeries of: GSE99000
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA386939
^PLATFORM = GPL13112
!Platform_title = Illumina HiSeq 2000 (Mus musculus)
!Platform_geo_accession = GPL13112
!Platform_status = Public on Feb 02 2011
!Platform_submission_date = Feb 02 2011
!Platform_last_update_date = Mar 19 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Mus musculus
!Platform_taxid = 10090
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM2629483
!Sample_title = Mbd1-ChIPSeq 1 (ChIP-Seq)
!Sample_geo_accession = GSM2629483
!Sample_status = Public on May 15 2018
!Sample_submission_date = May 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Dentate gyrus
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: dentate gyrus
!Sample_characteristics_ch1 = strain: C57BL6
!Sample_characteristics_ch1 = chip antibody: anti-FLAG (Sigma, catalog# F1804)
!Sample_growth_protocol_ch1 = All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for ChIP-Seq
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
!Sample_extract_protocol_ch1 = Samples that met the Illumina sample input guidelines were prepared according the TruSeq¨ ChIP Sample Preparation kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were size selected for an average size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip and Qubit¨ dsDNA HS Assay Kit, respectively.   Libraries were standardized to 2_M.  Cluster generation was performed using standard Cluster Kits (v3) and the Illumina Cluster Station.  Single 100bp sequencing was performed, using standard SBS chemistry (v3) on an Illumina HiSeq2000 sequencer.  Images were analyzed using the standard Illumina Pipeline, version 1.8.2.
!Sample_description = FLAG tagged-Mbd1 mouse line
!Sample_data_processing = ChIP and input samples were aligned with bowtie (version 0.12.7) under the parameter setting (-k 1 -m 1 --best --strata –sam).
!Sample_data_processing = Peaks were called with R package mosaics (version 2.9.8, using the hmm mode) (Chung et al., 2014; Kuan et al., 2011) with parameters binSize=200, capping=0 for each replicate (Rep1 and Rep2) against their matched input controls at a false discovery rate of 0.2
!Sample_data_processing = The average fragment length parameters were computed using strand cross-correlation and set as 290, 270, 295, and 280 bps for Rep 1 ChIP and input and Rep2 ChIP and input samples, respectively. The rest of the mosaics parameters were set to their default values.
!Sample_data_processing = We also generated a pooled sample (Rep0) by simply concatenating the reads from the two replicates and called peaks for the combined sample under the same setting. The three peak sets were consolidated by taking the intersection of Rep1 and Rep2 peaks and intersecting these with the Rep0 peaks. The final peak boundaries for the intersection peaks were taken from Rep0 peaks.
!Sample_data_processing = We used logMinP >= -log10(0.05) and aveLog2Ratio >= log2(1.5) from the mosaics output to require minimum posterior probability of enrichment within a peak to be at least 0.95 and average normalized ChIP to input fold-change to be at least 1.5.
!Sample_data_processing = Genome_build: mm9
!Sample_data_processing = Supplementary_files_format_and_content: Peak file in text format
!Sample_platform_id = GPL13112
!Sample_contact_name = Xinyu,,Zhao
!Sample_contact_email = xinyu.zhao@wisc.edu
!Sample_contact_department = Department of Neuroscience
!Sample_contact_institute = University of Wisconsin-Madison
!Sample_contact_address = 1500 HIGHLAND AVE, T513 Waisman Center
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53705
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = ChIP-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07134894
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2830131
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE98975
!Sample_series_id = GSE99001
!Sample_data_row_count = 0
^SAMPLE = GSM2629484
!Sample_title = Input DNA 1 (ChIP-Seq)
!Sample_geo_accession = GSM2629484
!Sample_status = Public on May 15 2018
!Sample_submission_date = May 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Dentate gyrus
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: dentate gyrus
!Sample_characteristics_ch1 = strain: C57BL6
!Sample_characteristics_ch1 = chip antibody: none
!Sample_growth_protocol_ch1 = All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for ChIP-Seq
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
!Sample_extract_protocol_ch1 = Samples that met the Illumina sample input guidelines were prepared according the TruSeq¨ ChIP Sample Preparation kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were size selected for an average size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip and Qubit¨ dsDNA HS Assay Kit, respectively.   Libraries were standardized to 2_M.  Cluster generation was performed using standard Cluster Kits (v3) and the Illumina Cluster Station.  Single 100bp sequencing was performed, using standard SBS chemistry (v3) on an Illumina HiSeq2000 sequencer.  Images were analyzed using the standard Illumina Pipeline, version 1.8.2.
!Sample_description = FLAG tagged-Mbd1 mouse line
!Sample_data_processing = ChIP and input samples were aligned with bowtie (version 0.12.7) under the parameter setting (-k 1 -m 1 --best --strata –sam).
!Sample_data_processing = Peaks were called with R package mosaics (version 2.9.8, using the hmm mode) (Chung et al., 2014; Kuan et al., 2011) with parameters binSize=200, capping=0 for each replicate (Rep1 and Rep2) against their matched input controls at a false discovery rate of 0.2
!Sample_data_processing = The average fragment length parameters were computed using strand cross-correlation and set as 290, 270, 295, and 280 bps for Rep 1 ChIP and input and Rep2 ChIP and input samples, respectively. The rest of the mosaics parameters were set to their default values.
!Sample_data_processing = We also generated a pooled sample (Rep0) by simply concatenating the reads from the two replicates and called peaks for the combined sample under the same setting. The three peak sets were consolidated by taking the intersection of Rep1 and Rep2 peaks and intersecting these with the Rep0 peaks. The final peak boundaries for the intersection peaks were taken from Rep0 peaks.
!Sample_data_processing = We used logMinP >= -log10(0.05) and aveLog2Ratio >= log2(1.5) from the mosaics output to require minimum posterior probability of enrichment within a peak to be at least 0.95 and average normalized ChIP to input fold-change to be at least 1.5.
!Sample_data_processing = Genome_build: mm9
!Sample_data_processing = Supplementary_files_format_and_content: Peak file in text format
!Sample_platform_id = GPL13112
!Sample_contact_name = Xinyu,,Zhao
!Sample_contact_email = xinyu.zhao@wisc.edu
!Sample_contact_department = Department of Neuroscience
!Sample_contact_institute = University of Wisconsin-Madison
!Sample_contact_address = 1500 HIGHLAND AVE, T513 Waisman Center
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53705
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = ChIP-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07134897
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2830132
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE98975
!Sample_series_id = GSE99001
!Sample_data_row_count = 0
^SAMPLE = GSM2629485
!Sample_title = Mbd1-ChIPSeq 2 (ChIP-Seq)
!Sample_geo_accession = GSM2629485
!Sample_status = Public on May 15 2018
!Sample_submission_date = May 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Dentate gyrus
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: dentate gyrus
!Sample_characteristics_ch1 = strain: C57BL6
!Sample_characteristics_ch1 = chip antibody: anti-FLAG (Sigma, catalog# F1804)
!Sample_growth_protocol_ch1 = All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for ChIP-Seq
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
!Sample_extract_protocol_ch1 = Samples that met the Illumina sample input guidelines were prepared according the TruSeq¨ ChIP Sample Preparation kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were size selected for an average size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip and Qubit¨ dsDNA HS Assay Kit, respectively.   Libraries were standardized to 2_M.  Cluster generation was performed using standard Cluster Kits (v3) and the Illumina Cluster Station.  Single 100bp sequencing was performed, using standard SBS chemistry (v3) on an Illumina HiSeq2000 sequencer.  Images were analyzed using the standard Illumina Pipeline, version 1.8.2.
!Sample_description = FLAG tagged-Mbd1 mouse line
!Sample_data_processing = ChIP and input samples were aligned with bowtie (version 0.12.7) under the parameter setting (-k 1 -m 1 --best --strata –sam).
!Sample_data_processing = Peaks were called with R package mosaics (version 2.9.8, using the hmm mode) (Chung et al., 2014; Kuan et al., 2011) with parameters binSize=200, capping=0 for each replicate (Rep1 and Rep2) against their matched input controls at a false discovery rate of 0.2
!Sample_data_processing = The average fragment length parameters were computed using strand cross-correlation and set as 290, 270, 295, and 280 bps for Rep 1 ChIP and input and Rep2 ChIP and input samples, respectively. The rest of the mosaics parameters were set to their default values.
!Sample_data_processing = We also generated a pooled sample (Rep0) by simply concatenating the reads from the two replicates and called peaks for the combined sample under the same setting. The three peak sets were consolidated by taking the intersection of Rep1 and Rep2 peaks and intersecting these with the Rep0 peaks. The final peak boundaries for the intersection peaks were taken from Rep0 peaks.
!Sample_data_processing = We used logMinP >= -log10(0.05) and aveLog2Ratio >= log2(1.5) from the mosaics output to require minimum posterior probability of enrichment within a peak to be at least 0.95 and average normalized ChIP to input fold-change to be at least 1.5.
!Sample_data_processing = Genome_build: mm9
!Sample_data_processing = Supplementary_files_format_and_content: Peak file in text format
!Sample_platform_id = GPL13112
!Sample_contact_name = Xinyu,,Zhao
!Sample_contact_email = xinyu.zhao@wisc.edu
!Sample_contact_department = Department of Neuroscience
!Sample_contact_institute = University of Wisconsin-Madison
!Sample_contact_address = 1500 HIGHLAND AVE, T513 Waisman Center
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53705
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = ChIP-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07134896
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2830133
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE98975
!Sample_series_id = GSE99001
!Sample_data_row_count = 0
^SAMPLE = GSM2629486
!Sample_title = Input DNA 2 (ChIP-Seq)
!Sample_geo_accession = GSM2629486
!Sample_status = Public on May 15 2018
!Sample_submission_date = May 16 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Dentate gyrus
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: dentate gyrus
!Sample_characteristics_ch1 = strain: C57BL6
!Sample_characteristics_ch1 = chip antibody: none
!Sample_growth_protocol_ch1 = All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for ChIP-Seq
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
!Sample_extract_protocol_ch1 = Samples that met the Illumina sample input guidelines were prepared according the TruSeq¨ ChIP Sample Preparation kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were size selected for an average size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip and Qubit¨ dsDNA HS Assay Kit, respectively.   Libraries were standardized to 2_M.  Cluster generation was performed using standard Cluster Kits (v3) and the Illumina Cluster Station.  Single 100bp sequencing was performed, using standard SBS chemistry (v3) on an Illumina HiSeq2000 sequencer.  Images were analyzed using the standard Illumina Pipeline, version 1.8.2.
!Sample_description = FLAG tagged-Mbd1 mouse line
!Sample_data_processing = ChIP and input samples were aligned with bowtie (version 0.12.7) under the parameter setting (-k 1 -m 1 --best --strata –sam).
!Sample_data_processing = Peaks were called with R package mosaics (version 2.9.8, using the hmm mode) (Chung et al., 2014; Kuan et al., 2011) with parameters binSize=200, capping=0 for each replicate (Rep1 and Rep2) against their matched input controls at a false discovery rate of 0.2
!Sample_data_processing = The average fragment length parameters were computed using strand cross-correlation and set as 290, 270, 295, and 280 bps for Rep 1 ChIP and input and Rep2 ChIP and input samples, respectively. The rest of the mosaics parameters were set to their default values.
!Sample_data_processing = We also generated a pooled sample (Rep0) by simply concatenating the reads from the two replicates and called peaks for the combined sample under the same setting. The three peak sets were consolidated by taking the intersection of Rep1 and Rep2 peaks and intersecting these with the Rep0 peaks. The final peak boundaries for the intersection peaks were taken from Rep0 peaks.
!Sample_data_processing = We used logMinP >= -log10(0.05) and aveLog2Ratio >= log2(1.5) from the mosaics output to require minimum posterior probability of enrichment within a peak to be at least 0.95 and average normalized ChIP to input fold-change to be at least 1.5.
!Sample_data_processing = Genome_build: mm9
!Sample_data_processing = Supplementary_files_format_and_content: Peak file in text format
!Sample_platform_id = GPL13112
!Sample_contact_name = Xinyu,,Zhao
!Sample_contact_email = xinyu.zhao@wisc.edu
!Sample_contact_department = Department of Neuroscience
!Sample_contact_institute = University of Wisconsin-Madison
!Sample_contact_address = 1500 HIGHLAND AVE, T513 Waisman Center
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53705
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = ChIP-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07134895
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2830134
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE98975
!Sample_series_id = GSE99001
!Sample_data_row_count = 0
^SAMPLE = GSM2629854
!Sample_title = WT 1 (FAIRE-Seq)
!Sample_geo_accession = GSM2629854
!Sample_status = Public on May 15 2018
!Sample_submission_date = May 17 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = WT
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: dentate gyrus
!Sample_characteristics_ch1 = strain: C57BL6
!Sample_characteristics_ch1 = genotype/variation: Mbd1 KO
!Sample_growth_protocol_ch1 = All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for Faire-Seq
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = The fixed dentate gyri from  were sonicated and then preceded to phenol chloroform extraction and the top layer was transferred to a new tube. TE buffer was then added to the old tube, followed by one more phenol chloroform extraction. The top layer was transferred and combined with the saved top layer, the combined top layers were then followed by two more rounds of phenol chloroform extraction. The purified DNA is FAIRE-seq DNA.
!Sample_extract_protocol_ch1 = The FAIRE-seq libraries were constructed using Nugen Ovation ultralow system V2 Kit according to its manual. Single 50bp sequencing was performed, using an Illumina HiSeq2000 sequencer.
!Sample_description = UWBC_Zhao_1
!Sample_data_processing = Reads were aligned to the mm9 genome with bowtie using the following command: bowtie -S -p 8 -v 2 -m 4 mm9 UWBC_Zhao_1_L000_R1_001.fastq UWBC_Zhao_1_L000_R1_001.sam
!Sample_data_processing = SAM files were converted to BAM files using the following command: samtools view -bS UWBC_Zhao_1_L000_R1_001.sam > UWBC_Zhao_1_L000_R1_001.bam
!Sample_data_processing = BAM files were sorted using the following command: samtools sort UWBC_Zhao_1_L000_R1_001.bam > UWBC_Zhao_1_L000_R1_001.sorted.bam
!Sample_data_processing = BAM file indices were generated using the following command: samtools index UWBC_Zhao_1_L000_R1_001.sorted.bam
!Sample_data_processing = MACS2 was used to call peaks using the following command: macs2 callpeak -t UWBC_Zhao_1_L000_R1_001.sorted.bam -n sample1 -f BAM -g mm
!Sample_data_processing = Genome_build: Pre-built mm9 indices were downloaded from the Johns Hopkins University's Center for Computational Biology (ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/)
!Sample_data_processing = Supplementary_files_format_and_content: The summit BED files contain genomic coordinates of FAIRE-seq peak summits.
!Sample_platform_id = GPL13112
!Sample_contact_name = Xinyu,,Zhao
!Sample_contact_email = xinyu.zhao@wisc.edu
!Sample_contact_department = Department of Neuroscience
!Sample_contact_institute = University of Wisconsin-Madison
!Sample_contact_address = 1500 HIGHLAND AVE, T513 Waisman Center
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53705
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = FAIRE-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07136281
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2831010
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2629nnn/GSM2629854/suppl/GSM2629854_sample1_summits.bed.gz
!Sample_series_id = GSE99000
!Sample_series_id = GSE99001
!Sample_data_row_count = 0
^SAMPLE = GSM2629855
!Sample_title = WT 2 (FAIRE-Seq)
!Sample_geo_accession = GSM2629855
!Sample_status = Public on May 15 2018
!Sample_submission_date = May 17 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = WT
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: dentate gyrus
!Sample_characteristics_ch1 = strain: C57BL6
!Sample_characteristics_ch1 = genotype/variation: WT
!Sample_growth_protocol_ch1 = All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for Faire-Seq
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = The fixed dentate gyri from  were sonicated and then preceded to phenol chloroform extraction and the top layer was transferred to a new tube. TE buffer was then added to the old tube, followed by one more phenol chloroform extraction. The top layer was transferred and combined with the saved top layer, the combined top layers were then followed by two more rounds of phenol chloroform extraction. The purified DNA is FAIRE-seq DNA.
!Sample_extract_protocol_ch1 = The FAIRE-seq libraries were constructed using Nugen Ovation ultralow system V2 Kit according to its manual. Single 50bp sequencing was performed, using an Illumina HiSeq2000 sequencer.
!Sample_description = UWBC_Zhao_2
!Sample_data_processing = Reads were aligned to the mm9 genome with bowtie using the following command: bowtie -S -p 8 -v 2 -m 4 mm9 UWBC_Zhao_1_L000_R1_001.fastq UWBC_Zhao_1_L000_R1_001.sam
!Sample_data_processing = SAM files were converted to BAM files using the following command: samtools view -bS UWBC_Zhao_1_L000_R1_001.sam > UWBC_Zhao_1_L000_R1_001.bam
!Sample_data_processing = BAM files were sorted using the following command: samtools sort UWBC_Zhao_1_L000_R1_001.bam > UWBC_Zhao_1_L000_R1_001.sorted.bam
!Sample_data_processing = BAM file indices were generated using the following command: samtools index UWBC_Zhao_1_L000_R1_001.sorted.bam
!Sample_data_processing = MACS2 was used to call peaks using the following command: macs2 callpeak -t UWBC_Zhao_1_L000_R1_001.sorted.bam -n sample1 -f BAM -g mm
!Sample_data_processing = Genome_build: Pre-built mm9 indices were downloaded from the Johns Hopkins University's Center for Computational Biology (ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/)
!Sample_data_processing = Supplementary_files_format_and_content: The summit BED files contain genomic coordinates of FAIRE-seq peak summits.
!Sample_platform_id = GPL13112
!Sample_contact_name = Xinyu,,Zhao
!Sample_contact_email = xinyu.zhao@wisc.edu
!Sample_contact_department = Department of Neuroscience
!Sample_contact_institute = University of Wisconsin-Madison
!Sample_contact_address = 1500 HIGHLAND AVE, T513 Waisman Center
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53705
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = FAIRE-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07136284
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2831011
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2629nnn/GSM2629855/suppl/GSM2629855_sample2_summits.bed.gz
!Sample_series_id = GSE99000
!Sample_series_id = GSE99001
!Sample_data_row_count = 0
^SAMPLE = GSM2629856
!Sample_title = Mbd1 KO 1 (FAIRE-Seq)
!Sample_geo_accession = GSM2629856
!Sample_status = Public on May 15 2018
!Sample_submission_date = May 17 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Mbd1 KO
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: dentate gyrus
!Sample_characteristics_ch1 = strain: C57BL6
!Sample_characteristics_ch1 = genotype/variation: Mbd1 KO
!Sample_growth_protocol_ch1 = All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for Faire-Seq
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = The fixed dentate gyri from  were sonicated and then preceded to phenol chloroform extraction and the top layer was transferred to a new tube. TE buffer was then added to the old tube, followed by one more phenol chloroform extraction. The top layer was transferred and combined with the saved top layer, the combined top layers were then followed by two more rounds of phenol chloroform extraction. The purified DNA is FAIRE-seq DNA.
!Sample_extract_protocol_ch1 = The FAIRE-seq libraries were constructed using Nugen Ovation ultralow system V2 Kit according to its manual. Single 50bp sequencing was performed, using an Illumina HiSeq2000 sequencer.
!Sample_description = UWBC_Zhao_3
!Sample_data_processing = Reads were aligned to the mm9 genome with bowtie using the following command: bowtie -S -p 8 -v 2 -m 4 mm9 UWBC_Zhao_1_L000_R1_001.fastq UWBC_Zhao_1_L000_R1_001.sam
!Sample_data_processing = SAM files were converted to BAM files using the following command: samtools view -bS UWBC_Zhao_1_L000_R1_001.sam > UWBC_Zhao_1_L000_R1_001.bam
!Sample_data_processing = BAM files were sorted using the following command: samtools sort UWBC_Zhao_1_L000_R1_001.bam > UWBC_Zhao_1_L000_R1_001.sorted.bam
!Sample_data_processing = BAM file indices were generated using the following command: samtools index UWBC_Zhao_1_L000_R1_001.sorted.bam
!Sample_data_processing = MACS2 was used to call peaks using the following command: macs2 callpeak -t UWBC_Zhao_1_L000_R1_001.sorted.bam -n sample1 -f BAM -g mm
!Sample_data_processing = Genome_build: Pre-built mm9 indices were downloaded from the Johns Hopkins University's Center for Computational Biology (ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/)
!Sample_data_processing = Supplementary_files_format_and_content: The summit BED files contain genomic coordinates of FAIRE-seq peak summits.
!Sample_platform_id = GPL13112
!Sample_contact_name = Xinyu,,Zhao
!Sample_contact_email = xinyu.zhao@wisc.edu
!Sample_contact_department = Department of Neuroscience
!Sample_contact_institute = University of Wisconsin-Madison
!Sample_contact_address = 1500 HIGHLAND AVE, T513 Waisman Center
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53705
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = FAIRE-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07136283
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2831012
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2629nnn/GSM2629856/suppl/GSM2629856_sample3_summits.bed.gz
!Sample_series_id = GSE99000
!Sample_series_id = GSE99001
!Sample_data_row_count = 0
^SAMPLE = GSM2629857
!Sample_title = Mbd1 KO 2 (FAIRE-Seq)
!Sample_geo_accession = GSM2629857
!Sample_status = Public on May 15 2018
!Sample_submission_date = May 17 2017
!Sample_last_update_date = May 15 2019
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Mbd1 KO
!Sample_organism_ch1 = Mus musculus
!Sample_taxid_ch1 = 10090
!Sample_characteristics_ch1 = tissue: dentate gyrus
!Sample_characteristics_ch1 = strain: C57BL6
!Sample_characteristics_ch1 = genotype/variation: WT
!Sample_growth_protocol_ch1 = All animal procedures were performed according to protocols approved by the University of Wisconsin-Madison Care and Use Committee. Mice were group housed up to 5 per cage with the same gender and maintained on a 12-h light/dark cycle with food and water available ad libitum. mice around 9 weeks old were used for Faire-Seq
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = The fixed dentate gyri from  were sonicated and then preceded to phenol chloroform extraction and the top layer was transferred to a new tube. TE buffer was then added to the old tube, followed by one more phenol chloroform extraction. The top layer was transferred and combined with the saved top layer, the combined top layers were then followed by two more rounds of phenol chloroform extraction. The purified DNA is FAIRE-seq DNA.
!Sample_extract_protocol_ch1 = The FAIRE-seq libraries were constructed using Nugen Ovation ultralow system V2 Kit according to its manual. Single 50bp sequencing was performed, using an Illumina HiSeq2000 sequencer.
!Sample_description = UWBC_Zhao_4
!Sample_data_processing = Reads were aligned to the mm9 genome with bowtie using the following command: bowtie -S -p 8 -v 2 -m 4 mm9 UWBC_Zhao_1_L000_R1_001.fastq UWBC_Zhao_1_L000_R1_001.sam
!Sample_data_processing = SAM files were converted to BAM files using the following command: samtools view -bS UWBC_Zhao_1_L000_R1_001.sam > UWBC_Zhao_1_L000_R1_001.bam
!Sample_data_processing = BAM files were sorted using the following command: samtools sort UWBC_Zhao_1_L000_R1_001.bam > UWBC_Zhao_1_L000_R1_001.sorted.bam
!Sample_data_processing = BAM file indices were generated using the following command: samtools index UWBC_Zhao_1_L000_R1_001.sorted.bam
!Sample_data_processing = MACS2 was used to call peaks using the following command: macs2 callpeak -t UWBC_Zhao_1_L000_R1_001.sorted.bam -n sample1 -f BAM -g mm
!Sample_data_processing = Genome_build: Pre-built mm9 indices were downloaded from the Johns Hopkins University's Center for Computational Biology (ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/)
!Sample_data_processing = Supplementary_files_format_and_content: The summit BED files contain genomic coordinates of FAIRE-seq peak summits.
!Sample_platform_id = GPL13112
!Sample_contact_name = Xinyu,,Zhao
!Sample_contact_email = xinyu.zhao@wisc.edu
!Sample_contact_department = Department of Neuroscience
!Sample_contact_institute = University of Wisconsin-Madison
!Sample_contact_address = 1500 HIGHLAND AVE, T513 Waisman Center
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53705
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = FAIRE-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07136282
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2831013
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2629nnn/GSM2629857/suppl/GSM2629857_sample4_summits.bed.gz
!Sample_series_id = GSE99000
!Sample_series_id = GSE99001
!Sample_data_row_count = 0