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| Status |
Public on Dec 20, 2019 |
| Title |
Marmoset_PrefrontalCortex_H3K4me3_2 |
| Sample type |
SRA |
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| Source name |
Marmoset Prefrontal Cortex
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| Organism |
Callithrix jacchus |
| Characteristics |
chip antibody: anti-H3K4me3 (Abcam, catalog#: ab8580)
tissue: Prefrontal Cortex
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
TruSeq DNA sample preparation kit (Illumina)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
RNA-seq: Sequencing reads were aligned using HISAT2 version 2.0.5. Reads that mapped to multiple locations and duplicate reads were removed using Samtools version 1.3.1. Reads in genes were counted using the featureCount function of the Rsubread package in R. The GTF file of Marmoset genes was obtained here: ftp://ftp.ensembl.org/pub/release-91/gtf/callithrix_jacchus.
Genome_build: Homo sapiens: hg38, Pan troglodytes: panTro5, Macaca mulatta: rheMac8, Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac bigwig files are in .bw; RNA-seq count values are in _RNAseq.txt;
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| Submission date |
May 08, 2019 |
| Last update date |
Dec 20, 2019 |
| Contact name |
Menno P Creyghton |
| E-mail(s) |
m.creyghton@hubrecht.eu
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| Organization name |
Hubrecht Institute
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| Lab |
Creyghton
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL17712 |
| Series (1) |
| GSE130871 |
Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients |
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| Relations |
| BioSample |
SAMN11604040 |
| SRA |
SRX5806019 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3755475_Marmoset_PrefrontalCortex_H3K4me3_2_calJac3.bw |
127.1 Mb |
(ftp)(http) |
BW |
| GSM3755475_Marmoset_PrefrontalCortex_H3K4me3_2_peaks.narrowPeak.gz |
678.4 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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