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Sample GSM3755485 Query DataSets for GSM3755485
Status Public on Dec 20, 2019
Title Marmoset_WhiteMatter_RNAseq_1
Sample type SRA
 
Source name Marmoset White Matter
Organism Callithrix jacchus
Characteristics tissue: White Matter
Extracted molecule total RNA
Extraction protocol TruSeq Stranded mRNA Library Preparation (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
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;
 
Submission date May 08, 2019
Last update date Dec 20, 2019
Contact name Menno P Creyghton
E-mail(s) m.creyghton@hubrecht.eu
Organization name Hubrecht Institute
Lab Creyghton
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
 
Platform ID GPL26636
Series (1)
GSE130871 Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients
Relations
BioSample SAMN11604030
SRA SRX5806029

Supplementary file Size Download File type/resource
GSM3755485_Marmoset_WhiteMatter_1_RNAseq.txt.gz 142.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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