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Sample GSM2481043 Query DataSets for GSM2481043
Status Public on May 10, 2017
Title NT2D1p37 H3K4me3 ChIP rep1
Sample type SRA
Source name Embryonal carcinoma stem cells
Organism Homo sapiens
Characteristics cell type: NT2D1
passages: p37
genotype: 46 XY +complex
chip antibody: anti-H3K4me3 (C15410003, Diagenode)
Growth protocol hESC (S1-13): mTeSR1+matrigel, NT2D1 (S14-16): DMEM+15%FCS
Extracted molecule genomic DNA
Extraction protocol Qiagen all prep for smallRNA (S7-13) and mRNA (S1-6), ChIP-DNA (S14-18): Qiagen MinElute PCR Purification Kit
smallRNA-seq (S7-13): Illumina TruSeq smallRNA, mRNA-seq (S1-6): Illumina TruSeq mRNA, ChIP-seq (S14-18): Diagenode Microplex Library Preparation kit v2
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
Data processing SmallRNA reads were trimmed using trim_galore to remove primer sequences, low-quality bases from read ends, and to discard trimmed reads < 18bp. The reads were then mapped to hg19 reference transcriptome (with tRNAs) using tophat2 (v2.0.13) with default parameters. PolyA+ reads were mapped to hg19 transcriptome using tophat2 (v2.0.13) with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by using the total exon length of the isoform with the longest total exon length and normalizing by this length and sequencing depth (according to the number of uniquely mapped reads obtained from htseq). For smallRNA-seq, genes with length > 250bp were excluded.
ChIP-seq data: reads with average quality below 20 were removed and reads with length 20-50 bp were retained with Trimmomatic 0.32, the reads were mapped to hg19 genome with Bowtie2 2.2.6 and non-unique reads were discarded, the ChIP peaks were called with MACS 1.0.1. with default parameters, except arbitrary shift size of 100 bp was used instead of shifting model and p-value cut off was 1.00E-04 for POL peak detection.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample in RNA-seq data or RPM in smallRNA-seq data, in ChIP-seq data the bigwig files contain the enrichment intensities and bed files the peaks with p-value =<0.0001.
Submission date Feb 08, 2017
Last update date May 15, 2019
Contact name Riikka Lund
Organization name Turku Centre for Biotechnology, University of Turku
Street address Tykistökatu 6
City Turku
ZIP/Postal code FI-20520
Country Finland
Platform ID GPL21290
Series (1)
GSE94696 POLR3G Dependent PolyA+ and smallRNA Transcriptomes in Human Pluripotent Stem Cells
BioSample SAMN06313013
SRA SRX2546085

Supplementary file Size Download File type/resource
GSM2481043_H3K4me3_rep1_NT2D1p37_MACS.bed.gz 366.3 Kb (ftp)(http) BED
GSM2481043_H3K4me3_rep1_NT2D1p37_Wig_BedGraph-to-bigWig.bigwig 159.4 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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