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| Status |
Public on May 10, 2017 |
| Title |
NT2D1p39 POLR3G ChIP rep2 |
| Sample type |
SRA |
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| Source name |
Embryonal carcinoma stem cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: NT2D1
passages: p39
genotype: 46 XY +complex
chip antibody: anti-POLR3G (SZ3070, Prof. Nouria Hernandez)
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| Growth protocol |
hESC (S1-13): mTeSR1+matrigel, NT2D1 (S14-16): DMEM+15%FCS
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| 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.
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| Submission date |
Feb 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Riikka Lund |
| Organization name |
Turku Centre for Biotechnology, University of Turku
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| Street address |
Tykistökatu 6
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| City |
Turku |
| ZIP/Postal code |
FI-20520 |
| Country |
Finland |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE94696 |
POLR3G Dependent PolyA+ and smallRNA Transcriptomes in Human Pluripotent Stem Cells |
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| Relations |
| BioSample |
SAMN06313009 |
| SRA |
SRX2546087 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2481045_POL_rep2_LowEnrichment_NT2D1p39_MACS.bed.gz |
22.5 Kb |
(ftp)(http) |
BED |
| GSM2481045_POL_rep2_LowEnrichment_NT2D1p39_Wig_BedGraph-to-bigWig.bigwig |
474.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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