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Sample GSM1967865 Query DataSets for GSM1967865
Status Public on Jun 03, 2016
Title 4sU-Seq rep1
Sample type SRA
 
Source name K562 cells
Organism Homo sapiens
Characteristics passage: 3-5
cell line: K562
Treatment protocol Cells were labeled in media for 5 min with 500 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 2 min at 3,000 rpm.
Growth protocol K562 cells were acquired from DSMZ (Braunschweig, Germany). Cells were grown in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated FBS (Gibco) and 1% Penicillin/Streptomycin (100x, PAA) at 37°C under 5% CO2
Extracted molecule total RNA
Extraction protocol RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Dolken et al., RNA, 2008.
fragmentation: no
NuGEN Human Whole Blood RNA-Seq System
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Sequencing data processing. Paired-end 50 base reads with additional 6 base reads of barcodes were obtained for each of the samples, i.e. total RNA (RNA-Seq), total fragmented RNA (RNA-Frag-Seq), labeled RNA (4sU-Seq), labeled fragmented RNA (TT-Seq) and ChIP-Seq samples (N20 and S2P). Reads were demultiplexed and mapped with STAR 2.3.0 (for RNA-Seq) (Dobin and Gingeras, Current protocols in bioinformatics, 2015) and Bowtie 2.1.0. (Langmead and Salzberg, Nat Methods, 2012) (for ChIP-Seq) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li et al., Bioinformatics, 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further processing of the RNA-Seq data was carried out using the R/Bioconductor environment. For visualization purposes piled-up read counts for every genomic position were summed up over replicates, size factors for each condition were calculated as described in (Anders and Huber, Genome Biol, 2010) and used to correct for library size and sequencing depth variations.
Genome_build: hg20/hg38 (GRCh38)
Supplementary_files_format_and_content: The file binned_count_table.txt gives the fragment counts for all experiments using the binning_anno.txt annotation file
Supplementary_files_format_and_content: The Series file README.txt includes information about the contents of the processed data files.
 
Submission date Dec 08, 2015
Last update date May 15, 2019
Contact name Björn Schwalb
E-mail(s) bschwal@gwdg.de
Organization name MPI
Street address Fassberg 11
City Göttingen
ZIP/Postal code 37077
Country Germany
 
Platform ID GPL18460
Series (1)
GSE75792 TT-Seq captures the human transient transcriptome
Relations
BioSample SAMN04325065
SRA SRX1470564

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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