GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1708034 Query DataSets for GSM1708034
Status Public on Jun 10, 2018
Title siRNF20-8Min-384-4sUDRBseq
Sample type SRA
Source name Human cervical carcinoma, HeLa cell
Organism Homo sapiens
Characteristics cell line: HeLa
time: 8 minutes
treatment: 3 h DRB, release - 8 min, 4sU -12 min
condition: siRNF20
replicate: 384
Treatment protocol Cells were treated with DRB for 3hr and harvested after DRB removal. Cells were also labeld with 4sU for 12 min before harvested.
Growth protocol HeLa cells were grown in DMEM supplemented with 10% bovine serum supplemented with antibiotics
Extracted molecule total RNA
Extraction protocol 4sU labled RNA was tagged with Biotion, and enriched with Streptavidin magnetic beads. cDNA libraries were prepared with Illumina TruSeq RNA sample preparation v2 kit according to the manufacturer's instructions but without the polyA isolation stage
4sUDRBseq: cDNA libraries were prepared with Illumina TruSeq RNA sample preparation v2 kit according to the manufacturer’s instructions but without the polyA isolation stage
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
Description Nascent RNA labled with 4sU
Data processing All reads were aligned to the human reference genome (hg19, GRCh37) using the bowtie 2 aligner with default parameters (only setting –N 1)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (bw) files contains aligned read for 4sUDRBseq with masked exons
Submission date Jun 10, 2015
Last update date May 15, 2019
Contact name Eran Rosenthal
Organization name Hebrew University
Department Computer Science
Lab Tommy Kaplan
Street address Givat Ram
City Jerusalem
ZIP/Postal code 91904
Country Israel
Platform ID GPL16791
Series (1)
GSE69738 Gene body H2B1ub regulates RNA Polymerase II pause release and is not needed for transcription elongation
BioSample SAMN03768428
SRA SRX1055095

Supplementary file Size Download File type/resource 26.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap