GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3900163 Query DataSets for GSM3900163
Status Public on Feb 01, 2021
Title HeLa_4sU_siWdr82_rep2
Sample type SRA
Source name 4sU-RNAseq HeLa siWdr82 rep 2
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: human cervix, epitheloid carcinoma
treatment: siWdr82
Treatment protocol 4-thio-uridine was added to the medium at a final concentration of … for 45 min before harvesting the cells.
Growth protocol HeLa cells were cultured in DMEM containing 10% South American FBS, 1% L-Glutamax solution and 1% Pen/Strep solution.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol whereafter nascent 4sU-labelled RNA was extracted as described (Austenaa et al. 2015 )
Library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007) starting from ca. 100-300 ng of nascent 4sU-labelled RNA, without ribosomal depletion.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description 4sU-RNAseq HeLa siWdr82 rep 2
Data processing After quality filtering according to the Illumina pipeline and after checking reads quality using FastQC v0.11.2 (, strand specific single end reads (76 bp) were aligned using TopHat v2.1.0 1 (PMID:23618408), allowing up to two mismatches and using the option --b2-very- sensitive --library-type fr-firststrand. Indels due to sequencing errors were identified using Bowtie2 v 2.2.6 (PMID: 19261174). Reads originating from the two strands were separated according to the XS:A:+/XS:A:-flag provided by TopHat2 (PMID:23618408).
SICER v2 (PMID: 24743992) was used to detect the extra-genic transcripts regulated in cells depleted of individual factors. The entire genome was partitioned into blocks of non-overlapping 500 bp windows with a gap size <1000 nt. An effective genome fraction of 1, a fragment size of 0 and a False Discovery Rate (FDR) cut-off <0.01 were used.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v.3.1.3 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Genome_build: hg38 (GENCODE)
Supplementary_files_format_and_content: Strand specific tracks (bigWig)
Submission date Jun 20, 2019
Last update date Feb 02, 2021
Contact name Viviana Piccolo
Organization name European Institute of Oncology (IEO)
Department Department of Experimental Oncology
Lab Gioacchino Natoli Lab
Street address Via Adamello 16
City Milano
State/province Milano
ZIP/Postal code 20139
Country Italy
Platform ID GPL18573
Series (2)
GSE133107 A first exon termination checkpoint that preferentially suppresses extragenic transcription [RNASEQ_HELA_4sU]
GSE133109 A first exon termination checkpoint that preferentially suppresses extragenic transcription
BioSample SAMN12100448
SRA SRX6099334

Supplementary file Size Download File type/resource 94.5 Mb (ftp)(http) BW 90.4 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