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Sample GSM3900161 Query DataSets for GSM3900161
Status Public on Feb 01, 2021
Title HeLa_4sU_siZc3h4_rep1
Sample type SRA
 
Source name 4sU-RNAseq HeLa siZc3h4 rep 1
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: human cervix, epitheloid carcinoma
treatment: siZc3h4
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 siZc3h4 rep 1
Data processing After quality filtering according to the Illumina pipeline and after checking reads quality using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), 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) https://www.gencodegenes.org/human/release_33.html
Supplementary_files_format_and_content: Strand specific tracks (bigWig)
 
Submission date Jun 20, 2019
Last update date Feb 02, 2021
Contact name Viviana Piccolo
E-mail(s) viviana.piccolo@ieo.it
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
Relations
BioSample SAMN12100450
SRA SRX6099332

Supplementary file Size Download File type/resource
GSM3900161_HeLa_4sU_siZc3h4_hg38_SID101761_RID102947_R1.FORW.bw 121.5 Mb (ftp)(http) BW
GSM3900161_HeLa_4sU_siZc3h4_hg38_SID101761_RID102947_R1.REV.bw 113.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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