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Sample GSM3900862 Query DataSets for GSM3900862
Status Public on Feb 01, 2021
Title HeLa_polyA_siCtl_rep2
Sample type SRA
 
Source name polyA-RNAseq HeLa siCtl rep 2
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: human cervix, epitheloid carcinoma
treatment: siCtl
Treatment protocol Cells were untreaded.
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 the Zymo kit with on-column DNAse digestion.
After oligodT-based selection of polyadenylated transcripts from 3-5 ug total RNA, library preparation was performed using the TruSeq Stranded Total RNA sample preparation kit (Illumina RS-122-9007).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description polyA-RNAseq HeLa siCtl rep 2
Data processing Strand specific paired end reads (76nt) were trimmed for removing the adapter sequence and discarding low quality bases using Trimmomatic v0.27 with PE option (PMID:24695404)
Read quality was then checked for each sample using FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High-quality reads were then aligned with TopHat2 v2.1.0 (–very-sensitive --library-type fr-firststrand -r 200 --segment-length 35 --microexon-search --no-mixed --no-discordant -g 1 --coverage-search) (PMID:23618408). Indels due to sequencing errors were identifies using Bowtie2 v.2.6 (PMID: 19261174).
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 21, 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)
GSE133109 A first exon termination checkpoint that preferentially suppresses extragenic transcription
GSE133139 A first exon termination checkpoint that preferentially suppresses extragenic transcription [RNASEQ_HELA_polyA]
Relations
BioSample SAMN12107298
SRA SRX6102512

Supplementary file Size Download File type/resource
GSM3900862_HeLa_polyA_siCtl_hg38_SID101769_RID102962_R2.FORW.bw 100.5 Mb (ftp)(http) BW
GSM3900862_HeLa_polyA_siCtl_hg38_SID101769_RID102962_R2.REV.bw 96.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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