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Sample GSM3900860 Query DataSets for GSM3900860
Status Public on Feb 01, 2021
Title HeLa_polyA_siWdr82_rep1
Sample type SRA
Source name polyA-RNAseq HeLa siWdr82 rep 1
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: human cervix, epitheloid carcinoma
treatment: siWdr82
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 siWdr82 rep 1
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 ( 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)
Supplementary_files_format_and_content: Strand specific tracks (bigWig)
Submission date Jun 21, 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)
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]
BioSample SAMN12107300
SRA SRX6102510

Supplementary file Size Download File type/resource 98.5 Mb (ftp)(http) BW 93.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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