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Sample GSM4872226 Query DataSets for GSM4872226
Status Public on Feb 01, 2021
Title HeLa_polyA_siZc3h4_rep3
Sample type SRA
Source name HeLa
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: human cervix, epitheloid carcinoma
treatment: siZc3h4
Treatment protocol Cells were left untreated.
Growth protocol HeLa cells were cultured in DMEM containing 10% South American origin Foetal Bovine Serum, 1% L-Glutamax solution and 1% PenicillinStreptomycin solution.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Zymo Quick-RNA Mini Prep kit (Cat no. R1055) 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 NovaSeq 6000
Description polyA-RNAseq HeLa siZc3h4 rep 3
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 Oct 28, 2020
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 GPL24676
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 SAMN16584291
SRA SRX9391085

Supplementary file Size Download File type/resource 133.2 Mb (ftp)(http) BW 127.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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