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Sample GSM4889429 Query DataSets for GSM4889429
Status Public on Mar 22, 2021
Title HEPG2_siI1_3
Sample type SRA
Source name liver cancer derived cell line
Organism Homo sapiens
Characteristics cell line: HepG2
sirna: siRNA pool against IGF2BP1
passages: harvested 72h upon transfection
Treatment protocol 72 hours upon transfection cells were harvested for RNA extraction.
Growth protocol HepG2 cells were cultured in DMEM supplemented with 10% FBS. BE(2)-C cells were cultured in EMEM:DMEM/F12 (1:1) medium supplemented with 10% FBS. Cells were grown at 37°C in 5% CO2.
Extracted molecule polyA RNA
Extraction protocol RNA extraction was performed using TRIZOL according to manufacturer's protocol.
Poly-A RNA was enriched using oligo(dT) beads. RNAs are fragmented randomly by adding fragmentation buffer. cDNA is synthesized by using random hexamers primer followed by second strand synthesis. Strand-specific double-stranded cDNA libraries are completed by size selection (250-300bp) and PCR enrichment.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description DE_HEPG2_C_vs_I1_all.csv
Data processing Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 --trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.30.3) using TMM normalization and FPKM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including FPKM, log2 fold change and false discovery rate values for each sample
Submission date Nov 09, 2020
Last update date Mar 22, 2021
Contact name Markus Glaß
Organization name Martin Luther University Halle-Wittenberg
Department Institute of Molecular Medicine
Lab Huettelmaier Lab
Street address Kurt-Mothes-Str. 3a
City Halle
ZIP/Postal code 06120
Country Germany
Platform ID GPL24676
Series (2)
GSE161086 IGF2BP1, a conserved regulator of RNA turnover in cancer [polyA RNA]
GSE161101 IGF2BP1, a conserved regulator of RNA turnover in cancer
BioSample SAMN16709222
SRA SRX9461496

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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