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Sample GSM4889609 Query DataSets for GSM4889609
Status Public on Mar 22, 2021
Title BE2C_1
Sample type SRA
 
Source name neuroblastoma derived cell line
Organism Homo sapiens
Characteristics cell line: BE(2)C
sirna: parental cell line
passages: harvested 48h upon seeding
Treatment protocol A549, ES2, MV3, PANC1 and HepG2 cells were harvested for RNA extraction 48 hours upon seeding. BE(2)C cells were harvested 24 hours upon seeding for RNA extraction.
Growth protocol A549, ES2, MV3, PANC1 and 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 total RNA
Extraction protocol RNA extraction was performed using TRIZOL according to manufacturer's protocol.
For A549, ES2, MV3 and PANC1 cells, 50ng of total RNA served as input using the NEXTflex Small RNA Library Prep Kit v3 (Bioo Scientific). Small RNA-seq libraries for HepG2 and B(E)2C cells were prepared by Novogene (Hong Kong).
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 1500
 
Description BE2C_WT_miRNA_CPM.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 16
Trimmed reads were mapped against the human genome (hg38 UCSC) using Bowtie2 (v 2.3.2) with parameters -p 6 -N 1 --un-gz
alignments were sorted using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -1 -t miRNA -g ID and miRBase annotations (v 21, GRCh 38)
Gene expression was assessed using R/edgeR (v 3.30.3) using TMM normalization and CPM transformation
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file containing CPM values
 
Submission date Nov 09, 2020
Last update date Mar 22, 2021
Contact name Markus Glaß
E-mail(s) markus.glass@medizin.uni-halle.de
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 GPL18460
Series (2)
GSE161099 IGF2BP1, a conserved regulator of RNA turnover in cancer [miRNA-seq]
GSE161101 IGF2BP1, a conserved regulator of RNA turnover in cancer
Relations
BioSample SAMN16709480
SRA SRX9461674

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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