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Sample GSM2537110 Query DataSets for GSM2537110
Status Public on Feb 22, 2018
Title M27H4 empty vector empty vector control, biological rep2, technical replicate 2
Sample type SRA
 
Source name murine cell line derived from a mammary gland tumor of the C3(1)SV40 TAg mouse model
Organism Mus musculus
Characteristics cell line: M27H4
genotype/variation: empty vector control
Treatment protocol LNA antisense Gapmer-mediated knockdown of Esrp2-as in the M6 cell line, and overexpression of Esrp2-as in M27H4 and 3T3-L1 cell lines
Growth protocol DMEM +10% FCS in a humidified atmosphere at 5% CO2 and 37°C
Extracted molecule total RNA
Extraction protocol Total RNA isolation with RNeasy Mini Kit (Qiagen), ribodepletion with Ribo-Zero® Gold rRNA Removal Kit, purification with RNAeasy MinElute Kit (Qiagen)
SureSelect Strand-Specific Library Preparation Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description M27-vec2b
processed data column: AS-145087-LR-20283
Data processing adapter trimming with cutadapt
alignment with HISAT2 --rna-strandness RF, --max-intronlen 20000, --no-unal, --dta
transcript assembly with Stringtie -eB
calculate raw counts with Stringtie prepDE
calculate logcpm values with edgeR
Genome_build: mm10, GRCm38 assembly (release 85)
Supplementary_files_format_and_content: Raw count data in a comma-separated .csv file and cpm data in .txt file
 
Submission date Mar 15, 2017
Last update date May 15, 2019
Contact name Reka Toth
E-mail(s) r.toth@dkfz-heidelberg.de
Phone +496221424322
Organization name DKFZ
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL21103
Series (1)
GSE96641 Genome-wide Screen for Differentially Methylated Long Noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as Regulated by Enhancer DNA Methylation with Prognostic Relevance for Human Breast Cancer
Relations
BioSample SAMN06603890
SRA SRX2642139

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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