|
Status |
Public on Feb 22, 2018 |
Title |
M27H4 Esrp2-as overexpression, biological rep1 |
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: Esrp2-as overexpression
|
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-oe1 processed data column: AS-143051-LR-20284
|
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 |
SAMN06603875 |
SRA |
SRX2642133 |