|
| Status |
Public on Jan 05, 2017 |
| Title |
Rnf40_WT_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Rnf40+/+
passages: 3
|
| Treatment protocol |
For RNF40 knockout, MEFs were passaged into GlutaMAX™-DMEM supplemented with 250nM of 4-hydroxitamoxifen (4-OHT) for 5 days, and then cultured for 3 days without 4-OHT.
|
| Growth protocol |
Primary MEFs were cultured in high-glucose GlutaMAX™-DMEM (Invitrogen) supplemented with 10% FBS Superior (Biochrom), 1% penicillin–streptomycin (Sigma-Aldrich), and 1% non-essential amino acids (Invitrogen) at 37°C, 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated using QIAzol Lysis Reagent (QIAGEN)
Libraries were prepared from 1 µg of total RNA using NEXTflex™ Rapid Directional RNA-Seq Kit according to the manufactures introduction (Bioo Scientific).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were mapped to mouse reference transcriptome (UCSC mm9) using bowtie 2 (version 2.1.0) with parameters --threads 11 --very-sensitive --omit-sec-seq
Read counts for each sample and each gene were aggregated using a custom Ruby script
DESeq (version 1.14.0) was used for measuring differential expression
Genome_build: mm9
Supplementary_files_format_and_content: The table includes gene normalized counts for each sample
|
| |
|
| Submission date |
Aug 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven A Johnsen |
| E-mail(s) |
steven.johnsen@med.uni-goettingen.de
|
| Organization name |
University Medical Center Göttingen
|
| Department |
Clinic for General, Visceral and Pediatric Surgery
|
| Lab |
AG Tumorepigenetics
|
| Street address |
Robert Koch Strasse 40
|
| City |
Göttingen, Niedersachsen |
| State/province |
Niedersachsen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE72238 |
Genome-wide H2B monoubiquitination regulates gene expression by coordinating H3K4me3 and H3K27me3 [RNA-Seq Data Set] |
| GSE72239 |
Genome-wide H2B monoubiquitination regulates gene expression by coordinating H3K4me3 and H3K27me3 |
|
| Relations |
| BioSample |
SAMN04003035 |
| SRA |
SRX1160459 |
