|
| Status |
Public on Oct 01, 2015 |
| Title |
473 - KO |
| Sample type |
SRA |
| |
|
| Source name |
mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
strain: C57BL/6
Sex: male
day: 4
clone: E3
genotype: Trim-/-
|
| Treatment protocol |
Trim71 conditional ("WT") cells were treated with 500 nM 4-OHT for 2 days to induce Trim71 mutation. Cells were further cultivated before cell harvest for at least 7 days to minimize indirect effects of the drug treatment.
|
| Growth protocol |
mES cells were cultivated in complete mES medium (FCS+LIF). Before analysis, harvested cells were subjected to SSEA-1 MACS sorting to correct for spontanious differentiation during culture. Two different mES cell clones were used in this study (with each WT and KO condition)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells lysed in TRIZOL (Invitrogen), and total RNA was extracted according to the manufactures’ protocol
Illumina TruSeq RNA Sample Preparation Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
base calling and de-multipexing using CASAVA version 1.8
Alignment withTopHat2 version v2.0.11 and Bowtie2 version 2.2.1 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on April 2014
Normalization using DeSeq2
Genome_build: mm10
|
| |
|
| Submission date |
Oct 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Joachim Schultze |
| E-mail(s) |
j.schultze@uni-bonn.de
|
| Organization name |
LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
|
| Department |
Genomics and Immunoregulation
|
| Street address |
Carl-Troll-Strasse 31
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE62398 |
mRNA sequencing of Trim71 conditional ("WT") and Trim71 KO mES cells |
|
| Relations |
| BioSample |
SAMN03112802 |
| SRA |
SRX734160 |
