|
| Status |
Public on May 27, 2024 |
| Title |
E14tg2a, CtbpDKO_Dox_d0_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
E14tg2a
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14tg2a
cell type: Embryonic stem cells
genotype: CtbpDKO
time: d0
|
| Growth protocol |
E14tg2a cells were maintained in GMEM with 10%FBS and LIF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using a PureLinkTM RNA Mini Kit (Ambion, Inc.) Genomic DNAs were evtracted using Wizard® SV Genomic DNA Purification System 602 (Promega).
RNA-seq libraries were contructed using CollibriTM Stranded RNA library prep for ilIuminaTM Systems 582 (ThermoFisher Scientific). RRBS libraries were constructed using Premium RRBS kit V2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
iCt2_d0_1
iCt2_counts.txt
|
| Data processing |
(RNA-seq) Sequence reads were trimmed using trimgalore (R-package) with option (-q 20 -j 4)
(RNA-seq) Trimed fasq files were aligned by Hisat2 to mm10 genome with defaults setting.
(RNA-seq) Read counts were extracted using R package FeatureCounts using mm10 KnownGenes.
(RRBS) Sequence reads were trimmed using trimgalore (R-package) with option (--rrbs --non_directional --paired --length 15)
(RRBS) Trimed fasq files were aligned using bismark with option (-- pbat)
(RRBS) CpG methylation was extracted using bismark_methylation_extractor
Assembly: mm10
Supplementary files format and content: tab-delimited files (RNA-seq)
Supplementary files format and content: BedGraph (RRBS)
|
| |
|
| Submission date |
Jan 22, 2024 |
| Last update date |
May 27, 2024 |
| Contact name |
Yoshiyuki Seki |
| E-mail(s) |
yseki@kwansei.ac.jp
|
| Organization name |
Kwansei Gakuin University
|
| Department |
School of Biological and Environmental Sciences
|
| Street address |
1, Gakuen Uegahara
|
| City |
Sanda |
| State/province |
hyogo |
| ZIP/Postal code |
6691330 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE253944 |
The disruption of CtBP regulates DUX-dependent and -independent genetic program for the 2-cell-like state in murine embryonic stem cells [RNA-seq and RRBS] |
|
| Relations |
| BioSample |
SAMN39551568 |
| SRA |
SRX23354044 |
