|
| Status |
Public on Dec 31, 2022 |
| Title |
EtOH_Control_72h_RNASeq_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
parental esc line: E14
zbtb11 locus genotype: Zbtb11lox/lox
rosa26 locus genotype: ERt2-Cre
treatment: ethanol
|
| Treatment protocol |
To induce Zbtb11 KO, growth media was supplemented with 4-hydroxytamoxifen (4OHT) pre-slubilised in ethanol. 4OHT was added to a final concentration of 250nM from a 1000x stock solution. As control, Zbtb11lox/lox Rosa26ERt2-Cre were treated with the carrier ethanol, or Zbtb11WT/WT Rosa26WT were treated with 4OHT.
|
| Growth protocol |
Mouse embryonic stem cells were maintained in feeder-free conditions, on gelatin-coated plates, in KO DMEM supplemented with 10% foetal bovine serum, LIF, L-Glutamine, 2-mercaptoethanol, non-essential amino acids, penicillin and streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1μg total RNA was used as starting material for each library. rRNA was depleted using the NEBNext rRNA Depletion Kit (E6310, New England Biolabs)
Directional RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420, New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
total RNA (rRNA-depleted)
|
| Data processing |
ChIP-seq: Reads were trimmed and filtered using Cutadapt applying a Phred quality threshold of 25 and a minimal read length of 25 bases. Filtered reads were aligned to the mouse genome (NCBI37/mm9 assembly) with Bowtie 1.1.2 keeping only uniquely aligned reads while allowing a maximum of 2 mismatches (-v 2 -m 1). MACS2 was set to discard PCR/optical duplicates and was used as peak caller within the Irreproducibility Discovery Rate (IDR) pipeline implemented by the ENCODE consortium. The final set of peaks was considered the conservative set for IDR <0.02. From this set we removed blacklisted sites. Peak overlap analysis was carried out in R and normalised read coverage values were obtained using the DiffBind Bioconductor package.
RNA-seq: Bases with a Phred quality score lower than 25 were trimmed from read ends with Cutadapt, and polyA tails were removed using PRINSEQ. Filtered reads were aligned to the mouse transcriptome with STAR using 2-pass mapping, and gene-level counts were generated with HTSeq. Differential gene expression analysis was carried out using the Bioconductor package EdgeR.
Genome_build: mm9
|
| |
|
| Submission date |
Jan 14, 2019 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Vlad Cezar Seitan |
| E-mail(s) |
vlad.seitan@kcl.ac.uk
|
| Organization name |
King's College London
|
| Department |
Medical & Molecular Genetics
|
| Lab |
Seitan Lab
|
| Street address |
Guy's Hospital
|
| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE130292 |
The roles of Zbtb11 in embryonic stem cell proliferation and survival |
|
| Relations |
| BioSample |
SAMN10741410 |
| SRA |
SRX5770338 |
