|
| Status |
Public on May 31, 2021 |
| Title |
ERT2-Cre_Pcgf6_Control_EB_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
EB
|
| Organism |
Mus musculus |
| Characteristics |
tamoxifen treatment: without 4-OHT
genotype: ERT2-Cre;Pcgf6f/f
cell type: embryoid body
replicate: 1
|
| Growth protocol |
Embryonic stem cells (ESCs) were cultured with LIF (1U: Laboratory made), SU5402 (Altair corporation), PD184352 (Altair corporation) and CHIR99021 (Altair corporation) on MEF. For Embryoid Body (EB) formation, ESCs were cultured without LIF, SU5402, PD184352, CHIR99021 for 2 days on low attach culture dish. For epiblast stem cell (EpiSC) establishment, Embryoid Body (day2) are dispersed. And the cells were cultured on MEF with ActivinA (Peprotech), bFGF (Wako) and IWP-2 (Wako) on MEF in F12 medium (Gibco) 1%KSR (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using simplyRNA Tissue Kit (Promega).
Sequencing libraries were generated according to NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing was performed with either 75 bp single-end read by NextSeq500 (run by Kazusa DNA Research Institute) or 50 bp single-end read by HiSeq1500 (run in RIKEN-IMS NGS facility).
The data were mapped onto UCSC-mm9 from illumina igenome and counted the reads on exon using STAR (version 2.5.2b: --outSAMtype BAM SortedByCoordinate), and the counted reads are normalized to TPM(Transcripts Per Million).
Each gene reads on exon were normalized by DESeq2 for fold change and p-value calculation.
Genome_build: mm9
Supplementary_files_format_and_content: tpm values
|
| |
|
| Submission date |
Dec 04, 2019 |
| Last update date |
May 31, 2021 |
| Contact name |
Hiroki Sugishita |
| E-mail(s) |
hiroki.sugishita@riken.jp
|
| Organization name |
RIKEN
|
| Department |
IMS
|
| Lab |
Laboratory for Developmental Genetics
|
| Street address |
1-7-22, Suehiro-cho
|
| City |
Tsurumi-ku,Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE141487 |
Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes [RNA-seq] |
| GSE141488 |
Variant PCGF1-PRC1 links PRC2 recruitment with induced transcriptional inactivation at target genes |
|
| Relations |
| BioSample |
SAMN13482352 |
| SRA |
SRX7268367 |
