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Sample GSM4204646 Query DataSets for GSM4204646
Status Public on May 31, 2021
Title ERT2-Cre_Pcgf1_Mutant_EB_rep3
Sample type SRA
Source name EB
Organism Mus musculus
Characteristics tamoxifen treatment: with 4-OHT
genotype: ERT2-Cre;Pcgf1delta/delta
cell type: embryoid body
replicate: 3
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 HiSeq 1500
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
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 GPL18480
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
BioSample SAMN13482335
SRA SRX7268384

Supplementary file Size Download File type/resource
GSM4204646_Pcgf1_Mutant_EB_rep3_tpm.tsv.gz 236.6 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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