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Sample GSM4007611 Query DataSets for GSM4007611
Status Public on May 18, 2021
Title ESCs, Ss18-KO.8h.RNA-seq
Sample type SRA
 
Source name mouse embryonic stem cells (mESCs)
Organism Mus musculus
Characteristics cell type: OG2 transgenetic mouse embryonic stem cells (OG2ES)
strain: 1/2 129SVJ+3/8 C57B6+1/8 CBA
genotype: c-Jun_TetOn_Ss18-KO_mESC
treatment: treated with doxycycline for 8h
passage: P12
Treatment protocol Treated with 2µg/ml doxycycline
Growth protocol Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)
Extracted molecule total RNA
Extraction protocol TRIzol, according to the manufacturers instructions
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Ss18-KO&WT.RNA-seq.merge.csv
Data processing bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM13) transcriptome using Bowtie2 (v2.2.5) and RSEM (v1.3.0)
Gene expression level was calculated using EDASeq (v2.4.1) GC-normalized method
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated value file containing GC-normalized RNA-seq data
 
Submission date Aug 05, 2019
Last update date May 18, 2021
Contact name kuang junqi
E-mail(s) kuangjunqi@westlake.edu.cn
Organization name westlake University
Street address No.18 Shilongshan Road
City hangzhou
ZIP/Postal code 310024
Country China
 
Platform ID GPL19057
Series (2)
GSE135397 SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation [RNA-Seq]
GSE135451 SS18 is a phase-separation protein relocating from pluripotent to somatic loci during mESC differentiation
Relations
BioSample SAMN12497444
SRA SRX6657657

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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