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Sample GSM4664589 Query DataSets for GSM4664589
Status Public on Dec 08, 2020
Title SETDB1_KO_chromRNA_Input_rep1
Sample type SRA
Source name Embryonic stem cells
Organism Mus musculus
Characteristics cell type: Embryonic stem cells
genotype: SETDB1 KO
Growth protocol E14Tg2a murine embryonic stem cells (mES) were cultured in Dulbecco’ s Modified Eagle’ s Medium (DMEM) supplemented with 10% fetal bovine serum (FBSGibco #16000-044), 1% MEM non-essential amino acid (Gibco #11140), 55 mM β-Mercaptoethanol (Gibco#21985-023), 100 U/mL Penicillin/Streptomycin (Hyclone #SV30010), 1000 units/mL LIF (Millipore #ESG1107,) and MEK inhibitor PD0325901 (1μM) and GSK3β inhibitor CH99021 (3μM) at 37℃ with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNAs were isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instruction.
Strand specific total RNA library preparation was performed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420S).
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model HiSeq X Ten
Data processing Raw reads were aligned to the mm10 genome using TopHat (v2.1.1) with parameter “--max-multihits 1”.
PCR duplicates were removed using samtools (v1.7) rmdup.
Strand specific reads were separated by samtools (v1.7) view with specific flags 99, 147, 83, 163.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage bigwig files
Submission date Jul 09, 2020
Last update date Dec 08, 2020
Contact name Yang Shi
Organization name Fudan university
Street address NO. 138, Yi-Xue-Yuan Road
City Shanghai
ZIP/Postal code 200032
Country China
Platform ID GPL21273
Series (2)
GSE126243 RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs
GSE154138 RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (MeRIP-Seq)
BioSample SAMN15497057
SRA SRX8701315

Supplementary file Size Download File type/resource 104.0 Mb (ftp)(http) BW 109.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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