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Sample GSM4664594 Query DataSets for GSM4664594
Status Public on Dec 08, 2020
Title YTHDC1_KO_total_RNA_rep2
Sample type SRA
 
Source name Embryonic stem cells
Organism Mus musculus
Characteristics cell type: Embryonic stem cells
genotype: YTHDC1 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 RNA-Seq
Library source transcriptomic
Library selection cDNA
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
E-mail(s) yshi@hms.harvard.edu
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
GSE154139 RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (total RNA-Seq 2)
Relations
BioSample SAMN15497070
SRA SRX8701320

Supplementary file Size Download File type/resource
GSM4664594_YTHDC1_KO_total_RNA_rep2_neg.bw 85.2 Mb (ftp)(http) BW
GSM4664594_YTHDC1_KO_total_RNA_rep2_pos.bw 87.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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