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Sample GSM3594170 Query DataSets for GSM3594170
Status Public on Dec 08, 2020
Title rescue_WT_total_RNA_rep1
Sample type SRA
 
Source name Embryonic stem cells
Organism Mus musculus
Characteristics cell type: Embryonic stem cells
genotype: METTL3 KO+WT METTL3
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 Bowtie2 (v 2.2.5) with parameter “-k 1” to keep only one locus when a read mapped to multiple genomic regions.
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 Feb 07, 2019
Last update date Dec 10, 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)
GSE126242 RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs (total RNA-seq)
GSE126243 RNA m6A modification mediated by METTL3 is important for IAP heterochromatin integrity in mESCs
Relations
BioSample SAMN10884476
SRA SRX5347802

Supplementary file Size Download File type/resource
GSM3594170_rescue_WT_total_RNA_rep1_neg.bw 70.0 Mb (ftp)(http) BW
GSM3594170_rescue_WT_total_RNA_rep1_pos.bw 71.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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