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Sample GSM4218633 Query DataSets for GSM4218633
Status Public on Jun 23, 2020
Title Abhd11 KO(P3)-1
Sample type SRA
Source name mESC
Organism Mus musculus
Characteristics cell type: mESC
passage: passage 3
phenotype: Abhd11 knock-out
Treatment protocol Control and Abhd11 KO ESCs were cultured in the absence of Doxycycline; Abhd11 RES ESCs were cultured in the presence of 1ng/ml Dox; Abhd11 OE ESCs were cultured in the presence of 1000ng/ml Dox.
Growth protocol murine ESCs were on 0.2% gelatin-coated plates in ESC maintenance medium containing high glucose Dulbecco-modified Eagle medium (DMEM), 5% fetal bovine serum (FBS), 15% KnockOut Serum Replacement (KSR), 2mM Glutamax, 1mM sodium pyruvate, 0.1mM  NEAA, 0.1mM b-mercaptoethanol, 100U/ml penicillin, 100U/ml streptomycin (all from Invitrogen) and 10ng/ml LIF (Millipore) at 37°C under 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol Reagent(Invitrogen,Cat:15596026) and a miRNeasy Micro Kit (QIAGEN,Cat:217084) according the manufacturer's manual. The RNA quality were measured using Agilent 4200 TapeStation.
RNA samples were send to Genminix Informatic Ltd. (Shanghai, China) for mRNA sequencing on Illumina Hiseq platform (Illumina, San Diego, California, USA) with 6Gbps.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Description Abhd11 KO ESCs cultured in the absence of Doxycyline (passage 3)
Data processing Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2(version:2.0.4).
Strings (version: 1.3.0) were used to count the number of Fragments for each gene after Hisat2 alignment, and then normalized by DESeq2 method. Finally, the count reads value of each gene was calculated.
Genome_build: mm10(GRCm38)
Submission date Dec 16, 2019
Last update date Jun 26, 2020
Contact name Rui Jian
Phone +8613627696789
Organization name Third Military Medical University
Department Department of Histology and Embryology
Lab Laboratory of Stem Cell and Developmental Biology
Street address Gaotanyan Street
City Chongqing
ZIP/Postal code 400038
Country China
Platform ID GPL21273
Series (1)
GSE142067 Gene expression of Abhd11 knock-out or over-expression embryonic stem cells
BioSample SAMN13569009
SRA SRX7376190

Supplementary file Size Download File type/resource
GSM4218633_L_A316_dox_6D_181203.csv.gz 275.2 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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