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Sample GSM2718944 Query DataSets for GSM2718944
Status Public on Dec 01, 2017
Title control_mESC_serum_1_lane4
Sample type SRA
 
Source name mESC_Serum
Organism Mus musculus
Characteristics culture condition: Serum
strain/cell type: J1 mESC
treatment: none
Treatment protocol Dnmt1 tet/tet mESCs (R1 strain) were treated with 10µM EPZ6438 for 9 days prior to harvesting.
Growth protocol Dnmt1 tet/tet mESCs (R1 strain) were cultured in DMEM supplemented with 15% foetal calf serum, 0.1mM non-essential amino acids, 1mM sodium pyruvate, 1% penicillin/streptomycin, 2mM L-glutamine, 0.1mM beta-mercaptoethanol and LIF at 1000U/mL. mESCS were passaged every 2-3 days with trypsin/EDTA and plated on 0.2% gelatin coated flasks.
Extracted molecule total RNA
Extraction protocol RNA extracted usisng RNeasy kit (Qiagen). For RNA quantification, samples were treated with DNase (Ambion) and random hexamer cDNA synthesized by reverse transcription. Assays-on-demand gene expression TaqMan® MGB 6FAM dye-labeled products (Applied Biosystems) were used for relative quantification of cDNA.
Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out on a NextSeq-550 sequencer
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Description HM06.coverage.bedGraph.gz
Data processing Paired ends aligned using FASTQ paired-end parser
Quality control and Tophat 2 Alignment
General sequence statistics calculated
Genome_build: mm9
Supplementary_files_format_and_content: .bw
 
Submission date Jul 26, 2017
Last update date May 15, 2019
Contact name J Thomson
E-mail(s) s0236078@googlemail.com
Organization name University of Edinburgh
Department IGMM
Street address Crewe Road
City Edinburgh
ZIP/Postal code Eh4 2XU
Country United Kingdom
 
Platform ID GPL21626
Series (1)
GSE101928 RNAseq analysis between mouse ESCs cultured in serum or plus the EZH2 inhibitor EPZ.
Relations
BioSample SAMN07418348
SRA SRX3040600

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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