|
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 |