|
| Status |
Public on May 01, 2020 |
| Title |
ESC(Ctrl)1 biological replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
passage: p 5-8
strain: 129/BL6 F1
developmental potential: normal
|
| Treatment protocol |
none
|
| Growth protocol |
ESCs were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs) in standard ESC medium (DMEM (Invitrogen) with 15% FCS (PAN Biotech), 4mM GlutaMax (Gibco), 1X non essential amino acids (Gibco), 20 mM Hepes buffer (Gibco), 0.1 mM b-mercaptoethanol (Gibco), 1.5x103 U/ml LIF (Millipore) in a 37°C humidified incubator with 5% CO2. When 70-80% confluent, the cells were passaged.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Mini Kit
Library preparation was performed using the Illumina TruSeqHT kit according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Datasets for each sample were concatenated into a single file
Reads were trimmed using Fastx Trimmer by 8 and 4 bases at the start and end of each read respectively to improve quality
TopHat2 Galaxy Version 0.9 with default settings was used to align reads to the mouse genome (bam files)
Reads that mapped uniquely were used for downstream analysis. htseq-count Version 0.6.1galaxy1 was applied to count the number of reads mapping to each gene. Intersection-strict mode was chosen to exclude reads that overlap more than one gene or reads that do not intersect a given gene with each read position. The Gencode release M7 was used to annotate the genome.
Normalization of read counts and differential expression analysis was subsequently performed with DESeq2 Galaxy Version 2.1.8.3 (default parameters).
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 output
|
| |
|
| Submission date |
Apr 30, 2020 |
| Last update date |
May 01, 2020 |
| Contact name |
William Henry Colledge |
| E-mail(s) |
whc23@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Street address |
Dowing Street
|
| City |
CAMBRIDGE |
| ZIP/Postal code |
CB2 3EG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE149628 |
Hypermethylation and reduced expression of Gtl2, Rian and Mirg at the Dlk1-Dio3 imprinted locus as a marker for poor developmental potential of mouse embryonic stem cells |
|
| Relations |
| BioSample |
SAMN14776815 |
| SRA |
SRX8213364 |
