 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 30, 2019 |
| Title |
MEF1 |
| Sample type |
SRA |
| |
|
| Source name |
MEF
|
| Organism |
Mus musculus |
| Characteristics |
cell type: MEF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with Trizol Lysis Reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy Micro kit (Qiagen) per manufacturer's instructions. The RNA integrity (RNA Integrity Score >= 7) and quantity determined on the Agilent 2100 Bioanalyzer (Agilent; Palo Alto, CA, USA) per manufacturer's recommendation and subjected to Illumina library prep for RNAseq.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mm10 genome using Bowtie version 2.1.0.0 (Phred 33)
Count files generated using HTSeq: http://bioinformatics.oxfordjournals.org/content/31/2/166 and EdgeR: Empirical analysis of digital gene expression data in R, see http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample
|
| |
|
| Submission date |
Mar 20, 2015 |
| Last update date |
Jun 30, 2019 |
| Contact name |
Paul A Wilson |
| E-mail(s) |
paul.a.wilson@gsk.com
|
| Organization name |
GSK
|
| Department |
Target Sciences
|
| Lab |
Computational Biology
|
| Street address |
GlaxoSmithKline Medicine Research Centre
|
| City |
Stevenage |
| State/province |
Hertfordshire |
| ZIP/Postal code |
SG1 2NY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE67117 |
Identifying signals from the skeletal muscle niche that regulate satellite cell function |
|
| Relations |
| BioSample |
SAMN03435918 |
| SRA |
SRX962816 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
