|
| Status |
Public on May 27, 2016 |
| Title |
Control rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
HDF-a_Control
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Adult Dermal Fibroblasts (HDF-a)
transfected with: empty control vector
|
| Biomaterial provider |
sciencell (#2320)
|
| Growth protocol |
All cells were grown at 37oC in a 5% CO2 humidified incubator on poly-l-lysine coated plastic in Fibroblast Medium (Sciencell #2301)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a RNeasy Mini Kit following the manufactures instructions with the addition of an on-column DNAse treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq; each library split across two lanes HiSeq4000, 15 half-libraries per lane
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Libraries for all samples were combined in a 15 samples multiplex which were then split across two lanes.
|
| Data processing |
Reads for each sample were combined and aligned to the reference hg38 genome using the STAR genome aligner with default commands with the addition of --outFilterMultimapNmax 15 --outSAMstrandField intronMotif
Raw read counts for refseq annotated genes were generated using featurecounts using gene annotations from GRCh38.p2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including default output from featurecounts
|
| |
|
| Submission date |
Apr 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Dunwell |
| Organization name |
University of Oxford
|
| Department |
Zoology
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3PS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE80282 |
Evolutionary origin and functional divergence of stem cell homeobox genes in eutherian mammals |
|
| Relations |
| BioSample |
SAMN04859246 |
| SRA |
SRX1704915 |
