|
Status |
Public on May 27, 2016 |
Title |
LEUTX rep 3 |
Sample type |
SRA |
|
|
Source name |
HDF-a_LEUTX
|
Organism |
Homo sapiens |
Characteristics |
cell type: Human Adult Dermal Fibroblasts (HDF-a) transfected with: LEUTX
|
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 |
SAMN04859256 |
SRA |
SRX1704925 |