|
| Status |
Public on Jun 25, 2017 |
| Title |
RNA-seq Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 6 |
| Sample type |
SRA |
| |
|
| Source name |
Primary Epidermal Keratinocyte - Differentiation Day 6
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary epidermal keratinocyte
differentiation state: Late differentiation (Day 6)
individual: Donor2
Sex: male
|
| Treatment protocol |
None
|
| Growth protocol |
Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiated for three or six days as previously described (Zarnegar et al., 2012)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were frozen at -80 C, and RNA was later purified using Qiagen RNeasy Mini Kit.
The TruSeq Stranded mRNA Library Prep Kit was used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 6
|
| Data processing |
Paired end RNA-seq reads were aligned to the Gencode V19 transcriptome in hg19 using STAR aligner version 2.4.1d with default settings.
RSEM version 1.2.21 was then used to calculate expected read counts per protein-coding gene.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file contains RSEM read count estimates for each Gencode V19 mRNA, in addition to transcription start site and transcription end site positions.
|
| |
|
| Submission date |
Jul 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul Khavari |
| Organization name |
Stanford University
|
| Street address |
269 Campus Drive, CCSR 2150
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE84661 |
Dynamic and stable enhancer-promoter contacts regulate terminal differentiation [RNA-Seq] |
| GSE84662 |
Dynamic and stable enhancer-promoter contacts regulate terminal differentiation |
|
| Relations |
| BioSample |
SAMN05425819 |
| SRA |
SRX1967843 |
