|
| Status |
Public on Apr 01, 2019 |
| Title |
Control-2 |
| Sample type |
SRA |
| |
|
| Source name |
Neonatal foreskin
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary human epidermal keratinocytes
genotype/variation: shCTRL
passage: 7-10
|
| Treatment protocol |
Primary keratinocytes were infected with lentivirus expressing scramble control short hairpin RNA (shCTRL) or HOPX-targeting short hairpn RNA (shHOPX), selected with puromycin for two days, then differentiated for six days by plating keratinocytes in culture confluence in the presence of 1.2 mM calcium.
|
| Growth protocol |
Normal primary human keratinocytes were isolated from neonatal foreskins and cultured in a 50:50 mixture of 154 medium and KSFM medium (Life Technologies) with recommended manufacturer supplements, penicillin/streptomycin, and amphotericin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from shCTRL and shHOPX differentiated keratinocytes was extracted with Trizol reagent and purified using the Direct-zol RNA Miniprep Kit (Zymo Research, R2052).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Removal of adaptor sequences and low-quality reads
Read alignment using STAR (2.5.3a).
Quantification by Partek E/M annotation model onto hg19 - RefSeq Transcripts v87
Genome_build: hg19
Supplementary_files_format_and_content: Counts, ratio
|
| |
|
| Submission date |
Jan 16, 2019 |
| Last update date |
Apr 01, 2019 |
| Contact name |
Bryan Sun |
| E-mail(s) |
bryansun@ucsd.edu
|
| Organization name |
UC San Diego
|
| Street address |
9500 Gilman Drive MC 0869
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0869 |
| Country |
USA |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE125152 |
Whole transcriptome sequencing of HOPX-depleted neonatal human keratinocytes |
|
| Relations |
| BioSample |
SAMN10754791 |
| SRA |
SRX5254200 |
