|
| Status |
Public on Nov 10, 2021 |
| Title |
shCTR2 |
| Sample type |
SRA |
| |
|
| Source name |
epidermal progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: neonatal foreskin
cell type: primary keratinocytes
genotype: control
|
| Treatment protocol |
shCTR (non-targeting), shRACK1-A, shRACK1-J knockdown
|
| Growth protocol |
Epidermal progenitor cells were grown on culture dishes and maintained in keratinocyte Epilife medium plus HKGS (Life technologies)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using GeneJET RNA purification kit (Thermo Scientific)
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Illumina Nextseq2000 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using STAR.
Aligned reads were mapped to RefSeq and normalized using Partek Flow. Genes with reads less than 10 were excluded in every sample.
Statistics were calculated by ANOVA and differential genes was selected based on p-values <0.05 and with a >2 fold change (+/-).
Genome_build: hg19
Supplementary_files_format_and_content: txt file with normalized gene read counts
|
| |
|
| Submission date |
Aug 01, 2021 |
| Last update date |
Nov 10, 2021 |
| Contact name |
George Sen |
| E-mail(s) |
gsen@health.ucsd.edu
|
| Organization name |
University of Californai San diego
|
| Department |
Dermatology
|
| Lab |
George Sen
|
| Street address |
9452 Medical Center Dr
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE181265 |
RACK1 prevents premature differentiation of epidermal progenitors by inhibiting IRF6 expression |
|
| Relations |
| BioSample |
SAMN20514841 |
| SRA |
SRX11623463 |
