|
| Status |
Public on Dec 15, 2016 |
| Title |
Gata6 WT4 |
| Sample type |
SRA |
| |
|
| Source name |
epidermal keratinocytes
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT (K14CreERT2-;Gata6 fl/fl)
treatment: tamoxifen 6 hours
passage: 8-10
|
| Treatment protocol |
Passage 8-10, cells were treated with 1 uM 4-hydroxytamoxifen for 6 hours
|
| Growth protocol |
Cells were grown in low calcium E media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by TRIzol and purified with Qiagen RNeasy mini spin columns
Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare libraries from 2 ug of total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were trimmed and filtered to remove low quality reads using FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), then mapped to mm10 assembly using Tophat2 with the following parameters: "--segment-length 22 --segment-mismatches 0 --no-novel-juncs"
Gene level read counts wre measured using htseq-counts (http://www-huber.embl.de/HTSeq/) using default parameters.
DESeq2 package for R was used to normalize gene level read counts and analyze differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table and DESeq output
|
| |
|
| Submission date |
Apr 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alex Wang |
| Organization name |
Cornell University
|
| Department |
Molecular Biology and Genetics
|
| Street address |
260 Biotechnology Bldg
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE80354 |
Gata6 promotes hair follicle matrix progenitor cell renewal by genome maintenance via Edaradd/NF-κB |
|
| Relations |
| BioSample |
SAMN04859460 |
| SRA |
SRX1709604 |
