|
Status |
Public on Dec 15, 2016 |
Title |
Gata6 WT2 |
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 |
SAMN04859462 |
SRA |
SRX1709602 |