GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2125014 Query DataSets for GSM2125014
Status Public on Dec 15, 2016
Title Gata6 WT3
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 NextSeq 500
Data processing Sequenced reads were trimmed and filtered to remove low quality reads using 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 ( 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 GPL19057
Series (1)
GSE80354 Gata6 promotes hair follicle matrix progenitor cell renewal by genome maintenance via Edaradd/NF-κB
BioSample SAMN04859459
SRA SRX1709603

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap