NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4850933 Query DataSets for GSM4850933
Status Public on Feb 19, 2021
Title Chuong545: Ac WT dorsal epidermis RNA-seq
Sample type SRA
 
Source name dorsal epidermis
Organism Acomys cahirinus
Characteristics tissue: dorsal epidermis
post-wound day (pwd): 21
region: N.A.
genotype: WT
quality score: Phred+33
rna-seq read type: Non strand-specific single-end 75bp
Extracted molecule polyA RNA
Extraction protocol TRIzol
Illumina TruSeq RNA sample Prep kit v2 / Illumina TruSeq Stranded mRNA library prep kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Chuong545
Data processing Low quality of sequencing bases were trimmed based on the Phred+33 quality score (> 20) from both of the 5'- and 3'-ends of reads. After trimming, reads are discarded, if they are shorter than 30bp, or have one or more ambiguous base.
The mouse mm10 reference genome, and RefSeq genome annotation downloaded from the UCSC Genome Browser on 5 June, 2019 were used for RNA-Seq analysis
The alignment, quantification, normalization, and differential expression analysis were performed by STAR 2.4.1d, htseq-count 0.6.0, TMM, and edgeR 3, respectively.
Genes with count-per-million (CPM) values above 1 in at least two samples were retained, and genes with no or low expression levels were discarded.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: The tab-delimited text files: 25 files with count values of 24500 genes for each sample produced by htseq-count
 
Submission date Oct 23, 2020
Last update date Feb 19, 2021
Contact name Hans I-Chen Harn
E-mail(s) hharn@usc.edu
Organization name University of Southern California
Street address 2011 Zonal Ave. HMR304
City Los Angeles
State/province CA
ZIP/Postal code 90089
Country USA
 
Platform ID GPL24885
Series (2)
GSE159938 Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration [bulk RNA-seq]
GSE159939 Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration
Relations
BioSample SAMN16523300
SRA SRX9349900

Supplementary file Size Download File type/resource
GSM4850933_Chuong545.txt.gz 100.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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