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Sample GSM4850937 Query DataSets for GSM4850937
Status Public on Feb 19, 2021
Title Chuong534: Ac WT dorsal dermis RNA-seq
Sample type SRA
Source name dorsal dermis
Organism Acomys cahirinus
Characteristics tissue: dorsal dermis
post-wound day (pwd): 0
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 Chuong534
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
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
BioSample SAMN16523294
SRA SRX9349904

Supplementary file Size Download File type/resource
GSM4850937_Chuong534.txt.gz 95.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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