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| Status |
Public on Feb 19, 2021 |
| Title |
Chuong538: Ac WT dorsal epidermis RNA-seq |
| Sample type |
SRA |
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| Source name |
dorsal epidermis
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| Organism |
Acomys cahirinus |
| Characteristics |
tissue: dorsal epidermis
post-wound day (pwd): 28
region: N.A.
genotype: WT
quality score: Phred+33
rna-seq read type: Non strand-specific single-end 75bp
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
TRIzol
Illumina TruSeq RNA sample Prep kit v2 / Illumina TruSeq Stranded mRNA library prep kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Chuong538
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| 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
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| Submission date |
Oct 23, 2020 |
| Last update date |
Feb 19, 2021 |
| Contact name |
Hans I-Chen Harn |
| E-mail(s) |
hharn@usc.edu
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| Organization name |
University of Southern California
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| Street address |
2011 Zonal Ave. HMR304
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN16523296 |
| SRA |
SRX9349902 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4850935_Chuong538.txt.gz |
96.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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