|
| Status |
Public on Mar 17, 2016 |
| Title |
D10 fibrotic ear tissue Mus musculus |
| Sample type |
SRA |
| |
|
| Source name |
Ear Tissue
|
| Organism |
Mus musculus |
| Characteristics |
healing mechanism: ear tissue
tissue: D10 fibrotic ear tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
tissue was frozen in liquid nitrogen, homgenized with ceramic beads in TriZol and extracted following TriZol protocol
HudsonAlpha directional RNAseq with ribosomal RNA reduction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
D10 fibrotic ear tissue
haib14AWS2783
|
| Data processing |
Normalize raw data using Trinity
Build references for each species using RSEM
Calculate raw transcript expression for each time point in each species using RSEM
Calculate expression fold change and probability of differential expression using Ebseq
Genome_build: de novo-assembled transcriptome for Acomys, mm10 for Mus
Supplementary_files_format_and_content: .result files were generated for each species comparing all time points versus D0. Probability of differential expression and fold change are reported. Due to the method the data was processed in, fold changes reported in this list are D0/DX. To get DX/D0, the inverse of the reported fold change is used.
|
| |
|
| Submission date |
Aug 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ashley Seifert |
| E-mail(s) |
awseifert@uky.edu
|
| Organization name |
University of Kentucky
|
| Department |
Biology
|
| Street address |
675 Rose St.
|
| City |
Lexington |
| State/province |
Kentucky |
| ZIP/Postal code |
40508 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE71761 |
Comparing regeneration and fibrosis using Acomys and Mus |
|
| Relations |
| BioSample |
SAMN03959889 |
| SRA |
SRX1134547 |
