|
| Status |
Public on Dec 08, 2022 |
| Title |
Reindeer_3YD__Back__day_3 62158 |
| Sample type |
SRA |
| |
|
| Source name |
3YD
|
| Organism |
Rangifer tarandus |
| Characteristics |
tissue: Back
days post wound: 3
control: FALSE
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells were isolated with RNeasy Plus kit (QIAGEN).
Sequencing libraries were prepared following the LM-seq protocol (Hou et al., 2015).
Sequenced on Illumina HiSeq 2500 at a depth of 17 samples per lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Reindeer_3YD__Back__day_3
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts.
Sequencing reads were mapped using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: Bos Taurus transcriptome (NCBI: GCF_002263795.1_ARS-UCD1.2)
Supplementary_files_format_and_content: Collated rsem output into tab files, expected counts (ec) and transcripts per million (tpm's)
|
| |
|
| Submission date |
Mar 11, 2021 |
| Last update date |
Dec 08, 2022 |
| Contact name |
Jeff Biernaskie |
| E-mail(s) |
jabierna@ucalgary.ca
|
| Phone |
4032107306
|
| Organization name |
University of Calgary
|
| Department |
Comparative Biology and Experimental Medicine
|
| Lab |
Biernaskie Lab
|
| Street address |
3330 Hospital Drive NW
|
| City |
Calgary |
| State/province |
Alberta |
| ZIP/Postal code |
T2N4N1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL29839 |
| Series (2) |
| GSE168746 |
Bulk RNA-Seq datasets supporting fibroblast polarization drives skin regeneration versus fibrosis in adult reindeer |
| GSE168748 |
Skin regeneration is enabled in the absence of fibroblast inflammatory priming |
|
| Relations |
| BioSample |
SAMN18269812 |
| SRA |
SRX10321440 |
