|
| Status |
Public on Jan 03, 2018 |
| Title |
Rat_IFE_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Rat inter-follicular epidermis
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: skin
tissue compartment: epidermis
skin status: Normal skin
Stage: Adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole tissue was homogenized using Precellys in RLT buffer supplemented with beta-mercapto ethanol to preserve RNA integrity. Total RNA was isolated using Rneasy micro kit as per manufacturer's suggestions (Qiagen), including DNAse treatment. Total RNA was eluted in molecular grade water. RNAs with optimal RIN scores were considered for library preparation.
SMART-seq2 was performed on total RNA as described by Picelli et al. Briefly, 10 ng and 100 ng total RNA was used for RT. Resulting cDNA was pre-amplified for 12 and 10 cycles, respectively and tagmentation performed on 18 ng and 20 ng cDNA using the Nextera DNA Sample Preparation Kit (Illumina). Fragments were amplified for 8 continuous cycles. Libraries sequenced as single-end (86bp and 43bp) on a NextSeq 500 Illumina Sequencing Platform (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
protocol: SMART-seq2
processed data file: Rat_TPM.txt
|
| Data processing |
Sequenced reads were mapped to Ensembl v.87 transcriptomes of Mus musculus (mm10) and Rattus norvegicus (Rnor_6.0) using bowtie v1.0.0 with parameters: -S --offrate 1 -a -m 200 --best -p 8 -v 2
Transcripts per million (TPM) measurements for rat and mouse samples were obtained using read alignments to Ensembl v87 transcriptomes and rsem v1.2.31
Genome_build: mm10 or Rnor_6.0
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for mouse samples and rat samples separately.
|
| |
|
| Submission date |
Mar 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maksim V Plikus |
| E-mail(s) |
plikus@uci.edu
|
| Phone |
949-824-1260
|
| Organization name |
University of California, Irvine
|
| Department |
Developmental and Cell Biology
|
| Street address |
845 Health Sciences Road
|
| City |
Irvine |
| State/province |
California |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE97047 |
Wound regeneration deficit in rats correlates with low morphogenetic potential and distinct transcriptome profile of epidermis |
|
| Relations |
| BioSample |
SAMN06644961 |
| SRA |
SRX2674060 |
