|
| Status |
Public on Jan 30, 2023 |
| Title |
AloPmouse.RepD.AA.Vec12w.KT.04_S4 |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal skin (approx 50 mg), Alopecia, untreated
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C3H/HeJ
gender: Female
age: approx 30w at termination
genotype/variation: AA
group: Alopecia
tissue: Dorsal skin
treatment: None
replicate: RepD
|
| Treatment protocol |
4 week daily oral servings for free eating.
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared according to a standard phenol-chloroform total RNA extraction method where skin samples were homogenized in Qiazol®, added chloroform, vortexed and centrifuged for phase separation. The RNA containing phase was ethanol precipitated and purified on an Applied Biosystems 6100 Nucleic Acid Prep Station.
RNA was diluted to 50ng/ul and used as input to create RNA libraries using TruSeq Stranded Total RNA with RiboGold depletion (Illumina, CA, USA) following standard instructions with the exception that no fragmentation of samples were made due to low RIN-values. Libraries were validated on the Fragment Analyzer platform (AATI, IA, USA) using standard sensitivity NGS analysis kit. Sample libraries were pooled in equimolar concentrations and diluted and denatured according to Illumina guidelines. The pool was then sequenced using a High Output 2 x 76 bp kit on an Illumina NextSeq500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
S4
PolyA RNA
Processed data file: combined.counts.txt
Processed data file: combined.gene.sf.tpm.txt
|
| Data processing |
Base calling was done by bcl2fastq from Illumina.
Reads were mapped with Hisat2 (version 2.0.1-beta).
Counts were generated with featurecounts (1.4.4).
TPMs were generated using Sailfish (version 0.7.6).
All processing was wrapped together with bcbio 0.9.5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: combined.counts.txt: Tab-delimited text file includes counts.
Supplementary_files_format_and_content: combined.gene.sf.tpm.txt: Tab-delimited text file includes TPMs.
|
| |
|
| Submission date |
Jan 27, 2017 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Elisabeth Israelsson |
| E-mail(s) |
elisabeth.israelsson@astrazeneca.com
|
| Organization name |
AstraZeneca, IMED RIA
|
| Department |
Translational Biology
|
| Street address |
Pepparedsleden 1
|
| City |
Molndal |
| ZIP/Postal code |
SE-431 83 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE94236 |
Effect of systemic exposure of JAK1 Inhibition (AZ13748709) in C3H/HeJ Mice with Alopecia Areata In Vivo |
| GSE94237 |
JAK inhibition in human CD8+ T-cells and C3H/HeJ Mice with Alopecia Areata In Vivo |
|
| Relations |
| BioSample |
SAMN06277402 |
| SRA |
SRX2524336 |
