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Sample GSM2471381 Query DataSets for GSM2471381
Status Public on Jan 30, 2023
Title AloPmouse.RepF.AA.Vec12w.KT.06_S6
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: RepF
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 S6
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 SAMN06277405
SRA SRX2524338

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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