|
| Status |
Public on Jan 26, 2014 |
| Title |
β-cat Het |
| Sample type |
SRA |
| |
|
| Source name |
β-cat Het
|
| Organism |
Mus musculus |
| Characteristics |
tissue: back skin
Sex: Female
age: P99
strain: C57BL6/129Sv
genotype: Ctnnb1 Het (K15CrePGR;Ctnnb1+/fl; Rosa-YFPfl/stop/fl)
|
| Growth protocol |
HFSCs were FACS-purifed from the telogen back skins of indicated ages of mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs from FACS-sorted populations were purified using Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. Quality of the RNA for sequencing was determined using Agilent 2100 Bioanalyzer, all samples used had RNA integrity numbers (RIN) > 8.
Library preparation using Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility, and RNAs were sequenced on Illumina HiSeq 2000 machines.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-Seq reads (51bp, single-ended) were aligned to the mouse genome (NCBI37/mm9) using the software TopHat (version 2.0.4)
The resulting alignment data from Tophat were then fed to an assembler, Cufflinks (version 2.1.1) to assemble aligned RNA-Seq reads into transcripts.
These transcripts were compared to the gene model for annotated transcripts obtained from the Ensembl database (72/GRCm38).
The category of transcripts is described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html.
Transcript abundances were measured in FPKM (fragments per kilobase of exon per million fragments mapped). Expression profiles were quantile-normalized across samples for comparison.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Wen-Hui Lien |
| E-mail(s) |
wlien@rockefeller.edu
|
| Phone |
212-327-7482
|
| Organization name |
The Rockefeller Unoversity
|
| Department |
Mammalian cell biology and development
|
| Lab |
Elaine Fuchs
|
| Street address |
1230 York Ave Box#300
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE48878 |
In vivo transcriptional goverance of hair follicle stem cells by canonical Wnt regulators |
|
| Relations |
| BioSample |
SAMN02251377 |
| SRA |
SRX322878 |
