|
| Status |
Public on Dec 21, 2017 |
| Title |
L-GFP+ |
| Sample type |
SRA |
| |
|
| Source name |
Freshly purified mouse luminal label-retaining cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Prostate
cell type: luminal
age: 18 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The FACS purified mouse prostate luminal GFP+ and luminal GFP- epithelial cell populations are subject to total RNA extraction by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) was used with 400~1000 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.10) and Bowtie2 (version 2.1.0).
The number of fragments in each known gene from GENCODE Release M7 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.16.0).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq) for all the samples.
|
| |
|
| Submission date |
May 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dingxiao Zhang |
| E-mail(s) |
[email protected]
|
| Phone |
+86-15391542415
|
| Organization name |
Hunan University
|
| Department |
School of BioMedical Sciences
|
| Lab |
Zhang lab
|
| Street address |
Yuelushan
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410082 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE98760 |
Histone 2B-GFP Label-Retaining Prostate Luminal Cells Possess Progenitor Cell Properties and Are Intrinsically Resistant to Castration |
|
| Relations |
| BioSample |
SAMN06925963 |
| SRA |
SRX2794574 |
