|
| Status |
Public on Sep 25, 2016 |
| Title |
P_T2 |
| Sample type |
SRA |
| |
|
| Source name |
HPCa167N benign prostatic bulk cells cultured in PrEGM
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: HPCa167N
patient age (yrs): 67
tissue: Prostate
cell type: HPCa167N benign prostatic bulk cells cultured in PrEGM
|
| Growth protocol |
Either freshly disassociated bulk benign prostatic cells or purified subpopulations were culatured primarily in PrEGM or WIT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The PrEGM- and WIT-expanded cells from either bulk or FACS-purified human benign prostatic basal and luminal cells 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 1 ug 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 human genome (hg38) by TopHat (version 2.0.10) and Bowtie2 (version 2.1.0).
The number of fragments in each known gene from GENCODE Release 21 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: hg38
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 |
Nov 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Dingxiao Zhang |
| E-mail(s) |
zdx1980@hnu.edu.cn
|
| 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 |
GPL11154 |
| Series (1) |
| GSE74698 |
Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors That Can Function as a Cell of Origin for Prostate Cancer |
|
| Relations |
| BioSample |
SAMN04240901 |
| SRA |
SRX1418874 |
