|
| Status |
Public on Mar 02, 2018 |
| Title |
0 hour untreated cell 18 [Sample_1_18] |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP_0 hour untreated cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: LNCaP
cell type: prostate cancer cells
time point: 0 hour untreated cell
|
| Treatment protocol |
Cell were seeded at 4 x 105 per well of a 6-well dish, synchronized to the G1/S phase with double thymidine block and androgen deprived (in RPMI 1640 -phenol red and substituted charcoal-stripped fetal bovine serum) for ~24 hours. Treatment groups 2 and 3 were cultured in the absence and presence of androgen (1 nM R1881) for 12 hours, respectively. Treatment group 1 was a baseline comparison treatment group and was collected right after cell synchronization and androgen deprivation (considered 0 hour).
|
| Growth protocol |
LNCaP cells were cultured (typically 1–2 × 106 cells into a T75 flask ) in RPMI 1640 media (Gibco) supplemented fetal bovine serum and penecillin/streptomycin, 10% and 1% final concentrations respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were hand picked with a micromanipulator and ejected into SMARTseq2 cell lysis buffer. Reverse transcription and PCR amplification occured according to the SMARTseq2 protocol as described by Picelli et al. 2014. The Illumina Nextera XT DNA Library Prep Kit (Cat#FC-131-1096) and the Index Kit v2 set A (Cat#FC-131-2001) were used with 0.3 ng of amplified DNA per cell for the construction of sequencing libraries.
RNA libraries were manually prepared for sequencing. We created equimolar solutions from 96 uniquely indexed cells.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file:
raw.txt
rpkm.txt
results_de12_pvalues_beganwithGeneNames.txt
results_de13_pvalues_beganwithGeneNames.txt
|
| Data processing |
Raw fastq is mapped to human genome by TopHat using default parameters for paired end sequencing
Multiple-mapped reads are removed using samtools
HOMER is used to generate text file for rpkm and raw reads using default parameters
Collected the average read value for genes with mulitple transcript variants per cell
R package SCDE is used to detect differentially expressed genes between each two of the three groups of cell population
Genome_build: hg19
Supplementary_files_format_and_content: Raw.txt contains the raw reads generated by HOMER using default parameter. The rpkm.txt contains rpkm reads generated by HOMER using default parameter. The 'results_de12_pvalues_beganwithGeneNames.txt' contains the DESeq2 result between 0hr and 12hr untreated cells. The 'results_de23_pvalues_beganwithGeneNames.txt' contains the DESeq2 result between 12hr untreated and androgen-treated cells. The 'results_de13_pvalues_beganwithGeneNames.txt' contains the DESeq2 result between 0hr untreated and 12hr androgen-treated cells.
|
| |
|
| Submission date |
Jun 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim Hui-Miing Huang |
| E-mail(s) |
huangt3@uthscsa.edu
|
| Phone |
210-450-0025
|
| Organization name |
University of Texas Health San Antonio
|
| Department |
Molecular Medicine
|
| Street address |
8403 Floyd Curl Dr.
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE99795 |
Single-cell RNA-seq reveals a subpopulation of prostate cancer cells with enhanced cell cycle-related transcription and attenuated androgen response |
|
| Relations |
| BioSample |
SAMN07204153 |
| SRA |
SRX2894481 |
