|
| Status |
Public on Jun 21, 2019 |
| Title |
LX1740 |
| Sample type |
SRA |
| |
|
| Source name |
mouse prostate cells_Proximal Basal
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8~12-week-old
tissue: proximal ducts
cell type: prostate basal cells
|
| Treatment protocol |
Dissociated single murine and human prostate cells were incubated with florescence conjugated antibodies at 4 deg C for 30 minutes. FACS analyses and sorting were performed by using the BD LSR II, BD LSR Fortessa, Aria I or Aria III (BD Biosciences, San Jose, CA) and gating was confirmed using fluorescence minus one.
|
| Growth protocol |
8~12-week-old C57BL/6 mouse prostate tissues were digested and dissociated into single cells. Dissociated single cells were cultured in Biocoat Collage I-coated plates (Corning, Corning, NY) in Bfs medium (5% Nu-Serum, 5% FBS, 1×Insulin/Selenium, 1×L-Glutamine, 1×Penicillin/Streptomycin, and 1×10-10M DHT in DMEM medium) at 37°C with 5% CO2. When the cell confluency reached around 90%, cells were trypsinized into single cells with 0.25% Trypsin-EDTA (Invitrogen, Carlsbad, CA). Cells were replated in Biocoat Collage I-coated plates (Corning, Corning, NY) for 30 min at 37°C/5% CO2. Unattached cells were discarded and remaining cells were cultured in Bfs at 37°C/5% CO2 till 80-90% confluency. All the experiments in this study used fresh primary stromal cells within 3 weeks after single cell dissociation from prostates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NucleoSpin RNA Kit from Macherey-Nagel, using manufacturer's protocol.
Total RNA samples were made into cDNA using the NuGEN Ovation® RNA‑Seq System V2 kit (using both random priming and poly d(T) priming). cDNA from the NuGEN kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Proximal Basal#3
LX1740_AGGCAGAACTCTCTAT
|
| Data processing |
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9) with parameters -r 100. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0) with parameters -r 100. UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.
|
| |
|
| Submission date |
Jun 11, 2018 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Chad Creighton |
| E-mail(s) |
[email protected]
|
| Organization name |
Baylor College of Medicine
|
| Department |
Biostatistics, Ducan Cancer Center
|
| Street address |
One Baylor Plaza, Mail Stop: BCM305
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE115631 |
Gene expression profiling of prostate basal cells at proximal and distal ducts |
|
| Relations |
| BioSample |
SAMN09395170 |
| SRA |
SRX4194155 |
