|
| Status |
Public on Jun 28, 2023 |
| Title |
RD7-3 |
| Sample type |
SRA |
| |
|
| Source name |
prostate basal cell organoids
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: prostate basal cell organoids
treatment: basement medium plus R-spondin (500 ng/ml) and DHT (10-7M)
|
| Treatment protocol |
To make the basement medium (BM), the following components were added to advanced DMEM/F12: B27 (50× diluted), HEPES 1 M (100× diluted), GlutaMAX (100× diluted), Penicillin-streptomycin (100× diluted), N-acetylcysteine (1.25 mM), EGF (50 ng/ml), A83-01 (200 nM), Noggin (100 ng/ml), and Y-27632 dihydrochloride (10 μM). For R samples, 500 ng/ml R-spondin1 were added to BM. For RD7 samples, 500 ng/ml R-spondin1 and 10-7 M DHT were added to BM.
|
| Growth protocol |
Mouse prostate basal cells were flow-sorted and cultured as organoids using published protocol (Drost et al, Nature Protocol 2016) for 5 days before harvest.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Organoid mRNA was isolated using the RNeasy Micro Kit (Qiagen) based on the kit instructions.
RNA was reverse transcribed and amplified into cDNA using the Takara SmartSeq kit. Libraries were subsequently constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB,E7645L).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR v2.6.1a with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using featureCounts function from Rsubread (v1.30.7) and rpkm function of edgeR (v3.24.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Dec 08, 2022 |
| Last update date |
Jun 28, 2023 |
| Contact name |
wang jiawen |
| E-mail(s) |
wangjiawen2013@gmail.com
|
| Organization name |
National institute of biological sciences
|
| Street address |
7 Science Park Road ZGC Life Science Park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE220499 |
RNA-seq of mouse prostate basal cell organoids treated under different androgen and Wnt signaling conditions |
| GSE220501 |
RNA-seq and CUT&RUN of mouse prostate basal cell organoids |
|
| Relations |
| BioSample |
SAMN32109553 |
| SRA |
SRX18537464 |
