 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 06, 2022 |
| Title |
WT_intact_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
WT intact
|
| Organism |
Mus musculus |
| Characteristics |
treatment: intact
crispr status: WT
|
| Treatment protocol |
PTEN castrate mice were castrated at ~4 months, and PTEN castrate 4EBP1 mice were castrated and put on doxycycline at ~4 months. WT intact and PTEN intact mice were reared normally.
|
| Growth protocol |
Mice were reared according to standard protocols
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized at ~6 months, and ventral prostate lobe was extracted via dissection.
RNA libraries were prepared for sequencing using Single Cell Library Kit from 10x Genomics (P/N 120218) according to manufacturer's guidelines.
single cell RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
WT intact mice (rep3)
|
| Data processing |
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and used a standard Illumina dual-index, paired-end constructs with the single Cell 14 bp barcode in the i7 index read (14 nt), sample index sequences in the i5 index read (8 nt), and Read 1 (98 nt) and Read 2 (10 nt) with standard Illumina sequencing primers in paired-end sequencing.
raw bcl files were processed using cellranger mkfastq and kallisto-bustools was used to align the fastq files to hg19. The gene matrix (.mtx) , genes file (.genes.txt) and barcodes file (.barcodes.txt) are submitted as processed data for each sample.
fastq files from output of cell ranger mkfastq are submitted as raw files
Genome_build: hg19
Supplementary_files_format_and_content: barcodes.txt, genes.txt and matrix.mtx ( 3 files per sample, output from cellranger count) are submitted as processed files.
|
| |
|
| Submission date |
Apr 01, 2021 |
| Last update date |
Dec 08, 2022 |
| Contact name |
Sonali Arora |
| E-mail(s) |
sarora@fredhutch.org
|
| Organization name |
FHCRC
|
| Street address |
1100 Fairview Ave N,
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE171336 |
Defining Cellular Population Dynamics in Advanced Prostate Cancer using Single-cell RNA Sequencing |
|
| Relations |
| BioSample |
SAMN18589920 |
| SRA |
SRX10501320 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5223639_WT_intact_rep3_barcodes.tsv.gz |
956.1 Kb |
(ftp)(http) |
TSV |
| GSM5223639_WT_intact_rep3_genes.tsv.gz |
141.2 Kb |
(ftp)(http) |
TSV |
| GSM5223639_WT_intact_rep3_matrix.mtx.gz |
18.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
