|
| Status |
Public on Jul 23, 2021 |
| Title |
anti-CSF1 replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Orthotopically injected TMPRSS2-ERG+ expressing prostate tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Prostate
cell type: TMPRSS2-ERG+ expressing
treatment: alpha-CSF1
rin: 8.9
28s/18s (height): 1.6
28s/18s (area): 1.8
total rna area: 14.14
rrna area: 5.85
conc. [ng/ul]: 335
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extraction using RNeasy Plus micro kit. Genomic DNA was removed by DNase treatment.
RNA libraries were prepared for sequencing using NuGen Ovation Mouse RNA-Seq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
MRI-016-1
|
| Data processing |
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt (https://doi.org/10.14806/ej.17.1.200) (version 1.8.1), and mapped to mm10 reference genome using star v2.5.3a with default settings.
Uniquely mapped reads were counted at gene-level by htseq-count (version 0.6.1) using Gencode vm21 transcript annotations for mouse
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each sample
|
| |
|
| Submission date |
Jul 16, 2021 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Chia-Ho Cheng |
| E-mail(s) |
chia-ho.cheng@moffitt.org
|
| Organization name |
Moffitt Cancer Center
|
| Street address |
12902 USF Magnolia Drive
|
| City |
Tampa |
| ZIP/Postal code |
33647 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE180270 |
Macrophage-derived cholesterol contributes to therapeutic resistance in prostate cancer |
|
| Relations |
| BioSample |
SAMN20285879 |
| SRA |
SRX11485437 |
