|
| Status |
Public on Jan 13, 2016 |
| Title |
control for experiment with highly downregulated Satb1, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
WT_tumor-associated DC
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: bearing ID8-Defb29/Vegf-a
treated with: Non-Targeting (NT) siRNA
satb1 status: wildtype
cell type: Cancer-Associated Dendritic Cells (DCs)
replicate: 2
|
| Treatment protocol |
mice (C57BL/6) were treated for 32-38 days with 100 μg of Non-Targeting (NT) or Satb1 siRNA-Rhodamine conjugated polyethylenimine nanocomplexes (Satb1)
|
| Growth protocol |
mice (C57BL/6) bearing ID8-Defb29/Vegf-a grown for 32-38 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated for RNA-Seq using Trizol reagent.
RNA-Seq library was prepared using the TruSeq Stranded Total RNA Library Preparation kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
endogenous level of Satb1
high.NT.2
|
| Data processing |
RNA-Seq data analyzing was done with rsem(ver. 1.2.12) and mm9 genome with UCSC known gene set.
DESeq2 was used for differentail expression analysis
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and raw count values for all UCSC genes across 6 samples
|
| |
|
| Submission date |
Jan 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE76776 |
Satb1 Overexpression Drives Tumor-Promoting Activities In Cancer-Associated Dendritic Cells |
|
| Relations |
| BioSample |
SAMN04397439 |
| SRA |
SRX1528500 |
