|
| Status |
Public on Jun 11, 2015 |
| Title |
WT rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
ovarian cancer ascites_WT
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild type
tissue: ID8-based tumors (day 23)
cell type: sorted tumor-associated DCs
|
| Growth protocol |
in vivo tumor and ascites
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from sorted tumor-associated DCs (N=3/genotype) was independently isolated using the miRVANA kit Life Technologies and further purified and concentrated using minElute columns (Qiagen). RNA integrity was confirmed using an Agilent Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample_tDC1-WT
|
| Data processing |
Align to contamination (mm9 related) (chrM and Ribosomal RNA) and get rid of chrM and ribo mapped reads
None aligned reads from step 2 are the possible reads coming from mRNAs. Use these reads to estimate isoform/gene level raw read counts using RSEM package (1).
Normalize read raw counts from rsem using edgeR bioconductor R package (2).Filter low count genes from complete data set.Normalize using Upper quartile normalization
Use edgeR to find differentially expressed genes.
Result will be sorted based on adjusted p-value and genes has small adjusted p-value are considered as differentially expressed based on comparison.
Genome_build: MM9
Supplementary_files_format_and_content: text, csv - Estimated counts, Normalized estimated counts
|
| |
|
| Submission date |
May 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Juan R Cubillos-Ruiz |
| E-mail(s) |
jrcubillos@gmail.com
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Medicine
|
| Street address |
1300 York Ave, E-907
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE68472 |
Transcriptional profile of XBP1-deficient ovarian cancer-associated dendritic cells (DCs) |
|
| Relations |
| BioSample |
SAMN03579582 |
| SRA |
SRX1015890 |
