|
| Status |
Public on Dec 17, 2019 |
| Title |
MBC02.shLuc.Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Human Breast Cancer PDXs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Breast Cancer PDXs primary cells
growth protocol: DMEM supplemented with 10% Fetal Bovine Serum, 2mM L-Glutamine, 1% Pen/Strep, 10mM HEPES, 5 µg/ml Insulin, 0.5 µg/ml Hydrocortisone, 10 ng/ml EGF, 10 NG/ML Cholera Toxin
treatment: Cells were infected with pRSI-U6-shLuc-UbiC-TagRFP-2A-Puro vector and selectioned with 3µg/ml of Puromycin
|
| Treatment protocol |
See additional columns of the SAMPLES section
|
| Growth protocol |
See additional columns of the SAMPLES section
|
| Extracted molecule |
total RNA |
| Extraction protocol |
2.5x10^4 cells are lysed and processed according to TRUSeq RNA Sample Prep Kit Illumina protocol. Briefly, after cell lysis the poly-A containing mRNA molecules were purified using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis follows, using DNA Polymerase I and RNase H. The cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library for HiSeq 2000 Illumina sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
genes.counts.txt
genes.edgeR_results_MBC02.txt
|
| Data processing |
Reads were quality filtered according to the Illumina pipeline, then were aligned to o the human (hg19) and mouse (mm10) reference genome using TopHat2 with the option “--b2-very-sensitive”. After removing the reads aligned to the mouse genome, only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts (Rsubread version 1.5.1), summarized across all exons as annotated in the NCBI build 37.2, with default options
Differentially expressed genes in biological triplicates of shLuc and shWDR5 cancer cell line were identified using EdgeR R-package v3.2.2.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: The file gene.counts.txt contains the raw read counts for each samples. The file edgeR_results_*.txt contains differentially expressed genes in biological triplicates of shLuc and shWDR5 Breast Cancer PDXs.
|
| |
|
| Submission date |
Apr 17, 2018 |
| Last update date |
Dec 17, 2019 |
| Contact name |
Chiara Balestrieri |
| E-mail(s) |
balestrieri.c@gmail.com
|
| Organization name |
IRCCS San Raffaele Scientific Institute
|
| Department |
Center for Omics Sciences
|
| Street address |
Via Olgettina 58
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE113288 |
WDR5 regulates EMT and metastasis in breast cancer by activating TGFB pathway [RNA-seq PDX] |
| GSE113289 |
WDR5 regulates EMT and metastasis in breast cancer by activating TGFB pathway |
|
| Relations |
| BioSample |
SAMN08943219 |
| SRA |
SRX3958463 |
