|
| Status |
Public on Jan 15, 2018 |
| Title |
RNA Xeno 2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: breast cancer cell line MDA-MB-231
originating cell line: Control
sample type: Control Primary tumor, mouse number 2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bulk RNA was extracted from cells using the QIAShredder (Qiagen – 79654) and the RNA extraction kit (Qiagen – 74106) and sequenced using HiSeq4000 (Illumina Inc.).
[sequencing strategy] 101bp single end RNAseq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
fpkm.geneSymbols.csv
counts.geneSymbols.csv
|
| Data processing |
The quality of the raw FASTQ files were checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). For samples originating from mouse xenographs, FASTQ reads were classified as originating from either mouse or human genomes using xenome (https://www.ncbi.nlm.nih.gov/pubmed/22689758), and human-specific reads were used for mapping. Reads were mapped to human reference GRCh38 using STAR (v2.4.1d, 2-pass mode).
Gene expression was estimated using cufflinks (v2.2.1, default parameters) and HTSeq (v0.6.1). Differential expression analyses were performed using DESeq2 (v1.14.1).
Prior to any unsupervised analyses, expression counts were transformed using variance stabilizing transformation using the DESeq2 R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited files contain FPKM and read count values for each sample.
|
| |
|
| Submission date |
Aug 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Murphy |
| E-mail(s) |
murphy.charlesj@gmail.com
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
1300 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE98183 |
Chromosomal instability promotes metastasis through a cytosolic DNA response |
|
| Relations |
| BioSample |
SAMN07431340 |
| SRA |
SRX3052671 |
