|
| Status |
Public on Jan 15, 2018 |
| Title |
Ka |
| Sample type |
SRA |
| |
|
| Source name |
Human cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
chromosomal instability group: CIN-medium
genotype/variation: Overexpression of Kif2a, which does not affect the number of chromosome segregation errors during anaphase and serves as an additional control. Part of the CIN-medium group.
sequencing strategy: 75bp paired end RNAseq
|
| 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 HiSeq2500 or HiSeq4000 (Illumina Inc.).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file:
FPKM.geneSymbols.75bpPE.csv
VST.geneSymbols.75bpPE.csv
Counts.geneSymbols.75bpPE.csv
processed data column: Ka
|
| Data processing |
The quality of the raw FASTQ files were checked with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), then 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, counts, or variance stabalizing transformed values for each sample.
|
| |
|
| Submission date |
Apr 25, 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 |
GPL16791 |
| Series (1) |
| GSE98183 |
Chromosomal instability promotes metastasis through a cytosolic DNA response |
|
| Relations |
| BioSample |
SAMN06830446 |
| SRA |
SRX2764509 |
