|
| Status |
Public on Apr 29, 2020 |
| Title |
control_1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
origin: Breast Cancer ER +ve
shRNA: empty vector
|
| Growth protocol |
Stable gene expression Cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen mRNA kit
Illumina TruSeq Stranded total RNA kit according to the manufacturer’s protocol. The libraries were sequenced using 2x76 bases paired end protocol on Illumina HiSeq 3000 instrument. Two biological replicates per condition were sequenced, generating 45-58 million pairs of reads per sample. Each pair of reads represents a cDNA fragment from the library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
MCF7 cells stably expressing empty vector_1
|
| Data processing |
Basecalling was done by Illumina HiSeq Control Software (version 3.3.76).
The reads were mapped to the human genome (hg38) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release 32 (83) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genome_build: hg38
Supplementary_files_format_and_content: Number of fragments in each gene
Supplementary_files_format_and_content: raw counts
|
| |
|
| Submission date |
Mar 11, 2020 |
| Last update date |
Apr 29, 2020 |
| Contact name |
Janani Kumar |
| E-mail(s) |
jkumar@mdanderson.org
|
| Organization name |
MD Anderson Cancer Center
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE146769 |
KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells |
|
| Relations |
| BioSample |
SAMN14352212 |
| SRA |
SRX7891864 |
