|
| Status |
Public on Sep 30, 2013 |
| Title |
CTRL sh-lane1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF10A_CTRL sh_RNA-seq strand specific
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
cell type: breast epithelial cells
sample type: RNA-seq strand specific
molecule subtype: total RNA - ribosome depleted
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ScriptSeqv2 kit along with ScriptSeq Index PCR primers (Epicentre)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 6
processed data file: CTRLsh_Forward.wig
processed data file: CTRLsh_Reverse.wig
|
| Data processing |
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
alignment: BOWTIE v 0.12.7 (default parameters)
tag density files: genomeCoverageBed (from BEDTools suite)
Genome_build: hg 18
|
| |
|
| Submission date |
Sep 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Alessandro Gardini |
| E-mail(s) |
agardini@wistar.org
|
| Phone |
305-243-7394
|
| Organization name |
University of Miami
|
| Department |
Sylvester Comprehensive Cancer Center
|
| Lab |
Ramin Shiekhattar
|
| Street address |
1501 NW 10 Avenue
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE40591 |
Genome-wide analysis of BRCA1 and PALB2 [ChIP-seq and RNA-seq] |
| GSE45715 |
Genome-wide analysis of BRCA1 and PALB2 |
|
| Relations |
| SRA |
SRX182687 |
| BioSample |
SAMN01161911 |
