|
| Status |
Public on Jun 13, 2013 |
| Title |
N_172_BRCA2_44_SAGEseq |
| Sample type |
SRA |
| |
|
| Source name |
expression library from cd44+ cells from BRCA1 and BRCA2 mutation carriers
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: mammary gland
cell type: cd44+ cells from BRCA2 mutation carrier
|
| Treatment protocol |
cells isolated tissue after digesting and sequential filtration and bead purification or FACS purification
|
| Growth protocol |
not applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For SAGE-seq: mRNA isolated from atleast 50-100K cells were captured on oligo(dT) beads followed by cDNA synthesis. cDNA was then cleaved with anchoring enzyme NlAIII following ligation of adapter 1. cDNA was subsequently released by tagging enzyme MmeI and ligated to adapter 2. The resulting 85 bp DNA fragments were amplified by Primer 1 and Primer 2 and purified in 12% PAGE. Purified libraries were sequenced on the Illumina Solexa 1G platform. All the adapters and primers were from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
SAGE library prepared using Illumina adapters and primers using NLAIII fragmenting enzyme
|
| Data processing |
21 base pair (bp) of each read is used in this study. The first 4 bp is always CATG, as this is the recognition site of NlaIII. Our analysis was based around the alignment of the rest of the 17bp tags to human genome composed of segments between nearest NlaIII sites flanking BssHII recognition sites where as 17 bp SAGE tags were aligned to transcripts.
|
| |
|
| Submission date |
Apr 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
[email protected]
|
| Phone |
617-632-2106
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Polyak
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE32017 |
Molecular profiling of human mammary gland links breast cancer risk to a p27+ cell population with progenitor characteristics |
|
| Relations |
| SRA |
SRX259976 |
| BioSample |
SAMN01999071 |
