|
| Status |
Public on Dec 10, 2010 |
| Title |
ASSAGE_breast_epithelium_cancer_T1 |
| Sample type |
SRA |
| |
|
| Source name |
biopsy and surgery
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
cell type: epithelial cell
disease state: cancer
cell marker: CD24+
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
ASSAGE libraries were generated essentially as described (PMID: 19056939), except that we used polyA RNA. Briefly,we treated polyA RNA with bisulfite, which changes all cytidine residues to uridine residues. We generated cDNA from bisulfite-treated RNA with reverse transcriptase, the double-stranded cDNA was used to construct libraries for sequencing following Illumina's standard genomic DNA sample preparation instructions. The sequence of a bisulfite-treated RNA molecule can only be matched to one of the two possible DNA template strands.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
We generated a bisulfite-converted genome for both plus and minus strands (6.2 Gb) as a reference for ASSAGE reads. We used SeqMap (http://biogibbs.stanford.edu/~jiangh/SeqMap/)to align reads to the bisulfite-converted genome under default conditions, allowing up to two mismatches in 32-bp reads. We used reads that uniquely mapped to either plus or minus strand-derived sequences.
|
| |
|
| Submission date |
Dec 08, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| 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 (2) |
| GSE25292 |
Altered antisense-to-sense transcript ratios in breast cancer |
| GSE25932 |
Altered antisense-to-sense transcript ratios in breast cancer: ASSAGE |
|
| Relations |
| SRA |
SRX033236 |
| BioSample |
SAMN00149456 |
