|
| Status |
Public on Aug 01, 2015 |
| Title |
Pt.G.CA125- |
| Sample type |
SRA |
| |
|
| Source name |
high grade serous ovarian cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tumor subpopulation: CA125 negative
tumor state: solid tumor
cell storage: freshly isolated primary cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Primary human high grade serous ovarian cancers, dissociated to single cells and either used fresh or cryopreserved, were FACS isolated based on expression of CA125. RNA was isolated using the Qiagen allprep micro kit.
Isolated total RNAs (50 ng) were amplified to cDNA using the Clontech SMARTer kit (# 634820 ), then converted to indexed cDNA libraries using the Nextera DNA Library preparation kit (#FC-121-1030)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
JK006 minus
|
| Data processing |
Illumina RTA software used for basecalling.
Demultiplex data without allowing mismatches
Align to genome with Tophat with hg19 and Ensembl 75 gene annotation, allowing 2 mismatches and unique alignments only
Run alignment file (BAM format) through HTSeq-package script along with Ensembl 75 human gene annotation gtf file to create gene counts matrix, then run gene matrix though DESeq to normalize and test for differential expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts values for each Sample ...
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sanaz Memarzadeh |
| E-mail(s) |
smemarzadeh@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Obstetrics and Gynecology
|
| Lab |
3017 TLSB
|
| Street address |
610 Charles E Young Dr East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE70072 |
Apoptosis enhancing drugs overcome innate platinum resistance in CA125 negative tumor initiating populations of high grade serous ovarian cancer |
|
| Relations |
| BioSample |
SAMN03784937 |
| SRA |
SRX1067686 |
