|
| Status |
Public on Jun 17, 2014 |
| Title |
HCC2157_RNAseq_siJARID1B |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC2157
cell type: breast cancer cells
transfection: siJARID1B
|
| Treatment protocol |
Cells transfected with gene-specific or non-targeting siRNA pools were cultured for 5 days prior to the sample preparation.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).
PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.7 or 1.8.
RNA-Seq raw data was mapped by Tophat to hg19.
Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold.
|
| |
|
| Submission date |
Apr 03, 2013 |
| 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 |
GPL11154 |
| Series (2) |
| GSE45732 |
Gene expression analysis of breast cancer cell-lines |
| GSE46073 |
Gene expression and genome-wide location analysis of breast cancer cell-lines |
|
| Relations |
| SRA |
SRX259566 |
| BioSample |
SAMN01997750 |
