|
| Status |
Public on Jun 15, 2014 |
| Title |
siScram_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7, siScram
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer
|
| Treatment protocol |
MCF7 cells were reverse-transfected at a density of 5 x 105 per well in 6-well culture plates. Transfection was performed using 100 nM siRNA targeting ZNF217 (OnTarget plus SMARTpool, Dharmacon, cat # L-004987-01) or non-targeting pool (OnTarget plus non-targeting pool, Dharmacon, cat # D-001810-10) using RNAiMax (Invitrogen) per the manufacturer’s instructions. RNA wascollected at 48h post-transfection.
|
| Growth protocol |
The MCF7 breast cancer cell line was obtained from American Type Culture Collection and cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum, 2mM Lglutamine and 1% penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples from triplicate biological replicates of MCF7 cells treated with scrambled siRNA or siZNF217 were extracted using the RNAeasy Kit (Qiagen).
2 ug of RNA samples were processed with the TruSeq RNA Sample Prep Kit (Illumina) to make RNA libraries following the Low-Throughput protocol. Libraries were pooled and sequenced using the HiSeq2500 platform at the UC Davis DNA Technologies Core Facility (http://dnatech.genomecenter.ucdavis.edu).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
fastq files were aligned to the hg19 genome using Tophat 2.0.9 with default parameters. The resulting aligned .bam files were used for cufflinks abundance measurements and cuffdiff differential gene expression anlaysis using the 2.1.1 Cufflinks software.
Genome_build: hg19
Supplementary_files_format_and_content: matrix describing the mean gene transcript abundances and the differential gene expression between siZNF217 and siScramble replicate experiments including statistical measurements of differential expression
|
| |
|
| Submission date |
Jun 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Seth Frietze |
| E-mail(s) |
[email protected]
|
| Phone |
8026560569
|
| Organization name |
University of Vermont
|
| Department |
BHSC
|
| Street address |
106 Carrigan Drive
|
| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE58326 |
Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with Eralpha |
|
| Relations |
| BioSample |
SAMN02847876 |
| SRA |
SRX582009 |
