|
| Status |
Public on Jun 21, 2016 |
| Title |
MCF10A H2A.X-KO_2 |
| Sample type |
RNA |
| |
|
| Source name |
MCF10A, H2A.X-KO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10A
cell type: breast cell line
genotype/variation: H2A.X knockout
group: knockout
|
| Treatment protocol |
Cells were cultured for 48 hours and harvested for RNA extraction.
|
| Growth protocol |
MCF10A parental (WT) or MCF10A cells knockout for H2A.X gene (MCF10A H2A.X-KO) were cultured in special medium consisting of Dulbecco’s minimal essential medium/F-12 (DMEM/F12) (Invitrogen, Carlsbad, CA) supplemented with 5% horse serum (Sigma, St. Louis, MO), 500 ng/ml hydrocortisone (Sigma), 20 ng/ml EGF (R and D Systems, Minneapolis, MN), 100 ng/ml cholera toxin (Sigma), 10 μg/ml insulin (Sigma), and 100 mg/ml of penicillin-streptomycin (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from MCF10A cells were extracted using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) following manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 1 ug total RNA. RNA was reverse transcribed with T7-oligo(dT) primer and biotin-labeled using Affymetrix One Cycle Target Labeling kit following manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Five replicates of each group were prepared, labeled, and hybridized to Affymetrix Human Gene 2.0 ST arrays.
|
| Scan protocol |
GeneChips were scanned on Affymetrix GeneChip scanner 3000.
|
| Description |
F2
|
| Data processing |
Affymetrix Expression Console (EC) was used to generate CHP files from CEL files. Then, the CEL files were loaded into Partek Genomics Suite software, version 6.6 for normalization and differential expression analysis.
|
| |
|
| Submission date |
Apr 12, 2016 |
| Last update date |
Jun 21, 2016 |
| Contact name |
Urbain S Weyemi |
| E-mail(s) |
[email protected]
|
| Phone |
3015945093
|
| Organization name |
National Institutes of Health
|
| Department |
National Cancer Institute
|
| Lab |
Genome Integrity Group, Dev. Therapeutics Branch
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
| GSE80180 |
Twist1 and Slug mediate H2A.X-regulated epithelial-mesenchymal transition in breast cells |
|
