|
| Status |
Public on Mar 25, 2014 |
| Title |
C10-MSCV cells untreated, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
C10 cells transduced with empty vector, control
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pre-B cells
|
| Treatment protocol |
Biological duplicates of C10-MSCV and C10-HDAC7 cells were treated with 100nM β-estradiol in the presence of 10nM of IL-3 and CSF-1 and harvested for RNA extraction at various times thereafter. Uninduced C10-MSCV and C10-HDAC7 were maintained for 24h in 0.1% ethanol.
|
| Growth protocol |
C10-MSCV and C10-HDAC7 cells were cultured at 37ºC in RPMI 1640 without phenol red supplemented with 10% of charcoal treated fetal bovine serum, 2 mM glutamine, and 50 U/ml streptomycin/penicillin. For the generation of C10-MSCV and C10-HDAC7 cells, C10 cells were spin infected and 48 hours after were selected in the presence of 3ug/ml of puromycin. For transdifferentiation induction, cells were treated with 100nM β-estradiol in the presence of 10nM of IL-3 and 10nM of mCsf1 for the indicated periods of time.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with a combination of Trizol and RNeasy minikit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.
|
| |
|
| Hybridization protocol |
PCR amplified biotinylated cDNA were hybridized against Affymetrix HT MG-430 PM Array Plate (Mouse Genome 430 PM strip).
|
| Scan protocol |
GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
|
| Description |
Gene expression data from uninduced C10-MSCV cells
|
| Data processing |
Affymatrix CEL files were background corrected and normalized using Bioconductor package “affy”. Particularly we used Affy 'expresso' algorithm. Since the Affymetrix chip version used in this study contains only perfect match (pm) probes, for normalization and acquiring raw probe intensities to expression values we used following parameters: background correction method rma; normalization method constant; pm correct method pmonly; and summary method avgdiff. Normalized absolute values were conveter to Log2 intensities using R program.
|
| |
|
| Submission date |
Mar 27, 2012 |
| Last update date |
Mar 25, 2014 |
| Contact name |
Maribel Parra |
| E-mail(s) |
mparra@idibell.cat, khademul.islam@gmailcom
|
| Phone |
+34932607133
|
| Fax |
+34932607219
|
| URL |
http://www.pebc.cat/grupodetalle.php?idg=20
|
| Organization name |
Bellvitge Biomedical Research Institute (IDIBELL)
|
| Department |
Cancer Epigenetics and Biology Programme (PEBC)
|
| Lab |
Cellular Differentiation
|
| Street address |
Avda. Gran Via 199-203, L'Hospitalet de Llobregat
|
| City |
Barcelona |
| State/province |
Barcelona |
| ZIP/Postal code |
08908 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11180 |
| Series (1) |
| GSE36827 |
HDAC7 is a repressor of myeloid genes whose downregulation in pre-B cells is required for transdifferentiation into macrophages |
|
