|
| Status |
Public on Dec 31, 2014 |
| Title |
Gfi1b knock-out Ter119 positive cells 1 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse fetal liver 14.5 dpc
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Ter119 positive erythroid cells
genotype/variation: Gfi1b knock-out
|
| Treatment protocol |
untreated
|
| Growth protocol |
Mice were housed under Specific Pathogen Free (SPF) conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol (Invitrogen) was used to isolate total RNA following the manufacturers instructions.
|
| Label |
biotin
|
| Label protocol |
Target RNA was reverse transcried into cDNA and in-vitro transcription was performed according to the standard Affymetrix protocol from 10 ug total RNA to generate biotin-labeled cRNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized with Affymetrix Mouse Gene 1.0 ST Arrays and Scanned
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Description |
Gene expression data from fetal liver derived Gfi1b conditional knockout erythroid cells
|
| Data processing |
Data was processed using the AltAnalyze software V 2.08 (www.altanalyze.org) using the default parameters.
Cel Layout File: MoGene-1_0-st-v1.r4.clf
BackGround Probe File: MoGene-1_0-st-v1.r4.bgp
Probe Group File: MoGene-1_0-st-v1.r4.pgf
The MoGene-1_0-st arrays used allow for a limited splicing analysis, or for a gene level analysis. Here we provide the gene-level analysis calculated by AltAnalyze using exclusively default parameters. During the gene level analysis process, AltAnalyze automatically remaps the transcript cluster IDs to Ensemble gene IDs if not chosen differently in the parameter settings.
We used the following (default) Expression Dataset Parameters:
-Remove probesets with DABG p-value above: 0.05
-Remove probesets expressed below (non-log): 1
-Perform alternative exon analysis: yes (calculated, but not provided here)
-Organize samples in groups: yes
-Determine gene expression levels using: constitutive probesets
-Include replicate experiment values in export: yes
-Comparison group test statistic: moderate t-test
-Remove batch effects (Combat): no
-Predict condition specific biomarkers: yes
-Perform expression clustering and visual QC: yes
-Perform cell profiling with LineageProfiler: yes
-Analyze ontologies and pathways with GO-Elite: yes
-Select the primary relational gene database used: Ensembl
Probesets were remapped to Ensembl genes by AltAnalyze internally using the matrix file "Mm_Ensembl_probesets" as a part of the "Gene level Analysis" process.
|
| |
|
| Submission date |
Jan 17, 2014 |
| Last update date |
Dec 31, 2014 |
| Contact name |
Cyrus Khandanpour |
| E-mail(s) |
[email protected]
|
| Organization name |
University Hospital Of Essen
|
| Department |
Department of Hematology
|
| Lab |
WTZ-Forschungsgebäude 2.OG
|
| Street address |
Hufelandstr. 55
|
| City |
Essen |
| State/province |
NRW |
| ZIP/Postal code |
45147 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE54204 |
Growth factor independence 1b (Gfi1b) is required for erythroid cell maturation and regulates embryonic globin expression [MoGene-1_0] |
| GSE54206 |
Growth factor independence 1b (Gfi1b) is required for erythroid cell maturation and regulates embryonic globin expression |
|
