|
| Status |
Public on Jul 14, 2016 |
| Title |
HSA_INT_1 |
| Sample type |
RNA |
| |
|
| Source name |
E13 fetal liver progenitors
|
| Organism |
Mus musculus |
| Characteristics |
progenitors: a4b7-HSAint
development stage: Embryonic day 13
|
| Growth protocol |
Freshly isolated fetal liver cells were depleted of lineage positive cells and lymphoid progenitors were sorted on a FACS Aria III cell sorted directly to RLT buffer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isoalted using the MicroRNAeasy kit from Quiagen France that included a DNAse treatment according to the manufacture's instructions. RNA quality was checked in an Agilent 2100 Bioanalyzer platform (Agilent Technologies).
|
| Label |
Biotin
|
| Label protocol |
For microarray target material used in the study, 50 ng total RNA was reverse transcribed and amplified per the manufacturer’s protocols using the Ovation Pico WTA System v2 (Nugen Technologies, Inc. #3302-12), fragmented and biotin labeled using the Encore Biotin Module, (Nugen Technologies, Inc. #4200-12).
|
| |
|
| Hybridization protocol |
Gene expression was determined by hybridization of the labeled template to HuGene 1.0 ST microarrays (Affymetrix, Inc.,Santa Clara, CA). Hybridization cocktail and post-hybridization processing was performed according to the “Target Preparation for Affymetrix GeneChip® Eukaryotic Array Analysis” protocol found in the appendix of the Nugen protocol of the fragmentation kit. Arrays were hybridized for 18 hours and washed using fluidics protocol FS450_0007 on a GeneChip Fluidic Station 450 (Affymetrix, Inc.)
|
| Scan protocol |
Data was scanned with an Affymetrix Genechip Scanner 3000, generating CEL files for each array. Three (3) Biological replicates were run for each condition.
|
| Data processing |
Quality assessment and normalization of the arrays was performed with the tools available in Expression Console v1.1 (Affymetrix, Inc.,Santa Clara, CA) and Bioconductor packages
|
| |
|
| Submission date |
Jul 13, 2016 |
| Last update date |
Jul 14, 2016 |
| Contact name |
Ana Cumano |
| E-mail(s) |
[email protected]
|
| Phone |
+33145688255
|
| Organization name |
Pasteur Institute
|
| Department |
Immunology
|
| Lab |
Lymphopoiesis
|
| Street address |
25 Rue du Dr. Roux
|
| City |
Paris |
| ZIP/Postal code |
75724 |
| Country |
France |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE84366 |
Gene expression of E13 fetal liver of common lymphoid progenitors Flt3+ a4b7+ compared to a4b7-HSAint, a4b7-HSAhi or a4b7-HSAlow |
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