|
| Status |
Public on Apr 20, 2016 |
| Title |
HSPC_A |
| Sample type |
RNA |
| |
|
| Source name |
Hematopoietic stem/progenitor cells (HSPC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hematopoietic stem/progenitor cells (HSPC)
|
| Growth protocol |
Committed erythroid and myeloid progenitors/precursors (EPP and MPP) were isolated as pools of CD34lowCD36high and CD34-CD13+ populations, after induction for five days in culture in the presence of SCF, IL3 and either Epo or G-CSF, respectively
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy Plus Mini kit (QIAGEN) and reverse transcribed by GeneChip 3IVT Express kit.
|
| Label |
biotin
|
| Label protocol |
Affymetrix HG-U133 Plus 2.0 GeneChip arrays staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Affymetrix HG-U133 Plus 2.0 GeneChip arrays hybridization was performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).
|
| Scan protocol |
Affymetrix HG-U133 Plus 2.0 GeneChip arrays scanning was performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA). Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GeneChip Operating Software (GCOS) software.
|
| Data processing |
Preprocessing of the data and normalization was carried out in R ('Affy' package). Specifically, probe level signals have been converted to expression values using the robust multi?array average procedure (RMA); intensity levels have been background adjusted, normalized using quantile normalization, and log2 expression values calculated using median polish summarization. The arrays were annotated using a custom chip definition file, the Gene Annot CDF for Human Gene U133 Plus 2.0 arrays, and the corresponding Bioconductor libraries (GeneAnnot version 2.1.0).
|
| |
|
| Submission date |
Jan 12, 2015 |
| Last update date |
Apr 20, 2016 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
silvio.bicciato@unipd.it
|
| Phone |
+39-049-827-6108
|
| Organization name |
University of Padova
|
| Department |
Molecular Medicine
|
| Street address |
via U. Bassi 59/b
|
| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19633 |
| Series (2) |
| GSE64888 |
Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation [Microarray] |
| GSE70677 |
Genome-wide definition of regulatory elements in hematopoietic stem cell differentiation |
|
