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Series GSE7658 Query DataSets for GSE7658
Status Public on Apr 26, 2008
Title Gene Expression Profile of Hematopoietic Stem Cells during Zebrafish Development
Organism Danio rerio
Experiment type Expression profiling by array
Summary In order to detect transcriptional differences between primitive and definitive hematopoietic stem and progenitor cells during regular development in the zebrafish embryo, gata1-GFP+/+(18 somites), lmo2-GFP+/+ (18 somites and 35 hpf)1 and cd41-GFP+/+ (35 hpf) cells from transgenic embryos were individually separated from GFP-/- cells by flow cytometry at the indicated stages. For each individual population, pools of 600 - 1500 transgenic embryos were collected. After RNA extraction, labelled cRNA was hybridized onto Affymetrix microarrays. Individual experiments were performed with 2 or 3 biological replicates.
Keywords: cell type comparison
Overall design gata1-GFP+/+(18 somites), lmo2-GFP+/+ (18 somites and 35 hpf)1 and cd41-GFP+/+ (35 hpf)2 cells were separated from GFP-/- cells
by flow cytometry at the indicated stages. Sorting was based on propidium iodide exclusion, forward scatter, and GFP
fluorescence, using a FACSVantage flow cytometer (Beckton Dickinson). Sorted cell populations were run twice to optimize cell
purity. Total RNA from cell-sorted populations was extracted with TRIzol reagent (Invitrogen) and purified on RNeasy resins
(Qiagen) according to the manufacturer’s recommendations. Total RNA was subjected to two rounds of linear amplification
(Ambion) and hybridized to Affymetrix zebrafish Gene Chips, according to Affymetrix guidelines. After staining with a
streptavidin-phycoerythrin conjugate (Molecular Probes), the fluorescence of bound RNA was quantitated by using a Gene Chip
scanner (Affymetrix). The raw expression data were calculated and, after pairing of GFP+/+ and GFP-/- samples, statistically
analyzed using methods implemented in Bioconductor’s “affy” package and available custom scripts 3,4.
1. Zhu, H. et al. Regulation of the lmo2 promoter during hematopoietic and vascular development in zebrafish. Dev Biol 281,
256-69 (2005).
2. Lin, H. F. et al. Analysis of thrombocyte development in CD41-GFP transgenic zebrafish. Blood 106, 3803-10 (2005).
3. Choe, S. E., Boutros, M., Michelson, A. M., Church, G. M. & Halfon, M. S. Preferred analysis methods for Affymetrix
GeneChips revealed by a wholly defined control dataset. Genome Biol 6, R16 (2005).
4. Weber, G. J. et al. Mutant-specific gene programs in the zebrafish. Blood 106, 521-30 (2005).
Contributor(s) Weber GJ, Huang H, Mayhall EA, Zhou Y, Zon LI
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 27, 2007
Last update date Jan 25, 2018
Contact name Gerhard J Weber
Organization name Children's Hospital Boston, Harvard Medical School
Department Hematology / Oncology
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
Samples (8)
GSM184125 zebrafish-35hpf-cd41-sorted-GFP-pos+3_repl-1
GSM184126 zebrafish-35hpf-cd41-sorted-GFP-neg-3_repl-1
GSM184145 zebrafish-35hpf-cd41-sorted-GFP-pos+6_repl-2
BioProject PRJNA99755

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Supplementary file Size Download File type/resource
GSE7658_RAW.tar 17.7 Mb (http)(custom) TAR (of CEL, CHP)
Raw data provided as supplementary file
Processed data provided as supplementary file

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