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Sample GSM184149 Query DataSets for GSM184149
Status Public on Apr 26, 2008
Title zebrafish-35hpf-cd41-sorted-GFP-pos+9_repl-4
Sample type RNA
Source name transgenic zebrafish embryos at 35hpf
Organism Danio rerio
Characteristics strain background: AB. Genotype: cd41-GFP transgenic, isolated GFP positive cells
Age: 35 hours post fertilization
Biomaterial provider Gerhard J. Weber
Treatment protocol gata1-GFP+/+(12 somites), lmo2-GFP+/+ (12 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).
Growth protocol Embryos were obtained by pairwise matings of adult transgenic fish, raised at 28 ºC.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner.
Description Gene expression data from sorted zebrafish GFP positive cell populations at 35hours post fertilization.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Submission date Apr 24, 2007
Last update date Apr 27, 2007
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
Platform ID GPL1319
Series (1)
GSE7658 Gene Expression Profile of Hematopoietic Stem Cells during Zebrafish Development

Data table header descriptions
VALUE expression value
ABS_CALL Affymetrix absence presence call
DETECTION P-VALUE calculated p-value

Data table
AFFX-BioB-5_at 2612.89 P 4.42873e-05
AFFX-BioB-M_at 3243.74 P 4.42873e-05
AFFX-BioB-3_at 2505.91 P 7.00668e-05
AFFX-BioC-5_at 6324.33 P 4.42873e-05
AFFX-BioC-3_at 5025.25 P 4.42873e-05
AFFX-BioDn-5_at 12032.7 P 4.42873e-05
AFFX-BioDn-3_at 21849.1 P 4.42873e-05
AFFX-CreX-5_at 66807.1 P 4.42873e-05
AFFX-CreX-3_at 79266.8 P 4.42873e-05
AFFX-DapX-5_at 67.2892 A 0.216524
AFFX-DapX-M_at 54.0766 A 0.48511
AFFX-DapX-3_at 12.6194 A 0.737173
AFFX-LysX-5_at 6.71251 A 0.737173
AFFX-LysX-M_at 109.727 A 0.470241
AFFX-LysX-3_at 28.3201 A 0.227636
AFFX-PheX-5_at 3.73496 A 0.860518
AFFX-PheX-M_at 11.6524 A 0.868639
AFFX-PheX-3_at 32.6794 A 0.52976
AFFX-ThrX-5_at 22.2132 A 0.724854
AFFX-ThrX-M_at 60.6993 A 0.382599

Total number of rows: 15617

Table truncated, full table size 564 Kbytes.

Supplementary file Size Download File type/resource
GSM184149.CEL.gz 2.0 Mb (ftp)(http) CEL
GSM184149.CHP.gz 89.8 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file

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