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Sample GSM184146 Query DataSets for GSM184146
Status Public on Apr 26, 2008
Title zebrafish-35hpf-cd41-sorted-GFP-neg-6_repl-2
Sample type RNA
Source name transgenic zebrafish embryos at 35hpf
Organism Danio rerio
Characteristics strain background: AB. Genotype: cd41-GFP transgenic, isolated GFP negative 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 negative 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 1135.36 P 5.16732e-05
AFFX-BioB-M_at 1443.98 P 4.42246e-05
AFFX-BioB-3_at 1043.26 P 9.4506e-05
AFFX-BioC-5_at 2733.43 P 4.42873e-05
AFFX-BioC-3_at 2157.51 P 4.42873e-05
AFFX-BioDn-5_at 5601.35 P 4.42873e-05
AFFX-BioDn-3_at 13801.4 P 5.16732e-05
AFFX-CreX-5_at 33666.8 P 4.42873e-05
AFFX-CreX-3_at 41621.7 P 4.42873e-05
AFFX-DapX-5_at 58.7877 A 0.16584
AFFX-DapX-M_at 9.3457 A 0.737191
AFFX-DapX-3_at 10.4696 A 0.843268
AFFX-LysX-5_at 6.18392 A 0.824672
AFFX-LysX-M_at 44.5331 A 0.559354
AFFX-LysX-3_at 30.9676 A 0.239063
AFFX-PheX-5_at 3.88846 A 0.921998
AFFX-PheX-M_at 6.27425 A 0.921998
AFFX-PheX-3_at 17.9806 A 0.672921
AFFX-ThrX-5_at 9.19655 A 0.760937
AFFX-ThrX-M_at 30.0751 A 0.51489

Total number of rows: 15617

Table truncated, full table size 569 Kbytes.

Supplementary file Size Download File type/resource
GSM184146.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM184146.CHP.gz 87.8 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data provided as supplementary file

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