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Sample GSM324904 Query DataSets for GSM324904
Status Public on Oct 10, 2008
Title zSP2
Sample type RNA
Source name Adult zebrafish kidney
Organism Danio rerio
Characteristics Wild type
Extracted molecule total RNA
Extraction protocol Cells were sorted into lysis buffer directly, and total RNAs were extracted using Absolutely RNA Nanoprep Kit (Stratagene) according to manufacturer's instructions.
Label Biotin
Label protocol Biotinylated cRNA was generated by 2 round of in vitro transcription (IVT) using MessageAmp II aRNA Amplification Kit (Applyied Biosystems).
Hybridization protocol Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Lymphoid cells (FS-low, SS-low) from zebrafish kidney were subdivided into the SP and MP population (referred to as "zSP" and "zMP") based on the Hoechst fluorescence intensity.
Data processing Expression values were calculated by RMA algorithm using the affy package of Bioconductor (
Submission date Sep 29, 2008
Last update date Sep 30, 2008
Contact name Isao Kobayashi
Organization name Keio University
Department Cell Differentiation
Street address 35 Shinanoma-chi
City Shinjuku-ku
State/province Tokyo
ZIP/Postal code 160-8582
Country Japan
Platform ID GPL1319
Series (1)
GSE12955 Gene expression profile of zebrafish kidney side population (SP) cells

Data table header descriptions
VALUE Signal intensity

Data table
AFFX-BioB-3_at 7.684140769
AFFX-BioB-5_at 7.82913948
AFFX-BioB-M_at 7.903327506
AFFX-BioC-3_at 8.598613306
AFFX-BioC-5_at 8.715842494
AFFX-BioDn-3_at 11.48360522
AFFX-BioDn-5_at 9.625041166
AFFX-CreX-3_at 12.77546911
AFFX-CreX-5_at 12.10007758
AFFX-DapX-3_at 2.008237513
AFFX-DapX-5_at 3.041131836
AFFX-DapX-M_at 2.308949152
AFFX-Dr-AB076373-1_at 3.069894287
AFFX-Dr-acta1-3_at 6.511658233
AFFX-Dr-acta1-5_at 4.705149136
AFFX-Dr-acta1-5_x_at 5.708257854
AFFX-Dr-acta1-M_at 4.509301782
AFFX-Dr-AF292559-1_at 2.050817442
AFFX-Dr-AF292559-2_s_at 2.040097042
AFFX-Dr-AF292559-3_s_at 1.668085598

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.

Supplementary file Size Download File type/resource
GSM324904.CEL.gz 1.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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