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Sample GSM95613 Query DataSets for GSM95613
Status Public on Feb 17, 2006
Title Zebrafish Embryo_50% epiboly
Sample type RNA
Source name zebrafish at 50% epiboly stage
Organism Danio rerio
Characteristics strain: TLAB (Wild Type)
stage: 50% epiboly
Biomaterial provider Antonio Giraldez/Alex Schier
Treatment protocol no treatment
Growth protocol embryos were collected and grown in egg water (Stock salts: 40 g
Extracted molecule total RNA
Extraction protocol RNA was isolated from 20 embyros using Trizol (Invitrogen). 20-50 ng of sample was quality checked using the RNA 6000 NanoAssay and Bioanalyzer 2100 (Agilent). Samples with a 28S/18S ribosomal peak ratio of 1.8-2.0 were labled.
Label biotin
Label protocol 2 micrograms of total RNA was used for cDNA synthesis using an oligo(dT)-T7 primer and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Synthesis, linear amplification, and labeling of cRNA were accomplished by in vitro transcription using the MessageAmp aRNA Kit (Ambion) and biotinylated nucleotides(Enzo Diagnostics).
Hybridization protocol 10 micrograms of labeled and fragmented cRNA were hybridized to GeneChip at 45 degrees C for 16 hours. Post hybridization staining and washing were performed according to the manufacturer (Affymetrix).
Scan protocol GeneChips were scanned with a high-numerical Aperture and flying objective (FOL) lens in a GS3000 scanner (Affymetrix).
Description --
Data processing normalization of all arrays was performed by dChip v.3.1. The values were then calculated using dChip's PM/MM difference model (
Submission date Feb 04, 2006
Last update date Jun 03, 2013
Contact name Antonio J. Giraldez
Phone 203 785 5423
Organization name Yale University
Department Genetics
Lab Giraldez Lab
Street address 333 Cedar Street
City New Haven
State/province CT
ZIP/Postal code 06510
Country USA
Platform ID GPL1319
Series (1)
GSE4201 Zebrafish microRNA miR-430 promotes deadenylation and clearance of maternal mRNAs

Data table header descriptions
VALUE normalized across all samples by dChip (v1.3) and calculated using the dChip PM/MM Difference Model
ABS_CALL Absolute Call (P= present, A= Absent, M= marginal)
STANDARD ERROR Standard error of VALUE determined by dChip (v1.3)

Data table
AFFX-BioB-5_at 202.415 P 8.45643
AFFX-BioB-M_at 159.32 P 5.64315
AFFX-BioB-3_at 213.587 P 6.74079
AFFX-BioC-5_at 513.476 P 11.6886
AFFX-BioC-3_at 500.874 P 8.63099
AFFX-BioDn-5_at 847.051 P 18.6328
AFFX-BioDn-3_at 2327.09 P 46.6719
AFFX-CreX-5_at 6666.16 P 158.923
AFFX-CreX-3_at 8266.64 P 167.136
AFFX-DapX-5_at 98.7329 P 5.37466
AFFX-DapX-M_at 59.275 P 2.29869
AFFX-DapX-3_at 59.2909 A 2.44461
AFFX-LysX-5_at 78.0644 A 1.99842
AFFX-LysX-M_at 84.6037 A 5.03675
AFFX-LysX-3_at 66.2512 A 4.19895
AFFX-PheX-5_at 223.528 A 5.6749
AFFX-PheX-M_at 363.765 A 2.56714
AFFX-PheX-3_at 294.67 A 14.3634
AFFX-ThrX-5_at 69.0295 A 4.7729
AFFX-ThrX-M_at 143.979 A 3.84182

Total number of rows: 15617

Table truncated, full table size 526 Kbytes.

Supplementary file Size Download File type/resource
GSM95613.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM95613.EXP.gz 367 b (ftp)(http) EXP
Raw data provided as supplementary file

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