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Sample GSM95611 Query DataSets for GSM95611
Status Public on Feb 17, 2006
Title Zebrafish Embyro_16cell stage_Rep1
Sample type RNA
Source name zebrafish_16cell stage
Organism Danio rerio
Characteristics strain: TLAB (wild type)
embryos: 16 cell stage
Biomaterial provider Antonio Giraldez/Alex Schier
Treatment protocol no treatment
Growth protocol embryos were collected and grown in egg water (Stock salts: 40 g "Instant Ocean" Sea Salts added to 1 L distilled water
Egg water = 1.5 ml stock salts added to 1 L distilled water = 60 µg/ml final concentration) at 28 degrees Celcius prior to RNA extraction
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 This array data is obtained from zebrafish embryos at the 16 cell stage (Replicate 1).
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 147.739 P 8.57773
AFFX-BioB-M_at 117.044 P 5.16947
AFFX-BioB-3_at 147.969 P 8.41831
AFFX-BioC-5_at 349.624 P 15.6738
AFFX-BioC-3_at 333.405 P 11.2348
AFFX-BioDn-5_at 616.629 P 15.4932
AFFX-BioDn-3_at 1941.31 P 64.7013
AFFX-CreX-5_at 6595.98 P 178.473
AFFX-CreX-3_at 8217.41 P 185.05
AFFX-DapX-5_at 56.1559 A 3.39131
AFFX-DapX-M_at 50.4413 A 4.6145
AFFX-DapX-3_at 30.1811 A 5.7812
AFFX-LysX-5_at 79.9853 A 4.78139
AFFX-LysX-M_at 81.4272 A 7.44245
AFFX-LysX-3_at 106.258 A 18.5455
AFFX-PheX-5_at 344.732 A 8.46018
AFFX-PheX-M_at 220.427 A 8.14745
AFFX-PheX-3_at 101.914 A 11.1099
AFFX-ThrX-5_at 21.2716 A 5.0752
AFFX-ThrX-M_at 106.682 A 7.83118

Total number of rows: 15617

Table truncated, full table size 526 Kbytes.

Supplementary file Size Download File type/resource
GSM95611.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM95611.EXP.gz 365 b (ftp)(http) EXP
Raw data provided as supplementary file

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