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Sample GSM95625 Query DataSets for GSM95625
Status Public on Feb 17, 2006
Title Zebrafish_Wild Type_Rep3
Sample type RNA
 
Source name wild type embryos, 9 hours post fertilization
Organism Danio rerio
Characteristics TLAB wild type embryos collected 9 hour post fertilization
Biomaterial provider Antonio Giraldez/Alex Schier
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 --
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 (www.dchip.org)
 
Submission date Feb 05, 2006
Last update date Jun 03, 2013
Contact name Antonio J. Giraldez
E-mail(s) antonio.giraldez@yale.edu
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
ID_REF
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
ID_REF VALUE ABS_CALL STANDARD ERROR
AFFX-BioB-5_at 242.771 P 7.68173
AFFX-BioB-M_at 227.619 P 9.09018
AFFX-BioB-3_at 259.66 P 6.60329
AFFX-BioC-5_at 620.838 P 15.3349
AFFX-BioC-3_at 622.673 P 19.7308
AFFX-BioDn-5_at 1153.63 P 30.4387
AFFX-BioDn-3_at 3255.14 P 71.4168
AFFX-CreX-5_at 8309.17 P 189.676
AFFX-CreX-3_at 9839.38 P 275.824
AFFX-DapX-5_at 135.923 A 5.21135
AFFX-DapX-M_at 61.1573 A 3.49329
AFFX-DapX-3_at 76.6186 A 4.21758
AFFX-LysX-5_at 80.8748 A 2.58338
AFFX-LysX-M_at 95.4581 A 4.69333
AFFX-LysX-3_at 84.7154 A 5.18549
AFFX-PheX-5_at 254.488 A 3.36759
AFFX-PheX-M_at 470.019 A 3.92537
AFFX-PheX-3_at 333.74 A 11.3208
AFFX-ThrX-5_at 83.1334 A 9.90367
AFFX-ThrX-M_at 161.527 A 3.98974

Total number of rows: 15617

Table truncated, full table size 526 Kbytes.




Supplementary file Size Download File type/resource
GSM95625.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM95625.EXP.gz 508 b (ftp)(http) EXP
Raw data provided as supplementary file

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