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Sample GSM95624 Query DataSets for GSM95624
Status Public on Feb 17, 2006
Title Zebrafish_Wild Type_Rep2
Sample type RNA
 
Source name wild type embryos_9 hours post fertilization
Organism Danio rerio
Characteristics TLAB (wild type) embryos collected 9 hours 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 188.201 P 6.84219
AFFX-BioB-M_at 169.14 P 6.201
AFFX-BioB-3_at 208.175 P 5.62196
AFFX-BioC-5_at 549.801 P 8.21278
AFFX-BioC-3_at 466.002 P 11.982
AFFX-BioDn-5_at 953.352 P 32.2911
AFFX-BioDn-3_at 2646.83 P 69.8247
AFFX-CreX-5_at 7183.78 P 117.095
AFFX-CreX-3_at 9006.74 P 262.675
AFFX-DapX-5_at 137.647 A 4.59422
AFFX-DapX-M_at 61.7106 A 2.47093
AFFX-DapX-3_at 64.1092 A 2.80503
AFFX-LysX-5_at 74.0102 A 2.71402
AFFX-LysX-M_at 86.0298 A 4.31894
AFFX-LysX-3_at 75.5306 A 12.9586
AFFX-PheX-5_at 256.09 A 1.9499
AFFX-PheX-M_at 449.857 A 3.18554
AFFX-PheX-3_at 312.518 A 9.22831
AFFX-ThrX-5_at 98.5395 A 6.62966
AFFX-ThrX-M_at 148.002 A 3.07158

Total number of rows: 15617

Table truncated, full table size 526 Kbytes.




Supplementary file Size Download File type/resource
GSM95624.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM95624.EXP.gz 507 b (ftp)(http) EXP
Raw data provided as supplementary file

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