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Sample GSM95612 Query DataSets for GSM95612
Status Public on Feb 17, 2006
Title Zebrafish Embryo_16 cell stage_Rep2
Sample type RNA
 
Source name zebrafish_16 cell 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
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 04, 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 151.601 P 7.20874
AFFX-BioB-M_at 121.296 P 6.26874
AFFX-BioB-3_at 116.533 P 9.39392
AFFX-BioC-5_at 322.116 P 14.0849
AFFX-BioC-3_at 317.124 P 8.84455
AFFX-BioDn-5_at 571.142 P 13.0357
AFFX-BioDn-3_at 1918.91 P 58.8674
AFFX-CreX-5_at 6577.42 P 231.994
AFFX-CreX-3_at 7862.65 P 299.249
AFFX-DapX-5_at 56.3897 A 4.56864
AFFX-DapX-M_at 55.316 A 4.04707
AFFX-DapX-3_at 40.2471 A 5.19478
AFFX-LysX-5_at 65.9163 A 3.83169
AFFX-LysX-M_at 87.1227 A 3.91495
AFFX-LysX-3_at 113.711 A 17.5618
AFFX-PheX-5_at 382.564 A 6.30701
AFFX-PheX-M_at 234.843 A 3.65604
AFFX-PheX-3_at 106.247 A 10.1021
AFFX-ThrX-5_at 12.5615 A 8.79589
AFFX-ThrX-M_at 114.13 A 5.52222

Total number of rows: 15617

Table truncated, full table size 527 Kbytes.




Supplementary file Size Download File type/resource
GSM95612.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM95612.EXP.gz 366 b (ftp)(http) EXP
Raw data provided as supplementary file

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