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Sample GSM95616 Query DataSets for GSM95616
Status Public on Feb 17, 2006
Title Zebrafish_MZ Dicer_miR-430 injected_Rep3
Sample type RNA
 
Source name MZ Dicer mutants injected with miR-430
Organism Danio rerio
Characteristics Maternal zygotic Dicer mutants

embryos collected 9 hours post fertilization

injected with miR-430 microRNA at the one cell stage
Biomaterial provider Antonio Giraldez/Alex Schier
Treatment protocol injected at the one cell stage with miR-430 micro-RNA
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 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 255.876 P 8.78722
AFFX-BioB-M_at 223.164 P 8.11668
AFFX-BioB-3_at 245.139 P 5.05981
AFFX-BioC-5_at 633.35 P 9.8321
AFFX-BioC-3_at 606.854 P 13.0434
AFFX-BioDn-5_at 1033.27 P 18.4473
AFFX-BioDn-3_at 2636.82 P 66.2698
AFFX-CreX-5_at 6524.67 P 81.8906
AFFX-CreX-3_at 7305.02 P 146.515
AFFX-DapX-5_at 117.028 A 3.52489
AFFX-DapX-M_at 56.1743 A 2.86918
AFFX-DapX-3_at 48.8117 A 2.23399
AFFX-LysX-5_at 59.0917 A 3.19492
AFFX-LysX-M_at 66.7447 A 2.65504
AFFX-LysX-3_at 67.5683 A 6.03439
AFFX-PheX-5_at 229.281 A 2.9655
AFFX-PheX-M_at 380.79 A 4.31881
AFFX-PheX-3_at 160.636 A 11.806
AFFX-ThrX-5_at 69.4486 A 7.67887
AFFX-ThrX-M_at 120.341 A 3.00604

Total number of rows: 15617

Table truncated, full table size 526 Kbytes.




Supplementary file Size Download File type/resource
GSM95616.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM95616.EXP.gz 370 b (ftp)(http) EXP
Raw data provided as supplementary file

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