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Sample GSM3258634 Query DataSets for GSM3258634
Status Public on May 14, 2019
Title high density, replicate 1
Sample type RNA
 
Source name Ovary, high density
Organism Danio rerio
Characteristics strain/background: AB
gender: Female
age: 90 dpf
tissue: Ovary
condition: High density
Treatment protocol The high density effects were studied during gonadal development (6–90 dpf).
Growth protocol At 6 days post fertilization (dpf), fish were placed in 2.8-liter.
Extracted molecule total RNA
Extraction protocol At 90 dpf, fish were sacrificed and gonads were dissected and flash frozen. RNA was extracted by Trizol (Sigma).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol After fragmentation, 600 ng of labeled cRNA from each sample was hybridized to the array in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).
Scan protocol Scanned on an Agilent G2539A scanner at 5um resolution and 100% PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
Description 1G4x_1_1
Gene expression in zebrafish ovary exposed at high density at 90 dpf.
Data processing Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.
 
Submission date Jul 05, 2018
Last update date May 14, 2019
Contact name Alejandro Valdivieso
E-mail(s) valdivieso@icm.csic.es
Organization name Insituto de Ciencias del Mar
Street address PASSEIG MARÍTIM DE LA BARCELONETA, 37-49
City BARCELONA
State/province BARCELONA
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL14688
Series (1)
GSE116700 Valdivieso A, Ribas L, Piferrer F. Ovarian transcriptomic signatures of zebrafish females resistant to different environmental perturbations.

Data table header descriptions
ID_REF
VALUE Unlogged normalized intensity value

Data table
ID_REF VALUE
12 135.723483
13 3138.050556
14 100.5322317
15 101.9077694
16 3668.745314
17 5467.919773
18 94.7191358
19 6876.705276
20 2623.800911
21 884.8823565
22 23486.99204
23 417.7841839
24 124.7056956
25 5888.220204
26 166.5503655
27 1244.73227
28 17327.90214
29 33132.87124
30 1864.527887
31 152.7427275

Total number of rows: 43803

Table truncated, full table size 755 Kbytes.




Supplementary file Size Download File type/resource
GSM3258634_1G4x_1_1.txt.gz 9.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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