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Sample GSM1370128 Query DataSets for GSM1370128
Status Public on Apr 17, 2015
Title zebrafish neurons regenerated, bio rep 3
Sample type RNA
 
Source name cerebrospinal neurons that regenerated their axons
Organism Danio rerio
Characteristics tissue: brain
treatment: spinal cord transection
sample type: regenerated their axons
Extracted molecule total RNA
Extraction protocol The total RNA isolated using miRNeasy Micro Kit (cat.no. 217084, Qiagen Germantown, MD). The total RNA was then amplified using Ovation® Pico WTA System V2 (cat.no. 3302-12, NuGEN Technologies, Inc., San Carlos, CA)
Label biotin
Label protocol The amplified SPIA cDNA (5µg) was labeled using Encore Biotin Module V2 (cat.no. 4200-12, NuGEN Technologies, Inc., San Carlos, CA).
 
Hybridization protocol After labeling, 25 µg of cDNA were hybridized for 18 hours at 45°C to Genechip Zebrafish Genome Array. Genechips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix Genechip scanner 3000 with 7G upgrade
Description gene expression from cerebrospinal neurons that regenerated their axons
Data processing The .cel files were obtained with Affymetrix® GeneChip® Command Console® Software (AGCC). Data was analyzed in GeneSpring GX 12.6.1 (Agilent Technologies, Santa Clara, CA). Robust Multi-array Average (RMA) (Irizarry, 2003.) summarization algorithm (with Quantile Normalization and Median Polish probe summarization procedure) and baseline transformation (baseline to median of all 9 samples) was run on data using logarithmic scale. Probe sets were filtered by expression values based on percentiles (20th to 100th). For comparison of the 3 groups, ANOVA with Tukey HSD post-hoc test was done to identify statistically significant (p-value cutoff 0.05) differentially expressed transcripts. Statistical test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated with GeneSpring GX 12.6.1.
 
Submission date Apr 16, 2014
Last update date Apr 17, 2015
Contact name Katarina Vajn
E-mail(s) kav31@pitt.edu
Phone 4126483270
Organization name University of Pittsburgh
Street address 200 Lothrop St
City Pitsburgh
State/province PA
ZIP/Postal code 15213
Country USA
 
Platform ID GPL1319
Series (1)
GSE56842 Identification of axonal regeneration-associated genes after spinal cord injury in adult zebrafish

Data table header descriptions
ID_REF
VALUE RMA summarized, quantile normalized base 2 log of signal intensity.

Data table
ID_REF VALUE
AFFX-BioB-5_at 0.4236
AFFX-BioB-M_at 0.2189
AFFX-BioB-3_at 0.1963
AFFX-BioC-5_at 0.0540
AFFX-BioC-3_at 0.0437
AFFX-BioDn-5_at 0.0000
AFFX-BioDn-3_at 0.1070
AFFX-CreX-5_at -0.1126
AFFX-CreX-3_at -0.1391
AFFX-DapX-5_at 0.0565
AFFX-DapX-M_at 0.2029
AFFX-DapX-3_at 0.2112
AFFX-LysX-5_at 0.0128
AFFX-LysX-M_at 0.3743
AFFX-LysX-3_at 0.2796
AFFX-PheX-5_at 0.1987
AFFX-PheX-M_at 0.1887
AFFX-PheX-3_at 0.5131
AFFX-ThrX-5_at 0.5566
AFFX-ThrX-M_at 0.1341

Total number of rows: 15617

Table truncated, full table size 368 Kbytes.




Supplementary file Size Download File type/resource
GSM1370128_R4_Zebrafish_.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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