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Sample GSM1325396 Query DataSets for GSM1325396
Status Public on Apr 10, 2015
Title Uncut, 12h-cultured, P3/4, biological rep1
Sample type RNA
 
Source name Prothorasic leg discs of 100h-old male Drosophila larvae
Organism Drosophila melanogaster
Characteristics genotype: w/Y; AyGAL4, UAS-GFP/+; puc[E69-I]-GAL4/UAS-flp
gender: male
developmental stage: 100h after embryo laying
tissue: Prothoracic leg imaginal disc
treatment: Uncut, 12h-cultured
region: posterior 3/4
Treatment protocol To minimize the time variance among each sample preparation, disc fragmentation and transplantation were performed within one hour.
Growth protocol To obtain a stage-synchronized cohorts of larvae, embryos were collected in one hour and incubated for exactly 100 hours at 25˚C. Cut or uncut discs were cultured in female adult fly abdomens for exactly 12 or 24 hours at 25˚C.
Extracted molecule total RNA
Extraction protocol RNA of regenerating cells or control cells were extracted using PicoPureTM RNA Isolation Kit (ARCTRUS/Life Technologies).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocols of GeneChip® Two-Cycle CDNA Synthesis kit and GeneChip® IVT labeling kit (Affymetrix).
 
Hybridization protocol cRNA (10 µg) was hybridized for 16 hr at 45˚C on GeneChip® Drosophila Genome 2.0 Array. Following hybridization, the arrays were processed using a GeneChip Fluidics Station 400 (Affymetrix).
Scan protocol Fluorescent images of arrays were captured using the GeneChip® Scanner 3000 7G (Affymetrix)
Description Prothorasic leg discs of 100h-old male Drosophila larvae were 12h-cultured, and the correspondng region to P3/4 samples were isolated.
Data processing Microarray data were preprocessed and analyzed using R and BioConductor. First, diagnostic plots were produced and used to exclude spatial artifacts. Then, probeset level intensities were background subtracted and quantile-quantile normalized using RMA. Hierarchical clustering analysis of expression values indicated the presence of batch effects. Data were therefore adjusted for this systematic error by performing a gene-wise one-way analysis of variance using PAMR (Prediction Analysis of Microarrays, for R) (Tibshirani R. et al., PNAS 99:6567-6572 (2002)). Differential expression analysis was carried out by computing moderated F-statistics using limma. Test p-values were adjusted for multiple comparisons using the Benjamini-Hochberg correction and genes with adjusted p < 0.001 were deemed significantly differentially expressed in at least a core comparison (C12A-UC12A, C24A-UC24A, C12P-UC12P, or C24P-UC24P). Series supplementary files 'anova_p10-3_4core-comparisons_YableS1.txt' and 'anova_p10-3_4culturing.txt' list expression values, defined as gene-wise one-way ANOVA residuals (after batch effect removal with PAMR).
 
Submission date Feb 11, 2014
Last update date Apr 10, 2015
Contact name Tomonori Katsuyama
E-mail(s) [email protected]
Organization name ETH Zurich
Department D-BSSE
Street address Mattenstrasse 26
City Basel
ZIP/Postal code 4055
Country Switzerland
 
Platform ID GPL1322
Series (1)
GSE54868 JAK/STAT coordinates cell proliferation during disc regeneration with Dilp8-mediated developmental delay in Drosophila melanogaster

Data table header descriptions
ID_REF
VALUE PAMR-processed RMA data

Data table
ID_REF VALUE
1616608_a_at -0.052084227
1622892_s_at 0.12853598
1622893_at 0.045994171
1622894_at 0.101991238
1622895_at -0.278013142
1622896_at 0.074806257
1622897_at -0.132655427
1622898_a_at -0.410700542
1622899_at -0.011727392
1622900_at -0.02360272
1622901_at 0.173336495
1622902_at -0.05819966
1622903_s_at 0.023147903
1622904_at -0.021853379
1622905_at -0.067427294
1622906_at 0.18017295
1622907_at -0.008682118
1622908_a_at 0.323502976
1622909_at 0.087266058
1622910_at 0.020292287

Total number of rows: 18952

Table truncated, full table size 442 Kbytes.




Supplementary file Size Download File type/resource
GSM1325396_UC12P-1.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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