^SAMPLE = Drosophila_T0-1
!Sample_title = embryo at T0, biological rep1
!Sample_supplementary_file = Drosophila_T0-1.CEL
!Sample_table = Drosophila_T0-1.CHP
!Sample_source_name = Drosophila embryos before nuclear cycle 9 (maternal transcripts)
!Sample_organism = Drosophila melanogaster
!Sample_characteristics = Tissue: Dechorionated embryo
!Sample_characteristics = Genotype: yellow white and Oregon R parents
!Sample_characteristics = Age: embryos younger than nuclear cycle 9
!Sample_treatment_protocol = Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).
!Sample_growth_protocol = 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4. 
!Sample_molecule = total RNA
!Sample_extract_protocol = Trizol extraction of total RNA was performed according to the manufacturer's instructions.
!Sample_label = biotin
!Sample_label_protocol = Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
!Sample_hyb_protocol = Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.  
!Sample_scan_protocol = GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A. 
!Sample_description = Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
!Sample_data_processing = The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
^SAMPLE = Drosophila_T0-2
!Sample_title = embryo at T0, biological rep2
!Sample_supplementary_file = Drosophila_T0-2.CEL
!Sample_table = Drosophila_T0-2.CHP
!Sample_source_name = Drosophila embryos before nuclear cycle 9 (maternal transcripts)
!Sample_organism = Drosophila melanogaster
!Sample_characteristics = Tissue: Dechorionated embryo
!Sample_characteristics = Genotype: yellow white and Oregon R parents
!Sample_characteristics = Age: embryos younger than nuclear cycle 9
!Sample_treatment_protocol = Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).
!Sample_growth_protocol = 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4. 
!Sample_molecule = total RNA
!Sample_extract_protocol = Trizol extraction of total RNA was performed according to the manufacturer's instructions.
!Sample_label = biotin
!Sample_label_protocol = Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
!Sample_hyb_protocol = Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.  
!Sample_scan_protocol = GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A. 
!Sample_description = Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
!Sample_data_processing = The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
^SAMPLE = Drosophila_T1-1
!Sample_supplementary_file = Drosophila_T1-1.CEL
!Sample_table = Drosophila_T1-1.CHP
!Sample_title = embryo at T1, biological rep1
!Sample_source_name = Drosophila embryos in slow phase of cellularisation
!Sample_organism = Drosophila melanogaster
!Sample_characteristics = Tissue: Dechorionated embryo
!Sample_characteristics = Genotype: yellow white and Oregon R parents
!Sample_characteristics = Age: embryos in slow phase of cellularisation
!Sample_treatment_protocol = Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).
!Sample_growth_protocol = 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4. 
!Sample_molecule = total RNA
!Sample_extract_protocol = Trizol extraction of total RNA was performed according to the manufacturer's instructions.
!Sample_label = biotin
!Sample_label_protocol = Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
!Sample_hyb_protocol = Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.  
!Sample_scan_protocol = GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A. 
!Sample_description = Gene expression data from embryos in slow phase of cellularisation.
!Sample_data_processing = The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
^SERIES = Dros_embryo_timecourse
!Series_title = Expression data from early Drosophila embryo 
!Series_summary = Morphogenesis of epithelial tissues relies on the precise developmental control of cell polarity and architecture. In the early Drosophila embryo, the primary epithelium forms during cellularisation, following a tightly controlled genetic programme where specific sets of genes are up-regulated. Some of them, for instance, control membrane invagination between the nuclei anchored at the apical surface of the syncytium. 
!Series_summary = We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. 
!Series_overall_design = Drosophila embryos were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of embryos at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected embryos according to morphological criteria at five time-points: before pole cell formation, i.e. before zygotic transcription (T0), during the slow phase (T1) and the fast phase (T2) of cellularisation and at the beginning (T3) and the end (T4) of gastrulation. 
!Series_contributor = Jane,Doe
!Series_contributor = John,A,Smith
!Series_contributor = Hans,van Elton
!Series_contributor = John,Smithers Jr
!Series_contributor = Jie,D,Chen
!Series_sample_id = Drosophila_T0-1
!Series_sample_id = Drosophila_T0-2
!Series_sample_id = Drosophila_T1-1