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^SAMPLE = Drosophila_T0-1
!Sample_title = embryo at T0, biological rep1
!Sample_supplementary_file = Drosophila_T0-1.CEL
!Sample_source_name_ch1 = Drosophila embryos before nuclear cycle 9 (maternal transcripts)
!Sample_organism_ch1 = Drosophila melanogaster
!Sample_characteristics_ch1 = Genotype: yellow white and Oregon R parents
!Sample_characteristics_ch1 = Age: embryos younger than nuclear cycle 9, i.e. before pole cells budding
!Sample_treatment_protocol_ch1 = 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_ch1 = 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_ch1 = total RNA
!Sample_extract_protocol_ch1 = Trizol extraction of total RNA was performed according to the manufacturer's instructions.
!Sample_label_ch1 = biotin
!Sample_label_protocol_ch1 = 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_platform_id = GPL72
#ID_REF =
#VALUE = MAS5-calculated Signal intensity
#ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
#DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call
!Sample_table_begin
ID_REF VALUE ABS_CALL DETECTION P-VALUE
141200_at 36.6 A 0.818657
141201_at 41.5 A 0.703191
141202_at 607.3 P 0.000944
141203_at 1509.1 P 0.000762
141204_at 837.3 P 0.000613
141205_at 363.2 P 0.003815
141206_at 1193.6 P 0.000491
141207_at 346.6 P 0.001165
141208_at 257.8 P 0.006575
141209_at 337.1 P 0.002607
141210_at 48 A 0.150145
141211_at 130.7 P 0.005504
141212_at 1454.3 P 0.000491
141213_at 21.2 A 0.635055
142121_at 133.7 A 0.889551
142122_at 275.3 A 0.611218
142123_at 307.6 A 0.611218
142124_at 132.6 A 0.437646
142125_at 195.8 A 0.110449
142126_at 174.1 A 0.681117
142127_at 316.3 A 0.65838
!Sample_table_end
^SAMPLE = Drosophila_T0-2
!Sample_title = embryo at T0, biological rep2
!Sample_supplementary_file = Drosophila_T0-2.CEL
!Sample_source_name_ch1 = Drosophila embryos before nuclear cycle 9 (maternal transcripts)
!Sample_organism_ch1 = Drosophila melanogaster
!Sample_characteristics_ch1 = Genotype: yellow white and Oregon R parents
!Sample_characteristics_ch1 = Age: embryos younger than nuclear cycle 9, i.e. before pole cells budding
!Sample_treatment_protocol_ch1 = 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_ch1 = 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_ch1 = total RNA
!Sample_extract_protocol_ch1 = Trizol extraction of total RNA was performed according to the manufacturer's instructions.
!Sample_label_ch1 = biotin
!Sample_label_protocol_ch1 = 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_platform_id = GPL72
#ID_REF =
#VALUE = MAS5-calculated Signal intensity
#ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
#DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call
!Sample_table_begin
ID_REF VALUE ABS_CALL DETECTION P-VALUE
141200_at 70.3 A 0.216313
141201_at 38 A 0.635055
141202_at 831.8 P 0.000613
141203_at 2215.5 P 0.000944
141204_at 965.6 P 0.000491
141205_at 383.2 P 0.001432
141206_at 1195 P 0.000491
141207_at 413.7 P 0.000613
141208_at 447.3 P 0.000762
141209_at 294.4 P 0.004591
141210_at 81.7 M 0.054711
141211_at 84.9 P 0.005504
141212_at 1456.4 P 0.000491
141213_at 37 A 0.122747
142121_at 133.7 A 0.889551
142122_at 275.3 A 0.611218
142123_at 307.6 A 0.611218
142124_at 132.6 A 0.437646
142125_at 195.8 A 0.110449
142126_at 174.1 A 0.681117
142127_at 316.3 A 0.65838
!Sample_table_end
^SAMPLE = Drosophila_T1-1
!Sample_supplementary_file = Drosophila_T1-1.CEL
!Sample_title = embryo at T1, biological rep1
!Sample_source_name_ch1 = Drosophila embryos in slow phase of cellularisation
!Sample_organism_ch1 = Drosophila melanogaster
!Sample_characteristics_ch1 = Genotype: yellow white and Oregon R parents
!Sample_characteristics_ch1 = Age: embryos in slow phase of cellularisation
!Sample_treatment_protocol_ch1 = 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_ch1 = 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_ch1 = total RNA
!Sample_extract_protocol_ch1 = Trizol extraction of total RNA was performed according to the manufacturer's instructions.
!Sample_label_ch1 = biotin
!Sample_label_protocol_ch1 = 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.
!Sample_platform_id = GPL72
#ID_REF =
#VALUE = MAS5-calculated Signal intensity
#ABS_CALL = the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
#DETECTION P-VALUE = 'detection p-value', p-value that indicates the significance level of the detection call
!Sample_table_begin
ID_REF VALUE ABS_CALL DETECTION P-VALUE
141200_at 20.8 A 0.801637
141201_at 85.8 A 0.48748
141202_at 704.8 P 0.000613
141203_at 1036.6 P 0.000944
141204_at 700.3 P 0.000491
141205_at 462.4 P 0.003159
141206_at 1301.9 P 0.000491
141207_at 454.8 P 0.000944
141208_at 438.6 P 0.000944
141209_at 264.4 P 0.004591
141210_at 65.6 A 0.150145
141211_at 72.2 A 0.070073
141212_at 1200 P 0.000491
141213_at 13.7 A 0.635055
142121_at 133.7 A 0.889551
142122_at 275.3 A 0.611218
142123_at 307.6 A 0.611218
142124_at 132.6 A 0.437646
142125_at 195.8 A 0.110449
142126_at 174.1 A 0.681117
142127_at 316.3 A 0.65838
!Sample_table_end
^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_type = time course
!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
|
