title: Ova C3H 3 vs control C3H pool

description: Amplified RNA from lungs of ovalbumen sensitized and challenged C3H 3 mouse vs. pool of amplified RNA from lungs of control C3H mice.

source_name: Ova C3H 3

source_name: control C3H pool


title: 4mM H2O2:ctrl (1h)

status: Public on Apr 18 2003

type: RNA

city: Rockville

first: Helena

middle: I

last: Boshoff

state: MD

address: 12441 Parklawn Drive

department: LIG

country: USA

institute: NIAID/ NIH

description:
H37Rv treated for 1h with 4mM H2O2 in 7H9/ADC/Tween at OD650 = 0.3 versus control untreated cells
Sample_array_print_batch: Mtaa-03
Sample_image_analysis_software: Axon GenePix Pro
Sample_image_analysis_software_version: 3.0.6.66
Sample_microarray_scanner: GenePix 4000B [82425]
Sample_NIH_mAdb_system_expt_id: 24080
Sample_organism_strain: H37Rv
Sample_treatment_agent: hydrogen peroxide
Sample_treatment_dose: 4
Sample_treatment_dose_unit: mM
Sample_treatment_timepoint: 1
Sample_treatment_timepoint_unit: h
Sample_treatment_vehicle: None
Keywords = DNA damage

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: control


title: Timepoint9r

status: Public on Apr 16 2003

city: Cambridge

first: R.

middle: Michael

last: Raab

state: MA

address: 77 Massachusetts Avenue

department: Chemical Engineering

institute: Massachusetts Institute of Technology

description:
A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was
grown in T-25 tissue culture flasks (Corning) at 37 C in
5% CO2 under two conditions. The first condition was the control, which
contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine,
1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second
condition was identical to the first, however the glutamine concentration was
altered periodically.

Once the cells had grown to confluency, the experiment
began at 9:30 PM by exchanging the medium in all flasks. The control
flasks received the same medium, containing 4 mM glutamine, while the ex-
perimental flasks received identical medium with no glutamine. Twenty-four
hours later, the medium was exchanged again, however this time all flasks
received medium containing 4 mM glutamine. The first medium exchange was
repeated at 48 hours into the experiment, while the second was repeated
at 72 hours into the experiment. Hence the glutamine concentration of the
experimental flasks oscillated between 0 mM and 4 mM glutamine over 96
hours, while the glutamine concentration of the control flasks remained con-
stant at 4 mM glutamine. At regular intervals, the flasks were sampled.
Total RNA was isolated, medium samples were retained, and isotopic mea-
surements were performed from flasks fed different labelled compounds.
All samples taken during the experiment were analyzed.

The total RNA harvested was labeled and hybridized to DNA microarrays
to measure the abundance of transcripts present.  Total RNA control
samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA
experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during
reverse transcription.  For reverse transcription 10 ug of total RNA
was aliquoted into a 6 uL volume.  If concentration of the RNA was
necessary, this was conducted using a speed vacufuge (Eppendorf) at
60 ºC for 10 minutes.  The RNA sample was then mixed with 2 uL of 10X
Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First
Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP,
dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20
(Invitrogen), and 2 uL of Superscript II reverse transcriptase
(Invitrogen).  This reaction mixture was incubated at 42 ºC for
approximately two hours.  Following the reverse transcription reaction,
the RNA template was degraded by addition of 2 uL of 1 N NaOH and
incubation at 65 ºC for 10 minutes.  The alkaline conditions were then
neutralized by addition of 2 uL of 1 N HCl.  Samples from identical
time points that were to be compared on DNA microarrays were then
mixed.  The combined sample was cleaned to remove extra primers and
nucleotides using a QIAquick Nucleotide Removal kit as described by
the manufacturer's instructions.  Once cleaned, the sample was
concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65
ºC.  Following concentration, the sample was resuspended in 32 uL of
prewarmed hybridization buffer (Clontech Laboratories), 1 uL was
removed for quantitation, and hybridized to prepared oligonucleotide
microarrays.  Hybridization occurred overnight at 55 ºC using Corning
hybridization chambers.  The following day the arrays were washed in
Glass Hybridization Wash Solution (Clontech Laboratories), and then
in 1X SSC, and finally 0.1X SSC.  Each wash step was conducted for
20 minutes under high agitation.  The arrays were dried by
centrifugation and scanned using GenePix 4000B scanner (Axon
Instruments).  The resulting data was downloaded and formatted in
Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.).

The arrays used for hybridization were prepared using GAPS glass
slides (Corning), and a Virtek arrayer (Bio-Rad).  These arrays
contained 17,280 features, printed from a synthesized oligonucleotide
mouse library (Operon).  Briefly, the library was resuspended in
3X SSC, centrifuged, and loaded into the arrayer.  Arrays were
printed using 32 pins (Telechem), at approximately 50% humidity.
Once printed, the probes were crosslinked to the glass slides
using a UV Stratalinker (Stratagene).  The slides were then blocked
for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic
anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric
acid, pH 8.0.  They were cleaned by rinsing in 250 mL of milli-Q
water (X2), followed by 250 mL of 95% ethanol.  They were finally
dried using filtered air and stored in the dark at room temperature.
Keywords = mouse, liver, hepatoma, cell culture, glutamine, carbon metabolism

organism: Mus musculus

source_name: Hepa1-6 cells with and without glutamine

source_name: Hepa1-6 cells with glutamine


title: 4mM H2O2:ctrl (2h)_4

description:
H37Rv treated for 2h with 4mM H2O2 in 7H9/ADC/Tween at OD650 = 0.3 versus control untreated cells
Sample_array_print_batch: Mtaa-05
Sample_image_analysis_software: Axon GenePix Pro
Sample_image_analysis_software_version: 3.0.6.66
Sample_microarray_scanner: GenePix 4000B [82425]
Sample_NIH_mAdb_system_expt_id: 24084
Sample_organism_strain: H37Rv
Sample_treatment_agent: hydrogen peroxide
Sample_treatment_dose: 4
Sample_treatment_dose_unit: mM
Sample_treatment_timepoint: 2
Sample_treatment_timepoint_unit: h
Sample_treatment_vehicle: None
Keywords = DNA damage


title: Timepoint9


title: Timepoint8r


title: Timepoint8


title: Timepoint7r


title: Timepoint4r


title: Timepoint6r


title: Timepoint11


title: Timepoint10r


title: Timepoint6


title: Timepoint7


title: Timepoint1

description:
A mouse hepatoma cell line (Hepa1-6 cells, ATCC) was
grown in T-25 tissue culture flasks (Corning) at 37 C in
5% CO2 under two conditions. The first condition was the control, which
contained DMEM medium (Gibco BRL) with 25 mM glucose, 4 mM glutamine,
1% penicillin-streptomycin (Sigma), and 10% CPSR-3 (Sigma). The second
condition was identical to the first, however the glutamine concentration was
altered periodically.

Once the cells had grown to confluency, the experiment
began at 9:30 PM by exchanging the medium in all flasks. The control
flasks received the same medium, containing 4 mM glutamine, while the ex-
perimental flasks received identical medium with no glutamine. Twenty-four
hours later, the medium was exchanged again, however this time all flasks
received medium containing 4 mM glutamine. The first medium exchange was
repeated at 48 hours into the experiment, while the second was repeated
at 72 hours into the experiment. Hence the glutamine concentration of the
experimental flasks oscillated between 0 mM and 4 mM glutamine over 96
hours, while the glutamine concentration of the control flasks remained con-
stant at 4 mM glutamine. At regular intervals, the flasks were sampled.
Total RNA was isolated, medium samples were retained, and isotopic mea-
surements were performed from flasks fed different labelled compounds.
All samples taken during the experiment were analyzed.

The total RNA harvested was labeled and hybridized to DNA microarrays
to measure the abundance of transcripts present.  Total RNA control
samples were labeled using Cy3 dCTP (Perkin-Elmer), and total RNA
experimental samples were labeled using Cy5 dCTP (Perkin-Elmer) during
reverse transcription.  For reverse transcription 10 ug of total RNA
was aliquoted into a 6 uL volume.  If concentration of the RNA was
necessary, this was conducted using a speed vacufuge (Eppendorf) at
60 ºC for 10 minutes.  The RNA sample was then mixed with 2 uL of 10X
Cy-labeled dCTP, 2 uL of 100 mM DTT (Invitrogen), 4 uL of 5X First
Strand Buffer (Invitrogen), 2 uL of a dNTP mixture containing 5 mM dGTP,
dATP, dTTP and 2 mM dCTP (Invitrogen), 2 uL of 0.5 mg/ mL oligo-dT18-20
(Invitrogen), and 2 uL of Superscript II reverse transcriptase
(Invitrogen).  This reaction mixture was incubated at 42 ºC for
approximately two hours.  Following the reverse transcription reaction,
the RNA template was degraded by addition of 2 uL of 1 N NaOH and
incubation at 65 ºC for 10 minutes.  The alkaline conditions were then
neutralized by addition of 2 uL of 1 N HCl.  Samples from identical
time points that were to be compared on DNA microarrays were then
mixed.  The combined sample was cleaned to remove extra primers and
nucleotides using a QIAquick Nucleotide Removal kit as described by
the manufacturer's instructions.  Once cleaned, the sample was
concentrated using a speed vacufuge (Eppendorf) for 20 minutes at 65
ºC.  Following concentration, the sample was resuspended in 32 uL of
prewarmed hybridization buffer (Clontech Laboratories), 1 uL was
removed for quantitation, and hybridized to prepared oligonucleotide
microarrays.  Hybridization occurred overnight at 55 ºC using Corning
hybridization chambers.  The following day the arrays were washed in
Glass Hybridization Wash Solution (Clontech Laboratories), and then
in 1X SSC, and finally 0.1X SSC.  Each wash step was conducted for
20 minutes under high agitation.  The arrays were dried by
centrifugation and scanned using GenePix 4000B scanner (Axon
Instruments).  The resulting data was downloaded and formatted in
Excel (Microsoft), and then analyzed using Matlab (The MathWorks, Inc.).

The arrays used for hybridization were prepared using GAPS glass
slides (Corning), and a Virtek arrayer (Bio-Rad).  These arrays
contained 17,280 features, printed from a synthesized oligonucleotide
mouse library (Operon).  Briefly, the library was resuspended in
3X SSC, centrifuged, and loaded into the arrayer.  Arrays were
printed using 32 pins (Telechem), at approximately 50% humidity.
Once printed, the probes were crosslinked to the glass slides
using a UV Stratalinker (Stratagene).  The slides were then blocked
for 15 minutes in a 250 mL mixture containing 15.7 g/ L succinic
anhydride, 239 mL 1-methyl-2-pyrrolidinone, and 10.7 mL of 1 M boric
acid, pH 8.0.  They were cleaned by rinsing in 250 mL of milli-Q
water (X2), followed by 250 mL of 95% ethanol.  They were finally
dried using filtered air and stored in the dark at room temperature.
Keywords = mouse, liver, hepatoma, glutamine, cell culture, carbon metabolism

source_name: Hepa1-6 cells with or without glutamine


title: Timepoint 2


title: Timepoint3


title: Timepoint5


title: Timepoint3r


title: Timepoint10


title: Timepoint 1r


title: Timepoint 2r

source_name: Hepa1-6 cells grown with or without glutamine

source_name: Hepa1-6 cells grown with glutamine


title: Timepoint4

source_name: Hepa1-6 cells without glutamine


title: S67

status: Public on Apr 02 2003

city: Bethesda

first: Xin

middle: Wei

last: Wang

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description:
S67
mAdb experiment ID: 28328

organism: Homo sapiens

source_name: hepatocellular carcinoma

source_name: non-cancerous liver tissue


title: S64

description:
S64
mAdb experiment ID: 28326


title: S66

description:
S66
mAdb experiment ID: 28327


title: 60mJ/cm2 UV:ctrl (4h)

description:
H37Rv irradiated with UV at 60 mJ/cm2 in open Petri dish (2E+10 cells in 5mL 7H9/ADC/Tween) with 4h recovery in 50mL 7H9/ADC/Tween at 37C versus control unirradiated cells
Sample_array_print_batch: Mtaa-05
Sample_image_analysis_software: Axon GenePix Pro
Sample_image_analysis_software_version: 3.0.6.66
Sample_microarray_scanner: GenePix 4000B [82425]
Sample_NIH_mAdb_system_expt_id: 24092
Sample_organism_strain: H37Rv
Sample_treatment_agent: UV radiation
Sample_treatment_dose: 60
Sample_treatment_dose_unit: mJ/cm2
Sample_treatment_timepoint: 4
Sample_treatment_timepoint_unit: h
Sample_treatment_vehicle: None
Keywords = DNA damage

source_name: UV


title: S65

description:
S65
mAdb experiment ID: 28325


title: S51-PN1

description:
S51-PN1
mAdb experiment ID: 25492


title: 40mJ/cm2 UV:ctrl (8h)

description:
H37Rv irradiated with UV at 40 mJ/cm2 in open Petri dish (2E+10 cells in 5mL 7H9/ADC/Tween) with 8h recovery in 50mL 7H9/ADC/Tween at 37C versus control unirradiated cells
Sample_array_print_batch: Mtaa-04
Sample_image_analysis_software: Axon GenePix Pro
Sample_image_analysis_software_version: 3.0.6.73
Sample_microarray_scanner: GenePix 4000A [55478]
Sample_NIH_mAdb_system_expt_id: 25466
Sample_organism_strain: H37Rv
Sample_treatment_agent: UV radiation
Sample_treatment_dose: 40
Sample_treatment_dose_unit: mJ/cm2
Sample_treatment_timepoint: 8
Sample_treatment_timepoint_unit: h
Sample_treatment_vehicle: None
Keywords = DNA damage


title: S56-PN1

description:
S56-PN1
mAdb experiment ID: 25494


title: S52-PN1

description:
S52-PN1
mAdb experiment ID: 25488


title: S57-PN1

description:
S57-PN1
mAdb experiment ID: 25495


title: S47-PN2

description:
S47-PN2
mAdb experiment ID: 25485


title: S61

description:
S61
mAdb experiment ID: 28321


title: S52-PN2

description:
S52-PN2
mAdb experiment ID: 25489


title: S63

description:
S63
mAdb experiment ID: 28323


title: S47-PN1

description:
S47-PN1
mAdb experiment ID: 25484


title: S46-PN2

description:
S46-PN2
mAdb experiment ID: 25483


title: S45-PN2

description:
S45-PN2
mAdb experiment ID: 25481


title: S46-PN1

description:
S46-PN1
mAdb experiment ID: 25482


title: S53-PN1

description:
S53-PN1
mAdb experiment ID: 25490


title: S55-PN1

description:
S55-PN1
mAdb experiment ID: 25493


title: S44-PN2

description:
S44-PN2
mAdb experiment ID: 25479


title: 0.2ug/mL MMC:ctrl (4h)_2

description:
H37Rv treated for 4h with 0.2ug/mL MMC in 7H9/ADC/Tween at OD650 = 0.3 versus control untreated cells
Sample_array_print_batch: Mtaa-05
Sample_image_analysis_software: Axon GenePix Pro
Sample_image_analysis_software_version: 3.0.6.66
Sample_microarray_scanner: GenePix 4000B [82425]
Sample_NIH_mAdb_system_expt_id: 24078
Sample_organism_strain: H37Rv
Sample_treatment_agent: MMC
Sample_treatment_dose: 0.2
Sample_treatment_dose_unit: microgram/ml
Sample_treatment_timepoint: 4
Sample_treatment_timepoint_unit: h
Sample_treatment_vehicle: DMF (1/10000 dilution )
Keywords = DNA damage

source_name: MMC


title: S45-PN1

description:
S45-PN1
mAdb experiment ID: 25480


title: S44-PN1

description:
S44-PN1
mAdb experiment ID: 25478


title: S42-PN2

description:
S42-PN2
mAdb experiment ID: 25477


title: S53-PN2

description:
S53-PN2
mAdb experiment ID: 25491


title: 4mM H2O2:ctrl (2h)_3

description:
H37Rv treated for 2h with 4mM H2O2 in 7H9/ADC/Tween at OD650 = 0.3 versus control untreated cells
Sample_array_print_batch: Mtaa-04
Sample_image_analysis_software: Axon GenePix Pro
Sample_image_analysis_software_version: 3.0.6.66
Sample_microarray_scanner: GenePix 4000B [82425]
Sample_NIH_mAdb_system_expt_id: 24083
Sample_organism_strain: H37Rv
Sample_treatment_agent: hydrogen peroxide
Sample_treatment_dose: 4
Sample_treatment_dose_unit: mM
Sample_treatment_timepoint: 2
Sample_treatment_timepoint_unit: h
Sample_treatment_vehicle: None
Keywords = DNA damage


title: S49-PN2

description:
S49-PN2
mAdb experiment ID: 25487


title: S41-P1

description:
S41-P1
mAdb experiment ID: 25474


title: S42-PN1

description:
S42-PN1
mAdb experiment ID: 25476


title: S34-M1

description:
S34-M1
mAdb experiment ID: 25470


title: S34-P1

description:
S34-P1
mAdb experiment ID: 25471


title: S41-T2

description:
S41-T2
mAdb experiment ID: 25473


title: S32-M1

description:
S32-M1
mAdb experiment ID: 25464


title: S30-P1

description:
S30-P1
mAdb experiment ID: 25462


title: S30-M2

description:
S30-M2
mAdb experiment ID: 25459


title: S32-P1

description:
S32-P1
mAdb experiment ID: 25465


title: S29-M2

description:
S29-M2
mAdb experiment ID: 25456


title: S33-M1

description:
S33-M1
mAdb experiment ID: 25467


title: S30-M1

description:
S30-M1
mAdb experiment ID: 25461


title: S29-M1

description:
S29-M1
mAdb experiment ID: 25454


title: S28-P1

description:
S28-P1
mAdb experiment ID: 25453


title: S33-P1

description:
S33-P1
mAdb experiment ID: 25468


title: S29-P1

description:
S29-P1
mAdb experiment ID: 25455


title: S29-P2

description:
S29-P2
mAdb experiment ID: 25457


title: 25mJ/cm2 UV: ctrl (6h)

description:
H37Rv irradiated with UV at 25 mJ/cm2 in open Petri dish (2E+10 cells in 5mL 7H9/ADC/Tween) with 6h recovery in 50mL 7H9/ADC/Tween at 37C versus control unirradiated cells
Sample_array_print_batch: Mtaa-05
Sample_image_analysis_software: Axon GenePix Pro
Sample_image_analysis_software_version: 3.0.6.66
Sample_microarray_scanner: GenePix 4000B [82425]
Sample_NIH_mAdb_system_expt_id: 24093
Sample_organism_strain: H37Rv
Sample_treatment_agent: UV radiation
Sample_treatment_dose: 25
Sample_treatment_dose_unit: mJ/cm2
Sample_treatment_timepoint: 6
Sample_treatment_timepoint_unit: h
Sample_treatment_vehicle: None
Keywords = DNA damage


title: S49-PN1

description:
S49-PN1
mAdb experiment ID: 25486


title: S28-M2

description:
S28-M2
mAdb experiment ID: 25448


title: S27-M2

description:
S27-M2
mAdb experiment ID: 25446


title: S27-P1

description:
S27-P1
mAdb experiment ID: 25445


title: S27-P2

description:
S27-P2
mAdb experiment ID: 25447


title: S30-P2

description:
S30-P2
mAdb experiment ID: 25460


title: S28-M1

description:
S28-M1
mAdb experiment ID: 25452


title: S26-P2

description:
S26-P2
mAdb experiment ID: 25439


title: S26-P1

description:
S26-P1
mAdb experiment ID: 25442


title: S25-P2

description:
S25-P2
mAdb experiment ID: 25437


title: S25-M2

description:
S25-M2
mAdb experiment ID: 25436


title: S23-P2

description:
S23-P2
mAdb experiment ID: 25431


title: S27-M1

description:
S27-M1
mAdb experiment ID: 25443


title: S26-M2

description:
S26-M2
mAdb experiment ID: 25438


title: S25-M1

description:
S25-M1
mAdb experiment ID: 25434


title: S28-P2

description:
S28-P2
mAdb experiment ID: 25450


title: S25-P1

description:
S25-P1
mAdb experiment ID: 25435


title: S24-P1

description:
S24-P1
mAdb experiment ID: 25433


title: S26-M1

description:
S26-M1
mAdb experiment ID: 25441


title: S23-M2

description:
S23-M2
mAdb experiment ID: 25430


title: S23-M1

description:
S23-M1
mAdb experiment ID: 25428


title: S21-M1

description:
S21-M1
mAdb experiment ID: 25426


title: S24-M1

description:
S24-M1
mAdb experiment ID: 25432


title: S21-P1

description:
S21-P1
mAdb experiment ID: 25427


title: S21-P2

description:
S21-P2
mAdb experiment ID: 25425


title: S20-P2

description:
S20-P2
mAdb experiment ID: 25422


title: 40mJ/cm2 UV:ctrl (8h), H37Rv_2

description:
H37Rv irradiated with UV at 40 mJ/cm2 in open Petri dish (2E+10 cells in 5mL 7H9/ADC/Tween) with 8h recovery in 50mL 7H9/ADC/Tween at 37C versus control unirradiated cells
Sample_array_print_batch: Mtaa-04
Sample_image_analysis_software: Axon GenePix Pro
Sample_image_analysis_software_version: 3.0.6.73
Sample_microarray_scanner: GenePix 4000A [55478]
Sample_NIH_mAdb_system_expt_id: 25469
Sample_organism_strain: H37Rv
Sample_treatment_agent: UV radiation
Sample_treatment_dose: 40
Sample_treatment_dose_unit: mJ/cm2
Sample_treatment_timepoint: 8
Sample_treatment_timepoint_unit: h
Sample_treatment_vehicle: None
Keywords = DNA damage


title: S20-M2

description:
S20-M2
mAdb experiment ID: 25421


title: S20-P1

description:
S20-P1
mAdb experiment ID: 25420


title: S21-M2

description:
S21-M2
mAdb experiment ID: 25423


title: S20-M1

description:
S20-M1
mAdb experiment ID: 25419


title: S19-P1

description:
S19-P1
mAdb experiment ID: 25417


title: S17-M1

description:
S17-M1
mAdb experiment ID: 25412


title: S14-P1

description:
S14-P1
mAdb experiment ID: 25409


title: S17-P1

description:
S17-P1
mAdb experiment ID: 25413


title: S18-M1

description:
S18-M1
mAdb experiment ID: 25414


title: S15-M1

description:
S15-M1
mAdb experiment ID: 25410


title: S14-M1

description:
S14-M1
mAdb experiment ID: 25408


title: S12-P1

description:
S12-P1
mAdb experiment ID: 25407


title: S12-M1

description:
S12-M1
mAdb experiment ID: 25406


title: S15-P1

description:
S15-P1
mAdb experiment ID: 25411


title: BMM_C3H/HeJ_time2h

status: Public on Mar 28 2003

city: San Diego

first: Timothy

last: Ravasi

state: CA

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California-San Diego

description:
Total RNA was extracted using Qiagen RNeasy midi-kit from bone marrow macrophages in-vitro differentiated using human colony stimulator factor-1 (CSF-1) or from C57BL6/J 17.5 whole embryo.
The cDNA derived from the total RNA was labeled using the amino-alyll indirect labeling with Cy3 mono-reactive dye.

source_name: Total RNA from bone marrow derived macrophage from C3H/HeJ mice after 10ug/ml LPS (S. minnesota) stimulation for 2 hours

source_name: Total RNA from C57BL6/J 17.5 days whole embryo


title: S19-M1

description:
S19-M1
mAdb experiment ID: 25416


title: BMM_C3H/HeJ_time0.5h

source_name: Total RNA from bone marrow derived macrophage from C3H/HeJ mice after 10ug/ml LPS (S. minnesota) stimulation for 0.5 hours


title: BMM_C3H/HeJ_time7h

source_name: Total RNA from bone marrow derived macrophage from C3H/HeJ mice after 10ug/ml LPS (S. minnesota) stimulation for 7 hours


title: S18-P1

description:
S18-P1
mAdb experiment ID: 25415


title: BMM_C3H/HeJ_time0h

source_name: Total RNA from bone marrow derived macrophage from C3H/HeJ mice


title: S11-P1

description:
S11-P1
mAdb experiment ID: 25404


title: BMM_BalbC_time21h

source_name: Total RNA from bone marrow derived macrophage from BalbC mice after 10ug/ml LPS (S. minnesota) stimulation for 21 hours


title: BMM_C3H/HeJ_time21h

source_name: Total RNA from bone marrow derived macrophage from C3H/HeJ mice after 10ug/ml LPS (S. minnesota) stimulation for 21 hours


title: S11-M1

description:
S11-M1
mAdb experiment ID: 25405


title: BMM_BalbC_time0.5h

source_name: Total RNA from bone marrow derived macrophage from BalbC mice after 10ug/ml LPS (S. minnesota) stimulation for 0.5 hours


title: BMM_BalbC_time2h

source_name: Total RNA from bone marrow derived macrophage from BalbC mice after 10ug/ml LPS (S. minnesota) stimulation for 2 hours


title: BMM_C3H/ARC_time7h

source_name: Total RNA from bone marrow derived macrophage from C3H/ARC mice after 10ug/ml LPS (S. minnesota) stimulation for 7 hours


title: BMM_C3H/ARC_time21h

source_name: Total RNA from bone marrow derived macrophage from C3H/ARC mice after 10ug/ml LPS (S. minnesota) stimulation for 21 hours


title: 0.2ug/mL MMC:ctrl (8h), H37Rv_2

description:
H37Rv treated for 8h with 0.2ug/mL MMC in 7H9/ADC/Tween at OD650 = 0.3 versus control untreated cells
Sample_array_print_batch: Mtaa-04
Sample_image_analysis_software: Axon GenePix Pro
Sample_image_analysis_software_version: 3.0.6.73
Sample_microarray_scanner: GenePix 4000A [55478]
Sample_NIH_mAdb_system_expt_id: 25451
Sample_organism_strain: H37Rv
Sample_treatment_agent: MMC
Sample_treatment_dose: 0.2
Sample_treatment_dose_unit: microgram/ml
Sample_treatment_timepoint: 8
Sample_treatment_timepoint_unit: h
Sample_treatment_vehicle: DMF (1/10000 dilution )
Keywords = DNA damage

source_name: control


title: BMM_C3H/ARC_time2h

source_name: Total RNA from bone marrow derived macrophage from C3H/ARC mice after 10ug/ml LPS (S. minnesota) stimulation for 2 hours


title: HU10Kb482

status: Public on Feb 13 2003

city: Bordeaux

first: Richard

last: Iggo

address: 229 cours de l'Argonne

department: Bergonie Cancer Institute

country: France

institute: University of Bordeaux

description: HLFs were infected with lentivirus pAB303 expressing no insert from the H1 polIII promoter (control virus). RNA was amplified by one round of T7 transcription and labelled by reverse transcription in the presence of Cy3 and Cy5 dCTP.

source_name: Stratagene universal reference

source_name: Embryonic lung fibroblasts (HLFs)


title: S62

description:
S62
mAdb experiment ID: 28322

source_name: hepatocellular carcinoma

source_name: non-cancerous liver tissue


title: BMM_C3H/ARC_time0h

description:
Total RNA was extracted using Qiagen RNeasy midi-kit from bone marrow macrophages in-vitro differentiated using human colony stimulator factor-1 (CSF-1) or from C57BL6/J 17.5 whole embryo.
The cDNA derived from the total RNA was labeled using the amino-alyll indirect labeling with Cy3 mono-reactive dye.
Keywords = macrophages

source_name: Total RNA from bone marrow derived macrophage from C3H/ARC mice


title: BMM_C3H/ARC_time0.5h

source_name: Total RNA from bone marrow derived macrophage from C3H/ARC mice after 10ug/ml LPS (S. minnesota) stimulation for 0.5 hour

source_name: Total RNA from C57BL6/J 17.5 days whole embryo


title: HU10Kb480

description: HLFs were infected with lentiviruses pAB319 and pAB322 expressing MRG15 and MRGX small hairpin RNAs from the H1 polIII promoter. RNA was amplified by one round of T7 transcription and labelled by reverse transcription in the presence of Cy3 and Cy5 dCTP. The pAB319 shRNA induces an artefactual interferon response.


title: Embryo_04.5-5.5h_N=2_700ii29top

status: Public on Jan 06 2003

city: New Haven

first: Kevin

middle: P

last: White

state: CT

address: 333 Cedar Street

department: Department of Genetics

institute: Yale University School of Medicine

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_04.5-5.5h_N=2_700ii29top
Normalization Factor: Ratio of Medians=1.0628
Normalization Factor: Ratio of Means=1.07012
Normalization Factor: Median of Ratios=1.07439
Normalization Factor: Mean of Ratios=0.953832
Normalization Factor: Regression Ratio=1.1424
Ratio Formulation:W1/W2 (635 nm/532 nm)

organism: Drosophila melanogaster

source_name: reference


title: Embryo_22-23h_N=1_30054bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30054bot: Tmcrs; 22-23hr embryo  (bn)
Normalization Factor: Ratio of Medians=0.928324
Normalization Factor: Ratio of Means=0.923334
Normalization Factor: Median of Ratios=0.929839
Normalization Factor: Mean of Ratios=0.751551
Normalization Factor: Regression Ratio=1.08597
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: BMM_BalbC_time7h

source_name: Total RNA from bone marrow derived macrophage from BalbC mice after 10ug/ml LPS (S. minnesota) stimulation for 7 hours


title: Embryo_23-24h_N=2_700ii22topGN

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: ref. vs. 23-24h embryonic
Normalization Factor: Ratio of Medians=1.04154
Normalization Factor: Ratio of Means=1.01068
Normalization Factor: Median of Ratios=1.0863
Normalization Factor: Mean of Ratios=0.785921
Normalization Factor: Regression Ratio=1.17225
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_20-21h_N=2_700ii21botGN

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: ref. vs. 20-21h embryonic
Normalization Factor: Ratio of Medians=1.02958
Normalization Factor: Ratio of Means=1.00235
Normalization Factor: Median of Ratios=1.03635
Normalization Factor: Mean of Ratios=0.836655
Normalization Factor: Regression Ratio=1.0812
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_22-23h_N=2_700ii22botGN

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: ref. vs. 22-23h embryonic
Normalization Factor: Ratio of Medians=1.0893
Normalization Factor: Ratio of Means=1.06312
Normalization Factor: Median of Ratios=1.08461
Normalization Factor: Mean of Ratios=0.921582
Normalization Factor: Regression Ratio=1.14342
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_21-22h_N=2_700ii21topGN

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: ref. vs. 21-22h embryonic
Normalization Factor: Ratio of Medians=1.07709
Normalization Factor: Ratio of Means=1.04679
Normalization Factor: Median of Ratios=1.08894
Normalization Factor: Mean of Ratios=0.839872
Normalization Factor: Regression Ratio=1.16763
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_19-20h_N=1_30035topGNrm

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30035top:TmCrs; 19-20h (bn)
Normalization Factor: Ratio of Medians=0.976596
Normalization Factor: Ratio of Means=0.984041
Normalization Factor: Median of Ratios=0.982925
Normalization Factor: Mean of Ratios=0.844366
Normalization Factor: Regression Ratio=1.08848
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: BMM_BalbC_time0h

source_name: Total RNA from bone marrow derived macrophage from BalbC mice


title: Embryo_18-19h_N=2_700ii20botGN

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: ref. vs. 18-19h embryonic
Normalization Factor: Ratio of Medians=0.979616
Normalization Factor: Ratio of Means=0.963252
Normalization Factor: Median of Ratios=0.9867
Normalization Factor: Mean of Ratios=0.812442
Normalization Factor: Regression Ratio=1.0473
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_21-22h_N=1_30048top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30048top: Tmcrs; 21-22hr embryo  (bn)
Normalization Factor: Ratio of Medians=1.0563
Normalization Factor: Ratio of Means=1.05522
Normalization Factor: Median of Ratios=1.05931
Normalization Factor: Mean of Ratios=0.881086
Normalization Factor: Regression Ratio=1.17554
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_19-20h_N=2_700ii20topGN

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: ref. vs. 19-20h embryonic
Normalization Factor: Ratio of Medians=1.07462
Normalization Factor: Ratio of Means=1.0456
Normalization Factor: Median of Ratios=1.10437
Normalization Factor: Mean of Ratios=0.822893
Normalization Factor: Regression Ratio=1.19338
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_18-19h_N=1_30035botGNrm

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30035bot:TmCrs; 18-19h (bn)
Normalization Factor: Ratio of Medians=0.956228
Normalization Factor: Ratio of Means=0.976731
Normalization Factor: Median of Ratios=0.965324
Normalization Factor: Mean of Ratios=0.835389
Normalization Factor: Regression Ratio=1.09765
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_16-17h_N=2_700ii13botGN

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: ref. vs. 16-17h embryonic
Normalization Factor: Ratio of Medians=0.981052
Normalization Factor: Ratio of Means=1.00769
Normalization Factor: Median of Ratios=1.00761
Normalization Factor: Mean of Ratios=0.826536
Normalization Factor: Regression Ratio=1.11192
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_15-16h_N=1_30034botHNrm

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30034bot:TmCrs; 15-16h (bn)
Normalization Factor: Ratio of Medians=0.846467
Normalization Factor: Ratio of Means=0.856918
Normalization Factor: Median of Ratios=0.855585
Normalization Factor: Mean of Ratios=0.750659
Normalization Factor: Regression Ratio=0.948757
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_15-16h_N=2_700ii31top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_15-16h_N=2_700ii31top
Normalization Factor: Ratio of Medians=0.986464
Normalization Factor: Ratio of Means=1.01443
Normalization Factor: Median of Ratios=1.02159
Normalization Factor: Mean of Ratios=0.800407
Normalization Factor: Regression Ratio=1.15466
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_14-15h_N=2_700ii31bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_14-15h_N=2_700ii31bot
Normalization Factor: Ratio of Medians=0.919548
Normalization Factor: Ratio of Means=0.950302
Normalization Factor: Median of Ratios=0.942768
Normalization Factor: Mean of Ratios=0.786269
Normalization Factor: Regression Ratio=1.07699
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_17-18h_N=1_30031top2

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30031top: Tmcrs; 17-18hr embryo  (bn)
Normalization Factor: Ratio of Medians=1.09801
Normalization Factor: Ratio of Means=1.1011
Normalization Factor: Median of Ratios=1.09643
Normalization Factor: Mean of Ratios=0.974769
Normalization Factor: Regression Ratio=1.21236
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_16-17h_N=1_30034topGNrm

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30034top:TmCrs; 16-17h (bn)
Normalization Factor: Ratio of Medians=0.995916
Normalization Factor: Ratio of Means=1.00736
Normalization Factor: Median of Ratios=1.00472
Normalization Factor: Mean of Ratios=0.84355
Normalization Factor: Regression Ratio=1.13062
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_17-18h_N=2_700ii13topbGN

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: ref. vs. 17-18h embryonic
Normalization Factor: Ratio of Medians=1.01131
Normalization Factor: Ratio of Means=1.00529
Normalization Factor: Median of Ratios=1.02354
Normalization Factor: Mean of Ratios=0.819386
Normalization Factor: Regression Ratio=1.12807
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_09-10h_N=2_700ii14top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: E 09-10h N=2 700ii14top
Normalization Factor: Ratio of Medians=1.02932
Normalization Factor: Ratio of Means=1.0563
Normalization Factor: Median of Ratios=1.0469
Normalization Factor: Mean of Ratios=0.843212
Normalization Factor: Regression Ratio=1.21722
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_08-9h_N=2_700ii14bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_08-9h_N=2_700ii14bot
Normalization Factor: Ratio of Medians=0.803461
Normalization Factor: Ratio of Means=0.818275
Normalization Factor: Median of Ratios=0.828008
Normalization Factor: Mean of Ratios=0.666829
Normalization Factor: Regression Ratio=0.96967
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_23-24h_N=1_30054top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30054top: Tmcrs; 23-24hr embryo  (bn)
Normalization Factor: Ratio of Medians=1.04532
Normalization Factor: Ratio of Means=1.04356
Normalization Factor: Median of Ratios=1.04711
Normalization Factor: Mean of Ratios=0.815838
Normalization Factor: Regression Ratio=1.21971
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_06-7hr_N=2_70099bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: E 06-7h N=2 700ii99bot
Normalization Factor: Ratio of Medians=1.06289
Normalization Factor: Ratio of Means=1.0562
Normalization Factor: Median of Ratios=1.08477
Normalization Factor: Mean of Ratios=0.876296
Normalization Factor: Regression Ratio=1.17063
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_08-9h_N=1_700ii54top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_08-9h_N=1_700ii54top
Normalization Factor: Ratio of Medians=1.03525
Normalization Factor: Ratio of Means=1.0332
Normalization Factor: Median of Ratios=1.04055
Normalization Factor: Mean of Ratios=0.870165
Normalization Factor: Regression Ratio=1.1274
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_13-14h_N=1_30097top2

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [46501]
Comment: tmcrs: 13-14hr embryo (bn)
Normalization Factor: Ratio of Medians=1.20847
Normalization Factor: Ratio of Means=1.14949
Normalization Factor: Median of Ratios=1.16695
Normalization Factor: Mean of Ratios=0.892003
Normalization Factor: Regression Ratio=1.33636
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_12-13h_N=2_700ii27bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_12-13h_N=2_700ii27bot
Normalization Factor: Ratio of Medians=0.983125
Normalization Factor: Ratio of Means=0.997189
Normalization Factor: Median of Ratios=0.996649
Normalization Factor: Mean of Ratios=0.838871
Normalization Factor: Regression Ratio=1.10823
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_07-8h_N=1_700ii43bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_07-8h_N=1_700ii43bot
Normalization Factor: Ratio of Medians=1.00105
Normalization Factor: Ratio of Means=1.00885
Normalization Factor: Median of Ratios=1.01012
Normalization Factor: Mean of Ratios=0.882397
Normalization Factor: Regression Ratio=1.08349
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_10-11h_N=2_700ii25bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_10-11h_N=2_700ii25bot
Normalization Factor: Ratio of Medians=0.914651
Normalization Factor: Ratio of Means=0.925736
Normalization Factor: Median of Ratios=0.927803
Normalization Factor: Mean of Ratios=0.769794
Normalization Factor: Regression Ratio=1.03289
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_11-12h_N=1_30091top2

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [46501]
Comment: tmcrs: 11-12hr embryo (bn)
Normalization Factor: Ratio of Medians=1.21759
Normalization Factor: Ratio of Means=1.21274
Normalization Factor: Median of Ratios=1.22287
Normalization Factor: Mean of Ratios=1.04658
Normalization Factor: Regression Ratio=1.34939
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_10-11h_N=1_30091bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [46501]
Comment: tmcrs: 10-11hr embryo (bn)--lifter slip
Normalization Factor: Ratio of Medians=1.22098
Normalization Factor: Ratio of Means=1.19708
Normalization Factor: Median of Ratios=1.18671
Normalization Factor: Mean of Ratios=0.923889
Normalization Factor: Regression Ratio=1.47968
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_07-8h_N=2_700ii99top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_07-8h_N=2_700ii99top
Normalization Factor: Ratio of Medians=0.976052
Normalization Factor: Ratio of Means=0.960792
Normalization Factor: Median of Ratios=0.991822
Normalization Factor: Mean of Ratios=0.787477
Normalization Factor: Regression Ratio=1.05315
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_12-13h_N=1_30097bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [46501]
Comment: tmcrs: 12-13hr embryo (bn)--lifter slip
Normalization Factor: Ratio of Medians=1.16944
Normalization Factor: Ratio of Means=1.11421
Normalization Factor: Median of Ratios=1.14414
Normalization Factor: Mean of Ratios=0.922535
Normalization Factor: Regression Ratio=1.23765
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_09-10h_N=1_30077top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [46501]
Comment: Timecourse: cy5=9-10hr embryo  (bn)
Normalization Factor: Ratio of Medians=0.99991
Normalization Factor: Ratio of Means=1.11367
Normalization Factor: Median of Ratios=1.01832
Normalization Factor: Mean of Ratios=0.857193
Normalization Factor: Regression Ratio=1.32717
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: S23-P1

description:
S23-P1
mAdb experiment ID: 25429


title: Embryo_14-15h_N=1_30031botGN

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30031bot: Tmcrs; 14-15hr embryo  (bn)
Normalization Factor: Ratio of Medians=0.980796
Normalization Factor: Ratio of Means=0.979558
Normalization Factor: Median of Ratios=0.981282
Normalization Factor: Mean of Ratios=0.854126
Normalization Factor: Regression Ratio=1.07463
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_06-7h_N=1_700ii43top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_06-7h_N=1_700ii43top
Normalization Factor: Ratio of Medians=1.00643
Normalization Factor: Ratio of Means=1.00592
Normalization Factor: Median of Ratios=1.01258
Normalization Factor: Mean of Ratios=0.846094
Normalization Factor: Regression Ratio=1.10389
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_05.5-6.5h_N=2_700ii98top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_05.5-6.5h_N=2_700ii98top
Normalization Factor: Ratio of Medians=1.02958
Normalization Factor: Ratio of Means=1.03006
Normalization Factor: Median of Ratios=1.03907
Normalization Factor: Mean of Ratios=0.876305
Normalization Factor: Regression Ratio=1.10613
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_11-12h_N=2_700ii25top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: E 10-11h N=2 700ii25top
Normalization Factor: Ratio of Medians=0.958985
Normalization Factor: Ratio of Means=0.972225
Normalization Factor: Median of Ratios=0.988908
Normalization Factor: Mean of Ratios=0.762088
Normalization Factor: Regression Ratio=1.15506
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_05.5-6.5h_N=1_700ii38bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_05.5-6.5h_N=1_700ii38bot
Normalization Factor: Ratio of Medians=0.826888
Normalization Factor: Ratio of Means=0.844886
Normalization Factor: Median of Ratios=0.836889
Normalization Factor: Mean of Ratios=0.712913
Normalization Factor: Regression Ratio=0.9238
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_05-6h_N=2_700ii98bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_05-6h_N=2_700ii98bot
Normalization Factor: Ratio of Medians=1.03507
Normalization Factor: Ratio of Means=1.02816
Normalization Factor: Median of Ratios=1.03855
Normalization Factor: Mean of Ratios=0.921301
Normalization Factor: Regression Ratio=1.08517
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_00-1h_N=1_30053top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [47902]
Comment: Time Course cy5=0-1hr sample 1
Normalization Factor: Ratio of Medians=0.760798
Normalization Factor: Ratio of Means=0.743022
Normalization Factor: Median of Ratios=0.757187
Normalization Factor: Mean of Ratios=0.691764
Normalization Factor: Regression Ratio=0.777269
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_03-4h_N=1_30073top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [47902]
Comment: Time Course cy5=3-4hr sample 1
Normalization Factor: Ratio of Medians=1.09983
Normalization Factor: Ratio of Means=1.0692
Normalization Factor: Median of Ratios=1.07895
Normalization Factor: Mean of Ratios=0.956014
Normalization Factor: Regression Ratio=1.16446
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_02.5-3.5h_N=2_700ii24top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_02.5-3.5h_N=2_700ii24top
Normalization Factor: Ratio of Medians=1.07536
Normalization Factor: Ratio of Means=1.07703
Normalization Factor: Median of Ratios=1.08347
Normalization Factor: Mean of Ratios=0.897067
Normalization Factor: Regression Ratio=1.16998
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_03-4h_N=2_700ii5bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_03-4h_N=2_700ii5bot
Normalization Factor: Ratio of Medians=0.993096
Normalization Factor: Ratio of Means=0.986885
Normalization Factor: Median of Ratios=1.00059
Normalization Factor: Mean of Ratios=0.8409
Normalization Factor: Regression Ratio=1.07776
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_04-5h_N=1_30094bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [46501]
Comment: Timecourse: cy5=4-5hr embryo  (bn)
Normalization Factor: Ratio of Medians=0.86591
Normalization Factor: Ratio of Means=0.861419
Normalization Factor: Median of Ratios=0.861475
Normalization Factor: Mean of Ratios=0.783658
Normalization Factor: Regression Ratio=0.925885
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_02-3h_N=1_30095bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [46501]
Comment: Timecourse: cy5=2-3hr embryo  (bn)
Normalization Factor: Ratio of Medians=1.01918
Normalization Factor: Ratio of Means=1.03159
Normalization Factor: Median of Ratios=1.02274
Normalization Factor: Mean of Ratios=0.925964
Normalization Factor: Regression Ratio=1.1174
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_03.5-4.5h_N=2_700ii5top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_03.5-4.5h_N=2_700ii5top
Normalization Factor: Ratio of Medians=1.09025
Normalization Factor: Ratio of Means=1.11214
Normalization Factor: Median of Ratios=1.10848
Normalization Factor: Mean of Ratios=0.892474
Normalization Factor: Regression Ratio=1.24212
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_03.5-4.5h_N=1_30073bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [47902]
Comment: Time Course cy5=3.5-4.5hr sample 1
Normalization Factor: Ratio of Medians=0.934676
Normalization Factor: Ratio of Means=0.917368
Normalization Factor: Median of Ratios=0.920399
Normalization Factor: Mean of Ratios=0.801312
Normalization Factor: Regression Ratio=1.00757
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_0.5-1.5h_N=2_700ii9top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_0.5-1.5h_N=2_700ii9top
Normalization Factor: Ratio of Medians=0.943643
Normalization Factor: Ratio of Means=0.979043
Normalization Factor: Median of Ratios=0.9722
Normalization Factor: Mean of Ratios=0.770589
Normalization Factor: Regression Ratio=1.1222
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_02-3h_N=2_700ii24bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_02-3h_N=2_700ii24bot
Normalization Factor: Ratio of Medians=0.982293
Normalization Factor: Ratio of Means=0.989516
Normalization Factor: Median of Ratios=0.989689
Normalization Factor: Mean of Ratios=0.859457
Normalization Factor: Regression Ratio=1.06305
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_96h_N=2_700ii42bot

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Larvae_96h_N=2_700ii42bot
Normalization Factor: Ratio of Medians=1.11908
Normalization Factor: Ratio of Means=1.1214
Normalization Factor: Median of Ratios=1.12714
Normalization Factor: Mean of Ratios=0.994911
Normalization Factor: Regression Ratio=1.1949
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_01-2h_N=2_700ii15bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_01-2h_N=2_700ii15bot
Normalization Factor: Ratio of Medians=1.00366
Normalization Factor: Ratio of Means=1.03518
Normalization Factor: Median of Ratios=1.02898
Normalization Factor: Mean of Ratios=0.870221
Normalization Factor: Regression Ratio=1.13412
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_01-2h_N=1_700ii38top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_01-2h_N=1_700ii38top
Normalization Factor: Ratio of Medians=0.920207
Normalization Factor: Ratio of Means=0.957098
Normalization Factor: Median of Ratios=0.949573
Normalization Factor: Mean of Ratios=0.75212
Normalization Factor: Regression Ratio=1.07062
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_96h_N=1_30029top

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30029top Tmcrs; cy5=96--Eric's larval  (bn)
Normalization Factor: Ratio of Medians=1.69859
Normalization Factor: Ratio of Means=1.65768
Normalization Factor: Median of Ratios=1.66584
Normalization Factor: Mean of Ratios=1.38037
Normalization Factor: Regression Ratio=1.78398
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_72h_N=1_30064top

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30064top: Tmcrs; 72hr larvae (bn)
Normalization Factor: Ratio of Medians=1.23244
Normalization Factor: Ratio of Means=1.21814
Normalization Factor: Median of Ratios=1.23115
Normalization Factor: Mean of Ratios=1.01683
Normalization Factor: Regression Ratio=1.346
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_0.5-1.5h_N=1_30053bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [47902]
Comment: Time Course cy5=0.5-1.5hr sample 1
Normalization Factor: Ratio of Medians=0.695357
Normalization Factor: Ratio of Means=0.68834
Normalization Factor: Median of Ratios=0.6973
Normalization Factor: Mean of Ratios=0.612147
Normalization Factor: Regression Ratio=0.754489
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_84h_N=1_30038topGNrm

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30038top:TmCrs; 84hr larvae  (bn)
Normalization Factor: Ratio of Medians=1.22206
Normalization Factor: Ratio of Means=1.1766
Normalization Factor: Median of Ratios=1.16224
Normalization Factor: Mean of Ratios=0.945016
Normalization Factor: Regression Ratio=1.26067
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_04-5h_N=2_700ii29bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_04-5h_N=2_700ii29bot
Normalization Factor: Ratio of Medians=0.955672
Normalization Factor: Ratio of Means=0.949803
Normalization Factor: Median of Ratios=0.961222
Normalization Factor: Mean of Ratios=0.836129
Normalization Factor: Regression Ratio=1.00714
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_49h_N=2_700ii37top

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Larvae_49h_N=2_700ii37top
Normalization Factor: Ratio of Medians=1.20217
Normalization Factor: Ratio of Means=1.20082
Normalization Factor: Median of Ratios=1.21167
Normalization Factor: Mean of Ratios=0.99433
Normalization Factor: Regression Ratio=1.31822
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_43h_N=2_700ii37bot

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Larvae_43h_N=2_700ii37bot
Normalization Factor: Ratio of Medians=1.21672
Normalization Factor: Ratio of Means=1.19332
Normalization Factor: Median of Ratios=1.21708
Normalization Factor: Mean of Ratios=1.06694
Normalization Factor: Regression Ratio=1.26033
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_02.5-3.5h_N=1_700ii54bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: E 02.5-3.5h 700ii54bot  N=1
Normalization Factor: Ratio of Medians=1.0199
Normalization Factor: Ratio of Means=1.02609
Normalization Factor: Median of Ratios=1.02629
Normalization Factor: Mean of Ratios=0.916046
Normalization Factor: Regression Ratio=1.08428
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_67h_N=2_700ii39top

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Larvae_67h_N=2_700ii39top
Normalization Factor: Ratio of Medians=1.36463
Normalization Factor: Ratio of Means=1.35029
Normalization Factor: Median of Ratios=1.36682
Normalization Factor: Mean of Ratios=1.17181
Normalization Factor: Regression Ratio=1.44565
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_01.5-2.5h_N=2_700ii15top

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Embryo_01.5-2.5h_N=2_700ii15top
Normalization Factor: Ratio of Medians=1.08287
Normalization Factor: Ratio of Means=1.11583
Normalization Factor: Median of Ratios=1.09917
Normalization Factor: Mean of Ratios=0.934794
Normalization Factor: Regression Ratio=1.2365
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_72h_N=2_700ii40bot

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: L 77h 700ii40bot
Normalization Factor: Ratio of Medians=1.40009
Normalization Factor: Ratio of Means=1.38683
Normalization Factor: Median of Ratios=1.39638
Normalization Factor: Mean of Ratios=1.23496
Normalization Factor: Regression Ratio=1.46243
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_00-1h_N=2_700ii9bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: E 0-1h N=2 700ii9bot
Normalization Factor: Ratio of Medians=0.962167
Normalization Factor: Ratio of Means=1.00367
Normalization Factor: Median of Ratios=0.985446
Normalization Factor: Mean of Ratios=0.840681
Normalization Factor: Regression Ratio=1.09902
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_57h_N=1_30029bot2

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: 30029botTmcrs; cy5=57--Eric's larval  (bn)
Normalization Factor: Ratio of Medians=1.5986
Normalization Factor: Ratio of Means=1.58951
Normalization Factor: Median of Ratios=1.60216
Normalization Factor: Mean of Ratios=1.31925
Normalization Factor: Regression Ratio=1.79073
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Embryo_01.5-2.5h_N=1_30070bot

description:
Embryo samples were collected as one-hour egg lays which were allowed to develop for the desired interval. At least two pre-lays were performed before each collection. The embryos were dechorionated and snap frozen in liquid nitrogen. Aliquots from each collection were taken prior to freezing and fixed for morphological verification of developmental stage. Only tightly staged embryo collections were used for RNA isolation.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000 [47902]
Comment: Time Course cy5=1.5-2.5hr sample 1
Normalization Factor: Ratio of Medians=1.16784
Normalization Factor: Ratio of Means=1.16887
Normalization Factor: Median of Ratios=1.1584
Normalization Factor: Mean of Ratios=1.06356
Normalization Factor: Regression Ratio=1.25891
Ratio Formulation:W1/W2 (635 nm/532 nm)


title: Larvae_84h_N=2_700ii40top

description:
Larvae were raised from 6-hour embryonic egg lays, synchronized at hatching, and aged appropriately and stage-verified by morphology.
Samples were prepared using the Canton S wild type strain and were raised and aged at 25°C. Total RNA was isolated using Trizol reagent (Gibco-BRL) and the PolyA+ was extracted using the PolyATtract mRNA isolation system (Promega). For more details on Materials and Methods, see http://www.sciencemag.org/cgi/data/297/5590/2270/DC1/1
Scanner:GenePix 4000A
Comment: Larvae_84h_N=2_700ii40top
Normalization Factor: Ratio of Medians=1.36885
Normalization Factor: Ratio of Means=1.35797
Normalization Factor: Median of Ratios=1.36695
Normalization Factor: Mean of Ratios=1.23086
Normalization Factor: Regression Ratio=1.42904
Ratio Formulation:W1/W2 (635 nm/532 nm)