title: Nm-PTZ+LEV 2nd day Replicate 3 (Dye swap)

status: Public on Mar 19 2008

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3.0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations

source_name: Drosophila melanogaster, unmated, untreated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labelled cRNA synthesis with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media for 2 days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC

value: 3-4 day old

value: Male

source_name: Drosophila melanogaster, unmated, treated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labelled cRNA synthesis with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 8mg/ml of PTZ and 5mg/ml of levetiracetam for 2 days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NM-PTZ+LEV 2nd day Replicate 4 (Dye swap)

type: RNA

city: Delhi

first: Abhay

last: Sharma

state: Delhi

address: Delhi University campus, Mall Road

department: Functional Genomics Unit

country: India

institute: CSIR-Institute of Genomics and Integrative Biology (IGIB)

description: The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data.

scan_protocol: Microarray slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices), using both green and red lasers. The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices).

molecule: total RNA

organism: Drosophila melanogaster

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from eight pools of frozen heads, each representing flies collected from four vials two times of which comprised a single parallel set of treatment, using TRI REAGENT (Sigma) according to the manufacturer’s protocol

tag: Strain

value: Oregon-R

tag: Age

tag: Sex

tag: Tissue

value: Head

source_name: unmated, 3-4 day old, untreated

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 8mg/ml of PTZ and 5mg/ml of levetiracetam for 2 days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NF-PTZ 2nd day Female Replicate 3 (Dye Swap)

status: Public on Mar 25 2008

description: The data in the file is ratio normalized. The ratio in the value column was derived from normalized data.

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) >= 0.6) and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3.0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations

source_name: Drosophila melanogaster, virgin, untreated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy5 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) for 2 days.Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

value: 3-4 days old

value: Female

source_name: Drosophila melanogaster, virgin, treated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 2 day .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NF-PTZ 12 hrs Female Replicate 1

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) 12 hours .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy3 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) for 12 hours .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NM-PTZ+LEV 2nd day Replicate 2


title: NF_PTZ 12 hrs Female Replicate 3 (Dye Swap)

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65 ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) 12 hours .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

value: Oregon-R Sex:Female Tissue:Head


title: NF-PTZ 2nd day female Replicate 1


title: NM-PTZ+LEV-PTZ 7th day (Dye Swap)

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media  for 4 days and then flies were shifted to Normal medium for 3 days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 8mg/ml of PTZ and 5mg/ml of levetiracetam for 4 days and again shifted to normal medium containing 8 mg/ml of PTZ for 3 days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NF-PTZ 2nd Day Female Replicate 4 (Dye Swap)

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals


title: Nm-PTZ+LEV 2nd day Replicate 1


title: Nm-PTZ+LEV-PTZ 7th day (Dye Swap)

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media for 4 days and again shifted to normal medium for 3 days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media containing 8mg/ml of PTZ and 5mg/ml of levetiracetam for 4 days and then flies were shifted to Normal medium containing 8 mg/ml of PTZ for 3 days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NF-PTZ 12 Hrs Female Replicate 4 (Dye Swap)

source_name: Drosophila melanogaster, Virgin, untreated

value: Oregon R


title: NM-PTZ+LEV 7th Day Replicate 1

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 8mg/ml of PTZ and 5mg/ml of levetiracetam for 4 days and then flies were shifted to Normal medium containing 8 mg/ml of PTZ for 3 days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media for 4 days and again shifted to normal medium for 3 days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NM-PTZ+LEV 7th day Replicate 2


title: Nm-PTZ+LEV 12 Hrs (Dye Swap)

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media for 12 hrs, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 8mg/ml of PTZ and 5mg/ml of levetiracetam for 12 hrs, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: Nm-PTZ+LEV 12 Hrs (Dye Swap)

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media for 12 hrs, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containg 8mg/ml of PTZ and 5mg/ml of levetiracetam for 12 hrs, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NF-PTZ 2nd day Female Replicate 2

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37 ºC for 16 hrs.


title: NA18517_vs_NA15510

status: Public on May 01 2008

type: genomic

city: Seattle

first: Jeffrey

middle: M

last: Kidd

state: WA

address: 1705 NE Pacific St

department: Department of Genome Sciences

country: USA

institute: University of Washington

description: Performed by NimbleGen following company specifications.

data_processing: normalized log2 Cy5/Cy3

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: Coriell

tag: NA18517, ABC7, female


title: NA18507_vs_NA15510

hyb_protocol: Performed by NimbleGen following company specifications.

tag: DNA from NA15510 female

tag: NA18507 (ABC8) male


title: Nm-PTZ+LEV 12 Hrs Replicate 1

description: The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereo microscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media containing 8mg/ml of PTZ and 5mg/ml of levetiracetam for 12 hrs, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC.

source_name: Drosophila melanogaster, unmated,  untreated.


title: HK-2 AngII+Cand

status: Public on Feb 28 2008

city: Liverpool

first: Rana

last: Rustom

address: Duncan Street

department: Metabolic and Cellular Medicine

country: United Kingdom

institute: University of Liverpool

description: Angiotensin II (AngII) is involved in the pathogenesis of progressive renal injury in varied kidney disease. The effects of AngII and candesartan, a specific innhibitor of AngII type 1 receptor, on the changes in gene protein expression stimulated by oxidative stress in PTC were assesed using cDNA microarrays.

hyb_protocol: According to user manual for Nylon Atlas cDNA Expression Arrays available at www.clontech.com

scan_protocol: The arrays were exposed to Storage Phosphor Screens (Amersham Pharmacia Biotech, Little Chalfont, UK). The phosphor screens were scanned using a Biorad Personal Molecular Imager FX (Biorad, Hercules, CA, USA).

data_processing: Values were normalized using Global normalization

source_name: Human renal proximal tubular epithelial cells

growth_protocol: Cells were cultured until 90-95% confluent in DMEM/Ham s F12 medium supplemented with 5.5 mM glucose, 2 mM L-glutamine, 5 ug/ml insulin, 5 ug/ml transferrin, 5 ng/ml sodium selenite, 0.4 ug/ml hydrocortisone, 5 ng/ml epidermal growth factor, 100 U/ml penicillin, 100 ug/ml streptomycin, 20 mM Hepes, and 10% FCS.

extract_protocol: Total RNA was isolated from HK-2 cells using Tri-reagent (Sigma, UK) as recommended by the manufacturer s protocol. The RNA content of the samples was measured using RiboGreen RNA Quantitation Reagent (Molecular Probes, Invitrogen, UK). The integrity of the total RNA was verified on a denaturing agarose-formaldehyde gel.

treatment_protocol: Cells were growth arrested for 48 h in serum-free DMEM/Ham's F-12 medium with 5.5 mM glucose, 2 mM L-glutamine,100 U/ml penicillin, 100 ug/ml streptomycin, 20 mM Hepes. Medium was refreshed and supplemented with 0.1 uM candesartan for 1h at 37C. Medium was refreshed again and supplemented with 0.1uM candesartan and 1 uM AngII. After further 24 h under standard cell culture conditions (37C, 5% CO2) cells were subjected to RNA extraction.

tag: Immortalised human renal proximal tubular epithelial cells


title: NA18956_vs_NA15510

scan_protocol: Performed by NimbleGen following company specifications.

tag: NA18956, ABC9, female


title: Nm-PTZ+LEV 12 Hrs Replicate 2

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 8mg/ml of PTZ and 5mg/ml of levetiracetam for 12 hrs, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media for 12 hrs, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NA18555_vs_NA15510

label_protocol: Performed by NimbleGen following company specifications.

tag: NA18555, ABC11, female


title: NA19240_vs_NA15510

tag: NA19240, ABC10, female


title: Nm-PILO Replicate 4 (Dye swap)

status: Public on Mar 18 2008

description: The data in the file is ratio normalized. The ratio in the Value column was derived from normalized.

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media containing Normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media containing 1.5 mg/ml of pilocarpine (PILO) for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NM-TEA Replicate3 (Dye Swap)

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) >= 0.6) and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3.0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 16 mg/ml of Tetraethylammonium chloride for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: Nm-PILO (Replicate2)

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 1.5 mg/ml of pilocarpine (PILO) for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy3 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing Normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NM-TEA (Replicate2)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy5 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 2-3 days in standard culture vials containing NF in batches of 30 individuals


title: Nm-STR Replicate3 (Dye Swap)

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 3.33 mg/ml of Strychnine (STR) for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: Nm-PILO Replicate3 (Dye swap)


title: Nm-STR (Replicate2)

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NM-STR (Replicate1)


title: NA12156_vs_NA15510

tag: NA12156, ABC14, female


title: NM-TEA (Replicate1)

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media containing 16 mg/ml of Tetraethylammonium chloride (TEA) for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: Nm-STR Replicate4 (Dye Swap)


title: NM-TEA Replicate4 (Dye Swap)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy5 dye (Amersham Biosciences), using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 24 +/- 1ºC in the treatment vessel in Normal media  for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: Nm-PILO (Replicate1)

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media containing 1.5 mg/ml of pilocarpine (PILO) for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel in normal media containing Normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: Q188Rfibroblasts_galactose_2days_rep2

status: Public on Nov 01 2007

city: Miami

first: Kent

last: Lai

state: FL

department: Pediatrics

institute: University of Miami

description: Cells were infected with lentiviral vector containing either GALT or GFP, barcode 251239127247

hyb_protocol: not provided by submitter

scan_protocol: not provided by submitter

data_processing: Data was normalized globally across the whole array (ratio) and locally (loess)

label_protocol: not provided by submitter

extract_protocol: not provided by submitter

tag: Repository # GM01703

tag: Gender

value: 9 month

value: human fibroblasts

tag: Gene Affected

tag: Mutation


title: NA19129_vs_NA15510

tag: NA19129, female (ABC13)


title: NA12878_vs_NA15510

tag: NA12878, ABC12, female


title: Q188Rfibroblasts_galactose_2days_rep1

description: Cells were infected with lentiviral vector containing either GALT or GFP, barcode 251239127246

tag: Age


title: Q188Rfibroblasts_hexosefree_2days_rep1

description: Cells were infected with lentiviral vector containing either GALT or GFP, barcode 251239125818


title: Q188Rfibroblasts_glucose_2days_rep1

description: Cells were infected with lentiviral vector containing either GALT or GFP, barcode 251239121715


title: NM-PM 7th Day Replicate 4 (Dye Swap)

status: Public on Oct 02 2007

hyb_protocol: The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65 ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37 ºC for 16 hrs.

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for labeling with Cy5 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from eight pools of frozen heads, each representing flies collected from four vials two times of which comprised a single parallel set of treatment, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC.

tag: Strain

tag: Age:3-4 days old

tag: Sex

source_name: Drosophila melanogaster, unmated, treated.

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for labeling with Cy3 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media containing 8 mg/ml of Pentylenetetrazol (PTZ) for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC.


title: NM-PM 7th Day Replicate 3 (Dye Swap)

tag: Age:3-4 day old

tag: Tissue


title: Q188Rfibroblasts_hexosefree_2days_rep2

description: Cells were infected with lentiviral vector containing either GALT or GFP, barcode 251239125774


title: Q188Rfibroblasts_glucose_2days_rep2

description: Cells were infected with lentiviral vector containing either GALT or GFP, barcode 251239121716


title: NM-PM 2nd Day Replicate 4 (Dye Swap)

growth_protocol: D. melanogaster Oregon-R wild type flie were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media  for two days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy3 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal containing 8 mg/ml of Pentylenetetrazol (PTZ) media for two days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC.


title: NM-PM 7th Day (Replicate 2)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for  labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 2-3 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media containing 8 mg/ml of Pentylenetetrazol (PTZ) for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC.

source_name: Drosophila melanogaster, unmated, untreated.

treatment_protocol: flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NM-PM 7th Day (Replicate 1)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA) were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1 ºC , 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC.


title: NM-levetiracetam Replicate 3 (Dye Swap)

status: Public on Oct 04 2007

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labelled cRNA synthesis with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flieswere grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days and then were shifted to vessale containg normal media for three days, heads were collected, snap frozen in liquid nitrogen and stored at –70 ºC

tag: sex

label_protocol: Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labelled cRNA synthesis with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products (cRNA)  were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days and then were shifted to vessale containg 5 mg/ml of levetiracetam for three days, heads were collected, snap frozen in liquid nitrogen and stored at –70 ºC

tag: on Sex


title: NM-levetiracetam Replicate 4 (Dye Swap)

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3,0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days and then were shifted to vessale containg normal media for another three days, heads were collected, snap frozen in liquid nitrogen and stored at –70 ºC

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days and then were shifted to vessale containg 5mg/ml of levetiracetam for three days, heads were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NM-levetiracetam Replicate 1

growth_protocol: D. melanogaster Oregon-R wild type flies, were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: flies were maintained at 24 +/- 1 ºC in the treatment vessel in normal media for seven days and then flies were shifted into vessle containg food mixed with 5 mg/ml of levetiracetam for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

treatment_protocol: flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days and then flies were shifted into vessle containg normal food for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NM-PM 2nd Day (Replicate 1)

data_processing: Data normalization was performed using Acuity 4.0 software (Molecular Devices). Ratio based normalization was used for all slides. All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) >= 0.6) and were detectable above background (SNR >= 3). Analyzable spots in at least three of four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3.0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutation

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for  labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4  days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old unmated adult males were grown in normal food containing 8 mg/ml of PTZ  for two days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

source_name: Drosophila melanogaster,  unmated, untreated

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies,were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old unmated adult males were grown in normal food (NF) for Two days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NM-PM 12 hrs Replicate 3 (Dye Swap)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for labeling with Cy5 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals.

treatment_protocol: 3-4 days old unmated adult males were grown in  normal food ( NF) for 12 Hrs.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for labeling with Cy3 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies, a laboratory stock of which was obtained and subsequently maintained by the corresponding author for around eight years, were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 2-3 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. 3-4 days old unmated adult males were grown in  normal food ( NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 12 Hours.


title: NM-PM 2nd Day Replicate 3 (Dye Swap)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products ( cRNA) were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel for the two day in normal media The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC.

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products ( cRNA) were purified by  were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 24 +/- 1 ºC in the treatment vessel for the two day in normal media containg 8 mg/ml pentylenettrazole (PTZ). The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC.


title: NM-NM 12 hrs (Replicate 3)

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: Control flies were maintained at 24 +/- 1 ºC in the treatment vessel for 12 hours. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

value: Oregon R Sex:Male Tissue:Head

source_name: Drosophila melanogaster, unmated, Untreated

growth_protocol: D. melanogaster Oregon-R wild type flieswere grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: Control flies were maintained at 24 +/- 1 ºC in the treatment vessel for 12 hours. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NM-NM 12 hrs (Replicate 4)

treatment_protocol: flies were maintained at 24 +/- 1 ºC in the treatment vessel for the 12 hours. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

value: Oregon R Age:3-4 days old Sex:Male Tissue:Head

source_name: Drosophila melanogaster, 3-4 day old, unmated, Untreated

treatment_protocol: flies were maintained at 24 +/- 1ºC in the treatment vessel for 12 hours. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC

value: oragon R Sex:Male Tissue:Head


title: NM-PM 12 hrs Replicate 4 (Dye Swap)

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: 3-4 days old unmated adult males were grown in food containing normal media for 12HRs. Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

growth_protocol:
D. melanogaster Oregon-R wild type flies, a laboratory stock of which was obtained and subsequently maintained by the corresponding author for around eight years, were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals
total RNA
Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from eight pools of frozen heads, each representing flies collected from four vials two times of which comprised a single parallel set of treatment, using TRI REAGENT (Sigma) according to the manufacturer’s protocol
Cy3
Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy3 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).
All Channels
The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

treatment_protocol: 3-4 days old unmated adult males were grown in normal food  containing 8 mg/ml pentylenetetazole  for 12HRs. Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NM-levetiracetam Replicate 2

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at  24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days and then were shifted to vessale containg 5mg/ml of levetiracetam for three days, heads were collected, snap frozen in liquid nitrogen and stored at –70 ºC

treatment_protocol: flies were maintained at 24 +/- 1 ºC in the treatment vessel in Normal media for seven days and then were shifted to vessale containg normal media again for three days, heads were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NM-PM 12 hrs (Replicate 1)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: The cultures were grown at 24 +/- 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old unmated adult males were grown in  normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) 12 hours  .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

label_protocol: Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old unmated adult males were grown in normal food (NF) for 12 hours .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NM-PM 2nd Day (Replicate 2)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old unmated adult males were grown in normal food  containing 8 mg/ml of PTZ for two days. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for labeling with Cy3 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies, were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals


title: NF-PTZ 14th day Female Replicate 4 (Dye Swap)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy5 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: The cultures were grown at 24 + 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) for 7 days then again flies were shifted to vials containing normal media  .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used cRNA synthesis for labeling with Cy3 dyes (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old virgin adult females were grown in normal food (NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 7 days and then flies were shifted to vials containing normal media  .Each vial contained 30 flies in the beginning of the treatment.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: NM-NM 12 hrs (Replicate 2)

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

treatment_protocol: flies were maintained at 24 +/- 1 ºC in the treatment vessel for 12 hours. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

growth_protocol: D. melanogaster Oregon-R wild type flies, a laboratory stock of which was obtained and subsequently maintained by the corresponding author for around eight years, were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals

value: Oregon R  Sex:Male Tissue:Head


title: 2091 mock vs. 2091 E2F4 IP

status: Public on Jan 01 2005

city: Boston

first: Jonghwan

last: Kim

state: MA

address: 1 Blackfan circle Karp-7

institute: HMS/CHB

description: 2091 mock vs. 2091 E2F4 IP

source_name: 2091 mock IP


title: NM-PM 12 hours (Replicate 2)

label_protocol: Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. The purified cDNA was used for cRNA synthesis and labeling with Cy5 dye (Amersham Biosciences),using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche).

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals.

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old unmated adult males were grown in  normal food ( NF) containing 8 mg/ml of pentylenetetrazol (PTZ) for 12 Hrs. The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC

treatment_protocol: The cultures were grown at 24 +/- 1 ºC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old unmated adult males were grown in  normal food ( NF) for 12 hours.The flies were collected, snap frozen in liquid nitrogen and stored at –70 ºC


title: 2091 mock vs. 2091 E2F4 IP set 2

description: 2091 mock vs. 2091 E2F4 IP


title: NM-NM 12 hrs (Replicate 1)

description: The data in the file is normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

hyb_protocol: Purified cDNA was used for labeling with Cy3 and Cy5 dyes (Amersham Biosciences), using Microarray RNA Target Synthesis Kit T7 (Roche) and labeled products were purified by Microarray Target Purification Kit (Roche). The two cRNA samples of each biological replicate, one labled with Cy3 and another with Cy5, were pooled together, precipitated, washed and air-dried. The dried pellet was dissolved in 18MΩ RNAase free water (Sigma). Hybridization solution was prepared by mixing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma) and added to the labeled product. This mixture was denatured at 65ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by lowering down a 24X60 mm coverslip (ESCO, Portsmouth, USA). Hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs.

data_processing: Data were normalized using the intensity ratio normalization algorithm implemented in Acuity 4.0 while ignoring the flagged values. Refer to the manuscript for further discussion of data handling.

source_name: Unmated, Drosophila melanogaster, males, untreated

growth_protocol: D. melanogaster Oregon-R wild type flies were grown in standard fly medium, i.e., NF, consisting of agar-agar, maize powder, brown sugar, dried yeast and nipagin, at 24 + 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. To obtain flies used in the experiments, individuals from identical cultures were first allowed to lay eggs in milk bottles containing normal fly media. Flies were shifted to fresh bottle every 12 hr. First 4 sets of bottles were discarded. Flies that emerged in subsequent bottles were only used. Those that emerged in the beginning were first discarded and then flies were collected within 1 day, at 4 hr interval. Flies were anesthetized with diethyl ether, and males and females separated immediately after collection using a stereomicroscope. Male flies were thereafter maintained for another 3-4 days in standard culture vials containing NF in batches of 30 individuals.

extract_protocol: Total RNA was isolated from eight pools of frozen heads, each representing flies collected from four vials two times of which comprised a single parallel set of treatment, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: Control flies were maintained at 24 +/- 1 ºC in the treatment vessel for 12 hours. The flies were collected, snap frozen in liquid nitrogen and head were collected and stored at –70ºC.

treatment_protocol: Control flies were maintained at 24 +/- 1 ºC in the treatment vessel for 6hrs. The flies were collected, snap frozen in liquid nitrogen and head were collected and stored at –70ºC.


title: Agilent 244k Chip 2

status: Public on Feb 29 2008

city: Houston

first: Omar

last: Alvi

state: TX

address: 1 Baylor Plaza

department: Human Genome Sequencing Center

institute: Baylor College of Medicine

description: CNV data for JW (Agilent Human Genome CGH 244K Array)

hyb_protocol: Experimental and reference targets for each hybridization were purified, pooled and incubated with human Cot-1 DNA (Invitrogen) and Blocking Agent (Agilent Technologies, Inc.)

scan_protocol: Slides were scanned into image files using an Axon microarray scanner (GenePix 4000B from Axon Instruments, Union City, CA, USA)

data_processing: Data was analyzed using the CGH Analytics software (Agilent Technologies, Inc.)

source_name: JW DNA extracted from blood

label_protocol: The labelling reaction was performed with Bioprime CGH labelling Module (Invitrogen) at 378C for 2 hours in the presence of Cy5-dCTP following standard Agilent protocal

extract_protocol: DNA extracted from blood using FlexiGene DNA kit from Qiagen

tag: Blood from JW

source_name: Reference DNA

label_protocol: The labelling reaction was performed with Bioprime CGH labelling Module (Invitrogen) at 378C for 2 hours in the presence of  Cy3-dCTP (PerkinElmer) following standard Agilent protocal

tag: Blood from reference DNA, Coriell number NA10851


title: PCA_wt_omcF_BR1A

status: Public on May 22 2008

city: Amherst

first: Derek

last: Lovley

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

description: total RNA was directly labeled with the Micromax ASA labeling kit, using 10 ug total RNA for each sample.

hyb_protocol: Combimatrix 100 ul volume cap

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work.  Background signal was calculated from a set of negative control spots incorporated into the array.  As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest.  To avoid this issue the negative control spots were ranked according to their total intensity.  The average of the lowest 30% was calculated.  Background signal was calculated as this mean + 2 standard deviations.  The background signal was then subtracted from the total intensity for each spot.  Probes whose signal was not greater than zero after background subtraction were omitted from further analysis.  For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3)  LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes.  Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001.  Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1.	Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2.	Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3.	Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geobacter sulfurreducens

source_name: OmcF-deficient mutant grown on fumarate

label_protocol: Micromax ASAP direct RNA labeling protocol

extract_protocol: Ambion RiboPure-Bacteria

tag: Geobacter sulfurreducens was grown anaerobically in steady-state chemostats with fumarate as the terminal electron acceptor and acetate as the electron donor.

source_name: wildtype grown on fumarate

extract_protocol: Ambion Ribopure-Bacteria kit


title: US-1078955 vs. HH-901

status: Public on May 08 2008

first: eric

middle: e

last: schadt

address: 401 Terry Ave N

department: Genetics

institute: Merck

description: Liver samples (1-2 g) were acquired from Caucasian individuals from three independent liver collections at tissue resource centers at Vanderbilt University, University of Pittsburg, and Merck Research Laboratories. All individuals were compared to a common pool created from equal portions of RNA from 191 (111 from Vanderbilt University and 80 from University of Pittsburg) samples.

hyb_protocol: Labeled cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides in the presence of 10 mM zinc chloride and adding a hybridization buffer containing 1 M sodium chloride, 0.5 percent sodium sarcosine, 50 mM morpholino-ethane sulfonic acid (pH 6.5), and formamide (final concentration, 30 percent at 40°C); After hybridization, the slides were washed

scan_protocol: slides were scanned using a confocal laser scanner (Agilent Technologies, Palo Alto, CA). Fluorescence intensities of the scanned images were quantified, normalized, and balanced

data_processing: Rosetta Resolver Ratio Experiment using Rosetta Resolver Agilent Error Model

source_name: Liver

label_protocol: One round of RT-IVT to cRNA

extract_protocol: Trizol Lysis + RNeasy Column

treatment_protocol: No treatment

tag: pool