title: NF-NaVP (Replicate 3-Dye Swap)

description: Array Number: 12926025. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in glass vials in media containing normal media for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

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 normal food in batches of 30 individuals, and then shifted to new vials with food containing 0.33 mg/ml of NaVP, for three days.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of NaVP treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in glass vials in media containing 0.33 mg/ml of sodium valproate (NaVP) for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NF-NaVP (Replicate 4-Dye Swap)

status: Public on Oct 05 2007

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: Array Number: 12926024. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.

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.

scan_protocol: 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).

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 2.21, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.

molecule: total RNA

organism: Drosophila melanogaster

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 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 10-11 days in standard culture vials containing normal food in batches of 30 individuals, and then shifted to new vials containing normal food, for three days.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of untreated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

tag: Strain

value: Oregon R

tag: Sex

value: Male

tag: Tissue

value: Head

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 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).

value: oragon R


title: NF-GBP (Replicate 1)

description: Array Number: 12917662. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.

source_name: Drosophila melanogaster, unmated, gabapentin treated

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 normal food in batches of 30 individuals, and then shifted to new vials with food containing 16 mg/ml of GBP, for three days.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of GBP treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in glass vials in media containing 16 mg/ml of Gabapentin (GBP) for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of untreated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in normal food for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NF-GBP (Replicate 2)

description: Array Number: 12926453. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.


title: NF-VGB (Relplicate 3-Dye Swap)

description: Array Number: 12926023. 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 stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing normal food in batches of 30 individuals, and then shifted to new vials containing normal food, for three days..

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 normal food in batches of 30 individuals, and then shifted to new vials with food containing 24 mg/ml of VGB, for three days..

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of VGB treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in glass vials in media containing 24 mg/ml of Vigabatrin (VGB) for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NF-GBP (Replicate 4-Dye Swap)

description: Array Number: 12926013. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of GBP treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol


title: NF-ETH (Replicate 4-Dye Swap)

description: Array Number: 12926016. 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 stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing normal food in batches of 30 individuals.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads,using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in normal food for three days.The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: 10-11 day old flies were maintained at 24 +/- 1ºC in glass vials in media containing 3.48 mg/ml of Ethosuximide (ETH) for three days.The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NF-NaVP (Replicate 2)

description: Array Number: 12926017. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.


title: NF-VGB (Replicate 1)

description: Array Number: 12917661. 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 stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing normal food in batches of 30 individuals, and then shifted to new vials with food containing 24 mg/ml of VGB, for three days.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads, which represented a single parallel set of four vials of VGB treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol


title: NF-NaVP (Replicate 1)

description: Array Number: 12917664. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.


title: S2 cells, not beta-eliminated, 4 mismatches tolerated on the pair of adapters

status: Public on Jan 22 2008

type: other

city: Worcester

first: Hervé

last: Seitz

state: MA

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

country: USA

institute: University of Massachusetts Medical School

description: This sample was not beta-eliminated before adapter ligation. The .sff files are not available for this submission.

hyb_protocol: (not applicable)

scan_protocol: (not applicable)

data_processing:
Inserts were extracted from the 454 reads, tolerating 0 mismatch on the pair of adapters (5´ adapter: AUCGUAGGCACCUGAAA; 3´ adapter: UUUAACCGCGAAUUCCAG); inserts of 18 to 30 nt long were selected.
The "ID_REF" column indicates the sequence of the small RNA; "VALUE" indicates the number of times that small RNA was detected in this sample.

molecule: other

source_name: S2 cells (with a stable transgene expressing mini-white and GFP, and: transiently transfected with a double-stranded RNA against GFP)

label_protocol: (not applicable)

extract_protocol: Total RNA was extracted using the miRVana kit (Ambion), then small RNAs (18 to 30-nt long) were gel-purified. 2S ribosomal RNA was depleted with a biotinylated, anti-2S DNA oligo, captured with streptavidin-coated paramagnetic beads (Dynal, M-270 beads).

tag: S2 cells containing the stably-integrated pKF63 construct (expressing the mini-white gene and GFP; described in Förstemann et al. (2005) PLoS Biol 3(7):e236) were transfected with a double-stranded RNA against GFP (described in Horwich et al. (2007) Curr. Biol. 17(14):1265).


title: NM-PM 14th Day (Replicate 4)

status: Public on Oct 02 2007

description: Array Number:12926021 The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

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).

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 2.21, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations

source_name: Drosophila melanogaster, 4-5 dy old, unmated, PTZ treated, 14th day

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, 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

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 25 +/- 1ºC in the treatment vessel in Normal media containing 8mg/ml Pentylenetetrazol (PTZ) forseven days and then flies were again shifted to normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

value: oragon R Age:4-5 days post-eclosion Sex:Male Tissue:Head

source_name: Drosophila melanogaster, 4-5 dy old, unmated, Untreated

treatment_protocol: Flies were maintained at 25 +/- 1ºC in the treatment vessel in Normal media seven days and then flies were again shifted to normal media for seven days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NF-ETH (Replicate 3-Dye Swap)

description: Array Number: 12926027. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.


title: NM-PM 14th Day (Replicate 3)

description: Array Number:12917682 The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.


title: NM-PM 10th Day (Replicate 2)

description: Array Number:13303863  The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

source_name: Drosophila melanogaster, 4-5 dy old, unmated, PTZ treated, 10th day

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 were purified by Microarray Target Purification Kit (Roche).

treatment_protocol: Flies were maintained at 25 +/- 1ºC in the treatment vessel containing normal media mixed with 8mg/ml of Pentylenetetrazol (PTZ) for seven days and then these flies were shifted to the normal media for three days, The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC

treatment_protocol: Flies were maintained at 25 +/- 1ºC in the treatment vessel containing normal media  for seven days and then these flies were shifted to normal media again for three days, The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NM-PM 14th Day (Replicate 1)

description: Array Number:12906480  The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.


title: NM-PM 10th Day (Replicate 3)

description: Array Number:13299442 The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

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).

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.

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 25 +/- 1ºC in the 8mg/ml of Pentylenetetrazol (PTZ) for seven days and then these flies were shifted to normal media for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: flies were maintained at 25 +/- 1ºC in the normal media for seven days and then these flies were shifted to normal media for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NM-PM 14th Day (Replicate 2)

description: Array Number:12917688 The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.


title: NM-PM 8th Day (Replicate 1)

description:
Array Number:12917670
The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

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) >= 0.5) 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 2.21, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.

source_name: Drosophila melanogaster, 4-5 dy old, unmated, PTZ treated, 8th day

treatment_protocol: Flies were maintained at 25 +/- 1ºC in the treatment vessel in Normal media containing 8 mg/ml of Pentylenetetrazol (PTZ) for seven days and then flies were shifted to normal media for one day. 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 Cy5 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 25 +/- 1ºC in the treatment vessel in Normal media for seven days and then again shfited to normal media for one day. The flies were collected , snap frozen in liquid nitrogen and stored at –70ºC.


title: NM-PM 10th Day (Replicate 4)

description: Array Number:13307448The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

treatment_protocol: Flies were maintained at 25 +/- 1ºC in the treatment vessel in Normal media containing 8mg/ml Pentylenetetrazol (PTZ) forseven days and then flies were again shifted to normal media for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.

treatment_protocol: Flies were maintained at 25 +/- 1ºC in the treatment vessel in Normal media seven days and then flies were again shifted to normal media for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC.


title: NM-PM 10th Day (Replicate 1)

description: Array Number:13303862 The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.

treatment_protocol: flies were maintained at 25 +/- 1ºC throughout the experiment in normal media containing Pentylenetetrazol (PTZ) for seven days and then in normal media for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC

treatment_protocol: flies were maintained at 25 +/- 1ºC throughout the experiment in normal media for seven days and then again shifted in normal media for three days. The flies were collected, snap frozen in liquid nitrogen and stored at –70ºC


title: NM-PM 8th Day (Replicate 2)

description:
Array Number:12926825
The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.


title: NM-PM 8th Day (Replicate 4)

description:
Array Number:12926458
The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.


title: NM-PM 8th Day (Replicate 3)

description:
Array Number:12926465
The data in the file is ratio normalized. The ratio in the Value column was derived from normalized data as discussed in the manuscript.


title: NF-ETH (Replicate 2)

description: Array Number: 12926030. 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 stereomicroscope. Male flies were thereafter maintained for another 10-11 days in standard culture vials containing normal food in batches of 30 individuals,and then shifted to new vials with food containing 3.48 mg/ml of ETH, for three days.

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads,which represented a single parallel set of four vials of ETH treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.

source_name: Drosophila melanogaster, unmated, Untreated

extract_protocol: Flies were frozen in liquid nitrogen, shaken, and the heads collected using cooled sieves. Total RNA was isolated from four pools of frozen heads,which represented a single parallel set of four vials of untreated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol.


title: NF-ETH (Replicate 1)

description: Array Number: 12917660. The data in the file is ratio normalized. The ratio in the 'Value' column was derived from normalized data as discussed in the manuscript.


title: U-2OS (decitabine treated) expression profile  (AffyChip U133A platform)

status: Public on Apr 05 2007

city: Toronot

first: Khaldoun

last: Al-Romaih

address: 610 University Ave

department: AMO

country: Canada

institute: Ontario Cancer Institute

description: non

hyb_protocol: For each case, 10 µg of RNA was labeled and hybridized to the Affymetrix HG-U133A GeneChips using the manufacturer’s protocol (Affymetrix, Santa Clara, CA) by the Center of Applied Genomics at the Hospital for Sick Children (Toronto, Canada).

scan_protocol: Data were extracted using the Microarray Suite (MAS) version 5.0 (Affymetrix) and linearly scaled to achieve an average intensity of 150 across each chip.

label: Biotin

organism: Homo sapiens

source_name: Human osteosarcoma cell line purchased from ATCC

label_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Germany) from U-2OS cells at Day3 after treatment with 1 µM decitabine or medium alone (control).  In each experiment RNA yields were pooled from two independent cultures per treatment arm to minimize experimental noise.  For each case, 10 µg of RNA was labeled using the two cycle target labeling assays as described by Affymetrix manual.

extract_protocol: RNAeasy kit from Qiagen

tag: bone tumor cell line exposed to 1 uM decitabine for 3 days.


title: NA15510_Sty_COMM_rep1

status: Public on Feb 12 2007

type: genomic

city: Santa Clara

first: Fan

last: Shen

state: CA

address: 3420 Central Expressway

institute: Affymetrix, Inc

description: Samples NA10851 or NA15510 were hybridized to 500K mapping arrays in triplicates

hyb_protocol: According to standard Affymetrix procedures

data_processing: Genotyes reported by dynamic modeling algorithm

label: DNA Labeling Reagent, Affymetrix, Inc.

molecule: genomic DNA

source_name: DNA was obtained from NIGHS Human Genetic Cell Repository

tag: Gender

value: Female	Cell lot number:4


title: NA15510_Sty_COMM_rep3

scan_protocol: According to standard Affymetrix procedures

extract_protocol: DNA was obtained from NIGHS Human Genetic Cell Repository


title: NA15510_Nsp_COMM_rep2

label_protocol: According to standard Affymetrix procedures


title: NA15510_Sty_COMM_rep2


title: NA19003_Sty_COMM

status: Public on Sep 30 2006

description: Hapmap samples used for identifying variable copy number regions in the genome

value: Female	Cell lot number:2


title: NA10851_Sty_COMM_rep3

value: Male	Cell lot number:3


title: NA15510_Nsp_COMM_rep3


title: NA10861_Sty_COMM


title: NA19238_Sty_COMM

value: Female	Cell lot number:1


title: NA12892_Sty_COMM


title: NA10851_Sty_COMM_rep1


title: NA19239_Sty_COMM

value: Male	Cell lot number:1


title: NA19240_Sty_COMM


title: NA19222_Sty_COMM


title: NA15510_Nsp_COMM_rep1


title: NA15510_Sty_EA_rep3

description: Samples used for parameter tuning and validation of algorithm


title: NA15510_Sty_EA_rep1


title: NA10851_Sty_COMM_rep2


title: NA19223_Sty_COMM


title: NA15510_Sty_EA_rep2


title: NA18637_Sty_COMM


title: NA19221_Sty_COMM


title: NA19211_Sty_COMM


title: NA10851_Nsp_COMM_rep1


title: NA10851_Nsp_COMM_rep3


title: NA10851_Nsp_COMM_rep2


title: NA19210_Sty_COMM


title: NA19209_Sty_COMM


title: NA10851_Sty_EA_rep2


title: NA19208_Sty_COMM


title: NA10851_Sty_EA_rep3


title: NA19207_Sty_COMM


title: NA19099_TechnicalReplicate_Sty_EA_rep1

description: Hapmap samples used as technical replicates to determine reproducibility


title: NA19206_Sty_COMM


title: NA19203_Sty_COMM


title: NA19205_Sty_COMM


title: NA19201_Sty_COMM


title: NA10851_Sty_EA_rep1


title: NA19202_Sty_COMM


title: NA18971_TechnicalReplicate_Sty_EA_rep3

value: Male	Cell lot number:2


title: NA19204_Sty_COMM


title: NA19099_TechnicalReplicate_Sty_EA_rep2


title: NA19099_TechnicalReplicate_Sty_EA_rep3


title: NA19193_Sty_COMM


title: NA18971_TechnicalReplicate_Sty_EA_rep2


title: NA19200_Sty_COMM


title: NA18971_TechnicalReplicate_Sty_EA_rep1


title: NA18860_TechnicalReplicate_Sty_EA_rep3


title: NA18980_TechnicalReplicate_Sty_EA_rep1


title: NA18980_TechnicalReplicate_Sty_EA_rep2


title: NA19192_Sty_COMM


title: NA18860_TechnicalReplicate_Sty_EA_rep1


title: NA19194_Sty_COMM


title: NA19172_Sty_COMM


title: NA19161_Sty_COMM


title: NA18621_TechnicalReplicate_Sty_EA_rep3


title: NA19173_Sty_COMM


title: NA19159_Sty_COMM


title: NA18980_TechnicalReplicate_Sty_EA_rep3


title: NA19154_Sty_COMM


title: NA19171_Sty_COMM


title: NA18860_TechnicalReplicate_Sty_EA_rep2


title: NA19160_Sty_COMM


title: NA18621_TechnicalReplicate_Sty_EA_rep2


title: NA18576_TechnicalReplicate_Sty_EA_rep2


title: NA19153_Sty_COMM


title: NA18621_TechnicalReplicate_Sty_EA_rep1


title: NA18500_TechnicalReplicate_Sty_EA_rep2


title: NA18500_TechnicalReplicate_Sty_EA_rep3


title: NA18576_TechnicalReplicate_Sty_EA_rep1


title: NA19143_Sty_COMM


title: NA19152_Sty_COMM


title: NA19144_Sty_COMM


title: NA19142_Sty_COMM


title: NA18576_TechnicalReplicate_Sty_EA_rep3


title: NA19145_Sty_COMM


title: NA19140_Sty_COMM


title: NA19137_Sty_COMM


title: NA19138_Sty_COMM


title: NA18500_TechnicalReplicate_Sty_EA_rep1


title: NA19141_Sty_COMM


title: NA12892_TechnicalReplicate_Sty_EA_rep1


title: NA19130_Sty_COMM


title: NA12892_TechnicalReplicate_Sty_EA_rep3


title: NA12892_TechnicalReplicate_Sty_EA_rep2


title: NA19145_Nsp_COMM


title: NA19129_Sty_COMM


title: NA12239_TechnicalReplicate_Sty_EA_rep3

value: Female	Cell lot number:3


title: NA19128_Sty_COMM


title: NA18562_Nsp_COMM


title: NA19119_Sty_COMM


title: NA19132_Sty_COMM


title: NA19116_Sty_COMM


title: NA19131_Sty_COMM


title: NA12239_TechnicalReplicate_Sty_EA_rep1


title: NA19120_Sty_COMM


title: NA18956_Nsp_COMM


title: NA19103_Sty_COMM


title: NA19127_Sty_COMM


title: NA12239_Nsp_COMM


title: NA19102_Sty_COMM


title: NA12239_TechnicalReplicate_Sty_EA_rep2


title: NA19101_Sty_COMM


title: NA19099_Sty_COMM


title: NA19094_Sty_COMM


title: NA12144_TechnicalReplicate_Sty_EA_rep3

value: Male	Cell lot number:4


title: NA12144_TechnicalReplicate_Sty_EA_rep2


title: NA19098_Sty_COMM


title: NA19100_Sty_COMM


title: NA19007_Sty_COMM


title: NA19238_Nsp_COMM


title: NA12144_TechnicalReplicate_Sty_EA_rep1


title: NA19092_Sty_COMM


title: NA19093_Sty_COMM


title: NA19239_Sty_EA


title: NA19139_Sty_COMM


title: NA19240_Sty_EA


title: NA19240_Nsp_COMM


title: NA19000_Sty_COMM


title: NA19012_Sty_COMM


title: NA19005_Sty_COMM

value: Male	Cell lot number:A1


title: NA19239_Nsp_COMM


title: NA19223_Nsp_COMM


title: NA18999_Sty_COMM


title: NA19222_Nsp_COMM


title: NA19223_Sty_EA


title: NA19238_Sty_EA


title: NA18998_Sty_COMM

value: Female	Cell lot number:A1


title: NA19221_Nsp_COMM


title: NA19222_Sty_EA


title: NA18995_Sty_COMM


title: NA19210_Nsp_COMM


title: NA19211_Nsp_COMM


title: NA18997_Sty_COMM


title: NA18992_Sty_COMM


title: NA19209_Nsp_COMM


title: NA18994_Sty_COMM


title: NA19208_Nsp_COMM


title: NA19206_Nsp_COMM


title: NA18987_Sty_COMM


title: NA18990_Sty_COMM


title: NA18981_Sty_COMM


title: NA19207_Nsp_COMM


title: NA19210_Sty_EA


title: NA18976_Sty_COMM


title: NA18980_Sty_COMM


title: NA19221_Sty_EA


title: NA18991_Sty_COMM


title: NA19208_Sty_EA


title: NA18973_Sty_COMM


title: NA19204_Nsp_COMM


title: NA18972_Sty_COMM


title: NA19206_Sty_EA


title: NA19209_Sty_EA


title: NA18975_Sty_COMM


title: NA18978_Sty_COMM


title: NA19207_Sty_EA


title: NA18974_Sty_COMM


title: NA18971_Sty_COMM


title: NA19205_Nsp_COMM


title: NA18970_Sty_COMM


title: NA19203_Nsp_COMM


title: NA19205_Sty_EA


title: NA18968_Sty_COMM


title: NA19211_Sty_EA


title: NA19202_Nsp_COMM


title: NA19201_Nsp_COMM


title: NA19204_Sty_EA


title: NA18965_Sty_COMM


title: NA18969_Sty_COMM


title: NA18967_Sty_COMM


title: NA18966_Sty_COMM


title: NA18964_Sty_COMM


title: NA19200_Nsp_COMM


title: NA19202_Sty_EA


title: NA18959_Sty_COMM


title: NA19201_Sty_EA


title: NA18961_Sty_COMM


title: NA19194_Sty_EA


title: NA19194_Nsp_COMM


title: NA18952_Sty_COMM


title: NA18960_Sty_COMM


title: NA18951_Sty_COMM


title: NA19192_Nsp_COMM


title: NA19193_Nsp_COMM


title: NA18956_Sty_COMM


title: NA19203_Sty_EA


title: NA19200_Sty_EA


title: NA19172_Nsp_COMM


title: NA19173_Nsp_COMM


title: NA18948_Sty_COMM


title: NA18945_Sty_COMM


title: NA18947_Sty_COMM


title: NA18953_Sty_COMM


title: NA18944_Sty_COMM


title: NA19193_Sty_EA


title: NA18940_Sty_COMM


title: NA18949_Sty_COMM


title: NA18942_Sty_COMM


title: NA19171_Nsp_COMM


title: NA19192_Sty_EA


title: NA18943_Sty_COMM


title: NA18913_Sty_COMM


title: NA18914_Sty_COMM


title: NA19161_Nsp_COMM


title: NA19159_Nsp_COMM


title: NA18872_Sty_COMM


title: NA18912_Sty_COMM


title: NA19160_Nsp_COMM


title: NA19161_Sty_EA


title: NA19154_Nsp_COMM


title: NA18870_Sty_COMM


title: NA19153_Nsp_COMM


title: NA19172_Sty_EA


title: NA18871_Sty_COMM


title: NA19171_Sty_EA


title: NA19160_Sty_EA


title: NA18863_Sty_COMM


title: NA19152_Nsp_COMM


title: NA18858_Sty_COMM


title: NA18862_Sty_COMM


title: NA19154_Sty_EA


title: NA19144_Nsp_COMM


title: NA18855_Sty_COMM


title: NA18860_Sty_COMM


title: NA19152_Sty_EA


title: NA18859_Sty_COMM


title: NA19173_Sty_EA


title: NA19143_Nsp_COMM


title: NA18857_Sty_COMM


title: NA18861_Sty_COMM


title: NA19144_Sty_EA


title: NA19153_Sty_EA


title: NA19141_Nsp_COMM


title: NA18852_Sty_COMM


title: NA18856_Sty_COMM


title: NA18854_Sty_COMM


title: NA19145_Sty_EA


title: NA18853_Sty_COMM


title: NA19143_Sty_EA


title: NA19142_Nsp_COMM


title: NA18624_Sty_COMM


title: NA19142_Sty_EA


title: NA19137_Nsp_COMM


title: NA18632_Sty_COMM


title: NA18622_Sty_COMM


title: NA19139_Nsp_COMM


title: NA19140_Nsp_COMM


title: NA18635_Sty_COMM


title: NA18623_Sty_COMM


title: NA19159_Sty_EA


title: NA18633_Sty_COMM


title: NA19140_Sty_EA


title: NA18636_Sty_COMM


title: NA18621_Sty_COMM


title: NA18620_Sty_COMM


title: NA18612_Sty_COMM


title: NA19132_Nsp_COMM


title: NA19138_Nsp_COMM


title: NA19141_Sty_EA


title: NA18611_Sty_COMM


title: NA19131_Nsp_COMM


title: NA19130_Nsp_COMM


title: NA19138_Sty_EA


title: NA18603_Sty_COMM


title: NA19139_Sty_EA


title: NA19137_Sty_EA


title: NA18594_Sty_COMM


title: NA18593_Sty_COMM


title: NA18609_Sty_COMM


title: NA19129_Nsp_COMM


title: NA18608_Sty_COMM


title: NA19132_Sty_EA


title: NA18592_Sty_COMM


title: NA19128_Nsp_COMM


title: NA19127_Nsp_COMM


title: NA18582_Sty_COMM


title: NA18605_Sty_COMM


title: NA19130_Sty_EA


title: NA19131_Sty_EA


title: NA18579_Sty_COMM


title: NA18576_Sty_COMM


title: NA19120_Nsp_COMM


title: NA18572_Sty_COMM


title: NA18577_Sty_COMM


title: NA19129_Sty_EA


title: NA19119_Nsp_COMM


title: NA18571_Sty_COMM


title: NA18573_Sty_COMM


title: NA18566_Sty_COMM


title: NA19128_Sty_EA


title: NA19116_Nsp_COMM


title: NA19103_Nsp_COMM


title: NA18570_Sty_COMM


title: NA18561_Sty_COMM


title: NA18563_Sty_COMM


title: NA19120_Sty_EA


title: NA18562_Sty_COMM


title: NA19101_Nsp_COMM


title: NA19119_Sty_EA


title: NA19116_Sty_EA


title: NA19127_Sty_EA


title: NA19102_Nsp_COMM


title: NA18555_Sty_COMM


title: NA18564_Sty_COMM


title: NA18552_Sty_COMM


title: NA18547_Sty_COMM


title: NA19099_Nsp_COMM


title: NA18558_Sty_COMM


title: NA18550_Sty_COMM


title: NA18545_Sty_COMM


title: NA19100_Nsp_COMM


title: NA19103_Sty_EA


title: NA19102_Sty_EA


title: NA18542_Sty_COMM


title: NA19094_Nsp_COMM


title: NA18532_Sty_COMM


title: NA19093_Nsp_COMM


title: NA18526_Sty_COMM


title: NA18537_Sty_COMM


title: NA18529_Sty_COMM


title: NA19092_Nsp_COMM


title: NA18523_Sty_COMM


title: NA18524_Sty_COMM


title: NA18522_Sty_COMM


title: NA19007_Nsp_COMM


title: NA19098_Sty_EA


title: NA18517_Sty_COMM


title: NA19100_Sty_EA


title: NA19101_Sty_EA


title: NA19094_Sty_EA


title: NA19099_Sty_EA


title: NA19098_Nsp_COMM


title: NA18540_Sty_COMM


title: NA18516_Sty_COMM


title: NA18521_Sty_COMM


title: NA19012_Nsp_COMM


title: NA19093_Sty_EA


title: NA18515_Sty_COMM


title: NA19092_Sty_EA


title: NA18508_Sty_COMM


title: NA19005_Nsp_COMM


title: NA19012_Sty_EA


title: NA18507_Sty_COMM


title: NA19003_Nsp_COMM


title: NA19000_Nsp_COMM


title: NA19007_Sty_EA


title: NA18506_Sty_COMM


title: NA18504_Sty_COMM


title: NA18505_Sty_COMM


title: NA18500_Sty_COMM


title: NA18501_Sty_COMM


title: NA12891_Sty_COMM


title: NA12875_Sty_COMM


title: NA18502_Sty_COMM


title: NA19000_Sty_EA


title: NA19005_Sty_EA


title: NA19003_Sty_EA


title: NA18503_Sty_COMM


title: NA18997_Nsp_COMM


title: NA18999_Sty_EA


title: NA18998_Nsp_COMM


title: NA18995_Nsp_COMM


title: NA12878_Sty_COMM


title: NA18999_Nsp_COMM


title: NA12874_Sty_COMM


title: NA12865_Sty_COMM


title: NA12864_Sty_COMM


title: NA12812_Sty_COMM


title: NA18994_Nsp_COMM


title: NA12813_Sty_COMM


title: NA18991_Nsp_COMM


title: NA12815_Sty_COMM


title: NA18994_Sty_EA


title: NA12802_Sty_COMM


title: NA18995_Sty_EA


title: NA18990_Nsp_COMM


title: NA12873_Sty_COMM


title: NA18991_Sty_EA


title: NA18990_Sty_EA


title: NA18998_Sty_EA


title: NA18981_Nsp_COMM


title: NA18992_Nsp_COMM


title: NA12814_Sty_COMM


title: NA12872_Sty_COMM


title: NA18997_Sty_EA


title: NA12763_Sty_COMM


title: NA12801_Sty_COMM


title: NA12761_Sty_COMM


title: NA18992_Sty_EA


title: NA18980_Nsp_COMM


title: NA18978_Nsp_COMM


title: NA12762_Sty_COMM


title: NA18987_Nsp_COMM


title: NA12752_Sty_COMM


title: L_310T

status: Public on Apr 10 2008

city: Basel

first: Wolfgang

middle: Ernst Gustav

last: Budach

address: Klybeckstrasse

department: BMD/NV&D

country: Switzerland

institute: Novartis Pharma AG

description: Tissue samples from a series of 41 chemotherapy-naïve non-small cell lung cancer patients and 15 control patients with inflammatory lung diseases.

hyb_protocol: A Tecan HS 4800 Hybridization station from Tecan, Inc. is used for prewash/hybridization/postwash of the microarrays. Prewash consists of 3 cycles with wash buffer at RT/75°C/50°C (each 20 s) followed by an additional 10 s wash with hybridization buffer at 50°C. One hundred L sample (100 ng labeled RNA) in hybridization buffer is then injected into the flow chambers at 50°C and agitated for 1 min. Subsequently, after 10 min at 75°C, the temperature is adjusted to 42°C for 16 h (agitation). The postwash consists in 4 cycles wash buffer at 42°C followed by an additional wash at 23°C (each 20 s). Finally, the slides are washed 3 times with diluted wash buffer at RT, dried in N2 stream, and scanned immediately with an Agilent LS fluorescence scanner (gain 80%).

scan_protocol: Agilent laser scanner at 100% gain, 10micron resolution, Cy5 channel. Files stored as 16bit TIF.

data_processing: The fluorescence images is analyzed by means of Array Pro (Mediacybernetics, Inc. US). Net signals is calculated by subtracting the 75 percentile of local corner background from trimmed mean of each spot (20% trimming on both sides of the intensity histogram). Individual samples are processed on separate slides in single color mode (Cy5). The 75 percentile of intensity histogram is adjusted to 200 counts (a.u.) for normalization of the microarrays. The image analysis is configured in a way that allowed an automated assessment of the quality of individual fluorescence spots (criteria: local fluorescence background, spots symmetry, presence in salt image/Print QC). Only microarrays with >98% qualified spots are used for further analysis.

source_name: Lung Biopsy

label_protocol: Commercial human reference RNA (Stratagene) was labeled per protocol and materials of the Ambion labelling kit (#1753). Labeling of RNA samples will be based on Ambion Amino Allyl MessageAmp II aRNA Amplification Kit (#q1753). 50 ng of total RNA was used for each labeling. The first step is a reverse transcription to synthesize first-strand cDNA with an oligo(dT) primer with a T7 promoter. Subsequently, the second-strand cDNA is synthesized. The cDNA was used for processing with the Ambion kit according to the protocol as template for in vitro transcription (IVT) with T7 RNA polymerase. During this amplification step, 5-(3- aminoallyl)-UTP (aaUTP) is incorporated into the cRNA. The resulting amplified RNA (aRNA) is then chemically coupled to N-hydroxysuccinimidyl ester-derivatized Cy5-dyes (NHS ester Cy5-dyes). Once purified, concentration and yield/dye incorporation are determined. The labeled products are aliquoted and stored at -80°C for further use

extract_protocol: Lysis and homogeneization is performed with 1 mL pre-warmed (60°C) TRIzol Reagent (Invitrogen Cat. No. 15596-026) and 5 mm stainless steel beads (Qiagen Cat. No. 69989, 2 times 2 min at 25 Hz in tissue lyser Mixer Mill 300 for 2-3 mm Ø biopsies). The extraction is completed by adding Phase Lock Gel (Eppendorf Cat. No. 0032007.970) during the phase extraction. Molecular biology grade glycogen (Roche Diagnostics GmbH, Cat. N. 901393) is added to the aqueous phase during the precipitation step. After purification step on RNeasy Microkit columns (Qiagen, Cat. No. 74004), the final cleaned total RNA is eluted in 14 µL of RNase free water and stored at -80°C. RNA levels, quality and purity are assessed with the use of RNA 6000 Nano and Pico assay on the Agilent 2100 Bioanalyzer.

tag: Phenotype

value: NSCLC-Adeno

tag: gender

tag: age

tag: status

tag: Surv

tag: stage

value: IIb

tag: T

tag: N

tag: M

tag: mat

value: tu

tag: Tumor Prop


title: NA12753_Sty_COMM


title: NA12750_Sty_COMM


title: NA18980_Sty_EA


title: NA18976_Nsp_COMM


title: NA18987_Sty_EA


title: NA12707_Sty_COMM


title: NA12751_Sty_COMM


title: NA12760_Sty_COMM


title: NA18981_Sty_EA


title: NA18975_Nsp_COMM


title: NA12716_Sty_COMM


title: NA12717_Sty_COMM

value: Female	Cell lot number:B3


title: NA18976_Sty_EA


title: NA12264_Sty_COMM


title: NA18973_Nsp_COMM


title: NA18974_Nsp_COMM


title: NA18978_Sty_EA


title: NA12740_Sty_COMM


title: NA12249_Sty_COMM


title: NA12248_Sty_COMM

value: Male	Cell lot number:A3


title: NA12234_Sty_COMM


title: Ago2 Hek293 FLAG-Ago2 Expression (4)

status: Public on Apr 08 2008

city: Stanford

first: Daniel

last: Hogan

address: 279 Campus Dr B439

institute: Stanford University

description:
Simple annotation: gene overexpression, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-08/76431.gif
Measurement: mass(absolute) 10 ug

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Daniel,,Hogan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.81; Parameter Scan Time = 13:13:36; Parameter PMT Volts = 305; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43340; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 2.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 24.81; Parameter Scan Time = 13:13:36; Parameter PMT Volts = 349; Parameter Scan Date = 2007-08-16; Parameter Pixel Size = 10; Parameter Laser on time = 43340; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 Autoloader [114773]; Parameter Laser Power = 3.03; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Daniel,,Hogan

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: UNIVERSAL REFERENCE

label_protocol: not provided

extract_protocol: not provided

tag: UNIVERSAL REFERENCE

source_name: amplified RNA from HEK293T cells

tag: amplified RNA from HEK293T cells


title: NA18972_Nsp_COMM


title: NA18971_Nsp_COMM


title: NA18970_Nsp_COMM


title: NA12239_Sty_COMM


title: NA18975_Sty_EA


title: NA18974_Sty_EA


title: NA18969_Nsp_COMM


title: NA12236_Sty_COMM

value: Female	Cell lot number:A3


title: NA18973_Sty_EA


title: NA12154_Sty_COMM


title: NA18970_Sty_EA


title: NA18971_Sty_EA


title: NA18967_Nsp_COMM


title: NA12057_Sty_COMM


title: NA12146_Sty_COMM


title: NA18966_Nsp_COMM


title: NA12056_Sty_COMM


title: NA12144_Sty_COMM


title: NA12155_Sty_COMM


title: NA12156_Sty_COMM


title: NA12043_Sty_COMM


title: NA12044_Sty_COMM


title: NA18965_Nsp_COMM


title: NA12005_Sty_COMM


title: NA12145_Sty_COMM


title: NA18968_Sty_EA


title: NA18968_Nsp_COMM


title: NA18967_Sty_EA


title: NA12003_Sty_COMM


title: NA12006_Sty_COMM


title: NA18969_Sty_EA


title: NA18966_Sty_EA


title: NA12004_Sty_COMM


title: NA18961_Nsp_COMM


title: NA11995_Sty_COMM


title: NA18960_Nsp_COMM


title: NA11993_Sty_COMM


title: NA18964_Nsp_COMM


title: NA18959_Sty_EA


title: NA11992_Sty_COMM


title: NA18953_Nsp_COMM


title: NA18972_Sty_EA


title: NA11994_Sty_COMM


title: HF1588EGF, chip HG-U133B

status: Public on Apr 02 2008

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.stembase.ca).  The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Samuel Weiss (weiss@ucalgary.ca; ) for analysis.
Stembase Experiment ID:			E244
Stembase Experiment ID link:		http://www.stembase.ca/?path=/browse/experiment&id=244
SCGP Sample ID:				S393
SCGP Sample ID link:			http://www.stembase.ca/?path=/browse/experiment&id=244#SAMPLE_393
Short description:			Three week old epidermal growth-factor generated neurospheres cultured from 20 week old human fetal brain tissue.
Estimated purity:				unknown
RNA concentration:			150 ng/ul
Sample volume:				~50 ul

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol  (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpha2=0.06

source_name: EGF-responsive neural stem cell, Fetal Brain

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

growth_protocol:
Growth medium:				DMEM:F12 N2
Media supplements:			2%B27
Culture conditions:			EGF 20ng/ul for 21 days

extract_protocol:
RNA prep method:				RNeasy
Amplification method:			N/A
Cell purification method:			Isolation based on neurosphere formation in response to EGF
Contaminating cell type:			unknown
Method for estimating purity:		N/A

tag: Strain:


title: NA18965_Sty_EA


title: NA18964_Sty_EA


title: NA18960_Sty_EA


title: NA11831_Sty_COMM


title: NA18952_Nsp_COMM


title: NA11881_Sty_COMM


title: NA18959_Nsp_COMM


title: NA11830_Sty_COMM


title: NA11882_Sty_COMM


title: NA11832_Sty_COMM


title: NA18961_Sty_EA


title: NA11829_Sty_COMM


title: NA11839_Sty_COMM

value: Male	Cell lot number:A2


title: NA18951_Nsp_COMM


title: NA10863_Sty_COMM

value: Female	Cell lot number:A2


title: NA18953_Sty_EA


title: NA18949_Nsp_COMM

value: Female	Cell lot number:2


title: NA11840_Sty_COMM


title: NA18948_Nsp_COMM


title: NA10859_Sty_COMM

value: Female	Cell lot number:A6


title: NA18947_Nsp_COMM

value: Female	Cell lot number:1


title: NA10855_Sty_COMM


title: NA10860_Sty_COMM

value: Male	Cell lot number:5


title: NA18951_Sty_EA


title: NA10851_Sty_COMM

value: Male	Cell lot number:3


title: NA18943_Nsp_COMM

value: Male	Cell lot number:1


title: NA18952_Sty_EA

value: Male	Cell lot number:2


title: NA10857_Sty_COMM


title: NA10854_Sty_COMM


title: NA10847_Sty_COMM

value: Female	Cell lot number:3


title: NA18949_Sty_EA


title: NA10856_Sty_COMM


title: NA18944_Nsp_COMM


title: NA18947_Sty_EA


title: NA10839_Sty_COMM


title: NA18956_Sty_EA


title: NA18940_Nsp_COMM


title: NA10846_Sty_COMM


title: NA18942_Nsp_COMM


title: NA10838_Sty_COMM


title: NA18914_Nsp_COMM


title: NA18948_Sty_EA


title: NA18945_Sty_EA


title: NA10831_Sty_COMM

value: Female	Cell lot number:5


title: NA10830_Sty_COMM

value: Male	Cell lot number:6


title: NA07348_Sty_COMM


title: NA18944_Sty_EA


title: NA18945_Nsp_COMM


title: U-2OS (no treatment) expression profile (AffyChip U133A platform)

description: non

data_processing: Data were extracted using the Microarray Suite (MAS) version 5.0 (Affymetrix) and linearly scaled to achieve an average intensity of 150 across each chip.

source_name: human Osteosarcoma cell line

tag: Bone tumor cell line U-2OS purchased from ATCC


title: NA18912_Nsp_COMM


title: NA07345_Sty_COMM

value: Female	Cell lot number:A4


title: NA07357_Sty_COMM


title: NA18913_Nsp_COMM


title: NA18943_Sty_EA


title: NA18942_Sty_EA


title: NA18872_Nsp_COMM


title: NA07055_Sty_COMM

value: Female	Cell lot number:B2


title: NA18914_Sty_EA


title: NA07022_Sty_COMM

value: Male	Cell lot number:4


title: NA06993_Sty_COMM


title: NA07048_Sty_COMM


title: NA07019_Sty_COMM


title: NA18912_Sty_EA


title: NA10835_Sty_COMM


title: NA07056_Sty_COMM

value: Female	Cell lot number:A1


title: NA18863_Nsp_COMM


title: NA07029_Sty_COMM

value: Male	Cell lot number:A1


title: NA07034_Sty_COMM

value: Male	Cell lot number:B3


title: NA18940_Sty_EA


title: NA18862_Nsp_COMM


title: NA06991_Sty_COMM


title: NA18870_Nsp_COMM


title: NA07000_Sty_COMM


title: NA18861_Nsp_COMM


title: NA15510_Nsp_EA_rep3

value: Female	Cell lot number:4


title: NA18871_Sty_EA


title: NA15510_Nsp_EA_rep1


title: NA06985_Sty_COMM

value: Female	Cell lot number:A5


title: NA18913_Sty_EA


title: NA18872_Sty_EA


title: NA18871_Nsp_COMM


title: NA10851_Nsp_EA_rep3


title: NA06994_Sty_COMM


title: NA19099_TechnicalReplicate_Nsp_EA_rep3


title: NA10851_Nsp_EA_rep2


title: NA15510_Nsp_EA_rep2


title: NA18870_Sty_EA


title: NA18858_Nsp_COMM


title: NA18980_TechnicalReplicate_Nsp_EA_rep3

value: Female	Cell lot number:2


title: NA18980_TechnicalReplicate_Nsp_EA_rep2


title: NA18859_Nsp_COMM


title: NA19099_TechnicalReplicate_Nsp_EA_rep2

value: Female	Cell lot number:1


title: NA18863_Sty_EA


title: NA18862_Sty_EA


title: NA18971_TechnicalReplicate_Nsp_EA_rep2


title: NA18857_Nsp_COMM


title: NA18856_Nsp_COMM


title: NA19099_TechnicalReplicate_Nsp_EA_rep1


title: NA18971_TechnicalReplicate_Nsp_EA_rep1


title: NA18980_TechnicalReplicate_Nsp_EA_rep1


title: NA18860_Sty_EA


title: NA18971_TechnicalReplicate_Nsp_EA_rep3


title: NA18860_TechnicalReplicate_Nsp_EA_rep2


title: NA18853_Nsp_COMM


title: NA18855_Nsp_COMM


title: NA18857_Sty_EA


title: NA18860_TechnicalReplicate_Nsp_EA_rep3


title: NA18621_TechnicalReplicate_Nsp_EA_rep3


title: NA18854_Nsp_COMM


title: NA18860_TechnicalReplicate_Nsp_EA_rep1


title: NA18859_Sty_EA


title: NA18852_Nsp_COMM


title: NA18637_Nsp_COMM


title: NA18576_TechnicalReplicate_Nsp_EA_rep3


title: NA18621_TechnicalReplicate_Nsp_EA_rep2


title: NA18856_Sty_EA


title: NA18855_Sty_EA


title: NA18636_Nsp_COMM


title: NA18576_TechnicalReplicate_Nsp_EA_rep1


title: NA18635_Nsp_COMM


title: NA18621_TechnicalReplicate_Nsp_EA_rep1


title: NA18500_TechnicalReplicate_Nsp_EA_rep1


title: NA12892_TechnicalReplicate_Nsp_EA_rep2


title: NA18500_TechnicalReplicate_Nsp_EA_rep3


title: NA18861_Sty_EA


title: NA18853_Sty_EA


title: NA12892_TechnicalReplicate_Nsp_EA_rep1


title: NA12892_TechnicalReplicate_Nsp_EA_rep3


title: NA18637_Sty_EA


title: NA18632_Nsp_COMM


title: NA18852_Sty_EA


title: NA18624_Nsp_COMM


title: NA12239_TechnicalReplicate_Nsp_EA_rep2


title: NA12144_TechnicalReplicate_Nsp_EA_rep3


title: NA12239_TechnicalReplicate_Nsp_EA_rep1


title: NA18623_Nsp_COMM


title: NA18854_Sty_EA


title: NA12144_TechnicalReplicate_Nsp_EA_rep2


title: NA18622_Nsp_COMM


title: NA18858_Sty_EA


title: NA18633_Nsp_COMM


title: NA18635_Sty_EA


title: NA18500_TechnicalReplicate_Nsp_EA_rep2


title: NA12239_TechnicalReplicate_Nsp_EA_rep3


title: NA12144_TechnicalReplicate_Nsp_EA_rep1


title: NA18633_Sty_EA


title: NA18632_Sty_EA


title: NA19238_Nsp_EA


title: NA19239_Nsp_EA


title: NA18620_Nsp_COMM


title: NA19240_Nsp_EA


title: NA18636_Sty_EA


title: NA18860_Nsp_COMM


title: NA19222_Nsp_EA


title: NA19221_Nsp_EA


title: NA18624_Sty_EA


title: NA19210_Nsp_EA


title: NA18623_Sty_EA


title: NA19211_Nsp_EA


title: NA18609_Nsp_COMM


title: NA18612_Nsp_COMM


title: NA18622_Sty_EA


title: NA19208_Nsp_EA


title: NA18621_Sty_EA


title: NA18611_Nsp_COMM


title: NA19204_Nsp_EA


title: NA19207_Nsp_EA


title: NA19206_Nsp_EA


title: NA18605_Nsp_COMM


title: NA19223_Nsp_EA


title: NA19209_Nsp_EA


title: NA18608_Nsp_COMM


title: NA18620_Sty_EA


title: NA18612_Sty_EA


title: NA18609_Sty_EA


title: NA19203_Nsp_EA


title: NA19201_Nsp_EA


title: NA18621_Nsp_COMM


title: NA19202_Nsp_EA


title: NA18603_Nsp_COMM


title: NA18611_Sty_EA


title: NA18594_Nsp_COMM


title: NA19205_Nsp_EA


title: NA19200_Nsp_EA


title: NA19173_Nsp_EA


title: NA18608_Sty_EA


title: NA18593_Nsp_COMM


title: NA19193_Nsp_EA


title: NA19194_Nsp_EA


title: NA18592_Nsp_COMM


title: NA19171_Nsp_EA


title: NA18605_Sty_EA


title: NA19172_Nsp_EA


title: NA18603_Sty_EA


title: NA19160_Nsp_EA


title: NA19154_Nsp_EA


title: NA19192_Nsp_EA


title: NA19161_Nsp_EA


title: NA18594_Sty_EA


title: NA19153_Nsp_EA


title: NA18593_Sty_EA


title: NA19145_Nsp_EA


title: NA19159_Nsp_EA


title: NA19152_Nsp_EA


title: NA18592_Sty_EA


title: NA19144_Nsp_EA


title: NA18573_Nsp_COMM


title: NA18576_Nsp_COMM


title: NA18582_Sty_EA


title: NA18579_Sty_EA


title: NA18579_Nsp_COMM


title: NA19143_Nsp_EA


title: NA18582_Nsp_COMM


title: NA18571_Nsp_COMM


title: NA19138_Nsp_EA


title: NA19141_Nsp_EA


title: NA18570_Nsp_COMM


title: NA18573_Sty_EA


title: NA19140_Nsp_EA


title: NA18572_Nsp_COMM


title: NA19131_Nsp_EA


title: NA18577_Nsp_COMM


title: NA19132_Nsp_EA


title: NA18576_Sty_EA


title: NA18577_Sty_EA


title: NA19137_Nsp_EA


title: NA19142_Nsp_EA


title: NA19130_Nsp_EA


title: NA19128_Nsp_EA


title: NA18564_Nsp_COMM


title: NA19139_Nsp_EA


title: NA18566_Nsp_COMM


title: NA18563_Nsp_COMM


title: NA18571_Sty_EA


title: NA19127_Nsp_EA


title: NA19129_Nsp_EA


title: NA19120_Nsp_EA


title: NA19102_Nsp_EA


title: NA18561_Nsp_COMM


title: NA18552_Nsp_COMM


title: NA19103_Nsp_EA


title: NA18570_Sty_EA


title: NA19099_Nsp_EA


title: NA19098_Nsp_EA


title: NA19101_Nsp_EA


title: NA19119_Nsp_EA


title: NA18550_Nsp_COMM


title: NA19100_Nsp_EA


title: NA18564_Sty_EA


title: NA19094_Nsp_EA


title: NA19093_Nsp_EA


title: NA18563_Sty_EA


title: NA18555_Nsp_COMM


title: NA18545_Nsp_COMM


title: NA18566_Sty_EA


title: NA19012_Nsp_EA


title: NA19092_Nsp_EA


title: NA18572_Sty_EA


title: NA18547_Nsp_COMM


title: NA18561_Sty_EA


title: NA18562_Sty_EA


title: NA18542_Nsp_COMM


title: NA19007_Nsp_EA


title: NA19116_Nsp_EA


title: NA18555_Sty_EA


title: NA18558_Sty_EA


title: NA18999_Nsp_EA


title: NA19000_Nsp_EA


title: NA19005_Nsp_EA


title: NA18540_Nsp_COMM


title: NA18550_Sty_EA


title: NA19003_Nsp_EA


title: NA18529_Nsp_COMM


title: NA18558_Nsp_COMM


title: NA18532_Nsp_COMM


title: NA18537_Nsp_COMM


title: NA18995_Nsp_EA


title: NA18994_Nsp_EA


title: NA18998_Nsp_EA


title: NA18547_Sty_EA


title: NA18526_Nsp_COMM


title: NA18997_Nsp_EA


title: NA18545_Sty_EA


title: NA18991_Nsp_EA


title: NA18990_Nsp_EA


title: NA18552_Sty_EA


title: NA18976_Nsp_EA


title: NA18542_Sty_EA


title: NA18992_Nsp_EA


title: NA18523_Nsp_COMM


title: NA18981_Nsp_EA


title: NA18540_Sty_EA


title: NA18987_Nsp_EA


title: NA18978_Nsp_EA


title: NA18980_Nsp_EA


title: NA18975_Nsp_EA


title: NA18537_Sty_EA


title: NA18532_Sty_EA


title: NA18524_Nsp_COMM


title: NA18522_Nsp_COMM


title: NA18529_Sty_EA


title: NA18971_Nsp_EA


title: NA18969_Nsp_EA


title: NA18974_Nsp_EA


title: NA18526_Sty_EA


title: NA18972_Nsp_EA


title: NA18516_Nsp_COMM


title: NA18524_Sty_EA


title: NA18970_Nsp_EA


title: NA18508_Nsp_COMM


title: NA18973_Nsp_EA


title: NA18517_Nsp_COMM


title: NA18967_Nsp_EA


title: NA18523_Sty_EA


title: NA18960_Nsp_EA


title: NA18515_Nsp_COMM


title: NA18522_Sty_EA


title: NA18965_Nsp_EA


title: NA18964_Nsp_EA


title: NA18961_Nsp_EA


title: NA18968_Nsp_EA


title: NA18507_Nsp_COMM


title: NA18506_Nsp_COMM


title: NA18959_Nsp_EA


title: NA18956_Nsp_EA


title: NA18966_Nsp_EA


title: NA18504_Nsp_COMM


title: NA18517_Sty_EA


title: NA18521_Sty_EA


title: NA18952_Nsp_EA


title: NA18505_Nsp_COMM


title: NA18951_Nsp_EA


title: NA18947_Nsp_EA


title: NA18516_Sty_EA


title: NA18503_Nsp_COMM


title: NA18949_Nsp_EA


title: NA18945_Nsp_EA


title: NA18506_Sty_EA


title: NA18515_Sty_EA


title: NA18508_Sty_EA


title: NA18953_Nsp_EA


title: NA18507_Sty_EA


title: NA18502_Nsp_COMM


title: NA18500_Nsp_COMM


title: NA18501_Nsp_COMM


title: NA18948_Nsp_EA


title: NA18914_Nsp_EA


title: NA18940_Nsp_EA


title: NA18943_Nsp_EA


title: NA12892_Nsp_COMM


title: NA18505_Sty_EA


title: NA18913_Nsp_EA


title: NA18872_Nsp_EA


title: NA12891_Nsp_COMM


title: NA18503_Sty_EA


title: NA18944_Nsp_EA


title: NA18504_Sty_EA


title: NA18912_Nsp_EA


title: NA18942_Nsp_EA


title: NA12878_Nsp_COMM


title: NA18871_Nsp_EA


title: NA18863_Nsp_EA


title: NA18862_Nsp_EA


title: NA18500_Sty_EA


title: NA12875_Nsp_COMM


title: NA18502_Sty_EA


title: NA12873_Nsp_COMM


title: NA18856_Nsp_EA


title: NA18870_Nsp_EA


title: NA12874_Nsp_COMM


title: NA18501_Sty_EA


title: NA18858_Nsp_EA


title: NA18855_Nsp_EA


title: NA18859_Nsp_EA


title: NA18860_Nsp_EA


title: NA18857_Nsp_EA


title: NA12892_Sty_EA


title: NA12891_Sty_EA


title: NA18861_Nsp_EA


title: NA12865_Nsp_COMM


title: NA12875_Sty_EA


title: NA12878_Sty_EA


title: NA18852_Nsp_EA


title: NA18853_Nsp_EA


title: NA18854_Nsp_EA


title: NA12864_Nsp_COMM


title: NA12872_Nsp_COMM


title: NA12814_Nsp_COMM


title: NA12872_Sty_EA


title: NA18637_Nsp_EA


title: NA18633_Nsp_EA


title: NA12815_Nsp_COMM


title: NA12802_Nsp_COMM


title: NA12874_Sty_EA


title: NA18632_Nsp_EA


title: NA12864_Sty_EA


title: NA12801_Nsp_COMM


title: NA18635_Nsp_EA


title: NA18612_Nsp_EA


title: NA12873_Sty_EA


title: NA18623_Nsp_EA


title: NA12813_Nsp_COMM


title: NA18620_Nsp_EA


title: NA12865_Sty_EA


title: NA12763_Nsp_COMM


title: NA18622_Nsp_EA


title: NA18611_Nsp_EA


title: NA18609_Nsp_EA


title: NA18624_Nsp_EA


title: NA18636_Nsp_EA


title: NA12812_Nsp_COMM


title: NA12814_Sty_EA


title: NA18621_Nsp_EA


title: NA12815_Sty_EA


title: NA18608_Nsp_EA


title: NA12762_Nsp_COMM


title: NA12761_Nsp_COMM


title: NA18605_Nsp_EA


title: NA18603_Nsp_EA


title: NA12760_Nsp_COMM


title: NA18593_Nsp_EA


title: NA18577_Nsp_EA


title: NA18594_Nsp_EA


title: NA18579_Nsp_EA


title: NA12801_Sty_EA


title: NA12753_Nsp_COMM


title: NA18592_Nsp_EA


title: NA12802_Sty_EA


title: NA12763_Sty_EA


title: NA12762_Sty_EA


title: NA18576_Nsp_EA


title: NA18573_Nsp_EA


title: NA12813_Sty_EA


title: NA12812_Sty_EA


title: NA18571_Nsp_EA


title: NA18572_Nsp_EA


title: NA18582_Nsp_EA


title: NA12761_Sty_EA


title: NA12752_Nsp_COMM


title: NA18570_Nsp_EA


title: NA18566_Nsp_EA


title: NA12751_Nsp_COMM


title: NA18562_Nsp_EA


title: NA18563_Nsp_EA


title: NA18555_Nsp_EA


title: NA18558_Nsp_EA


title: NA12751_Sty_EA


title: NA18561_Nsp_EA


title: NA12264_Nsp_COMM


title: NA12760_Sty_EA


title: NA12716_Nsp_COMM


title: NA12707_Nsp_COMM


title: NA12753_Sty_EA


title: NA12740_Nsp_COMM


title: NA18547_Nsp_EA


title: NA12249_Nsp_COMM


title: NA12750_Sty_EA


title: NA12752_Sty_EA


title: NA18540_Nsp_EA


title: NA12750_Nsp_COMM


title: NA18552_Nsp_EA


title: NA18545_Nsp_EA


title: NA18550_Nsp_EA


title: NA18537_Nsp_EA


title: NA18564_Nsp_EA


title: NA18542_Nsp_EA


title: NA12740_Sty_EA


title: NA12717_Nsp_COMM

value: Female	Cell lot number:B3


title: NA18532_Nsp_EA


title: NA18529_Nsp_EA


title: NA12717_Sty_EA


title: NA12248_Nsp_COMM

value: Male	Cell lot number:A3


title: NA12707_Sty_EA


title: NA12716_Sty_EA


title: NA18524_Nsp_EA


title: NA12156_Nsp_COMM

value: Female	Cell lot number:A3


title: NA12234_Nsp_COMM


title: NA12236_Nsp_COMM


title: NA18526_Nsp_EA


title: NA18522_Nsp_EA

value: Male	Cell lot number:1


title: NA12264_Sty_EA


title: NA18517_Nsp_EA


title: NA12155_Nsp_COMM

value: Male	Cell lot number:3


title: NA18516_Nsp_EA


title: NA12249_Sty_EA


title: NA12146_Nsp_COMM


title: NA12154_Nsp_COMM


title: NA18521_Nsp_EA


title: NA12239_Sty_EA

value: Female	Cell lot number:3


title: NA12248_Sty_EA


title: NA18523_Nsp_EA


title: NA18506_Nsp_EA


title: NA12145_Nsp_COMM


title: NA18507_Nsp_EA


title: NA18504_Nsp_EA


title: NA18505_Nsp_EA


title: NA18508_Nsp_EA


title: NA18515_Nsp_EA


title: NA12057_Nsp_COMM


title: NA18502_Nsp_EA


title: NA18503_Nsp_EA


title: NA12144_Nsp_COMM


title: NA12156_Sty_EA


title: NA12234_Sty_EA


title: NA18501_Nsp_EA


title: NA12892_Nsp_EA


title: NA18500_Nsp_EA


title: NA12875_Nsp_EA


title: NA12878_Nsp_EA


title: NA12056_Nsp_COMM


title: NA12044_Nsp_COMM


title: NA12154_Sty_EA


title: NA12155_Sty_EA


title: NA12146_Sty_EA


title: NA12865_Nsp_EA


title: NA12872_Nsp_EA


title: NA12236_Sty_EA


title: NA12891_Nsp_EA

value: Male	Cell lot number:2


title: NA12864_Nsp_EA


title: NA12006_Nsp_COMM


title: NA12873_Nsp_EA


title: NA12813_Nsp_EA


title: NA12874_Nsp_EA


title: NA12145_Sty_EA


title: NA12144_Sty_EA


title: NA12057_Sty_EA


title: NA12814_Nsp_EA


title: NA12815_Nsp_EA


title: NA12004_Nsp_COMM


title: NA12043_Nsp_COMM


title: NA12801_Nsp_EA


title: NA12812_Nsp_EA


title: NA12044_Sty_EA


title: NA12753_Nsp_EA


title: NA12005_Nsp_COMM


title: NA12043_Sty_EA


title: NA12802_Nsp_EA


title: NA12006_Sty_EA


title: NA11993_Nsp_COMM


title: NA12752_Nsp_EA


title: NA11992_Nsp_COMM


title: NA12005_Sty_EA


title: NA12760_Nsp_EA


title: NA12750_Nsp_EA


title: NA12763_Nsp_EA


title: NA12762_Nsp_EA


title: NA12056_Sty_EA


title: NA12751_Nsp_EA


title: NA12003_Nsp_COMM


title: NA12761_Nsp_EA


title: NA11994_Nsp_COMM


title: NA11995_Nsp_COMM


title: NA11882_Nsp_COMM


title: NA12740_Nsp_EA


title: NA12004_Sty_EA


title: NA12707_Nsp_EA


title: NA12716_Nsp_EA


title: NA12717_Nsp_EA


title: NA11881_Nsp_COMM


title: NA11840_Nsp_COMM


title: NA12003_Sty_EA


title: NA11832_Nsp_COMM


title: NA12264_Nsp_EA


title: NA12239_Nsp_EA


title: NA11839_Nsp_COMM

value: Male	Cell lot number:A2


title: NA12249_Nsp_EA


title: NA12248_Nsp_EA


title: NA10851_Nsp_EA_rep1


title: NA11994_Sty_EA


title: NA12234_Nsp_EA


title: NA12154_Nsp_EA


title: NA11830_Nsp_COMM


title: NA12156_Nsp_EA


title: NA11882_Sty_EA


title: NA11992_Sty_EA


title: NA12146_Nsp_EA


title: NA12236_Nsp_EA


title: NA11993_Sty_EA


title: NA11881_Sty_EA


title: NA12145_Nsp_EA


title: NA11831_Nsp_COMM


title: NA11995_Sty_EA


title: NA12057_Nsp_EA


title: NA10863_Nsp_COMM

value: Female	Cell lot number:A2


title: NA11840_Sty_EA


title: NA10861_Nsp_COMM


title: NA12155_Nsp_EA


title: NA12144_Nsp_EA

value: Male	Cell lot number:4


title: NA12056_Nsp_EA


title: NA10860_Nsp_COMM

value: Male	Cell lot number:5


title: NA11829_Nsp_COMM


title: NA12043_Nsp_EA


title: NA11839_Sty_EA


title: NA12044_Nsp_EA


title: NA12004_Nsp_EA


title: NA11831_Sty_EA


title: NA12006_Nsp_EA


title: NA11832_Sty_EA


title: NA12005_Nsp_EA


title: NA12003_Nsp_EA


title: NA11993_Nsp_EA


title: NA10856_Nsp_COMM


title: NA10857_Nsp_COMM


title: NA10863_Sty_EA


title: NA11830_Sty_EA


title: NA10859_Nsp_COMM

value: Female	Cell lot number:A6


title: NA11881_Nsp_EA


title: NA11992_Nsp_EA


title: NA11829_Sty_EA


title: NA10854_Nsp_COMM


title: NA11994_Nsp_EA


title: NA11840_Nsp_EA


title: NA10861_Sty_EA


title: NA10851_Nsp_COMM


title: NA11882_Nsp_EA

value: Female	Cell lot number:A1


title: NA11839_Nsp_EA


title: NA11995_Nsp_EA


title: NA10860_Sty_EA


title: NA10847_Nsp_COMM


title: NA18576_TechnicalReplicate_Nsp_EA_rep2


title: NA10855_Nsp_COMM


title: NA11832_Nsp_EA


title: NA11831_Nsp_EA


title: NA10863_Nsp_EA


title: NA10857_Sty_EA


title: NA11829_Nsp_EA


title: NA11830_Nsp_EA


title: NA10861_Nsp_EA

value: Female	Cell lot number:4


title: NA10856_Sty_EA


title: NA10835_Nsp_COMM


title: NA10839_Nsp_COMM


title: NA10859_Nsp_EA


title: NA10846_Nsp_COMM


title: NA10860_Nsp_EA


title: NA10855_Sty_EA


title: NA10856_Nsp_EA


title: NA10831_Nsp_COMM

value: Female	Cell lot number:5


title: NA10859_Sty_EA


title: NA10857_Nsp_EA


title: NA10854_Sty_EA

value: Female	Cell lot number:2


title: NA10851_Sty_EA


title: NA10846_Sty_EA


title: NA07357_Nsp_COMM


title: NA10839_Sty_EA


title: NA10855_Nsp_EA


title: NA10838_Nsp_COMM


title: NA10830_Nsp_COMM

value: Male	Cell lot number:6


title: NA10847_Sty_EA


title: NA10851_Nsp_EA


title: NA10854_Nsp_EA


title: NA10846_Nsp_EA


title: NA07345_Nsp_COMM

value: Female	Cell lot number:A4


title: NA10838_Sty_EA


title: NA10847_Nsp_EA


title: NA07056_Nsp_COMM


title: NA07348_Nsp_COMM


title: NA07055_Nsp_COMM

value: Female	Cell lot number:B2


title: NA10831_Sty_EA


title: NA10831_Nsp_EA


title: NA10830_Sty_EA


title: NA10839_Nsp_EA


title: NA10838_Nsp_EA


title: NA10835_Nsp_EA


title: NA07048_Nsp_COMM


title: NA07348_Sty_EA


title: NA07034_Nsp_COMM

value: Male	Cell lot number:B3


title: NA06994_Nsp_COMM


title: NA07048_Sty_EA


title: NA07348_Nsp_EA


title: NA10830_Nsp_EA


title: NA07055_Sty_EA


title: NA07019_Nsp_COMM


title: NA07345_Sty_EA


title: NA07357_Sty_EA


title: NA07056_Sty_EA


title: NA07029_Nsp_COMM

value: Male	Cell lot number:A1


title: NA07034_Sty_EA


title: NA07345_Nsp_EA


title: NA07022_Nsp_COMM


title: NA07000_Nsp_COMM


title: NA07056_Nsp_EA


title: NA07357_Nsp_EA

value: Male	Cell lot number:3


title: NA06993_Nsp_COMM


title: NA07029_Sty_EA


title: NA07055_Nsp_EA


title: NA06991_Nsp_COMM

value: Female	Cell lot number:3


title: NA06985_Nsp_COMM

value: Female	Cell lot number:A5


title: NA07019_Nsp_EA


title: NA07048_Nsp_EA


title: NA07034_Nsp_EA


title: NA07022_Nsp_EA


title: NA07000_Nsp_EA


title: NA06994_Nsp_EA


title: NA07022_Sty_EA


title: NA06993_Sty_EA


title: NA06994_Sty_EA


title: NA06991_Sty_EA


title: NA06985_Sty_EA


title: NA07000_Sty_EA


title: NA07029_Nsp_EA


title: NA06993_Nsp_EA


title: NA06985_Nsp_EA


title: NA06991_Nsp_EA


title: NA07019_Sty_EA


title: NA18521_Nsp_COMM

value: Male	Cell lot number:1


title: NA10835_Sty_EA