title: larval cyc0Kir LNvs at CT-3, biological rep3

status: Public on Sep 01 2012

city: New York

first: Marc

last: Ruben

address: 100 Washington Square East

institute: New York University

description:
Gene expression data from Kir and GFP expressing LNvs in the cyc0 mutant background LNvs at CT-3
cyc0Kir3

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 20 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Raw hybridization intensities from each CEL Affymetrix file (Drosophila 2.0 GeneChip) were analyzed using gcrma algorithm in Matlab. Intensities were quantile-normalized across all replicates and experiments to yield a single expression measure for each probeset on the chip.

source_name: Drosophila cyc0; Kir larval LNvs at CT-3

label_protocol: mRNA was amplified using the NuGen WT-Ovation™ Pico System to yield ~ 5ug biotin labeled, fragmented, single-stranded cDNA.

growth_protocol: All larval genotypes raised at 25C in 12:12hr Light/Dark cycle.

extract_protocol: The GFP+ cells were isolated by FACS, and sorted directly into Arcturus PicoPure RNA extraction buffer.

treatment_protocol: Dissected brains (L3 larvae) were transferred to Schneider’s Insect Medium (Sigma) in non-stick tubes (Neptune) and were kept on ice throughout. Prior to dissociation, brains were washed with ice-cold PBS buffer. For dissociation, we followed the method of Wegener et al: brains transferred to a 50:50 mix of 1X Collagenase (Sigma): 1X Dispase II (Roche) and incubated for 2hr at 25°C. After 2hr, the dissociation solution was replaced with Schneider’s medium with 10% FBS (Fetal Bovine Serum), brains were triturated 100x with a pipette, and strained through a 35mm nylon mesh filter. Cells in Schneider’s medium / 10% FBS were kept on ice for transport FACS.

value: L3 larval stage

value: Pdf > Kir2.1 + GFP; cyc0/cyc0

tag: tissue origin

value: brain

value: FACs-purified LNvs


title: 0-24 Hrs dMyc+ embryos, biological rep2

status: Public on Sep 15 2012

type: RNA

city: Charlotte

first: Kaveh

last: Daneshvar

state: NC

address: 9201 University City Blvd.

department: Biology

country: USA

institute: University of North Carolina at Charlotte

description: Gene expression data from embryos between 0 t0 24 hours old

hyb_protocol: Affymetrix hybridization protocol. Done by Expression Analysis (Durham, NC, USA)

scan_protocol: Affymetrix GeneChip Scannerl. Done by Expression Analysis (Durham, NC, USA)

data_processing: The data were analyzed using Affymetrix default analysis settings and global scaling as normalization method. Done by Expression Analysis (Durham, NC, USA)

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: 0-24 hour old embryos

label_protocol: 3” IVT Express kit was used. Done by Expression Analysis (Durham, NC, USA)

growth_protocol: For both genotypes (Control and dMyc+) 0-24 hours embryos were collected on a grape juice agar at 25C.

extract_protocol: Total RNA was extracted using Trizol solution (Invitrogen), according to manufacturer’s recommendation.

treatment_protocol: Embryos were dechorionated with 100% bleach, and washed with D.I. water several times. Washed and drained embryos were placed in the Trizol solution (Invitrogen).

tag: tissue

value: dechorionated embryo

tag: age

value: 0-24 hour old

tag: genotype/variation

value: Myc+ (flies over-expressing dMyc under UAS enhancer)


title: 0-24 Hrs control embryos, biological rep1

value: control (Gal 4 expressing animals)


title: larval cyc0Kir LNvs at CT-3, biological rep1

state: NY

description:
Gene expression data from Kir and GFP expressing LNvs in the cyc0 mutant background LNvs at CT-3
cyc0Kir1

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.


title: Flies on plain food, biological rep1

status: Public on Sep 05 2012

city: Albany

first: Haydeh

last: Payami

address: 150 New Scotland Ave.

department: Wadsworth Center

institute: NY State Department of Health

description:
dmel_control_1
Gene expression data from heads of flies exposed to plain food for 16 days.

hyb_protocol: The labeled cDNA was hybridized overnight to the GeneChip Drosophila 2.0 array (Affymetrix).

scan_protocol: The arrays were scanned on a GeneChip Scanner 30007G using standard protocols, and raw data were obtained using Affymetrix Command Console Software.

data_processing: The data were analyzed and normalized using the Bioconductor R packages affy and GCRMA (using the default options of quantile normalization, pmonly correction, and median polish summarization).

source_name: Drosophila adult female heads, 16 days on plain food

label_protocol: The cDNA was fragmented and biotin labeled using the Encore Biotin module according to standard protocols (NuGEN).

growth_protocol: Female D. melanogaster w1118 flies were collected up to 24 hours after eclosion and placed into food vials for pretreatment.

extract_protocol: Heads were dissected from 20 females per vial and pooled. Total RNA was extracted using Tri Reagent and the associated protocol, and RNA was cleaned using the Qiagen RNeasy Cleanup Kit and the associated protocol. Total RNA (50ng) was used to generate cDNA and amplified using a NuGEN 3'-Applause amplification system according to the manufacturer's instructions (NuGEN).

treatment_protocol: Flies were pretreated on food containing either 0 or 0.1 mg/ml nicotine for 10 days, and then treated on food containing either 0 or 5 mM paraquat plus the pretreatment dose of nicotine for 6 days. Flies were transferred to fresh food vials every other day.

tag: genotype

tag: Sex

value: female

tag: developmental stage

value: adult

value: head

tag: nicotine exposure

value: 0 mg/ml

tag: paraquat exposure

value: 0 mM


title: 0-24 Hrs control embryos, biological rep2


title: Flies on 5mM paraquat, biological rep2

description:
dmel_PQ_2
Gene expression data from heads of flies exposed to plain food for 10 days, followed by food with 5 mM paraquat for 6 days.

source_name: Drosophila adult female heads, 10 days on plain food and 6 days on food with paraquat

value: 5 mM


title: Flies on 0.1 mg/ml nicotine, biological rep3

description:
dmel_Nic_3
Gene expression data from heads of flies exposed to food with 0.1 mg/ml nicotine for 16 days.

source_name: Drosophila adult female heads, 16 days on food with nicotine

value: 0.1 mg/ml


title: Ovary_su(Hw)Pb/2_rep2

city: Iowa City

first: Alexey

middle: A

last: Soshnev

state: Iowa

address: 3159C MERF 375 Newton Rd

department: Biochemistry

institute: University of Iowa

description: Gene expression data from su(Hw)Pb/2 (sterile) young virgin female Drosophila embryos

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix hybridization buffer, placed onto Drosophila 2.0 arrays (Cat #900532), and incubated at 45º C for 18 h with 60 rpms rotation in an Affymetrix Model 640 Genechip Hybridization Oven.  Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc. Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) , and stained again with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), using the Affymetrix Model 450Fluidics Station (Affymetrix, Inc.) following the appropriate fluidics script protocol for the array

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade.

data_processing: Data were collected using the using the GeneChip operating software (GCOS) v1.4 and expression value estimates were generated using the microarray suite (MAS) v5.0 software.

label_protocol: Fifty nanograms total RNA was converted to SPIA amplified cDNA using the Ovation RNA Amplification System, v2 (NuGEN Technologies, Cat. #3100) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN.  3.75ug of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module,  (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

growth_protocol: Flies were raised on tandard cornmeal-agar medium at 25C. Newly eclosed virgin females were collected and aged for 4 hours prior to dissection of ovaries

extract_protocol: RNA was isolated with TRIzol from approximately 150 ovary pairs per replicate, DNase-treated (Qiagen DNaseI) and cleaned up (Qiagen RNeasy) according to the manufacturer instructions.

treatment_protocol: Ovaries were dissected in ice-cold PBS and stored at -80C until used.

value: ovary

value: 4-6 hours


title: Ovary_su(Hw)fv_rep3

description: Gene expression data from su(Hw)f/v (fertile) young virgin female Drosophila embryos

value: su(Hw)f/su(Hw)v


title: Ovary_su(Hw)2/v_rep3

description: Gene expression data from su(Hw)2/v (sterile) young virgin female Drosophila embryos


title: Ovary_su(Hw)Pb/2_rep1

source_name: su(Hw)Pb/2 (sterile) young virgin female Drosophila embryos


title: Ovary_su(Hw)Pb/2_rep3


title: Ovary_su(Hw)fv_rep1

source_name: su(Hw)f/v (fertile) young virgin female Drosophila embryos


title: larval cyc0Kir LNvs at CT-3, biological rep2

description:
Gene expression data from Kir and GFP expressing LNvs in the cyc0 mutant background LNvs at CT-3
cyc0Kir2

value: L3 larval stage

value: Pdf > Kir2.1 + GFP; cyc0/cyc0


title: Ovary_su(Hw)2/v_rep1

source_name: su(Hw)2/v (sterile) young virgin female Drosophila embryos


title: Ovaly_WT_rep2

description: Gene expression data from wild type young virgin female Drosophila embryos

value: su(Hw) wild type (Canton S)


title: Ovary_su(Hw)fv_rep2


title: Ovaly_WT_rep3

source_name: wild type young virgin female Drosophila embryos


title: Ovary_su(Hw)2/v_rep2


title: Ovaly_WT_rep1


title: larval Kir-LNvs at CT-15, biological rep2

description: Gene expression data from Kir-expressing LNvs at CT-15

source_name: Drosophila larval Kir-LNvs at CT-15

label_protocol: Affymetrix protocol

extract_protocol: The 0.01%-most RFP+ cells (150 - 300 cells) were isolated by FACS, and sorted directly into Arcturus PicoPure RNA extraction buffer. mRNA was amplified using the NuGen WT-Ovation™ Pico System to yield ~ 5ug biotin labeled, fragmented, single-stranded cDNA

value: FACs-purified LNvs

value: yw; Pdf-Gal4/UAS-Kir; Pdf-RFP


title: larval NCB--induced-LNvs at CT-15, biological rep3

description: Gene expression data from NCB-induced (30 degrees C) LNvs at CT-15

source_name: Drosophila larval NCB-induced LNvs at CT-15

growth_protocol: All larval genotypes raised at 25C in 12:12hr Light/Dark cycle.  Experiments were shifted to 30 degrees C when transferred to constant darkness.


title: larval per0 NCB-LNvs at CT-15, biological rep1

description: Gene expression data from per0 NCB-expressing LNvs at CT-15

source_name: Drosophila larval per0 NCB-LNvs at CT-15

value: per0, yw; Pdf-Gal4/UAS-NCB; Pdf-RFP


title: larval Kir-LNvs at CT-3, biological rep1

description: Gene expression data from Kir-expressing LNvs at CT-3

source_name: Drosophila larval Kir-LNvs at CT-3


title: larval per0 NCB-LNvs at CT-15, biological rep2


title: larval Kir-LNvs at CT-15, biological rep3


title: larval Kir-LNvs at CT-15, biological rep1


title: larval NCB-LNvs at CT-15, biological rep2

description: Gene expression data from NCB-expressing LNvs at CT-15

source_name: Drosophila larval NCB-LNvs at CT-15

value: yw; Pdf-Gal4/UAS-NCB; Pdf-RFP


title: larval WT-induced-LNvs at CT-15, biological rep3

description: Gene expression data from WT-induced (30 degrees C) LNvs at CT-15

source_name: Drosophila larval WT-induced LNvs at CT-15

value: yw; Pdf-Gal4/+; tub-Gal80ts/Pdf-RFP


title: larval per0 NCB-LNvs at CT-15, biological rep3


title: larval WT-induced-LNvs at CT-15, biological rep2


title: larval NCB-LNvs at CT-15, biological rep3


title: larval Kir-LNvs at CT-3, biological rep2


title: larval WT-induced-LNvs at CT-15, biological rep1


title: larval NCB-induced-LNvs at CT-15, biological rep1


title: larval NCB--induced-LNvs at CT-15, biological rep2


title: larval Kir-LNvs at CT-3, biological rep3


title: larval LNvs at CT-15, biological rep2

description: Gene expression data from wildtype LNvs at CT-15

source_name: Drosophila larval LNvs at CT-15

value: yw, Pdf-RFP


title: larval LNvs at CT-15, biological rep1


title: larval NCB-LNvs at CT-15, biological rep1


title: larval LNvs at CT-3, biological rep1

description: Gene expression data from wildtype LNvs at CT-3

source_name: Drosophila larval LNvs at CT-3


title: larval LNvs at CT-15, biological rep3


title: larval LNvs at CT-3, biological rep2


title: larval LNvs at CT-3, biological rep3


title: 0-24 Hrs control embryos, biological rep3

description: Gene expression data from embryos between 0 t0 24 hours old

value: dechorionated embryo

value: 0-24 hour old

value: control (Gal 4 expressing animals)


title: brains and imaginal discs from OregonR wild type 3rd instar Drosophila larvae, biological replicate 2

status: Public on Aug 20 2012

city: Oxford

first: Janina

last: Baumbach

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: Gene expression data from mitotic Drosophila wild type cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridised on Affymetrix Drosophila 2.0 GeneChips for 16 hrs at 45°C. Gene chips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip 3000 scanner.

data_processing: The data was analysed using the Bioconductor package limma. Probe intensities from Affymetrix image files (.CEL files)  were normalized using quantile normalisation, and expression signals of all probesets were calculated using GCRMA.

source_name: brains and imaginal discs from Drosophila 3rd instar larvae

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA using the Affymetrix 3’ IVT Express kit.

growth_protocol: Flies were kept on standard fly food at 25 degrees. Third instar wandering larvae were used for dissections.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Brains and imaginal discs were dissected in PBS under a dissecting scope and tissues from 10 larvae per sample were collected in a tube on dry ice.

value: OregonR wild type

value: brains and imaginal discs

value: 3rd instar larvae


title: gfp RNAi - Nov2010 - rep2

status: Public on Aug 30 2012

city: Barcelona

first: David

last: Rossell

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

hyb_protocol: 2.2 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Data from dates Oct_2009 and Nov_2010 were pre-processed separately. Data was quantile normalized and RMA summarized using Bioconductor.

source_name: GFP RNAi mutant

label_protocol: 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

growth_protocol: w1118, act5Cgal4>RNAi or lidk06801;act5Cgal4>lid RNAi larvae were grown at 25ºC until they became wall-climbing third instar larvae.

extract_protocol: RNA was extracted with a combination of Trizol and RNeasy minikit (Qiagen)

treatment_protocol: GFP RNAi and LID RNAi strains were obtained from NIG-FLY. For each condition, 30 wing imaginal discs were dissected in PBS and immediately transferred to Trizol

tag: RNAi

value: GFP

tag: genetic background

value: w1118, act5Cgal4> RNAi

value: third instar larva

tag: date


title: LID RNAi LID mutant - Nov2010 - rep1

source_name: LID RNAi mutant

value: LID

value: lidk06801;act5Cgal4>lid RNAi


title: brains and imaginal discs from Sak overexpressing 3rd instar Drosophila larvae, biological replicate 2

description: Gene expression data from mitotic Drosophila cells that have too many centrosomes

value: Sak overexpression


title: brains and imaginal discs from Sak overexpressing 3rd instar Drosophila larvae, biological replicate 3


title: LID RNAi LID mutant - Nov2010 - rep2


title: gfp RNAi - Nov2010 - rep1


title: wt - Nov2010 - rep2

source_name: wild type

value: w1118, act5Cgal4>RNAi


title: brains and imaginal discs from D-Sas4 mutant 3rd instar Drosophila larvae, biological replicate 1

description: Gene expression data from mitotic Drosophila cells that do not have centrioles

value: DSas-4 mutant


title: brains and imaginal discs from D-Sas4 mutant 3rd instar Drosophila larvae, biological replicate 2


title: brains and imaginal discs from w67 wild type 3rd instar Drosophila larvae, biological replicate 1

value: white wild type


title: brains and imaginal discs from D-Sas4 mutant 3rd instar Drosophila larvae, biological replicate 3


title: brains and imaginal discs from D-Ssas6 mutant 3rd instar Drosophila larvae, biological replicate 2

value: DSas-6 mutant


title: brains and imaginal discs from D-Ssas6 mutant 3rd instar Drosophila larvae, biological replicate 1


title: brains and imaginal discs from D-Ssas6 mutant 3rd instar Drosophila larvae, biological replicate 3


title: brains and imaginal discs from w67 wild type 3rd instar Drosophila larvae, biological replicate 3


title: brains and imaginal discs from OregonR wild type 3rd instar Drosophila larvae, biological replicate 1


title: brains and imaginal discs from Sak overexpressing 3rd instar Drosophila larvae, biological replicate 1


title: brains and imaginal discs from OregonR wild type 3rd instar Drosophila larvae, biological replicate 3


title: wt - Nov2010 - rep1


title: brains and imaginal discs from w67 wild type 3rd instar Drosophila larvae, biological replicate 2


title: camta1 root drought,biological replicate 2

status: Public on Aug 13 2012

city: lucknow

first: samir

middle: v

last: sawant

address: rana pratap marg

department: CPMB & GE

country: India

institute: national botanical research institute

description: Arabidopsis Thaliana mutant root in drought condition

hyb_protocol: According to affymatrix gene chip instruction manual using Fluidisc station 450.

scan_protocol: GeneChips were scanned using Affymatrix gene chip scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: 1 month old Arabidopsis plant

extract_protocol: Total RNA isolated from plant total RNA sigma kit

treatment_protocol: Plant sample collected under water and drought condition

value: root

tag: cultivar/ecotype


title: camta1 leaf drought,biological replicate 1

description: Arabidopsis Thaliana mutant leaf in drought condition

value: leaf


title: camta1 root water,biological replicate 3

description: Arabidopsis Thaliana  mutant root in water condition


title: camta1 leaf drought,biological replicate 3

source_name: Arabidopsis Thaliana mutant leaf in drought condition


title: camta1 root drought,biological replicate 1

source_name: Arabidopsis Thaliana mutant root in drought condition


title: camta1 root drought,biological replicate 3


title: camta1 root water,biological replicate 2

source_name: Arabidopsis Thaliana  mutant root in water condition


title: camta1 leaf drought,biological replicate 2


title: camta1 leaf water,biological replicate 2

description: Arabidopsis Thaliana mutant leaf in water condition


title: Col-0 root drought, biological replicate 1

description: Arabidopsis Thaliana root in drought condition


title: Col-0 root drought, biological replicate 2

source_name: Arabidopsis Thaliana root in drought condition


title: Col-0 leaf drought, biological replicate 1

description: Arabidopsis Thaliana leaf in drought condition


title: Col-0 root drought, biological replicate 3


title: Col-0 root water, biological replicate 3

description: Arabidopsis Thaliana root in water condition


title: Col-0 leaf drought, biological replicate 2

source_name: Arabidopsis Thaliana leaf in drought condition


title: camta1 leaf water,biological replicate 1

source_name: Arabidopsis Thaliana mutant leaf in water condition


title: Col-0 leaf water, biological replicate 3

description: Arabidopsis Thaliana leaf in water condition


title: Col-0 leaf drought, biological replicate 3


title: Col-0 leaf water, biological replicate 2

source_name: Arabidopsis Thaliana leaf in water condition


title: camta1 root water,biological replicate 1


title: Col-0 leaf water, biological replicate 1


title: camta1 leaf water,biological replicate 3


title: Col-0 root water, biological replicate 2

source_name: Arabidopsis Thaliana root in water condition


title: Col-0 root water, biological replicate 1


title: piffq 3d WL, biological rep 2

status: Public on Aug 02 2012

first: james

middle: m

last: tepperman

state: CA

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center/UC Berkeley

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: BioConductor software (RMA) to normalize and correct background on all the data.

source_name: pifq 2d seedling, 3d continuous white light (WL)

label_protocol: Standard Affymetrix procedures.

growth_protocol: Arabidopsis wild-type (WT) and pifq mutant (Leivar et al., 2008) seeds were plated on GM medium without sucrose at room temperature. During this procedure, the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, and then grown in WL (19 μmol/m2/s, R/FR ratio of 6.48) for 2 days at 21°C.

extract_protocol: Total RNA was extracted from ~400 mg (fw) tissue using the method of Chang et al. (Chang S, Puryear J & Cairney J (1993) Plant Mol. Biol. Rep. 11, 113-116), followed by further purification using Qiagen RNeasy columns.

treatment_protocol: No subsequent light treatment (WL0) (R:FR = 6.48); WL + FR  (R:FR=0.006) for 1h (FR1); WL + FR  (R:FR=0.006) for 3h (FR3); WL + FR  (R:FR=0.006) for 24h (FR24); 24h WL continuous, R:FR=6.48 (WL24).

value: pif1pif3pif4pif5 (pifq) mutant

value: whole seedling

tag: time in continuous light

value: 3 days

tag: time in fr light

value: 0 hr


title: piffq FR 24h, biological rep 2

source_name: pifq 2d seedling, 2d continuous white light (WL) + 24h FR light

value: 2 days

value: 24 hr


title: piffq FR 1h, biological rep 2

source_name: pifq 2d seedling, 2d continuous white light (WL) + 1h FR light

value: 1 hr


title: piffq FR 3h, biological rep 2

source_name: pifq 2d seedling, 2d continuous white light (WL) + 3h FR light

value: 3 hr


title: piffq 3d WL, biological rep 3


title: piffq FR 24h, biological rep 1


title: piffq FR 1h, biological rep 1


title: piffq FR 24h, biological rep 3


title: piffq 2d WL, biological rep 3

source_name: pifq 2d seedling, 2d continuous white light (WL)


title: piffq FR 3h, biological rep 3


title: WT 3d WL, biological rep 3

source_name: WT 2d seedling, 3d continuous white light (WL)

tag: ecotype

value: Columbia (Col-O)

value: WT


title: WT 3d WL, biological rep 2


title: WT FR 3h, biological rep 3

source_name: WT 2d seedling, 2d continuous white light (WL) + 3h FR light


title: piffq 2d WL, biological rep 1


title: piffq 3d WL, biological rep 1


title: piffq FR 3h, biological rep 1


title: WT 3d WL, biological rep 1


title: WT FR 24h, biological rep 1

source_name: WT 2d seedling, 2d continuous white light (WL) + 24h FR light


title: WT FR 3h, biological rep 2


title: WT FR 3h, biological rep 1


title: WT FR 1h, biological rep 3

source_name: WT 2d seedling, 2d continuous white light (WL) + 1h FR light


title: WT FR 1h, biological rep 2


title: WT 2d WL, biological rep 1

source_name: WT 2d seedling, 2d continuous white light (WL)


title: WT FR 24h, biological rep 2


title: WT FR 24h, biological rep 3


title: WT 2d WL, biological rep 3


title: WT 2d WL, biological rep 2


title: Mutant ssi2, biological rep3

status: Public on Aug 01 2012

city: LEXINGTON

first: Mihir

middle: Kumar

last: Mandal

state: KENTUCKY

address: 201 F Plant science Building

department: Plant Pathology

institute: University of Kentucky

description:
Columbia ecotype, 3-4 week old plants, grown in MTPS 144 conviron walk in Chamber at 22 degree C, 65% RH and 14 hr photoperiod
Gene expression data from mutant type ssi2 genotype

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: standard Affymetrix procedures Total RNA was isolated from four-week-old plants using TRIZOL method.  The experiment was carried out in triplicate and a separate group of plants was used for each set. RNA was processed and hybridized to the Affymetric Arabidopsis ATH1 genome array GeneChip following the manufacturers instructions. All probe sets on the Genechips were assigned hybridization signal above background using Affymetrix Expression Console Software v1.0.

label_protocol: standard Affymetrix procedures

extract_protocol: Trizol Method

treatment_protocol: Columbia ecotype, 3-4 week old plants, grown in MTPS 144 conviron walk in Chamber at 22 degree C, 65% RH and 14 hr photoperiod. Leaves were harvested from four week plants.

value: leaves

value: 4 wk


title: Wild type COL-0, biological rep1

description:
Columbia ecotype, 3-4 week old plants, grown in MTPS 144 conviron walk in Chamber at 22 degree C, 65% RH and 14 hr photoperiod
Gene expression data from Wild type Col-0 genotype

value: wild type


title: Mutant ssi2 act1, biological rep3

description:
Columbia ecotype, 3-4 week old plants, grown in MTPS 144 conviron walk in Chamber at 22 degree C, 65% RH and 14 hr photoperiod
Gene expression data from mutant type ssi2 act1 genotype

source_name: ssi2 act1-3

value: ssi2 act1


title: Mutant ssi2, biological rep2

growth_protocol: Columbia ecotype, 3-4 week old plants, grown in MTPS 144 conviron walk in Chamber at 22 degree C, 65% RH and 14 hr photoperiod


title: Mutant ssi2 sid2, biological rep3

description:
Columbia ecotype, 3-4 week old plants, grown in MTPS 144 conviron walk in Chamber at 22 degree C, 65% RH and 14 hr photoperiod
Gene expression data from mutant type ssi2 sid2 genotype

source_name: ssi2 sid2-3

value: ssi2 sid2


title: Mutant ssi2 sid2, biological rep1

source_name: ssi2 sid2-1


title: Mutant ssi2 act1, biological rep2

source_name: ssi2 act1-2


title: Mutant ssi2 act1, biological rep1

source_name: ssi2 act1-1


title: Wild type COL-0, biological rep2


title: Mutant ssi2 sid2, biological rep2

source_name: ssi2 sid2-2


title: Mutant ssi2, biological rep1


title: aerial organ explants, incubated on callus inducing medium, 96 h, replicate 2

status: Public on Jul 23 2012

city: beijing

first: Chongyi

last: XU

state: beijing

address: No.20 Nanxincun, Xiangshan

department: Center for signal transdution & metabolomics

country: China

institute: Institute of Botany, the Chinese Academy of Sciences

data_processing: Affymetrix Microarray Suite version 5.0

source_name: aerial organ explants, callus induction, 96 h

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets

growth_protocol: aerial organ segments seperated from 10-day-old seedlings grown on MS solid medium in growth chambers at 22 ºC with 16h light / 8h dark

extract_protocol: Total RNA was isolated from plant tissues using a guanidine thiocyanate extraction buffer as described (Hu et al., 2000, Plant J, 24: 693-701)

value: aerial organ explants

value: Columbia-0, wild-type

tag: treatment

value: 96 hours after incubating on callus inducing medium

tag: biological replicate

value: 2 of three


title: aerial organ explants, incubated on callus inducing medium, 48 h, replicate 3

source_name: aerial organ explants, callus induction, 48 h

tag: tissue

value: 48 hours after incubating on callus inducing medium

value: 3 of three


title: aerial organ explants, incubated on callus inducing medium, 24 h, replicate 2

source_name: aerial organ explants, callus induction, 24 h

value: 24 hours after incubating on callus inducing medium


title: aerial organ explants, incubated on callus inducing medium, 48 h, replicate 1

value: 1 of three


title: WT FR 1h, biological rep 1

value: whole seedling

value: 2 days

value: 1 hr


title: aerial organ explants, incubated on callus inducing medium, 24 h, replicate 3


title: aerial organ explants, incubated on callus inducing medium, 24 h, replicate 1


title: Wild type COL-0, biological rep3

tag: age


title: aerial organ explants, incubated on callus inducing medium, 48 h, replicate 2


title: aerial organ explants, incubated on callus inducing medium, 0 h, replicate 3

source_name: aerial organ explants, callus induction, 0 h

value: 0 hours after incubating on callus inducing medium


title: aerial organ explants, incubated on callus inducing medium, 96 h, replicate 1


title: aerial organ explants, incubated on callus inducing medium, 12 h, replicate 1

source_name: aerial organ explants, callus induction, 12 h

value: 12 hours after incubating on callus inducing medium


title: aerial organ explants, incubated on callus inducing medium, 0 h, replicate 2


title: aerial organ explants, incubated on callus inducing medium, 12 h, replicate 2


title: aerial organ explants, incubated on callus inducing medium, 96 h, replicate 3


title: aerial organ explants, incubated on callus inducing medium, 12 h, replicate 3


title: aerial organ explants, incubated on callus inducing medium, 0 h, replicate 1


title: piffq 2d WL, biological rep 2

source_name: pifq 2d seedling, 2d continuous white light (WL)

value: pif1pif3pif4pif5 (pifq) mutant

value: 0 hr


title: root explants, incubated on callus inducing medium, 48 h, replicate 1

source_name: root explants, callus induction, 48 h

growth_protocol: root segments seperated from 10-day-old seedlings grown on MS solid medium in growth chambers at 22 ºC with 16h light / 8h dark

value: root explants


title: root explants, incubated on callus inducing medium, 96 h, replicate 2

source_name: root explants, callus induction, 96 h


title: root explants, incubated on callus inducing medium, 24 h, replicate 2

source_name: root explants, callus induction, 24 h


title: root explants, incubated on callus inducing medium, 24 h, replicate 3


title: root explants, incubated on callus inducing medium, 12 h, replicate 2

source_name: root explants, callus induction, 12 h


title: root explants, incubated on callus inducing medium, 96 h, replicate 1


title: root explants, incubated on callus inducing medium, 12 h, replicate 3


title: root explants, incubated on callus inducing medium, 48 h, replicate 2


title: root explants, incubated on callus inducing medium, 48 h, replicate 3


title: root explants, incubated on callus inducing medium, 24 h, replicate 1


title: root explants, incubated on callus inducing medium, 0 h, replicate 1

source_name: root explants, callus induction, 0 h


title: root explants, incubated on callus inducing medium, 96 h, replicate 3


title: root explants, incubated on callus inducing medium, 12 h, replicate 1


title: root explants, incubated on callus inducing medium, 0 h, replicate 3


title: root explants, incubated on callus inducing medium, 0 h, replicate 2


title: L0.5h_mRNA_PL_rep3

status: Public on Jul 11 2012

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia sinica

description: 4-day etiolated seedling with white-light treatment for 0.5 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: etiolated Col-0, biological rep3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Seeds were surface sterilized and plated on 1/2 MS (0.8% agar, pH 5.7) plates.

extract_protocol: Total RNA was isolated as described previously [(Chang et al, Plant J 54, 205 (2008)]. Polysome RNA was isolated through a sucrose gradient and purified with phenol/chloroform extraction, LiCl precipitation and dissolved in RNase-free H2O.

treatment_protocol: Seedlings were grown under the dark with or without white-light (70~80 μmole m-2 sec-1) treatment.

value: seedlings (aerial parts)

value: white light

tag: time

tag: extract material

value: polysome-bound RNA


title: L0.5h_mRNA_PL_rep2

source_name: etiolated Col-0, biological rep2


title: L4h_mRNA_PL_rep2

description: 4-day etiolated seedling with white-light treatment for 4 h

value: 4 h


title: Dark_mRNA_PL_rep3

description: 4-day etiolated seedling

value: dark


title: L0.5h_mRNA_SS_rep3

value: steady-state RNA


title: piffq FR 1h, biological rep 3

source_name: pifq 2d seedling, 2d continuous white light (WL) + 1h FR light

tag: genotype


title: L4h_mRNA_SS_rep2


title: L4h_mRNA_SS_rep3


title: L0.5h_mRNA_PL_rep1

source_name: etiolated Col-0, biological rep1


title: L0.5h_mRNA_SS_rep1


title: L4h_mRNA_PL_rep1


title: Dark_mRNA_PL_rep2

description: 4-day etiolated seedling


title: Dark_mRNA_SS_rep2

description: 4-day etiolated seedling


title: L4h_mRNA_PL_rep3


title: L4h_mRNA_SS_rep1


title: L0.5h_mRNA_SS_rep2


title: Dark_mRNA_SS_rep3

description: 4-day etiolated seedling


title: motoneuron+glia_dSOD1_45d_rep3

status: Public on Jul 01 2012

city: Norman

first: Emily

middle: Louise

last: Kumimoto

state: OK

address: 730 Van Vleet Oval

department: Zoology

institute: University of Oklahoma

description: Gene expression data from 45 day old adult male flies expressing wild-type drosophila SOD1 in motoneurons and glia.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila_2 Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.  Hybridization was carried out by a service provider (Nottingham Arabidopsis Stock Centre International Affymetrix Service, Loughborough, United Kingdom)

scan_protocol: Scanning was carried out by a service provider (Nottingham Arabidopsis Stock Centre International Affymetrix Service, Loughborough, United Kingdom)

data_processing: CEL files were imported into ROBIN v1.1.5 (http://mapman.gabipd.org) and, using the default settings, the data were normalized by RMA, and linear models for microarray data (limma) was selected as the analysis strategy.

source_name: Drosophila 45 day old adult male with dSOD1 expressed in motoneurons and glia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Gene Chip 3' IVT Express Kit USer Manual, Affymetrix).  Labeling was carried out by a service provider (Nottingham Arabidopsis Stock Centre International Affymetrix Service, Loughborough, United Kingdom)

growth_protocol: Within 24 hours of eclosion, groups of 10 adult male flies were collected into vials containing standard cornmeal agar food and aged at 25C under 12 hours light and 12 hours dark.  Flies were transferred to new food vial every 5 to 7 days.

treatment_protocol: Flies were flash frozen in liquid nitrogen.

tag: gender

value: males

tag: developmental stage

value: adult

value: 45 days old

value: D42+M1B_Gal4 and UAS_dSOD1 parents

value: whole flies


title: motoneuron+glia_G85R_45d_rep3

description: Gene expression data from 45 day old adult male flies expressing mutant human SOD1 (G85R) in motoneurons and glia.

source_name: Drosophila 45 day old adult male with G85R expressed in motoneurons and glia

value: D42+M1B_Gal4 and UAS_G85R parents


title: motoneuron+glia_G85R_5d_rep2

description: Gene expression data from 5 day old adult male flies expressing mutant human SOD1 (G85R) in motoneurons and glia.

source_name: Drosophila 5 day old adult male with G85R expressed in motoneurons and glia

value: 5 days old


title: motoneuron+glia_dSOD1_5d_rep3

description: Gene expression data from 5 day old adult male flies expressing wild-type drosophila SOD1 in motoneurons and glia.

source_name: Drosophila 5 day old adult male with dSOD1 expressed in motoneurons and glia


title: motoneuron+glia_dSOD1_45d_rep2


title: motoneuron+glia_G85R_45d_rep1


title: motoneuron+glia_G85R_5d_rep1


title: motoneuron+glia_dSOD1_45d_rep1


title: motoneuron+glia_G85R_45d_rep2


title: Dark_mRNA_SS_rep1

description: 4-day etiolated seedling


title: glia_G85R_45d_rep3

description: Gene expression data from 45 day old adult male flies expressing mutant human SOD1 (G85R) in glia.

source_name: Drosophila 45 day old adult male with G85R expressed in glia

value: M1B_Gal4 and UAS_G85R parents


title: glia_dSOD1_5d_rep3

description: Gene expression data from 5 day old adult male flies expressing wild-type drosophila SOD1 in glia.

source_name: Drosophila 5 day old adult male with dSOD1 expressed in glia

value: M1B_Gal4 and UAS_dSOD1 parents


title: glia_G85R_5d_rep3

description: Gene expression data from 5 day old adult male flies expressing mutant human SOD1 (G85R) in glia.

source_name: Drosophila 5 day old adult male with G85R expressed in glia


title: glia_dSOD1_45d_rep1

description: Gene expression data from 45 day old adult male flies expressing wild-type drosophila SOD1 in glia.

source_name: Drosophila 45 day old adult male with dSOD1 expressed in glia


title: glia_G85R_45d_rep1


title: Dark_mRNA_PL_rep1

description: 4-day etiolated seedling


title: glia_G85R_5d_rep2


title: glia_G85R_45d_rep2


title: motoneuron+glia_dSOD1_5d_rep1


title: glia_dSOD1_45d_rep3


title: glia_dSOD1_5d_rep1


title: glia_dSOD1_5d_rep2


title: glia_G85R_5d_rep1


title: motoneuron+glia_dSOD1_5d_rep2


title: motoneuron_G85R_45d_rep3

description: Gene expression data from 45 day old adult male flies expressing mutant human SOD1 (G85R) in motoneurons.

source_name: Drosophila 45 day old adult male with G85R expressed in motoneurons

value: D42_Gal4 and UAS_G85R parents


title: motoneuron_G85R_5d_rep3

description: Gene expression data from 5 day old adult male flies expressing mutant human SOD1 (G85R) in motoneurons.

source_name: Drosophila 5 day old adult male with G85R expressed in motoneurons


title: motoneuron_G85R_5d_rep2


title: motoneuron_G85R_45d_rep1


title: motoneuron+glia_G85R_5d_rep3


title: motoneuron_G85R_45d_rep2


title: motoneuron_G85R_5d_rep1


title: motoneuron_dSOD1_45d_rep2

description: Gene expression data from 45 day old adult male flies expressing wild-type drosophila SOD1 in motoneurons.

source_name: Drosophila 45 day old adult male with dSOD1 expressed in motoneurons

value: D42_Gal4 and UAS_dSOD1 parents


title: motoneuron_dSOD1_5d_rep3

description: Gene expression data from 5 day old adult male flies expressing wild-type drosophila SOD1 in motoneurons.

source_name: Drosophila 5 day old adult male with dSOD1 expressed in motoneurons


title: motoneuron_dSOD1_45d_rep3


title: motoneuron_dSOD1_45d_rep1


title: motoneuron_dSOD1_5d_rep2


title: motoneuron_dSOD1_5d_rep1


title: seedling culture at 4 h_oligo_biol rep 1

status: Public on Jun 28 2012

city: Potsdam-Golm

first: Staffan

last: Persson

address: Am Mühlenberg 1

department: Institute of Molecular Plant Physiology

country: Germany

institute: Max Planck Institute

hyb_protocol: After verifying RNA integrity using the Agilent RNA 6000 Nano Kit and the Agilent 2100 Bioanalyzer, the labeled aRNA was hybridized to Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips at ATLAS Biolabs (Berlin, Germany).

scan_protocol: GeneChips were scanned by ATLAS Biolabs (Berlin, Germany).

data_processing: CEL files from the Affymetrix Chips were processed by use of the Robin program (Lohse et al., 2010). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding Robin function.

source_name: seedling culture_9 days_Long Day 16/8_1 day_dark treated

label_protocol: RNA was labelled with the MessageAMP II-Biotin Enhanced (Ambion) kit according to the manufactures protocol

growth_protocol: Around 100 seeds of Arabidopsis thaliana (L.) Heynh. Col-0 were inoculated into 80 ml of MS medium including 1% sucrose in 250 ml flask. Seedlings were grown at a 16/8 h day/night regime and 180 μmol m-2 s-1 light intensity on a shaker at 80 rpm.

extract_protocol: Total RNA isolation was done with the RNeasy Plant mini kit (Qiagen).

treatment_protocol: Seedlings were grown until day 9, then dark-treated for 24 h and kept in dark during treatment. For treatments, 80 µl of the stock were added to the seedling cultures for a final concentration of 10 µM, and an equal volume of EtOH was used as control. Seedlings were harvested, washed and directly frozen in liquid nitrogen.

tag: cultivar

value: seedling culture

value: 4 h_oligo


title: seedling culture at 4 h_oligo_biol rep 3


title: seedling culture at 4 h_EtOH_biol rep 2

value: 4 h_EtOH


title: seedling culture at 1 h_oligo_biol rep 3

value: 1 h_oligo


title: seedling culture at 1 h_EtOH_biol rep 1

value: 1 h_EtOH


title: seedling culture at 4 h_EtOH_biol rep 3


title: seedling culture at 1 h_EtOH_biol rep 2


title: Control

status: Public on Jun 20 2012

city: Beijing

first: Wenwen

last: Lv

address: Hai Dian

institute: Tsinghua university

description: Gene expression data of wing imaginal discs from en-Gal4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

source_name: Wing discs from 3rd-instar larvae

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Flies at 25℃

treatment_protocol: Drosophila wing imaginal discs from 3rd-instar larvae  were dissected in PBS.

value: Wing imaginal discs

value: yw; en-Gal4/+


title: seedling culture at 1 h_oligo_biol rep 2


title: seedling culture at 4 h_oligo_biol rep 2


title: glia_dSOD1_45d_rep2

value: males

value: adult


title: seedling culture at 4 h_EtOH_biol rep 1


title: seedling culture at 1 h_EtOH_biol rep 3


title: seedling culture at 1 h_oligo_biol rep 1


title: Root Phosphate starvation, biological rep2 [ATH1-121501]

status: Public on Jun 18 2012

city: No.12 Zhongguancun South Street, Haidian

first: Jun

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

hyb_protocol: Hybridization and scanning of all arrays were done at the Genomics Resource Center in the Rockefeller University following the manufacturer’s instructions (Affymetrix).

data_processing: Raw Signal intensity were normalized by quantile method using R statistical environment with affy package. The expression values are shown in log2 scale.

label_protocol: The efficiency of biotin labeling was confirmed by Gel-shift assay with NeutrAvidin (Pierce) as described in Genechip Whole transcript (WT) double-stranded target assay manual (Affymetrix).

growth_protocol: Non-sterile WT (Col-0) seeds were sowed on rock wool (Grodan Inc.) pre-soaked in basal MGRL hydroponic media24 and cold-treated at 4°C for 3 days. Plants were grown at 22°C under 150 μmol m-2 S-1 fluence rate and a 12hr:12hr light:dark cycle. To minimize environmental variation, plants were rotated in growth chambers once a day.

extract_protocol: Total RNAs extracted by RNA easy extraction kit (Qiagen) were used for Arabidopsis Genechip ATH1

treatment_protocol: In phosphate depleted media, 1.75 mM MES (pH 5.8) was used instead of 1.75 mM sodium phosphate (pH 5.8). All hydroponic media were aerated to maximize air supply during hydroponic culture. All plants were grown in basal MGRL hydroponic media for 20 days before being transferred to a phosphate-deficient medium. During the 10-day treatment, the phosphate-deficient medium was replaced every three days. For recovery experiments, plants previously grown in phosphate-deficient medium for 10 days were transferred to full-strength MGRL medium for an additional 3 days. Samples were collected on the 10th and 13th (10+3) day. Phosphate-starved shoot and root samples were collected separately at the indicated time point. Furthermore, all experiment procedures such as media replacement and sample collection were performed in the middle of day in order to minimize possible circadian effect. In parallel, control plants were grown in a full-strength MGRL media before sample collection on the 10th day after the initial 20-day growth period.

tag: organ

value: root

value: P_starvation, 10-day Phosphate starvation

value: 30 days


title: Hdac3 RNAi

description: Gene expression data of wing imaginal discs from Hdac3 RNAi flies

value: Hdac3 RNAi

tag: genetic background

value: yw; en-Gal4/+; UAS-Hdac3 RNAi/+


title: Root Phosphate recovery, biological rep1 [ATH1-121501]

scan_protocol: Hybridization and scanning of all arrays were done at the Genomics Resource Center in the Rockefeller University following the manufacturer’s instructions (Affymetrix).

value: Recovery, 10-day Phosphate starvation then transferred to full-strength MGRL medium for 3 days

value: 33 days


title: PI3K overexpression

description: Gene expression data of wing imaginal discs from PI3K overexpression flies

value: PI3K overexpressor

value: yw; en-Gal4/UAS-PI3K ov


title: Root Mock, biological rep3 [ATH1-121501]

description: Root Mock, biological rep3

source_name: Root Mock, biological rep3

value: Mock, 10-day full-strength MGRL medium


title: PI3K overexpression + Hdac3 RNAi

description: Gene expression data of wing imaginal discs from flies both  PI3K overexpression and Hdac3 RNAi

value: PI3K overexpressor and Hdac3 RNAi

value: yw; en-Gal4/UAS-PI3K ov; UAS-Hdac3 RNAi/+


title: Root Phosphate starvation, biological rep3 [ATH1-121501]


title: Root Mock, biological rep1 [ATH1-121501]

description: Root Mock, biological rep1

source_name: Root Mock, biological rep1


title: Root Mock, biological rep2 [ATH1-121501]

description: Root Mock, biological rep2

source_name: Root Mock, biological rep2


title: Shoot Phosphate recovery, biological rep1 [ATH1-121501]

value: shoot


title: Root Phosphate recovery, biological rep2 [ATH1-121501]


title: Root Phosphate recovery, biological rep3 [ATH1-121501]


title: Shoot Phosphate recovery, biological rep3 [ATH1-121501]


title: Shoot Phosphate starvation, biological rep3 [ATH1-121501]


title: Shoot Phosphate starvation, biological rep2 [ATH1-121501]


title: Shoot Phosphate starvation, biological rep1 [ATH1-121501]


title: Root Phosphate starvation, biological rep1 [ATH1-121501]


title: Shoot Mock, biological rep3 [ATH1-121501]

description: Shoot Mock, biological rep3

source_name: Shoot Mock, biological rep3


title: Shoot Mock, biological rep2 [ATH1-121501]

description: Shoot Mock, biological rep2

source_name: Shoot Mock, biological rep2


title: D.melanogaster_selection=R2_exposure=E5

status: Public on Jun 16 2012

city: Johnson City

first: Lev

last: Yampolsky

state: TN

address: ETSU

department: Biological Sciences

institute: East Tennessee State University

hyb_protocol: The cDNA was hybridized overnight to Drosophila Genome 2.0 arrays (Affymetrix, Santa Clara, CA U.S.A.), which were washed and stained with a fluorescent dye that binds to biotin (streptavidin, R-phycoerythrin conjugate).

scan_protocol: Arrays were scanned as recommended by Affymetrix using an Affymetrix Fluidics Station 450 and Scanner 3000.

data_processing: Raw expression .CEL files were normalized using the gcRMA algorithm (Wu et al. 2004) as implemented in the Affy package on Bioconductor (version 2.4) (Gentleman et al. 2004). We filtered out probe sets with low expression and variance by removing those whose mean, interquartile range among arrays, and standard deviation among arrays were each less than the median of the respective quantity over all probesets. After the filtering step, 12,236 out of the 18,769 original probe sets were left for further analysis.

source_name: D.melanogaster, selected: contol, exposure: ethanol

label_protocol: Total RNA was converted to biotin-labeled, fragmented cDNA with kits from NuGEN Technologies (Ovation Amplification System V2, FL-Ovation cDNA Biotin Module 2).

growth_protocol: To control for environmental effects on gene expression, flies from all populations were reared for at least two generations on standard medium at 25ºC before being used to lay eggs.

extract_protocol: RNA was extracted from groups of 50-200 larvae using the RNeasy mini kit and QIAshredder columns (QIAGEN Inc., Valencia, CA U.S.A.).  Extractions were conducted in three blocks on different days, at the same time each day to minimize circadian effects, with one sample per population and pre-treatment per block.  One RNA sample was lost due to technical error, leaving 35 samples for microarray hybridization.

treatment_protocol: Groups of 50-60 ca. one week old flies were allowed to lay eggs for three hours on apple juice agar medium (100 ml apple juice, 300 ml water, 6 g sucrose, 3.6 g agar) dispensed in 5 ml aliquots into the lids of 35 mm diameter Petri dishes. Each laying cap was then placed in a 60 mm Petri dish, to which 10 ml of either 18% ethanol (“exposure E”) or distilled water (“exposure W”) was added, with the result that the liquid just covered (by 1 mm or so) the surface of the agar (18% ethanol was used to result in an approximate final concentration of 12%, taking into account the volume of laying medium).  The dishes were covered, sealed with Parafilm, and placed on an orbital shaker at a gentle setting for 15 hours.  After this period, the caps were removed from the dishes and rinsed with distilled water, to remove any early hatching larvae.  Thereafter, newly-hatched larvae were collected at 45 minute intervals.

value: 50-200 1st instar larvae

tag: selection

value: contol

tag: exposure

value: ethanol


title: D.melanogaster_selection=E2_exposure=W2

source_name: D.melanogaster, selected: 12%ethanol, exposure: water

value: water


title: D.melanogaster_selection=E1_exposure=E5

source_name: D.melanogaster, selected: 12%ethanol, exposure: ethanol


title: D.melanogaster_selection=M2_exposure=E5

source_name: D.melanogaster, selected: variable, exposure: ethanol

value: variable


title: D.melanogaster_selection=E2_exposure=W5


title: D.melanogaster_selection=E1_exposure=W5


title: D.melanogaster_selection=R1_exposure=E5


title: Shoot Phosphate recovery, biological rep2 [ATH1-121501]


title: D.melanogaster_selection=R2_exposure=W5

source_name: D.melanogaster, selected: contol, exposure: water


title: D.melanogaster_selection=E2_exposure=E2


title: D.melanogaster_selection=M1_exposure=E5


title: D.melanogaster_selection=M1_exposure=W5

source_name: D.melanogaster, selected: variable, exposure: water


title: Shoot Mock, biological rep1 [ATH1-121501]

description: Shoot Mock, biological rep1

source_name: Shoot Mock, biological rep1


title: D.melanogaster_selection=R2_exposure=W2


title: D.melanogaster_selection=M2_exposure=W2


title: D.melanogaster_selection=M2_exposure=E2


title: D.melanogaster_selection=E2_exposure=E5


title: D.melanogaster_selection=M2_exposure=W5


title: D.melanogaster_selection=R1_exposure=W2


title: D.melanogaster_selection=M1_exposure=E2


title: D.melanogaster_selection=R1_exposure=W5


title: D.melanogaster_selection=R2_exposure=E2


title: D.melanogaster_selection=E1_exposure=W2


title: D.melanogaster_selection=R1_exposure=E2


title: D.melanogaster_selection=M2_exposure=W1


title: D.melanogaster_selection=E2_exposure=W1


title: D.melanogaster_selection=E2_exposure=E1


title: D.melanogaster_selection=E1_exposure=E2


title: D.melanogaster_selection=R2_exposure=E1


title: D.melanogaster_selection=E1_exposure=E1


title: D.melanogaster_selection=M1_exposure=E1


title: D.melanogaster_selection=E1_exposure=W1


title: D.melanogaster_selection=R1_exposure=E1


title: D.melanogaster_selection=R1_exposure=W1


title: D.melanogaster_selection=R2_exposure=W1


title: Adult Female Spermatheca Mated (REDONE) biological rep4

status: Public on Jun 07 2012

city: Glasgow

first: Jing

last: Wang or Venkat Chintapalli

state: Scotland

address: Dumbarton Road

department: Molecular Genetics

institute: University of Glasgow

description:
2-round
The female mated spermatheca surrounded by fatbody

hyb_protocol: Following fragmentation, 10 ug of cRNA (or according to the affy IVT protocol)  were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Adult Female Spermatheca Mated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: Wild-type Drosophila melanogaster (Canton S strain) were raised on standard medium on a 12:12 h L:D cycle, at 23C, and at 55% r.h. To facilitate the collection of accurately staged adults, a laying population of around 12 males and 12 females were transferred to fresh vials daily. When adults subsequently emerged, they were transferred to fresh vials on the day of emergence, and used 7 days later. Where larvae were used, these were third instar.

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Flies were anaesthetised briefly by chilling on ice, then immediately dissected.

tag: sample type

value: Canton-S, 60 female flies, 7 days old

value: Female Spermatheca Mated

tag: strain

value: Canton S


title: Adult Wings biological rep4

description:
1-round
Wings pulled from the body

source_name: Adult Wings

value: Canton-S, 50 female and  50 male flies, 7 days old

value: Wings


title: Adult Female Spermatheca Mated (REDONE) biological rep3

description:
1-round
The female mated spermatheca surrounded by fatbody


title: Adult Thoracic Muscle biological rep4

description:
1-round
Muscles extracted from the thorax

source_name: Adult Thoracic Muscle

value: Thoracic Muscle


title: Adult Thoracic Muscle biological rep3


title: Adult Female Spermatheca Mated (REDONE) biological rep1


title: Adult Wings biological rep2

description:
1-round
Wings pulled from the body


title: Adult Wings biological rep3

description:
1-round
Wings pulled from the body


title: Adult Female Spermatheca Mated (REDONE) biological rep2


title: D.melanogaster_selection=M1_exposure=W1


title: Adult Trachea biological rep4

description:
1-round
The major tracheal trunks, excluding spiracles and obvious adherent tissues.

source_name: Adult Trachea

value: Trachea


title: Adult Trachea biological rep1


title: Adult Thoracic Muscle biological rep1


title: Adult Wings biological rep1

description:
1-round
Wings pulled from the body


title: Adult Trachea biological rep3


title: Adult Thoracic Muscle biological rep2


title: Adult Trachea biological rep2


title: larval cyc0 LNvs at ZT-15, biological rep2

status: Public on Jun 01 2012

first: Marc

address: 100 Washington Square East

institute: New York University

description: Gene expression data from cyc0 LNvs at ZT-15

source_name: Drosophila larval cyc0 LNvs at ZT-15

label_protocol: see above (amplfication protocol)

growth_protocol: All larval genotypes raised at 25C in 12:12hr Light/Dark cycle.

extract_protocol: The 0.01%-most RFP+ cells (~1,000 cells) were isolated by FACS, and sorted directly into Arcturus PicoPure RNA extraction buffer. mRNA was amplified using the NuGen WT-Ovation™ RNA System to yield ~ 5ug biotin labeled, fragmented, single-stranded cDNA

value: FACs-purified LNvs

value: yw, Pdf-RFP, cyc0

value: L3 larval stage


title: larval per0 LNvs at ZT-15, biological rep2

description: Gene expression data from per0 LNvs at ZT-15

source_name: Drosophila larval per0 LNvs at ZT-15

value: yw, per0; Pdf-RFP


title: larval cyc0 LNvs at ZT-15, biological rep1


title: larval elav+ neurons at ZT-15, biological rep3

description: Gene expression data from elav+ neurons at ZT-15

source_name: Drosophila larval elav+ neurons at ZT-15

value: elav-Gal4, UAS-GFP;


title: larval LNvs at ZT-15, biological rep1

description: Gene expression data from wildtype LNvs at ZT-15

source_name: Drosophila larval LNvs at ZT-15

value: yw, Pdf-Gal4; UAS-GFP


title: larval LNvs at ZT-15, biological rep2


title: larval cyc0 LNvs at ZT-15, biological rep3


title: larval elav+ neurons at ZT-15, biological rep2


title: larval per0 LNvs at ZT-15, biological rep3


title: larval elav+ neurons at ZT-15, biological rep1


title: larval per0 LNvs at ZT-15, biological rep1


title: larval LNvs at ZT-3, biological rep3

description: Gene expression data from wildtype LNvs at ZT-3

source_name: Drosophila larval LNvs at ZT-3


title: larval LNvs at ZT-3, biological rep2


title: larval LNvs at ZT-15, biological rep3


title: larval LNvs at ZT-3, biological rep1

value: yellow white (yw), Pdf-Gal4; UAS-GFP


title: Ex 3 GFP 96

status: Public on May 20 2012

city: Los Angeles

first: William

middle: Alexander

last: Freije

address: 650 Charles Young Drive, South CHS B8-127

department: Obstetrics and Gynecology

institute: UCLA

description: Replicate 3, GFP transfected, 96 hour timepoint

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Standard Affymetrix scanning

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. MAS 5.0 output was then entered into dCHIP where the arrays were normalized to the median intensity array.

label: Biotin

source_name: GFP transfected, 96 hour timepoint

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: S2 cells cultrued in Schneider's media

extract_protocol: RNA extraction through Trizol followed by Rneasy Cleanup

treatment_protocol: Calcium phosphate transfection for siRNA specific for either GFP or COVA

tag: cell line


title: Ex 2 COVa 168

description: Replicate 2, COVA transfected, 168 hour timepoint

source_name: COVA transfected, 168 hour timepoint


title: Ex 3 GFP 72

description: Replicate 3, GFP transfected, 72 hour timepoint

source_name: GFP transfected, 72 hour timepoint


title: Ex 3 GFP 168

description: Replicate 3, GFP transfected, 168 hour timepoint

source_name: GFP transfected, 168 hour timepoint


title: Ex 2 COVa 96

description: Replicate 2, COVA transfected, 96 hour timepoint

source_name: COVA transfected, 96 hour timepoint


title: Ex 3 CoVa 168

description: Replicate 3, COVA transfected, 168 hour timepoint


title: Ex 2 GFP 120

description: Replicate 2, GFP transfected, 120 hour timepoint

source_name: GFP transfected, 120 hour timepoint


title: Ex 3 GFP 120

description: Replicate 3, GFP transfected, 120 hour timepoint


title: Ex 3 CoVa 96

description: Replicate 3, COVA transfected, 96 hour timepoint


title: Ex 2 GFP 96

description: Replicate 2, GFP transfected, 96 hour timepoint


title: Ex 2 GFP 168

description: Replicate 2, GFP transfected, 168 hour timepoint


title: Ex 2 COVa 72

description: Replicate 2, COVA transfected, 72 hour timepoint

source_name: COVA transfected, 72 hour timepoint


title: Ex 2 COVa 120

description: Replicate 2, COVA transfected, 120 hour timepoint

source_name: COVA transfected, 120 hour timepoint


title: Ex 1 COVa 48

description: Replicate 1, COVA transfected, 48 hour timepoint

source_name: COVA transfected, 48 hour timepoint


title: Ex 1 Control 48

description: Replicate 1, untransfected, 48 hour timepoint

source_name: untransfected, 48 hour timepoint


title: Ex 3 CoVa 120

description: Replicate 3, COVA transfected, 120 hour timepoint


title: Ex 3 CoVa 72

description: Replicate 3, COVA transfected, 72 hour timepoint


title: Ex 1 COVa 168

description: Replicate 1, COVA transfected, 168 hour timepoint


title: Ex 1 GFP 168

description: Replicate 1, GFP transfected, 168 hour timepoint


title: 8505

status: Public on May 11 2012

city: Marseille

first: Sylviane

last: Olschwang

address: 232 boulevard Sainte-Marguerite

department: Centre de Recherches en Cancérologie de Marseille

country: France

institute: Institut Paoli-Calmettes

description:
110706-16.CEL
gene expression data from primary colon adenocarcinoma after surgery only

hyb_protocol: Expression profiles were established with Affymetrix U133 Plus 2.0 human oligonucleotide microarrays

scan_protocol: Scanning was done with an Affymetrix GeneArray scanner and quantification with the Affymetrix GeneChip Operating Software (Affymetrix, Paris France).

data_processing: CEL files were processed in the R (v. 2.10.0)/Bioconductor (v 2.5) environment. Pre-processing steps (background adjustment, normalization and summarization) were performed with the GCRMA package (v.2.18.1)

organism: Homo sapiens

source_name: stage III_colon adenocarcinoma

extract_protocol: Enriched tumor zones were selected from frozen material on HE-stained cryosections to ensure a 60% minimum of tumor cells. Nucleic acids were extracted using QIAamp and RNeasy kits (Qiagen, Courtaboeuf France) according to the manufacturer's instructions. Quantification of samples was done with a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Illkirch France). RNA integrity was controlled on an Agilent Bioanalyzer (Agilent Technologies, Massy France).

treatment_protocol: Tissue samples were collected on fresh surgical specimens by pathologists within one hour after surgery from patients who underwent curative colonic resection, then flash frozen in liquid nitrogen and stored at -80°C until nucleic acids extraction.

tag: age at diagnosis

value: female

tag: localisation

value: left

tag: Stage

tag: date at surgery

tag: date at distant metastasis

tag: date at last contact

tag: center

value: IPC (Marseille Institut PAoli-Calmettes)

value: primary colon adenocarcinoma


title: 8336

description:
121206-14.CEL
gene expression data from primary colon adenocarcinoma after surgery only

source_name: stage II_colon adenocarcinoma

tag: gender

value: male

tag: tissue


title: Ex 1 GFP 48

description: Replicate 1, GFP transfected, 48 hour timepoint

source_name: GFP transfected, 48 hour timepoint


title: 12487

description:
110706-20.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 7094

description:
121206-24.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 97

description:
051206-15.CEL
gene expression data from primary colon adenocarcinoma after surgery only

value: CAL (Nice Lacassagne)


title: 8952

description:
080318-04.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 123

description:
070123-18.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: Ex 2 GFP 72

description: Replicate 2, GFP transfected, 72 hour timepoint


title: 7225

description:
121206-18.CEL
gene expression data from primary colon adenocarcinoma after surgery only

value: right


title: 315

description:
MFL_315b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 12371

description:
110706-19.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 629

description:
070123-02.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 60

description:
051206-09.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 53

description:
051206-01b.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 536

description:
070123-16.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 73

description:
051206-22.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 682

description:
070123-06.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 329

description:
070123-04.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 680

description:
070123-14.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 683

description:
070123-09.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 83

description:
051206-06.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 242

description:
070123-07.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 539

description:
070123-10.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 47

description:
051206-20.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 517

description:
070123-12.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 284

description:
MFL_284b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 20

description:
051206-23.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 179

description:
051206-12.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 163

description:
051206-21.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 186

description:
051206-08.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 456

description:
070123-08.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 202

description:
070123-13.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 164

description:
051206-11.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 129

description:
051206-10.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 81

description:
121206-13.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 182

description:
051206-13.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 197

description:
121206-03.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 244

description:
SOG_244_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 92

description:
121206-01.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 95

description:
121206-06.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 77

description:
070123-17.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 174

description:
121206-08.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 187

description:
121206-11.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: S1

description:
051206-04.CEL
gene expression data from primary colon adenocarcinoma after surgery only

value: APH (Marseille La Timone)


title: SA011853

description:
SOG_011853_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only

value: STA (Paris Saint-Antoine)


title: S5

description:
070123-01.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 241

description:
MFL_241_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 112

description:
121206-21.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA031373

description:
SOG_031373_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: L6

description:
070123-11.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 225

description:
MFL_225b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA034165

description:
SOG_034165_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: S3

description:
070123-15.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: Q1

description:
070123-03.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: L10

description:
051206-03.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA033888

description:
050805-04.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 106

description:
121206-12.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA031197

description:
SOG_031197_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 07C1421T

description:
SOG_1421b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only

value: NAN (Nancy Brabois)


title: 08C0535T

description:
SOG_535_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA010753

description:
SOG_010753_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA031424

description:
SOG_031424_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 08C0464T

description:
SOG_0464_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: B0201594

description:
SOG_47_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only

value: LAR (Paris Lariboisiare)


title: B9406375

description:
SOG_34_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 07C1415T

description:
SOG_1415_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 211

description:
MFL_211b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 08C0463T

description:
SOG_0463_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: B0115625

description:
SOG_46_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 9749

description:
SOG_9749_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 9848

description:
SOG_9848_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 9304

description:
SOG_9304_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 8612

description:
SOG_8612_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 8196

description:
SOG_8196_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 79

description:
SOG_79_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 538

description:
MFL_538b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 10937

description:
SOG_10937_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 625

description:
MFL_625b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 11196

description:
SOG_11196_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 9607

description:
SOG_9607_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 10602

description:
SOG_10602_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 10411

description:
SOG_10411_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 9243

description:
SOG_9243_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 9736

description:
SOG_9736_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 9184

description:
SOG_9184_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 533

description:
MFL_533b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 7610

description:
SOG_7610_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 208

description:
MFL_208b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 12266

description:
SOG_12266_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 534

description:
SOG_534_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 510

description:
SOG_510_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA033059

description:
050805-08.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA031610

description:
050805-07.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 206

description:
MFL_206b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA017456

description:
110706-24.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 519

description:
MFL_519b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 512

description:
MFL_512b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA014936

description:
111206-23.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 44

description:
SOG_44_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 684

description:
MFL_684b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA017579

description:
121206-07.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA013893

description:
051206-24.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 426

description:
MFL_426b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 21

description:
121206-05.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA012939

description:
110706-21.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA014500

description:
110706-23.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 27

description:
051206-16.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA031523

description:
050805-06.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA030625

description:
121206-16.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA031069

description:
050805-03.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 12

description:
121206-10.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 8246

description:
121206-19.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 33

description:
121206-15.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA016466

description:
051206-17.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 26

description:
121206-04.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA014040

description:
110706-22.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 14450

description:
090126-06.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 17

description:
051206-07.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: SA014736

description:
121206-02.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 48

description:
051206-14.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 13955

description:
090126-04.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 12248

description:
090126-03.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 386

description:
MFL_386b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 11697

description:
090126-01.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 10682

description:
090126-07.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 13070

description:
090126-02.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 14420

description:
090126-05.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 200

description:
MFL_200b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 363

description:
MFL_363b_U133_2.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 11501

description:
090126-08.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: 9700

description:
090126-09.CEL
gene expression data from primary colon adenocarcinoma after surgery only


title: Line8_Week4_Sham

status: Public on May 03 2012

city: Urbana

first: Jenny

last: Drnevich

state: IL

address: 1206 W. Gregory Dr.

institute: University of Illinois

description:
X936_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Drosophila 2.0 Genome Array using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Pre-processing was done using the GCRMA (v. 2.18.0) algorithm in R (v. 2.10.0) and Bioconductor packages (v. 2.6.0).

source_name: 4 week-old virgin female_Sham infected

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: Virgin females were collected from each line and maintained in vials containing cornmeal-molasses-yeast-agar medium (without live yeast) under standard conditions (25°C and 12 hr light: 12 hr dark cycles) until assayed at either one or four-weeks old.

extract_protocol: Total RNA was extracted using the TRIzol extraction method, followed by an RNeasy cleanup, according to the manufacturer’s instructions (Invitrogen/Qiagen).

treatment_protocol: Prior to injection, the bacterial culture was grown in LB broth + streptomycin (100µg/ml) from a single colony of a streptomycin resistant strain of Escherichia coli until OD600 reached 1.0 ± 0.1 (Beckman DU-65 Spectrophotometer, Beckman, Fullerton, CA, USA), corresponding to a final concentration of approximately 5.5x10^8 colony forming units/ml.  The bacterial solution was then loaded into pulled-glass capillary needles.  Bacteria-filled capillary needles were connected to an Eppendorf Femtojet microinjector (Eppendorf, Westbury, NY, USA) and flies were injected with the same volume of E. coli in the abdomen (microinjector settings: injection pressure = 0.46, injection time = 0.2s, and compensation pressure = 0.20) or were sham-injected with sterile Ringer's solution. Bacterially infected and sham-injected flies from each of the lines at each time point were frozen at -80°C six hours post-injection

tag: inbred line

value: Line 8

tag: age

value: 4 weeks post-eclosion

value: whole body

tag: infected with

value: sterile Ringer's solution (sham-infected)


title: Line19_Week4_Sham

description:
X728_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 19


title: Line3_Week4_Bact

description:
X735_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

source_name: 4 week-old virgin female_Bact infected

value: Line 3

value: E.coli culture (Bact infected)


title: Line8_Week4_Bact

description:
X805_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: female


title: Line13_Week1_Sham

description:
X813_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

source_name: 1 week-old virgin female_Sham infected

value: Line 13

value: 1 week post-eclosion


title: Line19_Week4_Bact

description:
X734_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line12_Week1_Sham

description:
X933_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 12


title: Line14_Week1_Bact

description:
X937_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

source_name: 1 week-old virgin female_Bact infected

value: Line 14


title: Line19_Week1_Bact

description:
X807_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line17_Week1_Bact

description:
X730_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 17


title: Line4_Week4_Bact

description:
X935_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 4


title: Line18_Week4_Bact

description:
X810_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 18


title: Line19_Week1_Sham

description:
X812_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line17_Week4_Sham

description:
X737_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line13_Week4_Bact

description:
X808_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line4_Week4_Sham

description:
X725_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line13_Week4_Sham

description:
X731_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line14_Week4_Bact

description:
X938_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line14_Week4_Sham

description:
X806_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line6_Week1_Sham

description:
X736_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 6


title: Line6_Week4_Bact

description:
X724_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line4_Week1_Sham

description:
X934_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line3_Week1_Sham

description:
X733_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line20_Week1_Sham

description:
X718_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 20


title: Line6_Week1_Bact

description:
X721_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line17_Week1_Sham

description:
X720_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line12_Week4_Bact

description:
X717_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line17_Week4_Bact

description:
X722_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line8_Week1_Sham

description:
X715_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 8


title: Line20_Week4_Sham

description:
X723_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: 4 weeks post-eclosion


title: Line13_Week1_Bact

description:
X703_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: whole body


title: Line3_Week4_Sham

description:
X714_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: sterile Ringer's solution (sham-infected)


title: Line4_Week1_Bact

description:
X716_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line8_Week1_Bact

description:
X697_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line1_Week1_Bact

description:
X707_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 1


title: Line14_Week1_Sham

description:
X709_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line1_Week4_Bact

description:
X696_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line1_Week4_Sham

description:
X702_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line12_Week4_Sham

description:
X706_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line18_Week4_Sham

description:
X695_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line3_Week1_Bact

description:
X693_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 3


title: Line20_Week4_Bact

description:
X705_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: E.coli culture (Bact infected)


title: control, S2 cells-2

city: Hachioji-shi

first: Sato

middle: M.

last: Yukiko

state: Tokyo

address: 1-1 Minami-Osawa

country: Japan

institute: Tokyo Metropolitan University

description: Gene expression data from Drosophila S2 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affimetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affimetrix default analysis settings and global scaling as normalization method.

source_name: Vehicle-treated Drosophila S2 cells

label_protocol: Biotylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Drosophila-derived S2 cells were cultured in Schneider’s Drosophila medium supplemented with insulin and 10 % fetal bovine serum. Briefly, 106 cells/well were seeded in six-well multiwall plates.

extract_protocol: Total RNA was isolated using the RNeasy Mini kit.

treatment_protocol: Drosophila S2 cells treated with 0.1 mM protocatechuic aldehyde for 2hr.

tag: cell type

value: S2 cells

tag: agent

value: Vehicle


title: PA, S2 cells-3

source_name: Protocatechuic aldehyde-treated Drosophila S2 cells

value: Protocatechuic aldehyde


title: Line18_Week1_Sham

description:
X698_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: female

value: 1 week post-eclosion


title: control, S2 cells-1


title: control, S2 cells-3


title: Line12_Week1_Bact

description:
X713_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)

value: Line 12


title: PA, S2 cells-2


title: PA, S2 cells-1


title: Line6_Week4_Sham

description:
X691_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: Line1_Week1_Sham

description:
X690_E.CEL
Pool of 8-15 individuals from an inbred line derived from a natural population in Raleigh, North Carolina (kindly provided by the laboratory of Dr. Trudy F. C. Mackay, NC State University)


title: PIF5ox low R/FR rep3

city: Lausanne

first: Markus

middle: Volker

last: Kohnen

state: Vaud

address: Genopode Building

department: Center for Integrative Genomics (CIG)

country: Switzerland

institute: Université de Lausanne

description: seedlings were kept for 1 h in high R/FR light in the morning and subsequently transfered to low R/FR for additional 2 h

hyb_protocol: Arabidopsis ATH1 Genome Array (Affymetrix, Santa Clara, CA, USA) were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

source_name: plant seedlings

label_protocol: 300ng of total RNA were amplified and labeled using the Message Amp II-biotin Enhanced reagents (Ambion; catalog #AM1791). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (www.affymetrix.com).

growth_protocol: Fifty seeds were plated on half MS and kept in the dark and cold for 3 days. Seedlings were grown under high R/FR conditions in 12:12 LD circles for 14 days.

extract_protocol: Seedlings were flash-frozen in liquid nitrogen, ground using a tissulyser (Qiagen) 2 times 30s, 30Hz without extraction buffer. RNAs were extracted using the Nucleo Spin for plant RNA kit (Machery-Nagel) following the manufacturer recommendations.

treatment_protocol: After 1h high R/FR treatment in the morning plants were transferred to low R/FR (supplemental FR) or kept in high R/FR for additional 2h.

value: seedlings

tag: genotype

value: PIF5 overexpressing

value: 14 days after germination

tag: genetic background

tag: treatment

value: low R/FR


title: PIF5ox low R/FR rep2


title: PIF5ox high R/FR rep2

description: seedlings were kept for 3 h in high R/FR light in the morning

value: high R/FR


title: PIF5ox low R/FR rep1


title: PIF5ox high R/FR rep1


title: PIF5ox high R/FR rep3


title: pif5 low R/FR rep2

value: pif5 mutant


title: pif5 high R/FR rep3


title: pif4pif5 low R/FR rep2

value: pif4pif5 double mutant


title: pif5 low R/FR rep1


title: pif5 high R/FR rep2


title: pif4pif5 low R/FR rep1


title: pif5 high R/FR rep1


title: pif4pif5 high R/FR rep3


title: pif4pif5 high R/FR rep2


title: pif5 low R/FR rep3


title: pif4pif5 high R/FR rep1


title: Col-0 low R/FR rep2

value: wild type


title: Col-0 low R/FR rep3


title: Col-0 low R/FR rep1


title: Col-0 high R/FR rep1


title: Col-0 high R/FR rep2


title: pif4pif5 low R/FR rep3