title: low R/FR, mock spray, biological rep 2

status: Public on May 01 2012

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

hyb_protocol: The (#900720) GeneChip Hybridization, Wash and Stain Kit was used for hybridization, washing, staining and scanning of the chips.

scan_protocol: The software program Affymetrix 'GeneChip Command Console (v3.1)' was used to operate the staning, washing and scanning of the GeneChips and visual inspection of the array images. Chips were scanned using the Affymetrix 3000G scanner

data_processing: Data were processed using the Bioconductor packages in R and using the RMA normalization algorithm.

source_name: Arabidopsis petioles, 2h low R/FR treatment

label_protocol: The Affymetrix 3'IVT-Express Labeling Kit was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labelling reactions.

growth_protocol: Arabidopsis thaliana plants were sown, stratified (4˚C) for 3 days and then transferred to a growth chamber (9 h. light (180 µmol / m2 / s, 20°C, 70% RH, R/FR = 2.2), 15 h dark) where they were transferred to individual pots after 10 d and gwon until 4 weeks old.

extract_protocol: Total RNA was isolated from homogenized material using the RNeasy plant mini kit (Qiagen) with on-column DNA digestion following the company’s instructions

treatment_protocol: Plants were put in each of the four conditions (control light with mock spray, control light with 0.1 mM JA spray, low R:FR (0.2) with mock spray, low R:FR (0.2) with 0.1 mM JA spray) for 2h. One petiole (approx. 5 mm length) per plant was harvested in liquid N2. 3 petioles/biological replicate were pooled.

tag: organ

value: petiole

tag: developmental stage

value: 4 weeks old plants

value: low R/FR, mock spray


title: high R/FR, mock spray, biological rep 2

type: RNA

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis petioles, 2h control treatment

tag: treatment

value: high R/FR, mock spray


title: low R/FR, mock spray, biological rep 1


title: Col-0 high R/FR rep3

status: Public on May 03 2012

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 3 h in high R/FR light in the morning

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.

tag: tissue

value: seedlings

tag: genotype

value: wild type

tag: age

value: 14 days after germination

tag: genetic background

value: high R/FR


title: low R/FR, JA spray, biological rep 3

source_name: Arabidopsis petioles, 2h low R/FR + JA treatment

value: low R/FR, JA spray


title: low R/FR, JA spray, biological rep 2


title: high R/FR, JA spray, biological rep 2

source_name: Arabidopsis petioles, 2h JA treatment

value: high R/FR, JA spray


title: low R/FR, JA spray, biological rep 1


title: high R/FR, JA spray, biological rep 1


title: low R/FR, mock spray, biological rep 3


title: high R/FR, mock spray, biological rep 1


title: high R/FR, JA spray, biological rep 3


title: Ws_root_2h_KCl_rep3

city: Santiago

first: Elena

middle: A

last: Vidal

address: Avenida Libertador Bernardo O'Higgins 340

department: Genetica Molecular y Microbiologia

country: Chile

institute: Pontificia Universidad Catolica de Chile

description: Ws wild-type seedlings, treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.

hyb_protocol: ATH1 chips were hybridized using the GeneChip Hybridization, Wash and Stain kit from Affymetrix

scan_protocol: Chips were scanned using the Affymetrix GeneChip Scanner 3000 7G and the Affymetrix GeneChip Command Console Scan Control 1.1.0.845 software

data_processing: The summarized probe set data was generated using R/bioconductor (affy library). Normalization of the data was performed using rma. Normalized data was subjected to a two-way ANOVA analysis with a false discovery rate of 5 %.

source_name: Ws roots, treated with 5 mM KCl for 2 hours

label_protocol: Bioitinylated cRNA was prepared using the GeneChip 3'IVT kit from Affymetrix

growth_protocol: Arabidopsis seedlings of the Ws and afb3-1 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 μE/m2/sec) and 8 hours of dark at 22°C for 14 days.

extract_protocol: Total RNA was extracted using the TriZol reagent as indicated by the manufacturer.

treatment_protocol: Plants were treated at the onset of the light period on day 15 with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Roots were cut and frozen on liquid nitrogen.

value: Arabidopsis root

value: Ws

value: 15-day old seedling

value: 2 hours of 5 mM KCl


title: Ws_root_2h_KNO3_rep2

description: Ws wild-type seedlings, treated with 5 mM KNO3 for 2 hours. Roots were cut and total RNA was extracted using TriZol.

source_name: Ws roots, treated with 5 mM KNO3 for 2 hours

value: 2 hours of 5 mM KNO3


title: Ws_root_2h_KCl_rep2


title: Ws_root_2h_KNO3_rep3


title: high R/FR, mock spray, biological rep 3


title: afb3-1_root_2h_KCl_rep2

description: Auxin receptor AFB3 mutant seedlings (afb3-1), treated with 5 mM KCl for 2 hours. Roots were cut and total RNA was extracted using TriZol.

source_name: afb3-1 roots, treated with 5 mM KCl for 2 hours

value: afb3-1 mutant


title: afb3-1_root_2h_KNO3_rep3

description: Auxin receptor AFB3 mutant seedlings (afb3-1), treated with 5 mM KNO3 for 2 hours. Roots were cut and total RNA was extracted using TriZol.

source_name: afb3-1 roots, treated with 5 mM KNO3 for 2 hours


title: afb3-1_root_2h_KCl_rep1


title: afb3-1_root_2h_KNO3_rep2


title: Ws_root_2h_KNO3_rep1


title: yw-18hr-WithoutIR_2

status: Public on Apr 18 2012

city: Boulder

first: Joseph

middle: K

last: Heimiller

state: CO

address: 347 UCB

department: MCDB

country: USA

institute: Univ of Colorado Boulder

hyb_protocol: Biotin-labeled amplified RNA was fragmented and hybridized onto the microarrays (Drosophila GeneChip 2.0) according to the Affymetrix protocol.

scan_protocol: Arrays were scanned using the Hewlett Packard Gene Array Scanner G2500A.

data_processing: The data were analyzed with the GCRMA method in R statistical environment 2.12.2.

organism: Drosophila melanogaster

source_name: yw 18hr without IR sample 2

label_protocol: RNA was biotin-labeled according to the Affymetrix protocol.

growth_protocol: 3rd instar larvae

extract_protocol: mRNA was isolated from wing imaginal discs using the RNeasy Plus kit (Qiagen)

treatment_protocol: 2 and 18 hr with and without ionizing irradiation of larvae with 4000R of X-rays

value: wing disc from 3rd instar larvae

tag: Sex

value: male and female

value: 3rd instar larvae

value: 18 hr without IR


title: yw-18hr-WithoutIR_1

source_name: yw 18hr without IR sample 1


title: yw-2hr-WithoutIR_2

source_name: yw 2hr without IR sample 2

value: 2 hr without IR


title: p53-2hr-WithoutIR_2

source_name: p53-mutant 2hr without IR sample 2


title: yw-2hr-WithIR_1

source_name: yw 2hr with IR sample 1

value: 2 hr with IR


title: proventriculus mRNA measured from F3 unchallenged larvae without past exposure

city: Rehovot

first: Shay

last: Stern

address: 234 Herzl Street

department: Biological Chemistry

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: log2, RMA-normalized signal, affymetrix expression console

label: standard affymetrix protocol

source_name: 3rd instar larvae proventriculus

label_protocol:
The standard protocol of affymetrix GeneChip drosophila 2.0 array was used to synthesize cDNA from total RNA by using the GeneChip 3 IVT Express Kit aRNA amplification procedure:
a. Reverse Transcription to Synthesize First-Strand cDNA is primed with T7 oligo(dT) primer to synthesize cDNA containing a T7 promoter sequence.
b. Second-Strand cDNA Synthesis converts the single-stranded cDNA into a double- stranded DNA (dsDNA) template for transcription. The reaction employs DNA polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA.
c. In Vitro Transcription to Synthesize Biotin-Modified aRNA with IVT Labeling Master Mix generates multiple copies of biotin-modified aRNA from the double-stranded cDNA templates; this is the amplification step.
d. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the biotin-modified aRNA.

extract_protocol: QIAGEN - MinElute Reaction Cleanup Kit

tag: stress

tag: strain

value: hairy-gal4 UAS-neoGFP

value: proventriculus

tag: Stage


title: yw-2hr-WithIR_2

source_name: yw 2hr with IR sample 2


title: yw-18hr_WithIR_2

source_name: yw 18hr with IR sample 2

value: 18 hr with IR


title: p53-2hr-WithoutIR_1

source_name: p53-mutant 2hr without IR sample 1


title: proventriculus mRNA measured from F3 unchallenged larvae with past exposure on F1


title: proventriculus mRNA measured from unchallenged larvae replicate 1

value: unchallenged larvae


title: p53-18hr-WithIR_2

source_name: p53-mutant 18hr with IR sample 2


title: p53-2hr-WithIR_1

source_name: p53-mutant 2hr with IR sample 1


title: yw-18hr_WithIR_1

source_name: yw 18hr with IR sample 1


title: yw-2hr-WithoutIR_1

source_name: yw 2hr without IR sample 1


title: p53-18hr-MinusIR_2

source_name: p53-mutant 18hr without IR sample 2


title: proventriculus mRNA measured from G418 challenged larvae replicate 2

value: G418 challenged larvae


title: proventriculus mRNA measured from unchallenged larvae replicate 2


title: p53-2hr-WithIR_2

source_name: p53-mutant 2hr with IR sample 2


title: p53-18hr-WithIR_1

source_name: p53-mutant 18hr with IR sample 1


title: proventriculus mRNA measured from G418 challenged larvae replicate 1


title: p53-18hr-MinusIR_1

source_name: p53-mutant 18hr without IR sample 1


title: MLX treatment, population 1, male 1

status: Public on Apr 17 2012

city: Lund

first: Jessica

middle: K.

last: Abbott

address: Sölvegatan 37

department: Dept. of Biology

country: Sweden

institute: Lund University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA (Robust Multichip Average) as implemented by the affy package in R 2.9 (BioConductor 2.4) using default settings.

label: Biotin

source_name: Drosophila male with paternally transmitted X-chromosome from MLX population 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All populations were maintained using the same culturing protocol as for the ancestral LHm population. Eggs are laid on day 0, adult flies eclose on day 9 or 10, and on day 12, adult flies are mixed between vials, and 16 pairs per vial are randomly selected to produce the next generation. These pairs interact for 48 hours in vials supplemented with live yeast, and then are transferred to new (yeastless) vials, and females are given an 18 hour window in which to lay eggs. At the end of this period, all adult flies are discarded (new day 0). The 48 hour period with controlled density of 16 pairs ensures that all adult flies experience the same conditions while competing for matings (males) or yeast (females).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by Qiagen purification.

treatment_protocol: Male-limited X-chromosome evolution is made possible in D. melanogaster by the use of DX females, which have two X-chromosomes that are linked at the centromere. This ensures father-son transmission of the X, but does not affect the transmission of the autosomes. MLX males experienced many generations of father-son transmission of the X-chromosome, potentially enabling adaptation to this altered transmission scheme. CDX males were produced by crossing a control male to a DX female, resulting in one generation of father-son transmission.

tag: gender

value: male

value: derived from LHm population

value: day 14 (4 days adult)

value: MLX

tag: population

value: whole body


title: MLX treatment, population 3, male 2

source_name: Drosophila male with paternally transmitted X-chromosome from MLX population 3


title: MLX treatment, population 3, male 1


title: MLX treatment, population 1, male 2


title: MLX treatment, population 2, male 1

source_name: Drosophila male with paternally transmitted X-chromosome from MLX population 2


title: MLX treatment, population 2, male 2


title: Control treatment, population 2, male 1

source_name: Drosophila male with normally transmitted X-chromosome from control population 2

value: control


title: Control treatment, population 1, male 2

source_name: Drosophila male with normally transmitted X-chromosome from control population 1


title: Control treatment, population 2, male 2


title: CDX treatment, population 3, male 2

source_name: Drosophila male with paternally transmitted X-chromosome from CDX population 3

value: CDX


title: Control treatment, population 1, male 1


title: CDX treatment, population 2, male 2

source_name: Drosophila male with paternally transmitted X-chromosome from CDX population 2


title: Control treatment, population 3, male 2

source_name: Drosophila male with normally transmitted X-chromosome from control population 3


title: CDX treatment, population 1, male 1

source_name: Drosophila male with paternally transmitted X-chromosome from CDX population 1


title: CDX treatment, population 2, male 1


title: Control treatment, population 3, male 1


title: yw ovaries at 25oC- biological replicate 3

status: Public on Apr 05 2012

city: Vancouver

first: Alireza

last: Baradaran-Heravi

state: BC

address: 950 West 28th Avenue, Room 218

department: Medical Genetics

country: Canada

institute: UBC

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing:
Bioconductor RMA
The yw expression data from both the base and high temperature states were used to determine a set of expressed transcripts using the maximum RMA value for each probe set across all individual yw samples. Probe sets were identified as being expressed when the maximum RMA value was greater than or equal to six.

source_name: yw (25oC)

label_protocol: One-cycle target labeling

growth_protocol: Flies from different genotypes were reared either at 20oC or 25oC incubators.

extract_protocol: QIAGEN RNeasy Mini Kit

treatment_protocol: Flies were either untreated (20oC) or heat stressed (25oC).

value: female

value: ovary

value: yw

tag: temperature


title: RpII2154/FM7;Marcal1del/del ovaries at 20oC- biological replicate 2

source_name: RpII2154/FM7;Marcal1del/del (20oC)


title: RpII2154/FM7;Marcal1del/del ovaries at 20oC- biological replicate 1


title: Marcal1del/del ovaries at 25oC- biological replicate 2

source_name: Marcal1del/del (25oC)


title: Marcal1del/del ovaries at 25oC- biological replicate 3


title: RpII2154/FM7 ovaries at 20oC- biological replicate 3


title: CDX treatment, population 1, male 2


title: Marcal1del/del ovaries at 25oC- biological replicate 1

description: del/del-HS- IG100212CBL037-2_01.CEL


title: RpII2154/FM7 ovaries at 20oC- biological replicate 2


title: CDX treatment, population 3, male 1


title: RpII2154/FM7;Marcal1del/del ovaries at 20oC- biological replicate 3


title: Marcal1del/del ovaries at 20oC- biological replicate 1

source_name: Marcal1del/del (20oC)


title: yw ovaries at 20oC- biological replicate 3

source_name: yw (20oC)


title: Marcal1del/del ovaries at 20oC- biological replicate 2


title: yw ovaries at 25oC- biological replicate 2


title: yw ovaries at 25oC- biological replicate 1


title: yw ovaries at 20oC- biological replicate 2


title: Marcal1del/del ovaries at 20oC- biological replicate 3


title: RpII2154/FM7 ovaries at 20oC- biological replicate 1


title: Adult_female_Df(2R)ED1770/+_biological_rep_3

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

institute: Umea University

description:
DP45.CEL
Gene expression data from adult females

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Raw data was normalized using RMA (R and Bioconductor).

label_protocol: Standard Affymetrix

growth_protocol: Flies were cultivated and crossed in vials with potato-yeast-agar medium at 25 ̊ C.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) followed by a purification using RNeasy kit (Qiagen) according to the instruction by the suppliers.

treatment_protocol: Each sample, containing 15 adult female flies in age 0-24h, were collected and frozen in -70 ̊ C prior to RNA extraction

value: adult (0-24hr)

tag: genotype/variation


title: Adult_female_Df(3R)ED7665/+_Df(2R)ED1612/+

description:
DP40.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED10953/+_biological_rep_3

description:
DP44.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED7665/+_biological_rep_2

description:
DP42.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED7665/+_Df(2L)ED4559/+

description:
DP37.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED7665/+_Df(2L)ED3/+

description:
DP41.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED3/+_biological_rep_3

description:
DP47.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED7665/+_Df(2R)ED1770/+

description:
DP39.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED7665/Df(3R)ED10953

description:
DP38.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED4559/+_biological_rep_3

description:
DP43.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED5071/Df(3R)ED10953

description:
DP31.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED5071/+_biological_rep_2

description:
DP36.CEL
Gene expression data from adult females


title: Adult_female_Df(2R)ED1612/+_biological_rep_3

description:
DP46.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED7665/+_biological_rep_1

description:
DP28.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED5071/+_Df(2R)ED1770/+

description:
DP32.CEL
Gene expression data from adult females


title: Adult_female_Df(2R)ED1770/+_Df(2L)ED3/+

description:
DP25.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED5071/+_Df(2R)ED1612/+

description:
DP33.CEL
Gene expression data from adult females


title: Adult_female_Df(2R)ED1612/+_biological_rep_2

description:
DP22.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED3/+_biological_rep_2

description:
DP23.CEL
Gene expression data from adult females


title: Adult_female_Df(2R)ED1612/+_Df(2L)ED3/+

description:
DP26.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED4559/+_biological_rep_2

description:
DP17.CEL
Gene expression data from adult females


title: Adult_female_Df(2R)ED1770/Df(2R)ED1612

description:
DP24.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED5071/+_Df(2L)ED4559/+

description:
DP30.CEL
Gene expression data from adult females


title: Adult_female_Df(2R)ED1770/+_biological_rep_2

description:
DP21.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED5071/+_biological_rep_1

description:
DP27.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED5071/+_Df(2L)ED3/+

description:
DP34.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED3/+_Df(3R)ED10953/+

description:
DP16.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED4559/Df(2L)ED3

description:
DP20.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED4559/+_Df(2R)ED1612/+

description:
DP19.CEL
Gene expression data from adult females


title: Adult_female_Df(2R)ED1612/+_biological_rep_1

description:
DP11.CEL
Gene expression data from adult females


title: Adult_female_Df(2R)ED1612/+_Df(3R)ED10953/+

description:
DP15.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED3/+_biological_rep_1

description:
DP12.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED10953/+_biological_rep_2

description:
DP14.CEL
Gene expression data from adult females


title: Adult_female_Df(2R)ED1770/+_biological_rep_1

description:
DP10.CEL
Gene expression data from adult females


title: Adult_female_Df(3R)ED10953/+_biological_rep_1

description:
DP7.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED4559/+_biological_rep_1

description:
DP8.CEL
Gene expression data from adult females


title: Adult_female_wild_type_biological_rep_5

description:
DP5.CEL
Gene expression data from adult females


title: Adult_female_wild_type_biological_rep_4

description:
DP4.CEL
Gene expression data from adult females


title: Adult_female_wild_type_biological_rep_2

description:
DP2.CEL
Gene expression data from adult females


title: Adult_female_wild_type_biological_rep_6

description:
DP6.CEL
Gene expression data from adult females


title: Adult_female_Df(2L)ED4559/+_Df(3R)ED10953/+

description:
DP13.CEL
Gene expression data from adult females


title: Adult_female_wild_type_biological_rep_1

description:
DP1.CEL
Gene expression data from adult females


title: Adult_female_wild_type_biological_rep_3

description:
DP3.CEL
Gene expression data from adult females


title: pft1 16C repB

status: Public on Apr 03 2012

city: Ciudad de Buenos Aires

first: Sabrina

last: Iñigo

state: Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir

hyb_protocol: The cRNA that was hybridized to the Affymetrix expression arrays (ATH1-121501) as described by the manufacturer (Affymetrix, http://www.affymetrix.com)

scan_protocol: standard Affymetrix protocol

data_processing: The expression set was obtained after RMA normalization using the affy package implemented in the R system v2.10

source_name: 10-day-old pft1-1 seedlings, grown on MS salts agar plates, at 16ºC under continuous light cool-white fluorescent light, 80 micromoles/sec m2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: 10-day-old seedlings, grown on MS salts agar plates, under continuous light cool-white fluorescent light, 80 micromoles/sec m2

extract_protocol: Total RNA was prepared using a plant RNAeasy kit (Qiagen, http://www.qiagen.com) according to manufacturer's instruction

treatment_protocol: Seedlings were harvested, weighed and frozen in liquid nitrogen before RNA extraction

value: seedling

value: Columbia

tag: growth conditions


title: pft1 23C repB

source_name: 10-day-old pft1-1 seedlings, grown on MS salts agar plates, at 23ºC under continuous light cool-white fluorescent light, 80 micromoles/sec m2


title: pft1 23C repC


title: WT 23C repB

source_name: 10-day-old Columbia (WT) seedlings, grown on MS salts agar plates, at 23ºC under continuous light cool-white fluorescent light, 80 micromoles/sec m2

value: wild type


title: WT 16C repB

source_name: 10-day-old Columbia (WT) seedlings, grown on MS salts agar plates, at 16ºC under continuous light cool-white fluorescent light, 80 micromoles/sec m2


title: WT 16C repC


title: pft1 16C repA


title: pft1 16C repC


title: WT 16C repA


title: WT 23C repC


title: WT 23C repA


title: whole body control (C) overfed middle-aged biological rep4

status: Public on Apr 01 2012

city: Leiden

first: Agnieszka

last: Doroszuk

address: Sylviusweg 72

department: Evolutionary Biology

institute: Leiden University

description: Gene expression data from 5 females (whole body)

hyb_protocol: Following fragmentation, 8 ug of cRNA were hybridized for 16 hr at 45C on GeneChipII Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data analysis was performed using R (version 2.7.0) and Bioconductor. The probe level data was summarized using the robust multi-array average (RMA) algorithm.

source_name: 5 Drosophila females

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

growth_protocol: Adult virgin females were placed in vials (five individuals per vial) with media where yeast and sugar content was manipulated to obtain diet treatments representing malnutrition, optimal food and overfeeding. The concentrations of yeast and sugar were relative to those of the standard medium (20 g agar, 9 g kalmus, 10 ml nipagin, 50 g saccharose and 35 g of granulated yeast per litre water).

extract_protocol: RNAwas isolated using the NucleoSpin RNA II kit (Macherey & Nagel).

treatment_protocol: Each sample was composed of five whole females snap-frozen in liquid nitrogen

tag: natural variant/selected line

value: Control

tag: diet

value: overfeeding (5x standard medium)

value: middle-aged (collected at 90% survival of the cohort)

value: whole organism


title: Adult_female_Df(2L)ED4559/+_Df(2R)ED1770/+

description:
DP18.CEL
Gene expression data from adult females


title: whole body control (C) overfed middle-aged biological rep1


title: pft1 23C repA


title: whole body control (C) overfed middle-aged biological rep3


title: whole body control (C) optimal food old biological rep1

value: optimal food (2x standard medium concentration)

value: old (sampled at 10% survival of the cohort)


title: whole body control (C) overfed middle-aged biological rep2


title: whole body control (C) optimal food middle-aged biological rep3


title: whole body control (C) overfed old biological rep2


title: whole body control (C) optimal food middle-aged biological rep1


title: whole body control (C) optimal food old biological rep2


title: whole body control (C) overfed old biological rep1


title: whole body control (C) optimal food old biological rep3


title: whole body control (C) optimal food old biological rep4


title: whole body control (C) overfed old biological rep3


title: whole body control (C) optimal food middle-aged biological rep4


title: whole body control (C) malnutritioned old biological rep3

value: malnutritioned (standard medium diluted 0.5x)


title: whole body control (C) optimal food middle-aged biological rep2


title: whole body control (C) malnutritioned middle-aged biological rep4


title: whole body control (C) malnutritioned middle-aged biological rep2


title: whole body control (C) malnutritioned old biological rep1


title: whole body control (C) malnutritioned middle-aged biological rep3


title: whole body starvation resistant (SR) overfed old biological rep2

value: Starvation resistant


title: whole body starvation resistant (SR) overfed old biological rep1


title: whole body starvation resistant (SR) overfed old biological rep4


title: whole body control (C) malnutritioned old biological rep2


title: whole body control (C) malnutritioned middle-aged biological rep1


title: whole body starvation resistant (SR) optimal food old biological rep4


title: whole body starvation resistant (SR) overfed middle-aged biological rep2


title: whole body starvation resistant (SR) optimal food old biological rep1


title: whole body starvation resistant (SR) optimal food middle-aged biological rep2


title: whole body starvation resistant (SR) optimal food old biological rep3


title: whole body starvation resistant (SR) overfed old biological rep3


title: whole body starvation resistant (SR) optimal food middle-aged biological rep3


title: whole body starvation resistant (SR) overfed middle-aged biological rep1


title: whole body starvation resistant (SR) optimal food middle-aged biological rep4


title: whole body starvation resistant (SR) malnutritioned old biological rep4


title: whole body starvation resistant (SR) overfed middle-aged biological rep3


title: whole body starvation resistant (SR) malnutritioned old biological rep1


title: whole body starvation resistant (SR) malnutritioned old biological rep2


title: whole body starvation resistant (SR) malnutritioned middle-aged biological rep4


title: whole body starvation resistant (SR) malnutritioned middle-aged biological rep3


title: whole body starvation resistant (SR) optimal food middle-aged biological rep1


title: whole body starvation resistant (SR) malnutritioned middle-aged biological rep1


title: whole body starvation resistant (SR) optimal food old biological rep2


title: whole body starvation resistant (SR) malnutritioned old biological rep3


title: whole body starvation resistant (SR) malnutritioned middle-aged biological rep2


title: phyABDE, 4-day dark growth followed by 2 hours of Rc50, biol rep 1

city: Davis

first: Wei

last: Hu

state: CA

address: One Shields Ave.

department: Department of Molecular and Cellular Biology

institute: Univ of California at Davis

description: gene expression data from dark-grown and 2hr Rc-treated phyABDE mutant

hyb_protocol: Fifteen micrograms (15 µg) of aRNA were fragmented, and used for hybridization for 16 hr at 45 degree on GeneChip Arabidopsis ATH1 Array in the Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the 3000 GeneChip Scanner with Autoloader.

data_processing: The data were analyzed in R/Bioconductor. Data were normalized with the 'RMA' function, ABS calls were obtained by Affymetrix GCOS algorithm, and statistical analysis were performed by LIMMA.

source_name: Arabidopsis 4-day-old seedling

label_protocol: Biotinylated aRNA were prepared using the GeneChip 3' IVT Express Kit (Affymetrix) from 500ng total RNA according to the manufacturer's instructions.

growth_protocol: Surface sterilized seeds were sown on 1x MS salt medium solidified with 0.8% phytoagar, imbibed in darkness at 4 degree for 4 days, then exposed to white light for 3 hours to promote germination, and finally wrapped with aluminum foil for dark growth, or put into LED red light growth chamber for continuous red light growth (50 µmol m-2 s-1 irradiance).

extract_protocol: QIAGEN RNeasy Plant Mini kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: After 4 days of growth, during the subjective morning time, continuous red light-grown seedlings (R50) were directly harvested under red light, dark-grown seedlings (D) were harvested under safe dim green light (approximately 1 µmol m-2 s-1 irradiance). For DR2h samples, dark-grown seedlings were exposed to red light (50 µmol m-2 s-1 irradiance) for 2 hours before harvest under red light.

value: whole seedling

value: phyABDE quadruple mutant

value: Ler

value: 4 d old

value: 4-day dark growth followed by 2 hours of red light


title: phyABDE, Rc50, biol rep 1

description: gene expression data from Rc50-grown phyABDE mutant

value: red light


title: phyABDE, Rc50, biol rep 3


title: phyABCDE, Rc50, biol rep 3

description: gene expression data from Rc50-grown phyABCDE mutant

value: phyABCDE quintuple mutant


title: phyABCDE, 4-day dark growth followed by 2 hours of Rc50, biol rep 2

description: gene expression data from dark-grown and 2hr Rc-treated phyABCDE mutant


title: phyABDE, Rc50, biol rep 2


title: phyABDE, Dark, biol rep 1

description: gene expression data from dark-grown phyABDE mutant

value: Dark


title: phyABCDE, 4-day dark growth followed by 2 hours of Rc50, biol rep 1


title: WT, Dark, biol rep 1

description: gene expression from dark-grown WT

value: wild type


title: phyABCDE, Dark, biol rep 1

description: gene expression data from dark-grown phyABCDE mutant


title: phyABDE, Dark, biol rep 3


title: phyABDE, Dark, biol rep 2


title: phyABCDE, Rc50, biol rep 1


title: phyABCDE, Dark, biol rep 3


title: yw ovaries at 20oC- biological replicate 1

description: yw Base-IG100212CBL027-2_01.CEL

value: female

value: ovary

value: yw


title: phyABCDE, Rc50, biol rep 2


title: Revertant larvae CNS, biological rep2

status: Public on Mar 31 2012

city: Huddinge

first: Hossain

last: Nawaz

state: Stockholm

address: Hälsovägen 7

department: LABMED

institute: Karolinska Institutet

description: Drosophila_Rev L2.CEL

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 400.

scan_protocol: GeneChips were scanned using the Genechip Scanner 30007G.

data_processing: RMA (R with Affy package for data normalization).

source_name: Drosophila third instar larvae

growth_protocol: Flies were raised on standard medium on a 12:12 h L:D cycle, at 23C, and at 55% r.h. Flies were collected irrespective of their age and sex, whereas the larvae used were third instar, wandering larvae.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Flies were anaesthetized briefly by using 5% CO2, then immediately dissected. The tissues dissected were the complete head, severed at the neck from the adult flies and the CNS (developing brain), including the optic lobes from the larvae

value: Revertant

value: dissected larvae CNS

value: Canton S parents

value: Third instar larvae


title: Revertant adult head, biological rep3

description: Drosophila_Rev H3.CEL

source_name: Drosophila adult head

value: decapitulated head

value: Adult


title: Revertant larvae CNS, biological rep3

description: Drosophila_Rev L3.CEL


title: Revertant adult head, biological rep2

description: Drosophila_Rev H2.CEL


title: Revertant larvae CNS, biological rep1

description: Drosophila_Rev L1.CEL


title: FicP larvae CNS, biological rep3

description: Drosophila_FicP L3.CEL

value: FicP


title: phyABCDE, Dark, biol rep 2

value: whole seedling

value: Ler


title: FicP adult head, biological rep3

description: Drosophila_FicP H3.CEL


title: FicP larvae CNS, biological rep1

description: Drosophila_FicP L1.CEL


title: phyABDE, 4-day dark growth followed by 2 hours of Rc50, biol rep 2

value: phyABDE quadruple mutant

value: 4 d old

value: 4-day dark growth followed by 2 hours of red light


title: FicP adult head, biological rep2

description: Drosophila_FicP H2.CEL


title: Revertant adult head, biological rep1

description: Drosophila_Rev H1.CEL


title: FicP adult head, biological rep1

description: Drosophila_FicP H1.CEL


title: FicP larvae CNS, biological rep2

description: Drosophila_FicP L2.CEL


title: 10min Reillumination Total RNA Rep2

city: Riverside

first: Piyada

last: Juntawong

address: 900 University ave

department: Botany and Plant Sciences

institute: University of California Riverside

description: 10 min reillumination total mRNA

hyb_protocol: Hybridizations against Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in a rotating platform, using 10 µg of Biotin-labeled cRNA.

scan_protocol: GeneChips were scanned by use of the Affymetrix GeneChip Workstation Scanner 3000.

data_processing: CEL files from the Affymetrix Chips were processed by use of the R program (http://cran.at.r-project.org/) and Bioconductor packages (http://www.bioconductor.org/). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding R function. Present, Marginal or Absent (P/M/A) calls were computed with the affy package.

source_name: 14d-old Arabidopsis Seedling, 10min Reillumination, total RNA, rep2

label_protocol: Total and polysomal RNA samples derived from two independent biological replicate experiments were used for microarray hybridization analysis. RNA samples (1.5 µg) were used to synthesize double stranded cDNA, using One-Cycle cDNA synthesis Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Arabidopsis 35S:HF-RPL18 (Col-0 ecotype), expressing an amino-terminally His6-FLAG (HF)-tagged ribosomal protein L18B (RPL18, At3g05590) under a control of the near-constitutive Cauliflower Mosaic Virus (CaMV) 35S promoter, was used to enable the immunoprecipitation of polysomes (Zanetti et al., 2005). Seeds were surfaced sterilized in a 15 mL Falcon tube with 10 mL 95% (v/v) ethanol for 5 min, 10 mL 20 % (v/v) household bleach plus 0.1 % (v/v) Tween-20 for 5 min, rinsed 3 times with 10 mL sterile water, and stratified in 10 mL sterile water at 4 °C for 48 h in darkness. Seeds were plated on sterile solid Murashige and Skoog (MS) medium containing 0.43 % (w/v) MS salts (Caisson Laboratories, North Logan, UT), 1 % (w/v) Sucrose, 1 % (w/v), Agar [pH 5.7] and vertically orientated in a growth chamber (model CU-36L5C8, Percival Scientific, Inc.) under a 16 h light (~60 μE sec−1 m−2) and 8 h dark cycle at 23 °C.

extract_protocol: Briefly, 7.5 mL of frozen packed tissue was thawed in 15 mL of Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA), 36 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene(23) lauryl ether (Brig® 35), 1% (v/v) Triton X-100, 1% (v/v) Tween-20, 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 1 mM dithiothreitol (DTT), 50 µg mL-1 cycloheximide, 50 µg mL-1 chloramphenicol), homogenized, and centrifuged at 16,000g for 20 min at 4 °C. Total extract was centrifuged at 16,000g for 20 min at 4 °C. The clarified supernatant of the extract was passed through Miracloth and 13 mL was combined with 400 µl EZ view Red Anti-FLAG affinity beads (Sigma, St. Louis, MO) that had been pre-washed twice with 6 mL PB. The mixture was incubated at 4 °C for 2 h with gentle shaking. The unbound fraction was removed by centrifugation in clinical centrifuge at 700g for 2 min and beads were washed 4 times with 6 mL PB for 5 min at 4 °C with gentle shaking. The elution was performed by incubation of beads with 600 μL PB containing 200 ng/μL 3x FLAG peptide (Sigma) for 30 min at 4 °C. Total RNA was extracted from 1 mL of the clarified extract. Both the total cell extract and immunoprecipitation eluate were subjected the TRIzol RNA extraction (Invitrogen, Carlsbad, CA). RNA was further purified by use of the RNaeasy Plant Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. RNA concentration and quality was determined by absorbance 260 and 280 nm by use of a spectrophotometer (ND-1000, Nanodrop, Wilmington, DE). The RNA integrity was examined with an Agilent Bioanalyzer 2100 on RNA 6000 nano chip (Agilent Teachnologies, Santa Clara, CA)

treatment_protocol: Fourteen-day old seedlings were subjected to 1h darkness treatment or reilluminate after 1 h darkness for 10 min. Treatment started at the middle of light period.

tag: ecotype

value: whole seedlings

value: 1 h darkness plus 10 min reillumination


title: 1 h Light IP RNA Rep2

type: other

description: 1 h light IP mRNA

molecule: other

source_name: 14d-old Arabidopsis Seedling, 1h light, IP RNA, rep2

tag: treatment

value: 1 h light control


title: 10min Reillumination IP RNA Rep1

description: 10 min reillumination IP mRNA

source_name: 14d-old Arabidopsis Seedling, 10min Reillumination, IP RNA, rep1

tag: tissue


title: 10min Reillumination IP RNA Rep2

description: 10 min reillumination IP mRNA

source_name: 14d-old Arabidopsis Seedling, 10min Reillumination, IP RNA, rep2


title: 1 h Light IP RNA Rep1

description: 1 h light IP mRNA

source_name: 14d-old Arabidopsis Seedling, 1h light, IP RNA, rep1


title: 1h Dark IP RNA Rep2

description: 1 h dark IP mRNA

source_name: 14d-old Arabidopsis Seedling, 1h dark, IP RNA, rep2

value: 1 h darkness


title: 10min Reillumination Total RNA Rep1

description: 10 min reillumination total mRNA

source_name: 14d-old Arabidopsis Seedling, 10min Reillumination, total RNA, rep1


title: High-grade osteosarcoma pre-chemotherapy biopsy L3449int

status: Public on Mar 28 2012

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

description: Gene expression data were exported from BeadStudio version 3.1.3.0 (Illumina) in GeneSpring probe profile format. Two supplementary/raw data files are present because each array that represents one Sample consists of 2 chips. The supplementary/raw data files represent the bead level data (2 raw .txt files per sample, containing all intensities per bead).

hyb_protocol: As per manufacturer's instructions.

scan_protocol: As per manufacturer's instructions.

data_processing: Data were analyzed using the statistical language R. As Illumina identifiers are not stable and consistent between different chip versions, raw oligonucleotide sequences were converted to nuIDs. Data were transformed using the variance stabilizing transformation (vst) algorithm and subsequently normalized using robust spline normalization. Conversion to nuIDs, variance stabilizing transformation, and normalization of the data were all carried out using the Bioconductor package lumi. Quality control was performed using the Bioconductor package arrayQualityMetrics. Poor quality arrays were removed from further analyses.

organism: Homo sapiens

label_protocol: As per manufacturer's instructions.

extract_protocol: RNA isolation, cDNA synthesis, cRNA amplification, Illumina Human-6 v2.0 Expression BeadChip hybridization, qPCR validation, and microarray data analysis were performed as previously described (Buddingh EP, Kuijjer ML, Duim RA, Burger H, Agelopoulos K, Myklebost O, et al. Tumor-infiltrating macrophages are associated with metastasis suppression in high-grade osteosarcoma: a rationale for treatment with macrophage-activating agents. Clin Cancer Res 2011 Apr 15;17(8):2110-2119).

tag: type

value: biopsy

value: F

value: 133 months

tag: histological subtype

value: fibroblastic osteosarcoma

tag: tumor location

value: femur

tag: huvos grade

tag: matching copy number data

value: no

tag: metastasis within 5yrs

value: yes


title: 1h Dark IP RNA Rep1

description: 1 h dark IP mRNA

source_name: 14d-old Arabidopsis Seedling, 1h dark, IP RNA, rep1

tag: age


title: 1h Dark Total RNA Rep2

description: 1 h dark total mRNA

source_name: 14d-old Arabidopsis Seedling, 1h dark, total RNA, rep2


title: High-grade osteosarcoma pre-chemotherapy biopsy L3444int

tag: gender

value: M

value: 264 months

value: humerus


title: High-grade osteosarcoma pre-chemotherapy biopsy L3534int

value: 180 months

value: sclerosing osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L3448int

value: 170 months

value: osteoblastic osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L3477int

value: 192 months

value: unknown


title: High-grade osteosarcoma pre-chemotherapy biopsy L3470int

value: 468 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L3475int

value: biopsy

value: 336 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L3445int

value: F

value: 696 months

value: telangiectatic osteosarcoma

value: tibia/fibula


title: High-grade osteosarcoma pre-chemotherapy biopsy L3443int

value: 204 months

value: fibroblastic osteosarcoma

value: no


title: 1 h Light Total RNA Rep1

description: 1 h light total mRNA

source_name: 14d-old Arabidopsis Seedling, 1h light, total RNA, rep1

value: whole seedlings

value: 1 h light control


title: High-grade osteosarcoma pre-chemotherapy biopsy L3447int

value: M

value: 162 months

value: humerus

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L3442int

value: 144 months

value: osteoblastic osteosarcoma

value: femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L3463int

value: biopsy

value: 948 months

value: unknown


title: High-grade osteosarcoma pre-chemotherapy biopsy L3440int

value: 264 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L3465int

value: F

value: 129 months

value: chondroblastic osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L3460int

value: 180 months

value: tibia/fibula

value: no


title: 1 h Light Total RNA Rep2

description: 1 h light total mRNA

source_name: 14d-old Arabidopsis Seedling, 1h light, total RNA, rep2

value: whole seedlings

value: 1 h light control


title: whole body starvation resistant (SR) overfed middle-aged biological rep4

value: Starvation resistant

value: overfeeding (5x standard medium)

value: middle-aged (collected at 90% survival of the cohort)

value: whole organism

value: female


title: High-grade osteosarcoma pre-chemotherapy biopsy L3438int

value: biopsy

value: M

value: 220 months

value: osteoblastic osteosarcoma

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L3436int

value: 205 months

value: femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L3434int

value: 181 months

value: sclerosing osteosarcoma


title: 1h Dark Total RNA Rep1

description: 1 h dark total mRNA

source_name: 14d-old Arabidopsis Seedling, 1h dark, total RNA, rep1

value: 1 h darkness


title: High-grade osteosarcoma pre-chemotherapy biopsy L2297int

value: F

value: 137 months

value: tibia/fibula

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L2620int

value: 217 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L2292int

value: 136 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L2618int

value: 96 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L2295int

value: biopsy

value: 487 months

value: anaplastic osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L3432int

value: M

value: 144 months

value: chondroblastic osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L2296int

value: 198 months

value: osteoblastic osteosarcoma

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L2616int

value: 218 months


title: wing disc control at 92hrs rep2

city: NICE cedex 2

first: julien

last: colombani

address: Centre de biochimie - Parc Valrose

department: Institut de Biologie Valrose (iBV)

country: France

institute: CNRS UMR7277

hyb_protocol: Following fragmentation,  cRNA were hybridized on Affimetrix Drosophila _2 Gene Array. GeneChips were washed and stained in the GeneChip Affymetrix Station.

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

data_processing: The data were analyzed with Partek®GSv.6.5) and using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set. The  robustness has been validated by independent methods (nonparametric SAM by Tibshirani and EBS form R/Bioconductor:limma)

source_name: drosophila wing disc_control at 92hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 2 hours egg collections of Rn>+ or Rn>Avl RNAi flies and development until 92, 116, or 168 hours at 25C .

extract_protocol: Qiazol extraction of total RNA was performed according to the manufacturer's instructions for Qiagen RNeasy lipid tissue microkit. RNA were analysed by electrophoresis with a Agilent Bioanalyzer.

treatment_protocol: Wing imaginal discs were dissected on ice and fast frozen in liquid N2.

tag: genotype

value: w-; elav-GAL80/+; Rn-GAL4/+

value: wing discs

tag: developmental stage

value: third larval instar at 92 hrs AED

tag: morphology

value: wild type

tag: genetic background


title: High-grade osteosarcoma pre-chemotherapy biopsy L3437int

value: 183 months

value: femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L3446int

value: 174 months

value: giant cell rich osteosarcoma


title: wing disc control at 116hrs rep1

source_name: drosophila wing disc_control at 116hrs

value: third larval instar at 116 hrs AED


title: wing disc control at 116hrs rep3


title: wing disc control at 92hrs rep3


title: wing disc control at 116hrs rep2


title: High-grade osteosarcoma pre-chemotherapy biopsy L2614int

value: biopsy

value: 165 months

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L3439int

value: M

value: 385 months

value: chondromyxoid fibroma-like osteosarcoma

value: humerus


title: High-grade osteosarcoma pre-chemotherapy biopsy L3433int

value: F

value: 204 months

value: osteoblastic osteosarcoma

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L2611int

value: 242 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L3431int

value: 81 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L2302int

value: 229 months

value: chondroblastic osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L2619int

value: 128 months

value: femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L3435int

value: biopsy

value: 200 months


title: High-grade osteosarcoma pre-chemotherapy biopsy L3441int

value: 228 months

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L2301int

value: M

value: 304 months

value: tibia/fibula


title: wing disc Rn>avl-RNAi at 116hrs rep2

source_name: drosophila wing disc_Rn>avl-RNAi at 116hrs

value: w-; elav-GAL80/+; Rn-GAL4,UAS Avl RNAi/+

value: wing discs

value: third larval instar at 116 hrs AED

value: neoplastic


title: wing disc Rn>avl-RNAi at 116hrs rep1


title: High-grade osteosarcoma pre-chemotherapy biopsy L1382int

value: 175 months

value: osteoblastic osteosarcoma

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L1376int

value: F

value: 164 months

value: telangiectatic osteosarcoma


title: wing disc Rn>avl-RNAi at92hrs rep2

source_name: drosophila wing disc_Rn>avl-RNAi at92hrs

value: third larval instar at 92 hrs AED


title: wing disc Rn>avl-RNAi at 116hrs rep3


title: High-grade osteosarcoma pre-chemotherapy biopsy L1385int

value: biopsy

value: 200 months

value: humerus

value: unknown


title: wing disc Rn>avl-RNAi at 92hrs rep3

source_name: drosophila wing disc_Rn>avl-RNAi at 92hrs


title: High-grade osteosarcoma pre-chemotherapy biopsy L1370int

value: M

value: 216 months

value: femur

value: no


title: High-grade osteosarcoma pre-chemotherapy biopsy L1372int


title: wing disc Rn>avl-RNAi at 168hrs rep1

source_name: drosophila wing disc_Rn>avl-RNAi at 168hrs

value: w-; elav-GAL80/+; Rn-GAL4,UAS Avl RNAi/+

value: wing discs

value: third larval instar at 168 hrs AED


title: wing disc Rn>avl-RNAi at 168hrs rep2

value: neoplastic


title: High-grade osteosarcoma pre-chemotherapy biopsy L1369int

value: 212 months

value: osteoblastic osteosarcoma

value: yes


title: wing disc Rn>avl-RNAi at 168hrs rep3


title: wing disc Rn>avl-RNAi at 92hrs rep1


title: High-grade osteosarcoma pre-chemotherapy biopsy L1085int

value: 223 months

value: chondroblastic osteosarcoma

value: tibia/fibula


title: 12 hour control (no chemical treatment) rep1

city: Taipei

first: Kevin Long-Chi

last: WANG

address: 128 Section 2, Academia Road

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

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

scan_protocol: 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.

data_processing: MAS5.0 signal intensity

source_name: 12 hours Arabidopsis seedling samples without chemical treatment

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: WT (Col-0) sown on 0.5x MS agar medium and stratified in the dark at 4 °C for 3 days and then germinated in the light condition (16 h light/8 h dark) for 5 days at 22 °C, and then transfer to the 0.5x MS solution one day for adapt the treatment condition.

extract_protocol: Qiagen RNAeasy mini kit (Qiagen) was used for RNA preparation

treatment_protocol: In DAG 6, final concentration 50 uM chemicals were added into the medium solution for chemical treatment. Seedlings collected before the chemicals added into the medium considered as the control sample. After chemicals added into the solution medium, samples were collected after designated time peroid (3 hour and 12 hour).

value: 6 Days after germination

tag: agent

value: no chemical treatment

tag: time

value: 12 hour


title: 12 hour control (no chemical treatment) rep2


title: High-grade osteosarcoma pre-chemotherapy biopsy L975int

value: biopsy

value: F

value: 244 months

value: anaplastic osteosarcoma


title: High-grade osteosarcoma pre-chemotherapy biopsy L997int

value: M

value: 217 months

value: no


title: 3 hour control (no chemical treatment) rep1

source_name: 3 hours Arabidopsis seedling samples without chemical treatment

value: 3 hour


title: 12 hour 5929745 treatment sample rep1

source_name: Arabidopsis seedling samples treated by 5929745 for 12 hours


title: 12 hour 5929745 treatment sample rep2


title: High-grade osteosarcoma pre-chemotherapy biopsy L1368int

value: 177 months

value: femur


title: High-grade osteosarcoma pre-chemotherapy biopsy L1386int

value: 101 months

value: osteoblastic osteosarcoma

value: yes


title: High-grade osteosarcoma pre-chemotherapy biopsy L1016int

value: 200 months

value: tibia/fibula


title: 12 hour 7606596 treatment sample rep1

source_name: Arabidopsis seedling samples treated by 7606596 for 12 hours

value: 6 Days after germination


title: 3 hour 7606596 treatment sample rep1

source_name: Arabidopsis seedling samples treated by 7606596 for 3 hours


title: High-grade osteosarcoma pre-chemotherapy biopsy L428int

value: 192 months


title: 3 hour 7606596 treatment sample rep2


title: 12 hour 7606596 treatment sample rep2

value: 12 hour


title: wing disc control at 92hrs rep1

value: w-; elav-GAL80/+; Rn-GAL4/+

value: wing discs

value: third larval instar at 92 hrs AED

value: wild type


title: 3 hour 5929745 treatment sample rep2

source_name: Arabidopsis seedling samples treated by 5929745 for 3 hours


title: 3 hour 5929745 treatment sample rep1


title: embryos from 2xbcd mother (control), biological rep3

status: Public on Mar 22 2012

city: Mishima

first: Kentaro

middle: M

last: Tanaka

country: Japan

institute: NIG

description: gene expression data in embryonic cell death

scan_protocol: scanning were performed following Affymetrix technical manuals

data_processing: The relative expression level of each probe set was analyzed by the Statistical Expression algorithm implemented in the GeneChip Operating System (GCOS, Affymetrix)

source_name: Drosophila st12-13 embryo

label_protocol: We used the GeneChip One-Cycle Target Labeling and Control reagents (Affymetrix) for labeling

extract_protocol: we extracted RNA from more than 100 eggs by the RNeasy Kit (Qiagen) with subsequent DNase I digestion procedure

tag: genotype/variation

value: TT16 males x  TT16 female

value: dechorionated embryo


title: time zero control (no chemical treatment) rep1

source_name: Time zero Arabidopsis seedling samples without chemical treatment

value: no chemical treatment

value: 0 hour


title: embryos from 2xbcd mother (control), biological rep2

value: TT16 males x TT16 female


title: embryos from 2xbcd mother (control), biological rep1


title: embryos from 6xbcd mother, biological rep1

value: TT16 males x bcd+t8 female


title: High-grade osteosarcoma pre-chemotherapy biopsy L432int

value: biopsy

value: F

value: 111 months

value: pleomorphic osteosarcoma

value: femur

value: no


title: embryos from 6xbcd mother, biological rep2


title: 3 hour control (no chemical treatment) rep2

value: 6 Days after germination

value: 3 hour


title: time zero control (no chemical treatment) rep2


title: GFP, control, rep 1

status: Public on Mar 19 2012

city: Boston

first: Joshua

middle: WK

last: Ho

state: MA

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

description: Background control for Sxl.RNAi.2 and Sxl.MSL2.RNAi.1

data_processing: Raw data are preprocessed with robust multiarray average (RMA) method.

source_name: Kc cells

extract_protocol: RNeasy Qiagen RNA extraction was performed according to the manufacturer's instructions.

tag: cell line

value: Kc cells

tag: knockdown

value: GFP control


title: embryos from 6xbcd mother, biological rep3

tag: tissue


title: Sxl RNAi KD, rep 3

description: Sxl RNAi KD

value: Sxl


title: Sxl RNAi KD, rep 1

description: Sxl RNAi KD


title: GFP, control, rep 3

description: Background control for Sxl.RNAi.3 and Sxl.MSL2.RNAi.2


title: Sxl RNAi KD, rep 2

description: Sxl RNAi KD


title: Sxl and MSL2 RNAi KD, rep 2

description: Sxl and MSL2 RNAi KD

value: Sxl and Msl2


title: genotype: P35S:rGRF3 overexpression - rep3

status: Public on Mar 13 2012

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: genotype=P35S:rGRF3 overexpression rep 3

hyb_protocol: Affymetrix GeneChip Hyb

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

source_name: root (genotype: P35S:rGRF3 overexpression)

label_protocol: Affymetrix one-cycle target labeling

growth_protocol: Growth Description:  Growth chamber: Plants were grown at 23°C under 16-h-light/8-h-dark conditions.

extract_protocol: Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up

tag: ecotype

value: ws

tag: transgenic description

value: Transgenic line overexpressing miR396-resistant variant of GRF3 under the control of CaMV 35S promoter

tag: organism part

tag: development stage

value: PO:0007033 whole plant growth stages

value: 2 week old plants

tag: growth media

value: modified Knopâ€™s medium


title: GFP, control, rep 2

description: Background control for Sxl.RNAi.1


title: Sxl and MSL2 RNAi KD, rep 1

description: Sxl and MSL2 RNAi KD


title: High-grade osteosarcoma pre-chemotherapy biopsy L436int

tag: type

value: biopsy

tag: age

value: 37 months

tag: histological subtype

value: osteoblastic osteosarcoma

tag: tumor location

value: tibia/fibula

tag: huvos grade

tag: matching copy number data

tag: metastasis within 5yrs


title: genotype: P35S:rGRF3 overexpression - rep2

description: genotype=P35S:rGRF3 overexpression rep 2


title: genotype: P35S:rGRF1 overexpression - rep1

description: genotype=P35S:rGRF1 overexpression rep 1

source_name: root (genotype: P35S:rGRF1 overexpression)

value: Transgenic line overexpressing miR396-resistant variant of GRF1 under the control of CaMV 35S promoter


title: genotype: P35S:rGRF1 overexpression - rep3

description: genotype=P35S:rGRF1 overexpression rep 3


title: genotype: Arabidopsis thaliana ecotypes WS - rep3

description: genotype=Arabidopsis thaliana ecotypes WS rep 3

source_name: root (genotype: Arabidopsis thaliana ecotypes WS)

value: wild type


title: genotype: Triple mutant grf1/grf2/grf3 - rep3

description: genotype=Triple mutant grf1/grf2/grf3 rep 3

source_name: root (genotype: Triple mutant grf1/grf2/grf3)

value: col-0 and ws

value: triple grf1/grf2/grf3 mutant


title: genotype: P35S:rGRF1 overexpression - rep2

description: genotype=P35S:rGRF1 overexpression rep 2


title: genotype: Arabidopsis thaliana ecotypes WS - rep1

description: genotype=Arabidopsis thaliana ecotypes WS rep 1


title: genotype: Arabidopsis thaliana ecotypes Col-0 - rep3

description: genotype=Arabidopsis thaliana ecotypes Col-0 rep 3

source_name: root (genotype: Arabidopsis thaliana ecotypes Col-0)


title: genotype: Triple mutant grf1/grf2/grf3 - rep2

description: genotype=Triple mutant grf1/grf2/grf3 rep 2


title: genotype: P35S:rGRF3 overexpression - rep1

description: genotype=P35S:rGRF3 overexpression rep 1


title: genotype: Arabidopsis thaliana ecotypes WS - rep2

description: genotype=Arabidopsis thaliana ecotypes WS rep 2


title: genotype: Arabidopsis thaliana ecotypes Col-0 - rep1

description: genotype=Arabidopsis thaliana ecotypes Col-0 rep 1


title: genotype: Triple mutant grf1/grf2/grf3 - rep1

description: genotype=Triple mutant grf1/grf2/grf3 rep 1


title: Col0-hCO2-Rep2

status: Public on Mar 07 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Sample was harvested 7h into the light period to ensure identical exposure to light at time of sampling

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45 °C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.

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

data_processing: RMA-normalized expression values as obtained with the affy package of BioConductor. The reported values are on log2-scale.

source_name: Col0, grown for five weeks at high CO2 concentration (300 ppm) in short day regime (8h light/16h dark)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA.

growth_protocol: Plants were grown for five weeks in soil at high CO2 concentration (3000 ppm) in a short day regime (8h light/16h dark), 20 °C/18 °C, 65% relative humidity, 200 umol.m-2.s-1 irradiance at the leaf surface.

extract_protocol: RNA was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA) and further purified using Qiagen RNeasy MiniElute Columns. Concentration and quality of the RNA was determined with a Nanodrop ND 1000 spectrophotometer and quality was examined using the RNA 6000 Nano Assay (Agilent Technologies 2100 Bioanalyzer).

treatment_protocol: No transfer to air

tag: genotype

tag: treatment group

value: rosette leaf material

value: five-week-old plants


title: Col0-hCO2-Rep3

value: grown for five weeks at high CO2 concentration (300 ppm) in short day regime (8h light/16h dark)


title: cat2-LD4-Rep3

source_name: cat2, transferred to air (400 ppm) for 4 days in long day regime (16h light/8h dark)

treatment_protocol: Transfer to air (400 ppm CO2) for 4 days in long day regime (16h light/8h dark)


title: cat2-LD4-Rep2

value: transferred to air (400 ppm) for 4 days in long day regime (16h light/8h dark)


title: cat2-hCO2-Rep1

source_name: cat2, grown for five weeks at high CO2 concentration (3000 ppm) in short day regime (8h light/16h dark)


title: cat2-hCO2-Rep3

value: grown for five weeks at high CO2 concentration (3000 ppm) in short day regime (8h light/16h dark)


title: Col0-LD4-Rep3

source_name: Col0, transferred to air (400 ppm) for 4 days in long day regime (16h light/8h dark)


title: genotype: Arabidopsis thaliana ecotypes Col-0 - rep2

description: genotype=Arabidopsis thaliana ecotypes Col-0 rep 2

tag: genotype/variation


title: Col0-SD4-Rep3

source_name: Col0, transferred to air (400 ppm) for 4 days in short day regime (8h light/16h dark)

treatment_protocol: Transfer to air (400 ppm CO2) for 4 days in short day regime (8h light/16h dark)


title: cat2-LD2-Rep3

source_name: cat2, transferred to air (400 ppm) for 2 days in long day regime (16h light/8h dark)

treatment_protocol: Transfer to air (400 ppm CO2) for 2 days in long day regime (16h light/8h dark)


title: cat2-LD4-Rep1


title: cat2-SD4-Rep3

source_name: cat2, transferred to air (400 ppm) for 4 days in short day regime (8h light/16h dark)


title: Col0-hCO2-Rep1


title: cat2-hCO2-Rep2


title: Col0-LD4-Rep1


title: cat2-SD2-Rep3

source_name: cat2, transferred to air (400 ppm) for 2 days in short day regime (8h light/16h dark)

treatment_protocol: Transfer to air (400 ppm CO2) for 2 days in short day regime (8h light/16h dark)


title: Col0-LD4-Rep2


title: Col0-LD2-Rep3

source_name: Col0, transferred to air (400 ppm) for 2 days in long day regime (16h light/8h dark)


title: cat2-LD2-Rep2

value: transferred to air (400 ppm) for 2 days in long day regime (16h light/8h dark)


title: cat2-SD2-Rep2

value: transferred to air (400 ppm) for 2 days in short day regime (8h light/16h dark)


title: cat2-LD2-Rep1


title: cat2-SD4-Rep2

value: transferred to air (400 ppm) for 4 days in short day regime (8h light/16h dark)


title: Col0-LD2-Rep1


title: Col0-SD4-Rep2


title: Col0-LD2-Rep2


title: cat2-SD4-Rep1


title: Col0-SD2-Rep2

source_name: Col0, transferred to air (400 ppm) for 2 days in short day regime (8h light/16h dark)


title: Col0-SD4-Rep1


title: cat2-SD2-Rep1


title: Col0-SD2-Rep1


title: Col0-SD2-Rep3


title: seedling 24h light, (+Lin), rep3

status: Public on Mar 02 2012

city: East Lansing

first: Michael

middle: E

last: Ruckle

state: MI

address: S-208 Plant Biology, Michigan State University

department: Plant Research Labs

institute: Michigan State University

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 24h after a fluence rate shift from 0.5 to 60 µmol m-2 s-8

hyb_protocol: For each sample, 15μg of labeled target cRNA was purified, fragmented, and hybridized to the GeneChip® Arabidopsis ATH1 Genome Array (Affymetrix) as recommended by the manufacturer. The GeneChip arrays were then washed and stained using a GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. In the manuscript, the data were normalized using GCRMA in R/Bioconductor (data provided as supplementary file: GSE24517.txt.gz).  Posterior probabilities were calculated using an empirical Bayes analysis on a per gene, per time point, and per treatment basis.  Samples Light_0h_(-LIN)_1 through Light_0h_(-LIN)_4 were used as the reference samples for -Lin at 0.5 h and 1 h.  Samples Light_0h_(+LIN)_1 through Light_0h_(+LIN)_4 were used as the reference samples for +Lin at 0.5 h and 1 h.  Samples Light_0h_(-LIN)_5 through Light_0h_(-LIN)_8 were used as the reference samples for -Lin at 4 h and 24 h.  Samples Light_0h_(+LIN)_5 through Light_0h_(+LIN)_8 were used as the reference samples for +Lin at 4 h and 24 h.

source_name: Arabidopsis seedlings, treated with lincomycin, 24h after the fluence shift

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA for each sample using the GeneChip One-Cycle Target Labeling (Affymetrix, Santa Clara CA).

growth_protocol: Col-0 seeds were surface-sterilized with ethanol, and plated on Linsmaier and Skoog medium containing 2% sucrose and 0.5% Phytoblend (Caisson Laboratories).  0.5mM lincomycin was included to the growth medium to block chloroplast biogenesis.  Seeds were stratified for 4 d at 4°C, irradiated with 125µmol m-2 s-1 red light for 1h at 21°C, incubated in the dark for 23h at 21°C, and incubated for 6 d in 0.5 µmol m-2 s-1 blue plus red (BR) light at 21°C.

extract_protocol: RNA was extracted with Qiagen Rneasy Plant Mini Kit (Qiagen, Valencia, CA) performed according to the manufacturer's instructions.

treatment_protocol: After 6 days of growth in 0.5 µmol m-2 s-1 blue plus red (BR) light, seedlings grown in the presence (+Lin) or absence (-Lin) of lincomycin were transferred to 60 µmol m-2 s-1 BR light.   50-100 seedlings were collected, frozen, and stored at -80°C before (0 h) and 0.5 h, 1 h, 4 h, and 24 h after the 0.5 to 60 µmol m-2 s-1 BR-fluence-rate shift.

value: seedlings

value: 7 days old


title: seedling 0h light, (+Lin), rep8

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-4

source_name: Arabidopsis seedlings, treated with lincomycin, before the fluence shift


title: seedling 4h light, (+Lin), rep2

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 4h after a fluence rate shift from 0.5 to 60 µmol m-2 s-7

source_name: Arabidopsis seedlings, treated with lincomycin, 4h after the fluence shift


title: seedling 0h light, (+Lin), rep5

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-1


title: seedling 4h light, (+Lin), rep1

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 4h after a fluence rate shift from 0.5 to 60 µmol m-2 s-6


title: seedling 24h light, (+Lin), rep2

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 24h after a fluence rate shift from 0.5 to 60 µmol m-2 s-7


title: seedling 4h light, (+Lin), rep4

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 4h after a fluence rate shift from 0.5 to 60 µmol m-2 s-9


title: seedling 0h light, (+Lin), rep6

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-2


title: seedling 24h light, (-Lin), rep1

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 24h after a fluence rate shift from 0.5 to 60 µmol m-2 s-1

source_name: Arabidopsis seedlings, not treated with lincomycin, 24 h after the fluence shift


title: seedling 4h light, (+Lin), rep3

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 4h after a fluence rate shift from 0.5 to 60 µmol m-2 s-8


title: seedling 4h light, (-Lin), rep4

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 4h after a fluence rate shift from 0.5 to 60 µmol m-2 s-4

source_name: Arabidopsis seedlings, not treated with lincomycin, 4 h after the fluence shift


title: seedling 24h light, (-Lin), rep3

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 24h after a fluence rate shift from 0.5 to 60 µmol m-2 s-3


title: seedling 24h light, (+Lin), rep4

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 24h after a fluence rate shift from 0.5 to 60 µmol m-2 s-9


title: seedling 4h light, (-Lin), rep2

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 4h after a fluence rate shift from 0.5 to 60 µmol m-2 s-2


title: seedling 4h light, (-Lin), rep3

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 4h after a fluence rate shift from 0.5 to 60 µmol m-2 s-3


title: seedling 0h light, (-Lin), rep6

description: Gene expression data from 7 day old seedlings not treated with the  chloroplast biogenesis inhibitor lincomycin (-Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-2

source_name: Arabidopsis seedlings, not treated with lincomycin, before the fluence shift


title: seedling 0h light, (-Lin), rep7

description: Gene expression data from 7 day old seedlings not treated with the  chloroplast biogenesis inhibitor lincomycin (-Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-3


title: seedling 0h light, (-Lin), rep8

description: Gene expression data from 7 day old seedlings not treated with the  chloroplast biogenesis inhibitor lincomycin (-Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-4


title: seedling 1h light, (+Lin), rep1

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 1h after a fluence rate shift from 0.5 to 60 µmol m-2 s-6

source_name: Arabidopsis seedlings, treated with lincomycin, 1h after the fluence shift


title: seedling 0.5h light, (+Lin), rep2

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 0.5h after a fluence rate shift from 0.5 to 60 µmol m-2 s-4

source_name: Arabidopsis seedlings, treated with lincomycin, 0.5h after the fluence shift


title: seedling 1h light, (+Lin), rep2

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 1h after a fluence rate shift from 0.5 to 60 µmol m-2 s-7


title: seedling 0.5h light, (+Lin), rep3

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 0.5h after a fluence rate shift from 0.5 to 60 µmol m-2 s-5


title: seedling 1h light, (+Lin), rep4

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 1h after a fluence rate shift from 0.5 to 60 µmol m-2 s-9


title: seedling 4h light, (-Lin), rep1

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 4h after a fluence rate shift from 0.5 to 60 µmol m-2 s-1


title: seedling 0.5h light, (+Lin), rep4

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 0.5h after a fluence rate shift from 0.5 to 60 µmol m-2 s-6


title: seedling 24h light, (-Lin), rep2

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 24h after a fluence rate shift from 0.5 to 60 µmol m-2 s-2


title: seedling 24h light, (+Lin), rep1

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 24h after a fluence rate shift from 0.5 to 60 µmol m-2 s-6


title: seedling 0h light, (-Lin), rep3


title: seedling 1h light, (-Lin), rep1

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 1h after a fluence rate shift from 0.5 to 60 µmol m-2 s-1

source_name: Arabidopsis seedlings, not treated with lincomycin, 1 h after the fluence shift


title: seedling 0.5h light, (-Lin), rep1

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 0.5h after a fluence rate shift from 0.5 to 60 µmol m-2 s-1

source_name: Arabidopsis seedlings, not treated with lincomycin, 0.5 h after the fluence shift


title: seedling 0h light, (+Lin), rep3

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-3


title: seedling 0h light, (+Lin), rep2

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-2


title: seedling 0h light, (+Lin), rep4

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-4


title: seedling 0.5h light, (+Lin), rep1

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) 0.5h after a fluence rate shift from 0.5 to 60 µmol m-2 s-3


title: seedling 1h light, (-Lin), rep2

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 1h after a fluence rate shift from 0.5 to 60 µmol m-2 s-2


title: seedling 1h light, (-Lin), rep4

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 1h after a fluence rate shift from 0.5 to 60 µmol m-2 s-4


title: seedling 0.5h light, (-Lin), rep4

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 0.5h after a fluence rate shift from 0.5 to 60 µmol m-2 s-4


title: seedling 0h light, (+Lin), rep1

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-1


title: seedling 0.5h light, (-Lin), rep2

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 0.5h after a fluence rate shift from 0.5 to 60 µmol m-2 s-2


title: seedling 1h light, (-Lin), rep3

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 1h after a fluence rate shift from 0.5 to 60 µmol m-2 s-3


title: seedling 0.5h light, (-Lin), rep3

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 0.5h after a fluence rate shift from 0.5 to 60 µmol m-2 s-3


title: seedling 0h light, (-Lin), rep5

description: Gene expression data from 7 day old seedlings not treated with the  chloroplast biogenesis inhibitor lincomycin (-Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-1


title: seedling 0h light, (-Lin), rep2

description: Gene expression data from 7 day old seedlings not treated with the  chloroplast biogenesis inhibitor lincomycin (-Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-2


title: seedling 0h light, (-Lin), rep4

description: Gene expression data from 7 day old seedlings not treated with the  chloroplast biogenesis inhibitor lincomycin (-Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-4


title: seedling 0h light, (-Lin), rep1


title: affy_eyedisc_control_2

status: Public on Feb 23 2012

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on Affymetrix Drosophila Genome 2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with GeneChip 3000.

data_processing: Affymetrix Drosophila Genome 2 arrays were analyzed in R, version 2.11.1, using the packages affy (Gautier et al., 2004), version 1.26.1, and limma (Smyth et al., 2005), version 3.4.3. Normalization was done using rma. Annotation information for the probes was taken from Ensembl 63.

label_protocol: Biotin labelling was done with 200 ng total RNA with the Ambion MessageAmp III kit.

growth_protocol: Flies were raised at 25 degrees celsius.  Eye imaginal discs were dissected from late 3rd instar larvae.

extract_protocol: Eye imaginal discs (~500) were dissected as quickly as possible in cold SFX medium and transferred into a microcentrifuge tube containing 500 ul SFX medium followed by centrifugation for 3 min, 300 x g at 4ºC in a microcentrifuge. The supernatant was carefully removed and 0.5 ml of 0.25% Trypsin solution with EDTA (solution needs to be at 37ºC) added. After preincubating the discs for 1 min at 37ºC they were mechanically disrupted with a needle (size 25G1) by sucking the solution up and down 9 times without creating bubbles. The resulting cell clumps were then incubated for another min (maximum 4 min) at 37ºC and the trypsinization stopped by adding 1 ml of cold medium. The cells were centrifuged for 5 min, 300 x g at 4ºC in a microcentrifuge and the supernatant carefully removed. The resulting cell pellet was resuspended in 1 ml of Schneider medium with 10% FBS and submitted for cytometry.Dissociated cells (eye-antenna imaginal discs) were separated based on their GFP fluorescing properties and sorted directly into TRIZOL (100,000 cells per 1 ml of TRIZOL). RNA (from dissociated cells) was purified based on a standard protocol from DGRC (Indiana University). The RNA pellet was suspended in 30 ul of RNAse free water. RNA from third instar larvae was purified by grinding 20 larvae with a plastic pestle in RLT buffer (Qiagen, RNeasy Kit). After passing the suspension over a QIAshredder column (Qiagen) samples were processed as described in the manual. The RNA was analyzed with an RNA nano chip from Agilent.

treatment_protocol: E(z) RNAi utilized UAS-E(z)-RNAi (Bloomington 27993).  The Jarid2 mutant (mb) is Jarid2MB00996/TM3 (Bloomington 22958).

value: eye-antenna imaginal disc


title: affy_larvae_ez-rnai_2

value: 3rd instar larvae


title: affy_eyedisc_control_1


title: affy_eyedisc_jarid2-mb_1

value: jarid2 mutant


title: affy_eyedisc_jarid2-mb_2


title: affy_larvae_jarid2-mb_2


title: affy_larvae_ez-rnai_1


title: affy_larvae_control_1


title: WT_root induction.12h.28C_rep2

status: Public on Feb 10 2012

city: Tokyo

first: Munetaka

last: Sugiyama

address: Hakusan 3-7-1, Bunkyo-ku

department: Botanical Gardens, Graduate School of Science

institute: The University of Tokyo

hyb_protocol: Hybridization, washing, and staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Technical Manual (Affymetrix).

scan_protocol: Scanning procedure was conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Technical Manual (Affymetrix).

data_processing: GCOS (MAS5.0).

source_name: WT explant

label_protocol: Biotinylated cRNA was prepared from total RNA with the GeneChip 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and purified with the RNeasy Micro Kit (QIAGEN).

treatment_protocol: Explants from 4-day-old seedlings were cultured on B5 medium supplemented with 0.5 mg/L IBA at 28C for 12 h for the induction of lateral root formation.

tag: strain

value: Landsberg erecta

value: cultured explant


title: eyedisc_tumor_biological replicate2

status: Public on Feb 20 2012

city: San Juan de Alicante

first: andres

last: garelli

address: c/Ramón y Cajal s/n

country: Spain

institute: instituto de neurociencias de alicante

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Gene Chip microarray scan protocol (Affymetrix Expression Analysis Technical Manual).

data_processing: The Affymetrix data were analyzed using CARMAweb tools and the raw data were processed with the gcRMA method. Differentially expressed genes were detected by SAM (Significance Analysis of Microarrays) with a  0.1378 FDR, and using the Benjamini and Hochberg correction for multiple hypothesis testing.

source_name: Drosophila L3 tumoral eyedisc

label_protocol: After DNAse digestion with RNAse-free Dnase set (Qiagen), cDNA was synthesized and purified with the One cycle cDNA synthesis kit (Affymetrix). The cRNA obtained was marked and purified with the IVT kit (Affymetrix), and 15 ug of cRNA were hybridized to Drosophila Genome 2.0 arrays (Affymetrix).

growth_protocol: Drosophila larvae were grown at 25ºC until wandering stage

extract_protocol: larvae were rinsed in PBS. Discs were dissected in the same buffer, transferred to RNA later and total RNA was isolated with the Trizol reagent and the RNeasy Mini Kit (Qiagen)

value: ey-Gal4 GS(2)88A8 UAS-Dl/+

tag: developmental stage

value: larva 3


title: rrd1_root induction.12h.28C_rep3

source_name: rrd1 explant

value: rrd1 mutant

tag: tissue


title: rrd2_root induction.12h.28C_rep1

source_name: rrd2 explant

value: rrd2 mutant


title: eyedisc_control_biological replicate1

source_name: Drosophila L3 control eyedisc


title: eyedisc_control_biological replicate2


title: rrd2_root induction.12h.28C_rep3


title: rrd1_root induction.12h.28C_rep1


title: rid4_root induction.12h.28C_rep2

source_name: rid4 explant

value: rid4 mutant


title: WT_root induction.12h.28C_rep1

value: wild type


title: WT_root induction.12h.28C_rep3


title: rid4_root induction.12h.28C_rep3


title: rid4_root induction.12h.28C_rep1


title: eyedisc_tumor_biological replicate3


title: rrd1_root induction.12h.28C_rep2


title: rrd2_root induction.12h.28C_rep2


title: eyedisc_tumor_biological replicate1


title: affy_larvae_control_2


title: Msh gain-of-function, rep1B

status: Public on Feb 08 2012

city: Bethesda

first: Brian

last: Busser

state: Md

address: 10 Center Drive

institute: NHLBI/NIH

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4, UAS-GFP and UAS-msh targeting GFP and msh to Twist expressing cells staged to late stage 11/early stage 12.
msh 1B

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: Bioconductor affy package in conjunction with the goldenspike package of Choe et al. (Choe et al. Genome Biol. 2005 (PMID 15693945)). The mean expression summary value from 8 different summary methods was determined (see http://www.elwood9.net/spike for details). The Slou gain-of-function samples were normalized against WT rep1A-C; the Msh gain-of-function samples were normalized against WT rep2A-C.

source_name: mesodermal cells, Msh gain-of-function

label_protocol: Approximately 2-5 ug of total RNA was processed to produce biotinylated cRNA targets.

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

tag: cell type

value: mesodermal cells

tag: background

value: Msh gain-of-function

value: late stage 11/early stage 12


title: Msh gain-of-function, rep1C

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4, UAS-GFP and UAS-msh targeting GFP and msh to Twist expressing cells staged to late stage 11/early stage 12.
msh 1C


title: WT mesodermal cells, rep2B

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4 and UAS-GFP insertions targeting GFP to Twist expressing cells staged to late stage 11/early stage 12.
WT 2B

source_name: mesodermal cells, wild type


title: WT mesodermal cells, rep2A

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4 and UAS-GFP insertions targeting GFP to Twist expressing cells staged to late stage 11/early stage 12.
WT 2A


title: Slou gain-of-function, rep1C

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4, UAS-GFP and UAS-S59 insertions targeting GFP and Slou to Twist expressing cells staged to late stage 11/early stage 12.
S59 1C

source_name: mesodermal cells, Slou gain-of-function

value: Slou gain-of-function


title: WT mesodermal cells, rep2C

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4 and UAS-GFP insertions targeting GFP to Twist expressing cells staged to late stage 11/early stage 12.
WT 2C


title: Slou gain-of-function, rep1B

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4, UAS-GFP and UAS-S59 insertions targeting GFP and Slou to Twist expressing cells staged to late stage 11/early stage 12.
S59 1B


title: Slou gain-of-function, rep1A

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4, UAS-GFP and UAS-S59 insertions targeting GFP and Slou to Twist expressing cells staged to late stage 11/early stage 12.
S59 1A


title: Msh gain-of-function, rep1A

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4, UAS-GFP and UAS-msh targeting GFP and msh to Twist expressing cells staged to late stage 11/early stage 12.
msh 1A


title: WT mesodermal cells, rep1A

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4 and UAS-GFP insertions targeting GFP to Twist expressing cells staged to late stage 11/early stage 12.
WT 1A


title: WT mesodermal cells, rep1B

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4 and UAS-GFP insertions targeting GFP to Twist expressing cells staged to late stage 11/early stage 12.
WT 1B


title: WT mesodermal cells, rep1C

description:
FACS-sorted GFP-positive cells from single cell suspensions of embryos with twi-gal4 and UAS-GFP insertions targeting GFP to Twist expressing cells staged to late stage 11/early stage 12.
WT 1C


title: Col-0 at -0.25 MPa, biological rep 3

status: Public on Feb 03 2012

first: Verslues

middle: Edwin

last: Paul

address: 128 Sec. 2, Academia Rd, Nankang, Taipei 11529 Taiwan, R.O.C.

description: Gene expression data of Col-0 at control condition.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on the GeneChip 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: Columbia at control condition

growth_protocol: Seedlings were grown on agar plates containing half-strength MS salts and 2 mM MES buffer. No sugar was added to the media.  Plates were positioned vertically for seeding growth along the surface of the agar and were kept in a growth chamber at 25 C, continuous light at 85-100 micromol photons m-2 sec-1 and high (80-90%) relative humidity.

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Seven-day-old seedlings were transferred from agar plates of control media to agar plates of fresh control media (water potential -0.25 MPa) or low water potential agar plates (-1.2 MPa).  Low water potential plates were prepared by overlaying a solution of polyethylene glycol (molecular weight 8000) on the control agar plates and equilibrating overnight.  Details of PEG-agar plate preparation can be found in Verslues et al., Plant J 45:523-539 2006.  After transfer to treatment plates, seedlings were returned to growth chamber for 96 h before sample collection.

value: WT

value: whole seedlings

tag: treatment

value: control


title: hai1-2 at -1.2 MPa condition, biological rep 1

description: Gene expression data of hai1-2 at low water potential condition.

source_name: hai1 at stress condition

value: hai1-2 mutant

value: low water potential stress


title: hai1-2 at -1.2 MPa condition, biological rep 2


title: Col-0 at -1.2 MPa condition, biological rep 1

description: Gene expression data of Col-0 at low water potential condition.

source_name: Columbia at stress condition


title: Col-0 at -1.2 MPa condition, biological rep 2


title: hai1-2 at -1.2 MPa condition, biological rep 3


title: hai1-2 at -0.25 MPa, biological rep 1

description: Gene expression data of hai1-2 at control condition.

source_name: hai1 at control condition


title: Mtd biological rep 2

status: Public on Feb 01 2012

first: Paula

last: Watnick

address: 300 Longwood Avenue

department: Infectious Diseases

institute: Children's Hospital, Boston

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Data processing was done using Gene Spring software. Statistical significance was determined using a one-way ANOVA with a threshold p value of 0.05

source_name: Mtd biological rep 2

label_protocol: Affymetrix protocol

growth_protocol: flies were raised in standard fly media at 24 degrees C prior to use in experiments

extract_protocol: Flies were homogenized in Trizol reagent.  One hundred flies were used per array.  Total RNA was extracted once, treated with DNaseI, and extracted again.  This was supplied to a core facility for hybridization to Affymetrix GeneCHIP Drosophila 2.0

treatment_protocol: 4-5 day old flies were placed in a fly vial with a cellulose plug at the bottom.  2mls of LB broth containing 10E8 V. cholerae per ml was added to the plug.  Flies were allowed to ingest the LB mixture for 24 hours and then RNA was extracted

value: Whole fly


title: Mtd biological rep 1

source_name: Mtd biological rep 1


title: Col-0 at -0.25 MPa, biological rep 2


title: hai1-2 at -0.25 MPa, biological rep 3


title: Mtd biological rep 3

source_name: Mtd biological rep 3


title: Col-0 at -1.2 MPa condition, biological rep 3


title: eyedisc_control_biological replicate3


title: hai1-2 at -0.25 MPa, biological rep 2


title: Key biological rep 1

source_name: Key biological rep 1


title: CTL fly biological rep 3

source_name: CTL fly biological rep 3

value: wildtype


title: seedling 0h light, (+Lin), rep7

description: Gene expression data from 7 day old seedlings treated with the chloroplast biogenesis inhibitor lincomycin (+Lin) before (0 h) a fluence rate shift from 0.5 to 60 µmol m-2 s-3

source_name: Arabidopsis seedlings, treated with lincomycin, before the fluence shift

value: seedlings

value: 7 days old


title: CTL fly biological rep 2

source_name: CTL fly biological rep 2


title: Key biological rep 2

source_name: Key biological rep 2


title: Key biological rep 3

source_name: Key biological rep 3


title: CTL fly biological rep 1

source_name: CTL fly biological rep 1


title: Col-0 at -0.25 MPa, biological rep 1


title: GFP-positive cells from twi-GAL4 UAS-2EGFP embryos, replicate 2

status: Public on Jan 30 2012

first: Shaad

middle: M.

last: Ahmad

state: MD

address: Building 10, Room 7N311, 10 Center Drive MSC 1654

department: Systems Biology Center

institute: National Heart Lung and Blood Institute

description: FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: The data were analyzed with the Bioconductor affy package, using the mas5 command with default settings, and log2 transformed.

source_name: FACS-sorted Drosophila cells

label_protocol: Approximately 2-5 µg of total RNA was processed to produce biotinylated cRNA targets

growth_protocol: Embryos were aged to late stage 11-early stage 12 at 29°C.

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

value: FACS-sorted GFP positive cells

tag: cell derivation


title: GFP-positive cells from twi-GAL4 UAS-2EGFP embryos, replicate 3

value: single cell suspensions of late stage 11/early stage 12 embryos

value: twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells


title: GFP-positive cells from twi-GAL4 UAS-2EGFP embryos, replicate 1


title: GFP-positive cells from twi-GAL4 UAS-2EGFP/UAS-jumu embryos, replicate 3

description: FACS-sorted GFP positive cells from single cell suspensions of late stage 11/early stage 12 embryos with twi-GAL4 and UAS-2EGFP insertions that target GFP fluorescence to Twist expressing mesodermal cells, as well as a UAS-jumu insertion that constitutively expresses Jumu within these Twist expressing cells.