title: Arabidopsis root section, longitudinal zone 1, pH 5.7, replicate 1

description: Gene expression data from root developmental stage zone 1


title: Whole root - Std pH 48H_rep1

status: Public on Nov 23 2011

type: RNA

city: Durham

first: Anjali

middle: S

last: Iyer-Pascuzzi

state: NC

department: Biology

country: USA

institute: Duke University

description: Expression profile of whole root exposed to pH 5.7 for 48H

hyb_protocol: hybs with fragmented cRNA were preformed by Expression Analysis (Durham, NC)

scan_protocol: scans were preformed by Expression Analysis (Durham, NC)

data_processing: CHP files contain MAS 5.0 probe set summarizations using Affymetrix default analysis settings and global scaling as normalization method. The mean target intensity of each array was set to 250.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: whole roots transferred to std pH, 48H

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from 1 ug total RNA

growth_protocol: Seedlings were grown for 5 days on standard (pH 5.7) media before transfer either to standard or low pH (pH 4.6) media for the indicated time

extract_protocol: Total RNA was extracted with Qiagen Rneasy Plant mini kit according to manufacturer's instructions

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media containing 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. At 5 days, seedlings were transferred to standard pH (pH 5.7) or low pH (pH 4.6) media for the indicated time. Low pH media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 3mM DMG, 1% sucrose, 1% agar and adjusted to pH 4.6 with KOH. Standard pH is the same except pH is adjusted to 5.7.

tag: developmental stage

value: whole root

tag: ecotype

value: Columbia

tag: treatment

value: pH 5.7 for 48 hr


title: Arabidopsis root section, longitudinal zone 2, pH 5.7, replicate 1

description: Gene expression data from root developmental stage zone 2

source_name: root tissue

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

growth_protocol: Seedlings were grown for 5 days on standard (pH 5.7) media before transfer either to standard or low pH (pH 4.6) media for 24 hours prior to dissection

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media containing 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. At 5 days, seedlings were transferred to standard pH (pH 5.7) or low pH (pH 4.6) media for 24 hours prior to dissection. Low pH media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 3mM DMG, 1% sucrose, 1% agar and adjusted to pH 4.6 with KOH. Standard pH is the same except pH is adjusted to 5.7.

tag: longitudinal zone

tag: age

value: 6 day old roots


title: Whole root - Std pH 3H_rep2

description: Expression profile of whole root exposed to pH 5.7 for 3H

source_name: whole roots transferred to std pH, 3H

value: pH 5.7 for 3 hr


title: Arabidopsis root section, longitudinal zone 1, pH 4.6, replicate 2


title: Arabidopsis root cells, stele, pH 5.7, replicate 3

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the stele

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix two-cycle protocol from total RNA isolated from sorted cells

growth_protocol: Seedlings were grown for 5 days (described in Birnbaum et al. 2005) on pH 5.7 media before transfer either to pH 5.7 or pH 4.6 media for 24 hours prior to protoplasting and FACS sorting

extract_protocol: Total RNA was extracted with Qiagen Rneasy micro kit according to manufacturer's instructions

treatment_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on media containing 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. At 5 days, seedlings were transferred to standard pH (pH 5.7) or low pH (pH 4.6) media for 24 hours prior to protoplasting and FACS sorting. Low pH media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 3mM DMG, 1% sucrose, 1% agar and adjusted to pH 4.6 with KOH. Standard pH is the same except pH is adjusted to 5.7.

tag: cell type

value: stele

value: cells from 6 day-old roots

tag: marker line


title: Arabidopsis root section, longitudinal zone 2, pH 4.6, replicate 2


title: Whole root - Std pH 1H_rep1

description: Expression profile of whole root exposed to pH 5.7 for 1H

source_name: whole roots transferred to std pH, 1H

value: pH 5.7 for 1 hr


title: Arabidopsis root section, longitudinal zone 2, pH 4.6, replicate 1


title: Arabidopsis root section, longitudinal zone 3, pH 4.6, replicate 1

description: Gene expression data from root developmental stage zone 3


title: Arabidopsis root section, longitudinal zone 1, pH 5.7, replicate 2


title: Arabidopsis root cells, stele, pH 5.7, replicate 2


title: Arabidopsis root cells, stele, pH 5.7, replicate 1


title: Arabidopsis root cells, epidermis and lateral root cap, pH 5.7, replicate 1

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the epidermis and lateral root cap

value: epidermis and lateral root cap


title: Arabidopsis root cells, endodermis and quiescent center, pH 4.6, replicate 2

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the endodermis and quiescent center

value: endodermis and quiescent center


title: Arabidopsis root cells, stele, pH 4.6, replicate 2


title: Arabidopsis root cells, cortex, pH 5.7, replicate 2

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the cortex

value: cortex


title: Arabidopsis root cells, cortex, pH 4.6, replicate 2


title: Arabidopsis root cells, stele, pH 4.6, replicate 1


title: Arabidopsis root cells, endodermis and quiescent center, pH 4.6, replicate 3


title: Arabidopsis root cells, endodermis and quiescent center, pH 5.7, replicate 1


title: Arabidopsis root cells, epidermis and lateral root cap, pH 5.7, replicate 3


title: Arabidopsis root cells, cortex, pH 5.7, replicate 1


title: Arabidopsis root cells, cortex, pH 4.6, replicate 1


title: Arabidopsis root cells, epidermis and lateral root cap, pH 4.6, replicate 2


title: Arabidopsis root cells, columella root cap, pH 5.7, replicate 2

source_name: Protoplasted and FACS sorted Arabidopsis root cells from the columella root cap

value: columella root cap


title: Arabidopsis root cells, epidermis and lateral root cap, pH 5.7, replicate 2


title: Arabidopsis root cells, columella root cap, pH 5.7, replicate 3


title: Arabidopsis root cells, cortex, pH 4.6, replicate 3


title: Arabidopsis root cells, endodermis and quiescent center, pH 5.7, replicate 2


title: Arabidopsis root cells, endodermis and quiescent center, pH 5.7, replicate 3


title: Arabidopsis root cells, epidermis and lateral root cap, pH 4.6, replicate 3


title: Arabidopsis root cells, cortex, pH 5.7, replicate 3


title: Arabidopsis root cells, stele, pH 4.6, replicate 3


title: Arabidopsis root cells, columella root cap, pH 4.6, replicate 1


title: Arabidopsis root cells, columella root cap, pH 5.7, replicate 1


title: Arabidopsis root cells, endodermis and quiescent center, pH 4.6, replicate 1


title: Arabidopsis root cells, epidermis and lateral root cap, pH 4.6, replicate 1


title: Arabidopsis root cells, columella root cap, pH 4.6, replicate 3


title: Arabidopsis root cells, columella root cap, pH 4.6, replicate 2


title: Drosophila_3d_Brain_CAA/G105_2

status: Public on Nov 22 2011

city: Philadelphia

first: Bonini

last: Nancy

state: PA

address: 415 S University Ave

institute: University of Pennsylvania

description: Age-matched control flies expressing non-toxic trinucleotide repeats

hyb_protocol: Encore Biotin Module  (NuGEN)

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

data_processing: Normalization of probe signal intensity levels across arrays was performed using the GCRMA algorithm implemented in Partek Genomic suite 6.2 beta.

organism: Drosophila melanogaster

source_name: 3d female fly brain expressing CAA/G105

label_protocol: Encore Biotin Module  (NuGEN)

growth_protocol: Flies were raised at 25C with 12hr/12hr light-dark cycle.

extract_protocol:
Total brain RNA was extracted and purified using TRIzol reagent (Invitrogen) and the RNeasy Mini system (Qiagen), and treated with RNase-free DNase I (Qiagen).
cDNA was amplifed using Ovation Pico WTA system (NuGEN)

treatment_protocol: Female fly brain tissue was dissected in cold phosphate buffered saline (PBS) and stored in Trizol reagent at -80C at 3 d.

tag: gender

value: female

tag: tissue

value: brain

tag: genotype

value: elav-GAL4; UAS-DsRed-CAA/G105 (2x)


title: Drosophila_3d_Brain_CAA/G105_3


title: Drosophila_3d_Brain_CAG100_2

description: flies expressing toxic CAG100 repeats

source_name: 3d female fly brain expressing CAG100

value: elav-GAL4; UAS-DsRed-CAG100 (5x)


title: Drosophila_3d_Brain_CAG100_3

description: flies expressing toxic CAG100 repeats


title: Drosophila_3d_Brain_CAG100_4

description: flies expressing toxic CAG100 repeats


title: Drosophila_3d_Brain_CAA/G105_4


title: Drosophila_3d_Brain_CAG0_3

description: age-matched control flies expressing only DsRed reporter

source_name: 3d female fly brain expressing CAG0

value: elav-GAL4; UAS-DsRed-CAG0


title: Drosophila_3d_Brain_CAG0_4


title: Drosophila_3d_Brain_CAG0_2


title: Drosophila_3d_Brain_CAA/G105_1


title: Drosophila_DL1 cells_nbr RNAi 5

status: Public on Nov 01 2011

description: 3766_24277_nbr5 Drosophila_2_(Drosophila_2)

hyb_protocol: Encore™ Biotin Module  (NuGEN)

source_name: DL1 cells nbr RNAi

label_protocol: Encore™ Biotin Module  (NuGEN)

growth_protocol: DL1 cells were grown at 25˚C.

extract_protocol:
Total RNA was extracted and purified using TRIzol reagent (Invitrogen)
cDNA was amplifed using Ovation Pico WTA system (NuGEN)

treatment_protocol: The cells were bathed in dsRNA to renilla or nbr, and grown at 25˚C for five days.

tag: days after dsrna bathing

tag: RNAi

value: nbr/CG9247 dsRNA


title: Drosophila_3d_Brain_CAG0_1


title: Drosophila_DL1 cells_control RNAi 2

description: 3766_24269_Renilla2 Drosophila_2_(Drosophila_2)

source_name: DL1 cells control RNAi

value: renilla dsRNA


title: Drosophila_DL1 cells_control RNAi 3

description: 3766_24270_Renilla3 Drosophila_2_(Drosophila_2)


title: Drosophila_DL1 cells_nbr RNAi 2

description: 3766_24274_nbr2 Drosophila_2_(Drosophila_2)


title: Drosophila_3d_Brain_CAG100_1

description: flies expressing toxic CAG100 repeats


title: Drosophila_DL1 cells_nbr RNAi 4

description: 3766_24276_nbr4 Drosophila_2_(Drosophila_2)


title: Drosophila_DL1 cells_control RNAi 4

description: 3766_24271_Renilla4 Drosophila_2_(Drosophila_2)


title: Drosophila_DL1 cells_nbr RNAi 3

description: 3766_24275_nbr3 Drosophila_2_(Drosophila_2)


title: Drosophila_DL1 cells_nbr RNAi 1

description: 3766_24273_nbr1 Drosophila_2_(Drosophila_2)


title: NSL1_RNAi_replicate2

status: Public on Oct 29 2011

city: Munich

first: Christian

last: Feller

address: Schillerstraße 44

department: Molecular Biology

country: Germany

institute: Adolf-Butenandt Institute at the LMU University Munich

description: Gene expression data from NSL1 RNAi-treated S2 cells.

hyb_protocol: Performed by Dietmar Martin and colleagues (Laboratory of Patrick Cramer, Gene Center, Munich, Germany).

data_processing: Raw signals were processed using the R package “gcrma” (Wu and Irizarry, 2005).

source_name: S2 cell line, NSL1 dsRNA

extract_protocol: RNA was isolated using Trizol (Invitrogen), followed by a purification using the RNeasy kit (Quiagen). RNA quality was checked using the Bioanalyzer (Agilent).

treatment_protocol: 1.5x10exp6 cells were treated with 10 µg dsRNA targeted against NSL1 or glutathione-S-transferase (control) for 1 hour in serum-free medium. Then, serum-containing Schneider medium was added, and cells were incubated for 6 days at 26°C before RNA extraction.

tag: cell line

tag: dsrna treatment

value: NSL1 dsRNA


title: GST_RNAi_replicate3

description: Gene expression data from control RNAi-treated S2 cells.

scan_protocol: Performed by Dietmar Martin and colleagues (Laboratory of Patrick Cramer, Gene Center, Munich, Germany).

source_name: S2 cell line, control dsRNA

value: GST dRNA


title: Drosophila_DL1 cells_control RNAi 5

description: 3766_24272_Renilla5 Drosophila_2_(Drosophila_2)


title: Drosophila_DL1 cells_control RNAi 1

description: 3766_24268_Renilla1 Drosophila_2_(Drosophila_2)


title: GST_RNAi_replicate2

label_protocol: Performed by Dietmar Martin and colleagues (Laboratory of Patrick Cramer, Gene Center, Munich, Germany).


title: NSL1_RNAi_replicate1


title: GST_RNAi_replicate1


title: Whole root - low pH 30min_rep1

description: Expression profile of whole root exposed to pH 4.6 for 30 min

source_name: whole roots transferred to low pH, 30min

value: whole root

value: Columbia

value: pH 4.6 for 30 min


title: Hypoxic-seedlings, Col-0, rep 2

status: Public on Oct 23 2011

city: Riverside

first: Takeshi

last: Fukao

state: CA

address: Department of Botany and Plant Sciences

institute: University of California, Riverside

description:
Col-0 seedlings treated with hypoxic conditions for 2h
Hypoxia_Col-0_2

hyb_protocol: Hybridization of 12 μg of biotin-labelled cRNA to each Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

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

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: Hypoxic-seedlings, Col-0

label_protocol: Biotin-labelled cRNA was synthesized from 500 ng total RNA with the Affymetrix 3’ IVT Express Labelling kit (Santa Clara, CA).

growth_protocol: Seeds used for this analysis  were after-ripened seeds obtained from plants grown at the same time within the same tray within the same controlled environment chambers to minimize differences in pre-harvest history. For pre-germinated seeds samples, seeds were surface sterilized for 5 min in 5% (v/v) bleach and then washed twice in distilled water. The seeds were then plated on square plates containing 0.5×Murashige and Skoog (MS, Sigma-Aldrich) salt mixture in 1% (w/v) bacto-agar and stratified at 4˚C for 48 h. Plates were incubated vertically at 22°C in 150 μmol m−2 s−1 constant light for 24 h and then whole seeds were sampled for total RNA extraction. For hypoxia-treated seedling samples, seeds were surface sterilized with 95 % (v/v) ethanol for 5 min, followed by 10 min submergence in bleach solution (20 % (v/v) bleach and 0.1 % (v/v) Tween-20), and finally rinsed three times with sterile water. Seeds were stored at 4°C for 3 days, and then plated on solid MS plates (0.43 % (w/v) Murashigi Skoog (MS) salts (Sigma, St. Louis, MO), 0.4 % (w/v) phytage, pH 5.75l (Sigma), 1 % (w/v) sucrose, pH 5.7), and placed at a vertical orientation in a growth chamber (Percival Scientific, Inc., http://www.percival-scientific.com/; model CU36L5C8) under long day conditions (16 h light at ~80 µmol photons m-2 s-1/ 8 h darkness) at 23 °C for 7 days.

extract_protocol: Total RNA was extracted by using QIAGEN RNeasy Plant Mini kit according to the manufacture's protocol. RNase-Free DNase treatment was conducted during the column purification process.

treatment_protocol: Hypoxia treatment commenced at the end of the 16 h light cycle under 6.5 µmol s–1 m–2 light, in open or sealed chambers. For hypoxia, 99.995% argon gas was bubbled through water and into the chamber for 2 h. Control plants were exposed to the same light and temperature conditions but maintained in air. Whole seedlings were frozen under liquid nitrogen within 3 min of release from treatment and stored at -80 oC until use.

value: seedlings

value: 7 d old

value: hypoxic conditions


title: Hypoxic-seedlings, Col-0, rep 1

description:
Col-0 seedlings treated with hypoxic conditions for 2h
Hypoxia_Col-0_1


title: Aerobic-seedlings, Col-0, rep 2

description:
Col-0 seedlings treated with aerobic (normal) conditions for 2h
Air_Col-0_2

source_name: Aerobic-seedlings, Col-0

value: aerobic (normal) conditions


title: Aerobic-seedlings, prt6-1, rep 1

description:
prt6-1 seedlings treated with aerobic (normal) conditions for 2h
Air_prt6_1

source_name: Aerobic-seedlings, prt6-1


title: Hypoxic-seedlings, prt6-1, rep 1

description:
prt6-1 seedlings treated with hypoxic conditions for 2h
Hypoxia_prt6_1

source_name: Hypoxic-seedlings, prt6-1


title: Hypoxic-seedlings, ate1 ate 2, rep 1

description:
ate1 ate2 seedlings treated with hypoxic conditions for 2h
Hypoxia_ate1 ate2_1

source_name: Hypoxic-seedlings, ate1 ate 2

value: ate1 ate2


title: Hypoxic-seedlings, prt6-1, rep 2

description:
prt6-1 seedlings treated with hypoxic conditions for 2h
Hypoxia_prt6_2


title: Pre-germinated seeds, Col-0, rep 3

description:
Col-0 seeds imbibed for 24 h
Seed_Col-0_3

source_name: Pre-germinated seeds, Col-0

value: Pre-germinated seeds

value: imbibed for 24 h


title: Pre-germinated seeds, Col-0, rep 1

description:
Col-0 seeds imbibed for 24 h
Seed_Col-0_1


title: Pre-germinated seeds, prt6-1, rep 1

description:
prt6-1 seeds imbibed for 24 h
Seed_prt6-1_1

source_name: Pre-germinated seeds, prt6-1


title: Aerobic-seedlings, Col-0, rep 1

description:
Col-0 seedlings treated with aerobic (normal) conditions for 2h
Air_Col-0_1


title: Aerobic-seedlings, ate1 ate2, rep 1

description:
ate1 ate2 seedlings treated with aerobic (normal) conditions for 2h
Air_ate1 ate2_1

source_name: Aerobic-seedlings, ate1 ate2


title: Pre-germinated seeds, Col-0, rep 2

description:
Col-0 seeds imbibed for 24 h
Seed_Col-0_2


title: amiRAP_aerobic_rep1

status: Public on Oct 14 2011

city: Pisa

first: Francesco

last: Licausi

address: Via Mariscoglio 34

department: Institute of Life Sciences

country: Italy

institute: Scuola Superiore Sant'Anna

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: GC-RMA algorithm

label: Biotin

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Seeds were sown in 6-cm diameter pots containing moisted Arabidopsis soil. The seeds were stratified at 4°C in the dark for 2 days and then the pots were moved in a growth chamber at short photoperiodic conditions (8h light 16 h darkness) with 18°C in the night and 22°C in the day.

extract_protocol: Total RNA was extracted from whole 5-week old plants using the RNeasy kit (Qiagen). RNA quality was assessed by agarose gel electrophoresis and spectrophotometry. RNA was processed for use on Affymetrix Arabidopsis Genome GeneChip arrays.

treatment_protocol: Plants were kept in the dark at a 21% O2 atmosphere for 1.5h starting the treatment at 10am in the morning, 2h after the start of the day

value: Columbia 0

value: 5-week old

value: aerobic


title: Aerobic-seedlings, ate1 ate2, rep 2

description:
ate1 ate2 seedlings treated with aerobic (normal) conditions for 2h
Air_ate1 ate2_2


title: amiRAP_aerobic_rep2


title: amiRAP_hypoxic_rep1

treatment_protocol: Plants were kept in the dark at a 1% O2 atmosphere for 1.5h starting the treatment at 10am in the morning, 2h after the start of the day

value: hypoxia


title: Pre-germinated seeds, prt6-1, rep 3

description:
prt6-1 seeds imbibed for 24 h
Seed_prt6-1_3


title: HARAP_hypoxic_rep3


title: amiRAP_hypoxic_rep3


title: Pre-germinated seeds, prt6-1, rep 2

description:
prt6-1 seeds imbibed for 24 h
Seed_prt6-1_2


title: amiRAP_hypoxic_rep2


title: amiRAP_aerobic_rep3


title: HARAP_hypoxic_rep2


title: HARAP_aerobic_rep2


title: HARAP_hypoxic_rep1


title: HARAP_aerobic_rep3


title: HARAP_aerobic_rep1


title: wildtype_aerobic_rep3

value: wild type


title: wildtype_aerobic_rep2


title: wildtype_hypoxic_rep3


title: wildtype_aerobic_rep1


title: Kas-1 -Fe 24h, biological rep3

status: Public on Oct 06 2011

city: Lincoln

first: Brian

middle: M

last: Waters

state: Nebraska

address: 279 Plant Sciences Hall

department: Agronomy and Horticulture

institute: University of Nebraska-Lincoln

description:
BrW_ATH1_121410_18_KmR24.CEL
Gene expression data from roots after 24h in -Fe solution

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 Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data was analyzed with GeneSpringX (Agilent) using the MAS5 algorithm

source_name: Arabidopsis Kas-1 roots after 24h in -Fe nutrient solution

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds were planted onto rockwool loosely packed into 1.5 ml centrifuge tubes with the bottoms removed. The tubes were floated in foam rafts in containers of nutrient solution. After 10 days, seedlings were transferred to holes in lids of containers contain nutrient solution with constant aeration for an additional 14 days before treatments.

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

treatment_protocol: Roots were collected after 24 or 48 h of exposure to complete (with 50 micromolar of Fe-EDDHA) or –Fe (without added Fe) solutions.

value: roots

value: 30 days old plants

tag: growth protocol

value: -Fe solution

tag: time


title: wildtype_hypoxic_rep2


title: Kas-1 -Fe 24h, biological rep2

description:
BrW_ATH1_121410_17_KmR24.CEL
Gene expression data from roots after 24h in -Fe solution


title: Tsu-1 +Fe 24h, biological rep1

description:
BrW_ATH1_121410_01_TpR24.CEL
Gene expression data from roots after 24h in complete solution

source_name: Arabidopsis Tsu-1 roots after 24h in complete nutrient solution

value: complete solution


title: Kas-1 +Fe 24h, biological rep1

description:
BrW_ATH1_121410_13_KpR24.CEL
Gene expression data from roots after 24h in complete solution

source_name: Arabidopsis Kas-1 roots after 24h in complete nutrient solution


title: Kas-1 +Fe 24h, biological rep2

description:
BrW_ATH1_121410_14_KpR24.CEL
Gene expression data from roots after 24h in complete solution


title: Tsu-1 -Fe 48h, biological rep3

description:
BrW_ATH1_121410_12_TmR48.CEL
Gene expression data from roots after 48h in -Fe solution

source_name: Arabidopsis Tsu-1 roots after 48h in -Fe nutrient solution


title: Kas-1 -Fe 48h, biological rep3

description:
BrW_ATH1_121410_24_KmR48.CEL
Gene expression data from roots after 48h in -Fe solution

source_name: Arabidopsis Kas-1 roots after 48h in -Fe nutrient solution


title: wildtype_hypoxic_rep1


title: Tsu-1 -Fe 48h, biological rep1

description:
BrW_ATH1_121410_10_TmR48.CEL
Gene expression data from roots after 48h in -Fe solution


title: Kas-1 +Fe 24h, biological rep3

description:
BrW_ATH1_121410_15_KpR24.CEL
Gene expression data from roots after 24h in complete solution


title: Kas-1 -Fe 24h, biological rep1

description:
BrW_ATH1_121410_16_KmR24.CEL
Gene expression data from roots after 24h in -Fe solution


title: Tsu-1 -Fe 24h, biological rep2

description:
BrW_ATH1_121410_05_TmR24.CEL
Gene expression data from roots after 24h in -Fe solution

source_name: Arabidopsis Tsu-1 roots after 24h in -Fe nutrient solution


title: Tsu-1 -Fe 24h, biological rep3

description:
BrW_ATH1_121410_06_TmR24.CEL
Gene expression data from roots after 24h in -Fe solution


title: SOS1_leaf_0mM NaCl_rep1 (wt + tg set)

city: Wuhan

first: Zhulong

last: Chan

state: Hubei

address: Wuchang District, Moshan

country: China

institute: Wuhan Botanic Garden, Chinese Academy of Sciences

description: Gene expression data in Col(gl) in the absence of salt

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: All the Affymetrix data files produced with Affymetrix GCOS software (*.CEL files) were analyzed using Bioconductor, a public source software for the analyses of genomic data rooted in the statistical computing environment R. The data were normalized by robust multioiarray normalization of probe-level data with RMA and analyzed using affylmGUI running on R software.

source_name: SOS1 OX plant, 0mM NaCl, 6 d

label_protocol: Ten µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Seeds of both transgenic and wild type plants were sown as described above with two replicate pots for each genotype and salt combination. Plants were grown at 23/18 °C in the growth chamber under a short-day cycle (10h light/14 h dark) at 350 μmol m-2s-1 and 70% relative humidity in order to increase seedling leaf area and growth while not promoting bolting. Sampling time was performed at 20 DAS by collecting developed but not senescent leaves (about 0.5cm width × 1.5cm length) from at least 15 seedlings.

extract_protocol: Total RNA was extracted and purified using QIAGEN-RNeasy Mini Kit according to guidelines specified by the manufacturer.

treatment_protocol: Plants subjected to salt stress were watered with NaCl solution which was dissolved in ½ Strength Hoagland Solution. Salt treatment started at 14 DAS . Plants were watered from below to field capacity and then sprayed with the same concentration of NaCl solution from the top, ensuring adequate leaching and preventing excess salinity. The concentrations of NaCl supplementation were increased stepwise by 50 mM every 2 days for each line, to the indicated maximum (0, 100 mM). Plants were then watered every 2 days with or without NaCl at the indicated concentrations. The flats were rotated in the growth chamber everyday to minimize the effect of growth condition.

value: leaf

value: 20 days after sowing

tag: genetic background

value: Col(gl)

value: 0mM NaCl


title: SOS1_leaf_100mM NaCl_rep2 (wt + tg set)

description: Gene expression data in Col(gl) in the presence of salt

source_name: SOS1 OX plant, 100mM NaCl, 6 d

value: 100mM NaCl


title: Tsu-1 +Fe 24h, biological rep3

description:
BrW_ATH1_121410_03_TpR24.CEL
Gene expression data from roots after 24h in complete solution


title: M6PR transgenic_leaf_100mM NaCl_rep2 (wt + tg set)

description: Gene expression data in Ws in the presence of salt

source_name: M6PR OX plant, 100mM NaCl, 6 d


title: Kas-1 -Fe 48h, biological rep1

description:
BrW_ATH1_121410_22_KmR48.CEL
Gene expression data from roots after 48h in -Fe solution


title: Tsu-1 -Fe 48h, biological rep2

description:
BrW_ATH1_121410_11_TmR48.CEL
Gene expression data from roots after 48h in -Fe solution


title: SOS1_leaf_100mM NaCl_rep1 (wt + tg set)


title: Kas-1 -Fe 48h, biological rep2

description:
BrW_ATH1_121410_23_KmR48.CEL
Gene expression data from roots after 48h in -Fe solution


title: Tsu-1 -Fe 24h, biological rep1

description:
BrW_ATH1_121410_04_TmR24.CEL
Gene expression data from roots after 24h in -Fe solution


title: M6PR transgenic_leaf_0mM NaCl_rep2 (wt + tg set)

description: Gene expression data in Ws in the absence of salt

source_name: M6PR OX plant, 0mM NaCl, 6 d


title: SOS1_leaf_0mM NaCl_rep2 (wt + tg set)


title: M6PR transgenic_leaf_0mM NaCl_rep1 (wt + tg set)


title: M6PR transgenic_leaf_100mM NaCl_rep1 (wt + tg set)


title: CBF3_leaf_100mM NaCl_rep2 (wt + tg set)

description: Gene expression data in Col in the presence of salt

source_name: CBF3 OX plant, 100mM NaCl, 6 d

value: Ws


title: CBF3_leaf_0mM NaCl_rep1 (wt + tg set)

description: Gene expression data in Col in the absence of salt

source_name: CBF3 OX plant, 0mM NaCl, 6 d


title: CBF3_leaf_0mM NaCl_rep2 (wt + tg set)


title: CBF3_leaf_100mM NaCl_rep1 (wt + tg set)


title: Base of Col, biological rep3

status: Public on Sep 30 2011

city: Vienna

first: Stefanie

last: Suer

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description:
Col-base_Rep3
Gene expression data from stem tissue at the base of wildtype stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.

hyb_protocol: Following fragmentation, the aRNAs were hybridized for 16 hr at 45C on the GeneChip ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed using the RMA method on the Bioconductor statistical package (R).

source_name: wildtype stem base

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown for 3 weeks on short days (8 hours light, 16 hours dark) under standard conditions and then switched to long days (16 hours light, 8 hours dark).

extract_protocol: Total RNA was extracted from frozen, grinded plant material by agitating with 1 ml of TRIZOL. After centrifuging, 900 µl of the supernatant was transferred to fresh tubes, containing 200 µl of chloroform each. Phases were separated by centrifugation for 15 min at maximum speed in a table centrifuge. Subsequenty, the aqueous layer was transferred to 500 µl isopropanol. RNA was precipitated and the pellet washed with 70% ethanol, prior to column purification using the RNeasy Mini Kit in combination with the RNase-Free DNase Set (QIAGEN) and following the manufacturer's instructions.

treatment_protocol: 15-20 cm tall wildtype Columbia and wox4-1 plants with a first internode of at least 3.5 cm in length were used for the experiment. Stem fragments of 0.5 cm in length were harvested from the base of Arabidopsis plants and from the region between 1.5 and 2.0 cm above the uppermost rosette leaf, respectively. RNA was extracted from 3 biological replicates per plant line and sample type, each consisting of a pool of 13-17 stem samples.

value: base of stem

value: Columbia

value: WT

tag: height


title: Stem of Col, biological rep1

description:
Col-stem_Rep1
Gene expression data from stem tissue from the first internode of wildtype stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.

source_name: wildtype stem, first internode

value: first internode of stem

tag: ecotype


title: Base of Col, biological rep1

description:
Col-base_Rep1
Gene expression data from stem tissue at the base of wildtype stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.


title: Stem of wox4, biological rep3

description:
wox4-stem_Rep3
Gene expression data from stem tissue from the first internode of wox4 stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.

source_name: wox4 stem, first internode

value: wox4-1 mutant


title: Stem of Col, biological rep2

description:
Col-stem_Rep2
Gene expression data from stem tissue from the first internode of wildtype stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.


title: Stem of Col, biological rep3

description:
Col-stem_Rep3
Gene expression data from stem tissue from the first internode of wildtype stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.


title: piwi trans-heterozygous mutant ovaries, repeat 2

status: Public on Sep 29 2011

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description:
piwi1_piwi2_R2
Transposable elements expression data from piwi trans-heterozygous mutant ovaries.

hyb_protocol: 10 micrograms of biotin-labeled cRNA were hybridized for 16 hrs onto the GeneChip Drosophila Genome 2.0 Arrays (Affymetrix).

scan_protocol: Affymetrix 7G GeneArray scanner.

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Genespring GX11 (Agilent) software. No further adjustments were made to the data in the table.

source_name: fly ovaries, piwi trans-heterozygous mutant

label_protocol: 100 ng total RNA was converted to biotinylated cRNA using the Affymetrix 3' IVT Express kit.

extract_protocol: The Qiagen RNeasy Plus Kit was used to extract total cellular RNA according to the manufacturer's protocol.

value: piwi trans-heterozygous

value: ovary

tag: sample type

value: mutant


title: aub heterozygous control ovaries, repeat 1

description:
aubHN2_CyO_R1
Transposable elements expression data from aub heterozygous control ovaries.

source_name: fly ovaries, aub heterozygous control

value: aub heterozygous

value: control


title: aub trans-heterozygous mutant ovaries, repeat 1

description:
aubHN2_aubQC42_R1
Transposable elements expression data from aub trans-heterozygous mutant ovaries.

source_name: fly ovaries, aub trans-heterozygous mutant

value: aub trans-heterozygous


title: Base of wox4, biological rep3

description:
wox4-base_Rep3
Gene expression data from stem tissue at the base of wox4-1 stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.

source_name: wox4 stem base


title: aub trans-heterozygous mutant ovaries, repeat 2

description:
aubHN2_aubQC42_R2
Transposable elements expression data from aub trans-heterozygous mutant ovaries.


title: Base of wox4, biological rep1

description:
wox4-base_Rep1
Gene expression data from stem tissue at the base of wox4-1 stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.


title: vret homozygous mutant ovaries, repeat 2

description:
vret148-60_vret148-60_R2
Transposable elements expression data from vret homozygous mutant ovaries.

source_name: fly ovaries, vret homozygous mutant

value: vret homozygous


title: piwi trans-heterozygous mutant ovaries, repeat 1

description:
piwi1_piwi2_R1
Transposable elements expression data from piwi trans-heterozygous mutant ovaries.


title: vret heterozygous control ovaries, repeat 1

description:
vret148-60_TM6b_R1
Transposable elements expression data from vret heterozygous control ovaries.

source_name: fly ovaries, vret heterozygous control

value: vret heterozygous


title: vret homozygous mutant ovaries, repeat 1

description:
vret148-60_vret148-60_R1
Transposable elements expression data from vret homozygous mutant ovaries.


title: Stem of wox4, biological rep1

description:
wox4-stem_Rep1
Gene expression data from stem tissue from the first internode of wox4 stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.


title: piwi heterozygous control ovaries, repeat 1

description:
piwi1_CyO_R1
Transposable elements expression data from piwi heterozygous control ovaries.

source_name: fly ovaries, piwi heterozygous control

value: piwi heterozygous


title: Base of wox4, biological rep2

description:
wox4-base_Rep2
Gene expression data from stem tissue at the base of wox4-1 stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.


title: Base of Col, biological rep2

description:
Col-base_Rep2
Gene expression data from stem tissue at the base of wildtype stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.


title: piwi heterozygous control ovaries, repeat 2

description:
piwi1_CyO_R2
Transposable elements expression data from piwi heterozygous control ovaries.


title: Stem of wox4, biological rep2

description:
wox4-stem_Rep2
Gene expression data from stem tissue from the first internode of wox4 stems.
Stem sections of 49 to 58 days old plants, harvested when the plant reached a height of 15 to 20 cm.
Pool of 13-17 stem samples.


title: vret heterozygous control ovaries, repeat 2

description:
vret148-60_TM6b_R2
Transposable elements expression data from vret heterozygous control ovaries.


title: aub heterozygous control ovaries, repeat 2

description:
aubHN2_CyO_R2
Transposable elements expression data from aub heterozygous control ovaries.


title: Body 48 hr fasted 4

status: Public on Sep 24 2011

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: Body missing the head

hyb_protocol: Nugen standard array protocol for cDNA hybridization (Nugen user guide)

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Body 48 hr fasted 3

label_protocol: Nugen’s FL-Ovation cDNA Biotin Module V2 protocol (Cat.# 4200-12)

extract_protocol: RNEasy Qiagen, amplified with Nugen Ovation® RNA Amplification System V2 (Cat.# 3100-12)

value: Body

tag: pool

tag: treatment

value: fasting


title: Body 24 hr fasted 4

description: Body missing the head

source_name: Body 24 hr fasted 4


title: Body 24 hr fasted 5

description: Body missing the head

source_name: Body 24 hr fasted 5


title: Body 0 hr fasted 4

description: Body missing the head

source_name: Body 0 hr fasted 4

value: 0 h

value: baseline


title: Body 0 hr fasted 5

description: Body missing the head

source_name: Body 0 hr fasted 5


title: Body 48 hr fasted 3

description: Body missing the head


title: Body 24 hr fasted 3

description: Body missing the head

source_name: Body 24 hr fasted 3


title: Body 48 hr fasted 2

description: Body missing the head

source_name: Body 48 hr fasted 2


title: Body 0 hr fasted 1

description: Body missing the head

source_name: Body 0 hr fasted 1


title: Palp-Proboscis 0 hr fasted 5

description: palp and proboscis combined

source_name: Palp-Proboscis 0 hr fasted 5

value: Palp


title: Palp-Proboscis 48 hr fasted 4

description: palp and proboscis combined

source_name: Palp-Proboscis 48 hr fasted 4


title: Palp-Proboscis 48 hr fasted 3

description: palp and proboscis combined

source_name: Palp-Proboscis 48 hr fasted 3


title: Body 24 hr fasted 2

description: Body missing the head

source_name: Body 24 hr fasted 2


title: Body 24 hr fasted 1

description: Body missing the head

source_name: Body 24 hr fasted 1


title: Palp-Proboscis 24 hr fasted 5

description: palp and proboscis combined

source_name: Palp-Proboscis 24 hr fasted 5


title: Body 0 hr fasted 3

description: Body missing the head

source_name: Body 0 hr fasted 3


title: Palp-Proboscis 24 hr fasted 1

description: palp and proboscis combined

source_name: Palp-Proboscis 24 hr fasted 1


title: Palp-Proboscis 0 hr fasted 2

description: palp and proboscis combined

source_name: Palp-Proboscis 0 hr fasted 2


title: Palp-Proboscis 48 hr fasted 1

description: palp and proboscis combined

source_name: Palp-Proboscis 48 hr fasted 1


title: Palp-Proboscis 0 hr fasted 4

description: palp and proboscis combined

source_name: Palp-Proboscis 0 hr fasted 4


title: Palp-Proboscis 0 hr fasted 3

description: palp and proboscis combined

source_name: Palp-Proboscis 0 hr fasted 3


title: Palp-Proboscis 24 hr fasted 2

description: palp and proboscis combined

source_name: Palp-Proboscis 24 hr fasted 2


title: Palp-Proboscis 24 hr fasted 4

description: palp and proboscis combined

source_name: Palp-Proboscis 24 hr fasted 4


title: Head 0 hr fasted 5

description: heads without chemosensory organs attached

source_name: Head 0 hr fasted 5

value: Head


title: Body 0 hr fasted 2

description: Body missing the head

source_name: Body 0 hr fasted 2


title: Palp-Proboscis 24 hr fasted 3

description: palp and proboscis combined

source_name: Palp-Proboscis 24 hr fasted 3


title: Palp-Proboscis 48 hr fasted 2

description: palp and proboscis combined

source_name: Palp-Proboscis 48 hr fasted 2


title: Body 48 hr fasted 1

description: Body missing the head

source_name: Body 48 hr fasted 1


title: Head 48 hr fasted 4

source_name: Head 48 hr fasted 4


title: Head 24 hr fasted 5

source_name: Head 24 hr fasted 5


title: Head 0 hr fasted 4

source_name: Head 0 hr fasted 4


title: Head 24 hr fasted 4

source_name: Head 24 hr fasted 4


title: Head 48 hr fasted 3

source_name: Head 48 hr fasted 3


title: Palp-Proboscis 0 hr fasted 1

description: palp and proboscis combined

source_name: Palp-Proboscis 0 hr fasted 1


title: Head 0 hr fasted 3

source_name: Head 0 hr fasted 3


title: Head 24 hr fasted 3

source_name: Head 24 hr fasted 3


title: Head 24 hr fasted 2

source_name: Head 24 hr fasted 2


title: Head 48 hr fasted 2

source_name: Head 48 hr fasted 2


title: Head 24 hr fasted 1

source_name: Head 24 hr fasted 1


title: Head 48 hr fasted 1

source_name: Head 48 hr fasted 1


title: Antenna 48 hr fasted 5

description: antenna dissection

source_name: Antenna 48 hr fasted 5

value: antenna


title: Antenna 0 hr fasted 3

description: antenna dissection

source_name: Antenna 0 hr fasted 3


title: Head 0 hr fasted 2

source_name: Head 0 hr fasted 2


title: Head 0 hr fasted 1

source_name: Head 0 hr fasted 1


title: Antenna 48 hr fasted 6

description: antenna dissection

source_name: Antenna 48 hr fasted 6


title: Antenna 0 hr fasted 1

description: antenna dissection

source_name: Antenna 0 hr fasted 1

value: Antenna


title: Antenna 0 hr fasted 4

description: antenna dissection

source_name: Antenna 0 hr fasted 4


title: Antenna 48 hr fasted 1

description: antenna dissection

source_name: Antenna 48 hr fasted 1


title: Antenna 24 hr fasted 6

description: antenna dissection

source_name: Antenna 24 hr fasted 6


title: Antenna 24 hr fasted 3

description: antenna dissection

source_name: Antenna 24 hr fasted 3


title: Antenna 24 hr fasted 4

description: antenna dissection

source_name: Antenna 24 hr fasted 4


title: Antenna 24 hr fasted 2

description: antenna dissection

source_name: Antenna 24 hr fasted 2


title: Antenna 48 hr fasted 3

description: antenna dissection

source_name: Antenna 48 hr fasted 3


title: Antenna 48 hr fasted 2

description: antenna dissection

source_name: Antenna 48 hr fasted 2


title: Antenna 0 hr fasted 2

description: antenna dissection

source_name: Antenna 0 hr fasted 2


title: seed germinating in countinuous light 48 h SL Replicate 3

status: Public on Sep 09 2011

city: Umeå

first: Simon

middle: R.

last: Law

state: Västerbotten

address: Umeå University

country: Sweden

institute: Umeå Plant Science Centre

description: Gene expression data from germinating seed

hyb_protocol: Following fragmentation, 12.5 µg of the labelled aRNA was hybridised rotating at 60 rpm, 16 hr at 45 °C on GeneChip ATH1 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned individually using a GeneChip Scanner 3000

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. Additionally, GC RMA normalisation was carried out using Partek Genomics Suite.

source_name: Arabidopsis seed germinating in countinuous light

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 80 mg of Arabidopsis thaliana seeds were surface steralised and plated on MS media. Stratification was carried out at 4 °C in darkness, light conditions were 100 µE m -2 sec-1 at 22 °C.

extract_protocol: RNA isolation was carried out using the Ambion Plant RNA isolation aid and RNAqeous RNA isolation kit.

treatment_protocol: Seed was collected freshly harvested (H), after 14 days of drying (0 h), 1, 12 and 48 h during stratification and 1, 6, 12, 24, 48 h in continuous light.

value: seed

value: germinating seed


title: seed germinating in countinuous light 12 h SL Replicate 3


title: seed germinating in countinuous light 24 h SL Replicate 1


title: seed germinating in countinuous light 48 h SL Replicate 2


title: seed germinating in countinuous light 12 h SL Replicate 2


title: seed germinating in countinuous light 48 h SL Replicate 1


title: seed germinating in countinuous light 24 h SL Replicate 2


title: seed germinating in countinuous light 1 h SL Replicate 3

value: 1 h


title: seed germinating in countinuous light 12 h SL Replicate 1


title: Antenna 24 hr fasted 1

description: antenna dissection

source_name: Antenna 24 hr fasted 1


title: seed germinating in countinuous light 24 h SL Replicate 3


title: seed germinating in countinuous light 6 h SL Replicate 2

value: 6 h


title: seed germinating in countinuous light 6 h SL Replicate 3


title: seed germinating in countinuous light 6 h SL Replicate 1


title: seed germinating in countinuous light 1 h SL Replicate 1


title: seed during stratification 48 h S Replicate 3

description: Gene expression data from seed during stratification

source_name: Arabidopsis seed during stratification

value: seed during stratification


title: seed during stratification 48 h S Replicate 2


title: seed during stratification 48 h S Replicate 1


title: seed during stratification 12 h S Replicate 3


title: seed during stratification 12 h S Replicate 2


title: seed during stratification 12 h S Replicate 1


title: seed during stratification 1 h S Replicate 3


title: dry seed 0 h Replicate 2

description: Gene expression data from dry seed

source_name: Arabidopsis dry seed (0 h)

value: dry seed


title: dry seed 0 h Replicate 1

description: Gene expression data from dry seed


title: dry seed 0 h Replicate 3

description: Gene expression data from dry seed


title: seed germinating in countinuous light 1 h SL Replicate 2


title: seed during stratification 1 h S Replicate 1


title: seed freshly harvested H Replicate 3

description: Gene expression data from freshly harvested seed

source_name: Arabidopsis seed freshly harvested (H)

value: freshly harvested seed


title: seed freshly harvested H Replicate 2


title: seed during stratification 1 h S Replicate 2


title: stage14_elav-dimm_rep2

status: Public on Sep 06 2011

city: Saint Louis

first: Tarik

last: Hadzic

state: MO

address: 660 S. Euclid Ave

department: Psychiatry

institute: Washington University in St Louis School of Medicine

hyb_protocol: Arrays were hybridized and washed by using standard Affymetrix reagents and protocols outlined in GeneChip® Expression Analysis Technical Manual provided by Affymetrix.

scan_protocol: Arrays were scanned by using standard Affymetrix reagents and protocols outlined in GeneChip® Expression Analysis Technical Manual provided by Affymetrix.

data_processing: Affymetrix CEL files raw probe intensity data was loaded into the statistical computing language R v. 2.12.1 for Snow Leopard (32-bit build) with the affy / simpleaffy libraries (ReadAffy). Microarrays were quality checked with the affyPLM and affycoretools libraries. Probe intensities were then log2 normalized with the gcrma algorithm version 2.22.0 (default settings). All eight arrays were gcrma-normalized together as one data set. Gcrma-normalized data sets were then processed with the limma package (Linear Models for Microarray Data) v. 3.6.9 and default limma settings (Smyth GK, 2004). Contrast matrices were set up to look for probes that were differentially expressed in the ED samples compared to E samples for each age: (ED3,ED4)-(E3,E4) and (ED1,ED2)-(E1,E2).

label_protocol: Following Affymetrix procedures outlined, an in vitro transcription (IVT) reaction was then done to produce biotin-labeled cRNA from the cDNA. The cRNA was fragmented before hybridization.

growth_protocol: Adult flies were reared on standard cornmeal/agar media supplemented with yeast and kept in a 25°C incubator.

extract_protocol: Total RNA was prepared from embryos by using a Qiagen RNeasy minicolumn. Double-stranded cDNA was synthesized from total RNA in accordance with GeneChip® Expression Analysis Technical Manual provided by Affymetrix.

treatment_protocol: For these experiments, we crossed UAS-dimm-myc flies (#2A3) with ones bearing the pan-neuronal driver, elav-GAL4. For microarray analysis, these were compared to the GAL4 parental line. Crosses and egg collections were maintained 18oC to minimize lethality.

value: dechorionated Embryos

tag: genotype/variation

tag: embryonic stage

value: Stage 14

tag: age

value: 22-26 hr after egg laying (AEL)


title: stage16_elav-dimm_rep2

tag: tissue

value: Stage 16

value: 28-32 hr after egg laying (AEL)


title: stage14_elav-dimm_rep1


title: GMR>miR-11, biological rep3

status: Public on Sep 01 2011

city: Chicago

first: Mary

last: Truscott

state: IL

address: 900 S Ashland Ave, room 2356

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: Gene expression data from third instar larval eye discs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GS3000.

data_processing: The data were normalized using the R-Bioconductor "affy" package. The quality and variability were analyzed with the "arrayQualityMetrics" Bioconductor package

source_name: Drosophila larval eye discs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: Flies were cultured at 25 degrees celcius

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

treatment_protocol: Crosses were set under standard conditions, and maintained at 25 degrees celcius

value: larval eye discs

tag: genotype


title: stage16_elav-dimm_rep1


title: GMR>dE2F1,dDP, biological rep1

value: GMR-Gal4/+; UAS-dE2F1,UAS-dDP/+


title: GMR>dE2F1,dDP,miR-11, biological rep3


title: stage14_control_rep2


title: stage16_control_rep1


title: GMR>miR-11, biological rep1


title: GMR>dE2F1,dDP, biological rep3


title: GMR>dE2F1,dDP,miR-11, biological rep1


title: stage14_control_rep1


title: GMR>WT, biological rep3


title: GMR>WT, biological rep2


title: GMR>dE2F1,dDP,miR-11, biological rep2


title: GMR>miR-11, biological rep2


title: GMR>WT, biological rep1


title: GMR>dE2F1,dDP, biological rep2


title: 15

city: Moffet Field

first: Sharmila

last: Bhattacharya

address: Bldg. 236, Room 213

institute: NASA Ames Research Center

description: 6 sets of 50 mid 3rd instar control larvae

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip¨ Expression Analysis Technical Manual)

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip¨ Expression Analysis Technical Manual)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label_protocol: Affymetrix One Cycle Target Labeling according to manufacturer's protocol (GeneChip¨ Expression Analysis Technical Manual)

extract_protocol: Qiagen RNeasy Kit

tag: strain

value: Hml-Gal4>;UAS-GFP transgenic line

tag: developmental stage

value: mid 3rd instar larvae

tag: environmental treatment group

value: control


title: 17

description: 3 sets of 20 adults each was prepared from adult females from the corresponding control cassettes

value: adult

tag: sex

value: females


title: 10

source_name: 6 sets of 50 mid 3rd instar control larvae


title: 12


title: 11


title: 14


title: seed freshly harvested H Replicate 1

value: seed


title: 13


title: stage16_control_rep2


title: 16

source_name: 3 sets of 20 adults each was prepared from adult females from the corresponding control cassettes


title: 18


title: 7

description: 3 sets of 20 adults each was prepared from adult females that emerged during the flight and within 4 hours of landing


title: 6

description: 6 sets of 50 mid 3rd instar larvae collected on the day of landing

value: collected on the day of landing


title: 2

source_name: 6 sets of 50 mid 3rd instar larvae collected on the day of landing


title: 5


title: Colon_RB45_1652

city: Roskilde

first: Morten

last: Thorsteinsson

address: Koegevej 7-13

department: Department of Surgery

country: Denmark

institute: Roskilde Hospital, University of Copenhagen

hyb_protocol: Standard Affymetrix protocols.

scan_protocol: Standard Affymetrix protocols.

data_processing: The processing and analysis of expression data were performed using the statistical software R and Bioconductor. For all Affymetrix CEL files the background were corrected and the expression were normalized using robust multiarray average (RMA).

organism: Homo sapiens

source_name: Colon adenocarcinoma

label_protocol: Standard Affymetrix protocols.

extract_protocol: RNA was extracted using mirVana® miRNA isolation Kit (Ambion, Applied Biosystems, USA) according to the manufacturers protocol.

tag: gender

value: female

tag: ethnicity

value: caucasian

tag: tumor location

value: right colon

tag: tnm-stage

value: II

tag: histology

value: adenocarcinoma

tag: grade

value: moderately diff.

tag: number of lymphnodes resected

tag: adjuvant chemotherapy

value: no

tag: relapse free survival time

value: 83.11 month

tag: recurrence

tag: death

value: yes


title: 4


title: 3


title: Colon_RB36_1646

tag: age

value: III


title: 8

source_name: 3 sets of 20 adults each was prepared from adult females that emerged during the flight and within 4 hours of landing

value: Hml-Gal4>;UAS-GFP transgenic line


title: Colon_RB29_1650

value: left colon

value: 42.05 month


title: 9

value: adult

value: emerged during the flight and within 4 hours of landing


title: Colon_RB33_1658

value: 99.19 month


title: Colon_RB50_182

value: male

value: 96.82 month


title: Colon_RB56_1653

value: female

value: caucasian

value: well diff.

value: 43.27 month


title: 1

value: mid 3rd instar larvae

value: collected on the day of landing


title: Colon_RB35_1659

value: right colon

value: II

value: adenocarcinoma

value: moderately diff.

value: no

value: 33.01 month


title: Colon_RB43_1648

value: 4.60 month

value: yes


title: Colon_RB51_183


title: Colon_RB01_14

value: III

value: mucinous adenocarcinoma


title: Colon_R54_1969

value: left colon

value: 36.59 month


title: Colon_R47_1963

value: female

value: caucasian

value: 36.36 month


title: Colon_RB24_1656

value: male


title: Colon_R42_1961

value: well diff.


title: Colon_RB06_165

value: right colon

value: 26.56 month


title: Colon_R55_1970

value: adenocarcinoma

value: 11.67 month


title: Colon_RB22_1655

value: moderately diff.

value: no


title: Colon_RB14_155

value: II

value: poor diff.

value: 6.41 month


title: Colon_R49_1965

value: III

value: yes

value: 36.10 month


title: Colon_R52_1967

value: left colon

value: 20.38 month


title: Colon_R43_1962

value: female

value: caucasian

value: mucinous adenocarcinoma

value: 40.60 month


title: Colon_R40_2367

value: male

value: right colon

value: 38.92 month


title: Colon_R41_1960

value: adenocarcinoma

value: moderately diff.

value: 40.11 month


title: Colon_R27_1673

value: II

value: well diff.

value: no

value: 29.88 month


title: Colon_R26_1671

value: III

value: 36.10 month


title: Colon_R22_1662

value: 38.73 month


title: Colon_R18_1665

value: female

value: left colon

value: 28.96 month

value: yes


title: Colon_R25_1668

value: caucasian

value: 36.23 month


title: Colon_R21_1667

value: 41.03 month


title: Colon_R14_2363

value: adenocarcinoma

value: 48.53 month


title: Colon_R29_1663

value: moderately diff.

value: 38.30 month


title: Colon_R31_2365

value: male

value: right colon

value: II

value: 36.03 month


title: Colon_R36_2366

value: III

value: poor diff.

value: no

value: 38.33 month


title: Colon_R15_2364

value: female

value: 5.29 month


title: Colon_R09_2362

hyb_protocol: Standard Affymetrix protocols

scan_protocol: Standard Affymetrix protocols

label_protocol: Standard Affymetrix protocols

value: Male

value: Caucasian

value: left colon

value: 48.45 month

value: No


title: Colon_R06_2361

value: Female

value: adenocarcinoma

value: Moderate diff.

value: yes

value: 47.80 month


title: Rosette of vtc1, biological rep3 (II)

status: Public on Aug 26 2011

city: Leeds

first: Pavel

last: Kerchev

address: Faculty of Biological Sciences University of Leeds

country: United Kingdom

institute: University of Leeds

description: Gene expression data from rosette of vtc1.

hyb_protocol: The target cRNAs were fragmented, combined with hybridization and spike controls, then hybridized to the Genechip Arabidopsis ATH1 Genome Array (Affymetrix, Inc., Santa Clara, CA) for 16 h. Following hybridization, the arrays were washed and stained with streptavidin phycoerythrin conjugate using an automated GeneChip® Fluidics Station 450

scan_protocol: GeneChips were scanned with a GeneChip® Scanner 3000 7G using a 570 nm excitation wavelength laser. Microarray quality controls were assessed using GeneChip® Operating Software (Affymetrix)..

data_processing:
Raw intensity values from the scanned Arabidopsis ATH1 Genome Arrays were analyzed using RMAExpress .
A significance test was undertaken by calculating a null hypothesis through a permuted modified t-statistic across the replicates for each array comparison. The log2 means of the normalized intensity values of the biological replicates were compared as ratios, where a log2 ratio of ±1.0 and a p-value of < 0.05 was selected as worthy of further study.

source_name: Rosette of vtc1, 42 days old

label_protocol: Double-stranded cDNA was generated from each of the ten total-RNA samples and transcribed to obtain biotin-labeled cRNA.

growth_protocol: Arabidopsis thaliana was grown on compost in controlled conditions. 8 h day, 60 % RH, 23/18°C day/night, light intensity 200 µmol/ m2 s

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

treatment_protocol: Whole rosettes were harvested at the indicated stage, frozen in liquid nitrogen and stored at −80°C.

tag: tissue

value: rosette

value: 42 days old

tag: genotype

value: vtc1 (vitamin C defective 1)


title: Rosette of abi4-102, biological rep2 (II)

description:
Gene expression data from rosette of abi4-102.
Samples (I) and (II) only share the same Title between GSE23329 & GSE23330. They are different samples from two independent experiments, and do not represent the same Affymetrix hybridizations.

source_name: Rosette of abi4, 42 days old

value: abi4-102 (aba insensitive 4)


title: Rosette of abi4 vtc2, biological rep6 (I)

description: Gene expression data from rosette of abi4 vtc2.

source_name: Rosette of abi4 vtc2, 42 days old

label_protocol: Double-stranded cDNA was generated from each of the seventeen total-RNA samples and transcribed to obtain biotin-labeled cRNA.

growth_protocol: Arabidopsis thaliana was grown on compost in controlled conditions. 10 h day, 60 % RH, 22 °C constant temperature, light intensity 350 µmol/ m2 s

value: abi4 vtc2 (double mutant)


title: Rosette of vtc1, biological rep4 (II)


title: Rosette of abi4-102, biological rep3 (II)


title: Rosette of vtc1, biological rep2 (II)


title: Rosette of vtc1, biological rep1 (II)


title: Rosette of Col 0, biological rep2 (II)

description:
Gene expression data from rosette of wild type Col 0.
Samples (I) and (II) only share the same Title between GSE23329 & GSE23330. They are different samples from two independent experiments, and do not represent the same Affymetrix hybridizations.

source_name: Rosette of Col 0, 42 days old

value: Col 0 (wild type)


title: Rosette of abi4 vtc2, biological rep4 (I)


title: Rosette of abi4-102, biological rep1 (II)


title: Rosette of Col 0, biological rep1 (II)


title: Rosette of abi4 vtc2, biological rep2 (I)


title: Rosette of Col 0, biological rep3 (II)


title: Rosette of abi4 vtc2, biological rep5 (I)


title: Rosette of abi4 vtc2, biological rep1 (I)


title: Rosette of abi4 vtc2, biological rep3 (I)


title: Rosette of vtc2, biological rep3 (I)

description: Gene expression data from rosette of vtc2.

source_name: Rosette of vtc2, 42 days old

value: vtc2 (vitamin C defective 2)


title: Rosette of vtc2, biological rep4 (I)


title: Rosette of vtc2, biological rep2 (I)


title: Rosette of vtc2, biological rep1 (I)


title: Rosette of abi4-102, biological rep4 (I)

description: Gene expression data from rosette of abi4-102.


title: Rosette of abi4-102, biological rep2 (I)


title: Rosette of abi4-102, biological rep3 (I)


title: Rosette of abi4-102, biological rep1 (I)


title: Rosette of Col 0, biological rep1 (I)


title: Rosette of Col 0, biological rep3 (I)


title: Rosette of Col 0, biological rep2 (I)


title: S2 RNAi-control  plus bacteria 180min rep2

status: Public on Aug 25 2011

city: Boston

first: Christine

last: Kocks

state: Massachusetts

address: 185 Cambridge St CPZN7.250

department: Pediatrics/Molecular Biology

institute: Massachusetts General Hospital

description: gene expression data from control RNAi-treated S2 cells in the presence of bacteria at 180 minutes of phagocytosis

hyb_protocol: Affymetrix standard protocol. Hybridization: 16 hour incubation; Wash & Stain: double amplified with phycoerythrin-tagged streptavidin

scan_protocol: Affymetrix standard protocol. Scan GeneChip: exitation: 488 nm, emission: 570 nm

data_processing: Data were analysed with freely available GenePattern version 2.0 Software on the BROAD public Server using CEL files as input. Background subtraction and normalization were performed with ExpressionFileCreator using GC-RMA and quantile normalization. Data were not filtered (no threshold/ceiling filters, no variance filters). Normalized data were preprocessed using MultiplotPreprocess (no replicate FC, no random data, no outlier elimination, but with Stats), analysed using Multiplot and means calculated from 3 independent biological replicates were visualized with scatter plots. Probability of differential expression was calculated by Multiplot from 3 independent biological replicates per sample using FDR (Hochberg) p-values adjusted for multiple hypothesis testing; probability of ≤ 0.05 was considered significant. [For quality control purposes, data were analysed with Microarray Suite version 5.0 (MAS 5.0).]

source_name: S2 cells, pBR322 RNAi, plus bacteria, 180 minutes phagocytosis 26.5˚C

label_protocol: Samples were processed by the Biopolymers Core Facility at Harvard Medical School using Full Affymetrix Service according to standard Affymetrix protocols. Complete sets of biological replicates (A-series, B-series, C-series) were processed in parallel to minimize technical day-to-day variations.  cRNA: biotin-labled via in vitro transcription

growth_protocol: Drosophila Schneider line 2 (S2) cells were maintained in the exponential growth phase at 26.5˚C in Schneider's Drosophila Medium (Invitrogen) containing 10% fetal bovine serum.

extract_protocol: Total RNA (10 to 20 µg per sample) was extracted according to the manufacturer's instructions using the RNeasy Plus Kit (Qiagen). RNA integrity was confirmed with a Agilent Bioanalyzer (Nano Kit).

treatment_protocol: For RNA interference (RNAi) 10^6 S2 cells were soaked with 15 µg double stranded RNAs as described (Chung & Kocks 2011 J Biol Chem 286:26524-26532). After 60 to 72 hours, cells were shifted to 0˚C (temperature non-permissive for phagocytosis). FITC-labeled, heat-inactivated Gram-positive and Gram-negative bacteria (Staphylococcus aureus and Serratia marcescens, respectively) were added; bacterial input was previously optimized to achieve 50% of cells binding to both kind of bacteria. Bacteria were briefly centrifuged onto the cells and incubated for 30 minutes on ice to maximize binding to cells. Cultures were shifted to 26.5˚C (temperature permissive for phagocytosis) and RNA was extracted at three different timepoints: 30 or 90 or 180 minutes at 26.5˚C. Parallel samples were analysed in all cases in phagocytosis assays with S. aureus and S. marcescens to confirm the expected biological effect of eater knockdown (betweeen 50 to 80% decreased phagocytosis).

tag: cell line

value: Schneider line 2 (S2) cells

tag: knockdown

value: pBR322 RNAi

tag: treatment

value: plus bacteria

tag: time

value: 180 minutes


title: S2 RNAi-control  plus bacteria 180min rep1


title: S2 RNAi-eater  plus bacteria 180min rep2

description: gene expression data from eater RNAi-treated S2 cells in the presence of bacteria at180 minutes of phagocytosis

source_name: S2 cells, eater-N RNAi, plus bacteria, 180 minutes phagocytosis 26.5˚C

value: eater-N RNAi


title: S2 RNAi-control  plus bacteria 90min rep3

description: gene expression data from control RNAi-treated S2 cells in the presence of bacteria at 90 minutes of phagocytosis

source_name: S2 cells, pBR322 RNAi, plus bacteria, 90 minutes phagocytosis 26.5˚C

value: 90 minutes


title: S2 RNAi-control  plus bacteria 180min rep3


title: S2 RNAi-control  plus bacteria 90min rep2


title: S2 RNAi-eater  plus bacteria 180min rep1


title: S2 RNAi-eater  plus bacteria 90min rep3

description: gene expression data from eater RNAi-treated S2 cells in the presence of bacteria at 90 minutes of phagocytosis

source_name: S2 cells, eater-N RNAi, plus bacteria, 90 minutes phagocytosis 26.5˚C


title: S2 RNAi-eater  plus bacteria 180min rep3


title: S2 RNAi-eater  plus bacteria 90min rep1


title: S2 RNAi-eater  plus bacteria 90min rep2


title: S2 RNAi-control  plus bacteria 30min rep2

description: gene expression data from control RNAi-treated S2 cells in the presence of bacteria at 30 minutes of phagocytosis

source_name: S2 cells, pBR322 RNAi, plus bacteria, 30 minutes phagocytosis 26.5˚C

value: 30 minutes


title: S2 RNAi-eater  plus bacteria 30min rep2

description: gene expression data from eater RNAi-treated S2 cells in the presence of bacteria at 30 minutes of phagocytosis

source_name: S2 cells, eater-N RNAi, plus bacteria, 30 minutes phagocytosis 26.5˚C


title: S2 RNAi-control  plus bacteria 90min rep1


title: S2 RNAi-eater  plus bacteria 30min rep1


title: S2 RNAi-control  plus bacteria 30min rep3


title: S2 RNAi-eater  no bacteria 30min rep3

description: gene expression data from eater RNAi-treated S2 cells in the absence of bacteria

source_name: S2 cells, eater-N RNAi, no bacteria, 30 minutes 26.5˚C

value: no bacteria


title: S2 RNAi-eater  plus bacteria 30min rep3


title: S2 RNAi-eater  no bacteria 30min rep2


title: S2 RNAi-control  no bacteria 30min rep3

description: gene expression data from control RNAi-treated S2 cells in the absence of bacteria

source_name: S2 cells, pBR322 RNA, no bacteria, 30 minutes 26.5˚C


title: S2 RNAi-eater  no bacteria 30min rep1


title: S2 RNAi-control  plus bacteria 30min rep1


title: S2 RNAi-control  no bacteria 30min rep1


title: S2 RNAi-control  no bacteria 30min rep2


title: ckh2_CK200_rep2

status: Public on Aug 17 2011

city: Okazaki

first: Minoru

last: Kubo

state: Aichi

address: 38NIshigonaka, Myoudaiji

department: ERATO

country: Japan

institute: JST

description: Hypocotyl segments of the ckh2-1 mutant was cultured for 3 days on CIM containing 100 ng/ml 2,4-D and high level (200 ng/ml) of kinetin.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The data were analyzed with Affymetrix Microarray Suite version 5.0 (MAS 5.0).

source_name: ckh2-1 mutant, cultured on CIM in the presence of high level of cytokinin.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA.

growth_protocol: The sterilized seeds were put on germination medium (GM) and stored at 4ºC for at least 1 day, and then moved to growth chambers at 23ºC. Seedlings to be used for the excision of hypocotyl segments for callus induction were grown for 10days under dim light (2.5 µEm-2s-1).

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

treatment_protocol: Callus induction medium (CIM) were GM supplemented with 1 mg/liter biotin, 100 ng/ml 2,4-D as auxin and kinetin as cytokinin at the specified concentrations or TSA. Hypocotyl segments of seedlings were cultured for 3 days on CIM under comtinuous illumination (100 µEm-2s-1) at 23ºC , and then collected and rapidly frozen by liquid nitrogen.

tag: sample type

value: tissue culture

value: ckh2-1 mutant


title: wild type (Ler)_TSA_rep1

description: Hypocotyl segments of the wild type (Ler) was cultured for 3 days on CIM containing 100 ng/ml 2,4-D and 100 ng/ml TSA.

source_name: wild type (Ler), cultured on CIM in the presence of TSA.

value: wild type (Ler)


title: ckh1_CK200_rep1

description: Hypocotyl segments of the ckh1-1 mutant was cultured for 3 days on CIM containing 100 ng/ml 2,4-D and high level (200 ng/ml) of kinetin.

source_name: ckh1-1 mutant, cultured on CIM in the presence of high level of cytokinin.

value: ckh1-1 mutant


title: ckh2_CK0_rep2

description: Hypocotyl segments of the ckh2-1 mutant was cultured for 3 days on CIM containing 100 ng/ml 2,4-D in the absence of kinetin.

source_name: ckh2-1 mutant, cultured on CIM in the absence of cytokinin.


title: wild type (Ler)_TSA_rep2

value: cultured for 3 days on CIM containing 100 ng/ml 2,4-D and 100 ng/ml TSA.


title: ckh2_CK200_rep1

value: cultured for 3 days on CIM containing 100 ng/ml 2,4-D and high level (200 ng/ml) of kinetin.


title: ckh2_CK25_rep1

description: Hypocotyl segments of the ckh2-1 mutant was cultured for 3 days on CIM containing 100 ng/ml 2,4-D and low level (25 ng/ml) of kinetin.

source_name: ckh2-1 mutant, cultured on CIM in the presence of low level of cytokinin.


title: ckh1_CK200_rep2


title: ckh2_CK0_rep1

value: cultured for 3 days on CIM containing 100 ng/ml 2,4-D in the absence of kinetin.


title: ckh2_CK25_rep2

value: cultured for 3 days on CIM containing 100 ng/ml 2,4-D and low level (25 ng/ml) of kinetin.


title: ckh1_CK25_rep2

description: Hypocotyl segments of the ckh1-1 mutant was cultured for 3 days on CIM containing 100 ng/ml 2,4-D and low level (25 ng/ml) of kinetin.

source_name: ckh1-1 mutant, cultured on CIM in the presence of low level of cytokinin.


title: ckh1_CK0_rep2

description: Hypocotyl segments of the ckh1-1 mutant was cultured for 3 days on CIM containing 100 ng/ml 2,4-D in the absence of kinetin.

source_name: ckh1-1 mutant, cultured on CIM in the absence of cytokinin.


title: ckh1_CK25_rep1


title: wild type (Ler)_CK0_rep1

description: Hypocotyl segments of the wild type (Ler) was cultured for 3 days on CIM containing 100 ng/ml 2,4-D in the absence of kinetin.

source_name: wild type (Ler), cultured on CIM in the absence of cytokinin.


title: ckh1_CK0_rep1


title: wild type (Ler)_CK200_rep1

description: Hypocotyl segments of the wild type (Ler) was cultured for 3 days on CIM containing 100 ng/ml 2,4-D and high level (200 ng/ml) of kinetin.

source_name: wild type (Ler), cultured on CIM in the presence of high level of cytokinin.


title: wild type (Ler)_CK0_rep2


title: wild type (Ler)_CK200_rep2


title: wild type (Ler)_CK25_rep1

description: Hypocotyl segments of the wild type (Ler) was cultured for 3 days on CIM containing 100 ng/ml 2,4-D and low level (25 ng/ml) of kinetin.

source_name: wild type (Ler), cultured on CIM in the presence of low level of cytokinin.


title: wild type (Ler)_CK25_rep2


title: Col_leaf_0mM NaCl_rep2

status: Public on Aug 16 2011

description:
Gene expression data in Col in the absence of salt
CEL data is identical to that assigned GEO accession GSM455427

source_name: Col plant, 0mM NaCl, 6 d

growth_protocol: Seeds were sown directly on soil in 26  × 26  × 6 cm flat pot filled with standard  planting medium (Baccto, Houston, TX, USA). Each flat pot was divided into 36 subsections and 5 seeds were pipetted onto wet soil surface carefully in each subsection.  The pots were covered with a transparent plastic cover and plants were grown at 23/18 °C in the growth chamber with a 10h light/14h dark cycle at 350 μmol m-2s-1 and 70% relative humidity. Half Strength Hoagland Solution was applied and watered from below once per week before the beginning of the salt treatment. At 14 DAS, the flats were thinned to 1 seedling per subsection.

value: leaf

value: Col

value: 20 days after sowing


title: Col_leaf_0mM NaCl_rep1

description:
Gene expression data in Col in the absence of salt
CEL data is identical to that assigned GEO accession GSM455426


title: Col_leaf_100mM NaCl_rep1

description:
Gene expression data in Col in the presence of salt
CEL data is identical to that assigned GEO accession GSM455428

source_name: Col plant, 100mM NaCl, 6 d


title: Col(gl)_leaf_100mM NaCl_rep2

description: Gene expression data in Col(gl) in the presence of salt

source_name: Col(gl) plant, 100mM NaCl, 6 d

value: Col(gl)


title: Col(gl)_leaf_100mM NaCl_rep1


title: Col(gl)_leaf_0mM NaCl_rep1

description: Gene expression data in Col(gl) in the absence of salt

source_name: Col(gl) plant, 0mM NaCl, 6 d


title: Col(gl)_leaf_0mM NaCl_rep2


title: Ws_leaf_100mM NaCl_rep2

description: Gene expression data in Ws in the presence of salt

source_name: Ws plant, 100mM NaCl, 6 d

value: Ws


title: Ws_leaf_0mM NaCl_rep1

description: Gene expression data in Ws in the absence of salt

source_name: Ws plant, 0mM NaCl, 6 d


title: Ws_leaf_0mM NaCl_rep2


title: Col_leaf_100mM NaCl_rep2

description:
Gene expression data in Col in the presence of salt
CEL data is identical to that assigned GEO accession GSM455429


title: seedling in dark treated with mock, biological rep3

status: Public on Aug 02 2011

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

data_processing: Raw microarray data were normalized using the robust multiarray analysis (RMA) algorithm in the BIOCONDUCTOR affy package. Then the microarray data were analyzed using Significance Analysis of Microarrays (SAM) method with default parameters as well as a manual setting of false discovery threshold (FDR) < 0.027 in D and <0.022 in FR.

source_name: Arabidopsis thaliana seedlings growing in dark for 4 days and  treated with mock for 2 hours

label_protocol: RNA quality was assessed with an Agilent 2100 Bioanalyzer, and hybridization to the Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays was performed according to the manufacturer’s instructions.

growth_protocol: FHY3p:FHY3-GR fhy3-4 transgenic seedlings grown in D or continuous FR light for 4 d

extract_protocol: total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: treated with 10 μM dexamethasone (DEX) or MOCK (equal volume of ethanol) for 2 h

tag: developmental stage

value: seedling

value: 4 days

tag: genotype/variation

value: FHY3p:FHY3-GR fhy3-4 transgenic line


title: seedling in far-red treated with mock, biological rep2

source_name: Arabidopsis thaliana seedlings growing in far-red light for 4 days and  treated with mock for 2 hours


title: seedling in far-red treated with DEX, biological rep4

source_name: Arabidopsis thaliana seedlings growing in far-red light for 4 days and  treated with DEX for 2 hours


title: seedling in far-red treated with mock, biological rep4


title: seedling in dark treated with mock, biological rep2


title: seedling in far-red treated with DEX, biological rep1


title: seedling in far-red treated with DEX, biological rep2


title: seedling in dark treated with mock, biological rep1


title: seedling in dark treated with DEX, biological rep2

source_name: Arabidopsis thaliana seedlings growing in dark for 4 days and  treated with DEX for 2 hours


title: seedling in dark treated with mock, biological rep4


title: seedling in far-red treated with mock, biological rep1


title: seedling in dark treated with DEX, biological rep3


title: seedling in far-red treated with DEX, biological rep3


title: seedling in dark treated with DEX, biological rep1


title: seu-3 ant-1 110826/59

status: Public on Aug 01 2011

city: Raleigh

first: April

middle: N

last: Wynn

address: Campus Box 7614

department: Genetics

institute: NC State University

description: each sample was pooled from 15-25 hand-dissected carpes

hyb_protocol: The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge which was incubated at 45°C for at least 16 hours in a rotating oven at 60 rpm.  GeneChips were washed and stained using a Fluidics station 450 using protocol: EukGE-WS2v4_450. Samples processed by Expression Analysis (Durham, NC).

scan_protocol: Hardware: Affymetrix GC3000 scanner with 7G upgrade, Factory PMT settings. Software: AGCC version 3.1.1, CHP files were scaled using a target intensity of 500. Samples processed by Expression Analysis (Durham, NC).

data_processing: The CHP files were generated in AGCC using the MAS 5.0 algorithm with a global scaling of 500. Samples were processed by Expression Analysis (Durham, NC).

source_name: floral stage 8-10 hand dissected carpels

growth_protocol: Plants were grown with long days (16 hrs) at 24 degrees C and randomized within the growth chamber.

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini Kit from Qiagen. Amplification, labeling, and fragmenting of the cDNA was carried out according to GeneChip 3' IVT Express Kit instructions from Affymetrix.

treatment_protocol: All inforescence apecies were collected from shoots that had produced between 10-20 mature (post anthesis) flowers below the inflorescenece apex.  Shoots younger or older than this were not used . Inforescence apicies were collected and placed immediately in 100% ice-cold ethanol, then stored in ethanol at -20 degrees C until reday for dissection. Dissections of the inflorescence apecies were completed within 6 days. Carpels/gynoecia from floral stages 8-10 were pooled with 15-25 gynoecia serving as one biological replicate.

value: seuss-3 aintegumenta-1


title: Ws_leaf_100mM NaCl_rep1


title: seu-3 110824/74

label_protocol: Amplification, labeling, and fragmenting of the cDNA was carried out according to GeneChip 3' IVT Express Kit instructions from Affymetrix.


title: seu-3 ant-1 110825/10


title: Colon_RB30_1651

source_name: Colon adenocarcinoma

tag: gender

value: male

tag: ethnicity

value: caucasian

tag: tumor location

value: right colon

tag: tnm-stage

value: II

tag: histology

value: adenocarcinoma

value: poor diff.

value: no

value: 38.14 month

value: yes


title: ant-1 110822/63


title: seu-3 110816/61


title: Col-0 110820/66


title: seu-3 ant-1 110818/47


title: seu-3 110823/33n


title: ant-1 110821/30


title: seu-3 ant-1 110817/7


title: Col-0 110819/40b


title: seu-3 110815/21


title: ant-1 110814/27


title: ant-1 110813/56


title: Col-0 110812/50


title: Col-0 110811/36b


title: female_restricted_diet_rep1

status: Public on Jul 21 2011

city: Providence

first: Michael

last: Antosh

state: RI

address: Brown University Box 1843

institute: Michael Antosh

hyb_protocol: The arrays are hybed overnight (16 hr) at 45C 60 rpm. Fluidics protocol is FS450_0002

scan_protocol: Arrays were scanned on a Affymetrix Gene Chip Scanner 3000 7G

data_processing: R/Bioconductor, normalized using GCRMA

source_name: female head/thorax, restricted diet

label_protocol: Standard Affymetrix protocol.

extract_protocol: Total RNA was isolated from at least 75 females using Trizol (Invitrogen) and further purified using RNeasy columns (QIAGEN). 5 μg total RNA was used with Affymetrix One Cycle DNA conversion Kit (Cat # 900431) and all steps were carried out according to the Affymetrix manual

value: female

value: head/thorax

tag: genetic background

value: canton-s

tag: diet

value: restricted

value: 10 days


title: female_restricted_diet_rep3

tag: age


title: female_normal_diet_plus_resveratrol_rep3

source_name: female head/thorax, normal diet plus resveratrol

tag: tissue

value: normal plus resveratrol


title: female_normal_diet_plus_resveratrol_rep2


title: female_normal_diet_rep3

source_name: female head/thorax, normal diet

value: normal


title: Drosophila_wt-3

status: Public on Jul 02 2011

city: Edmonton

first: Fred

middle: David

last: Mast

state: Alberta

address: Medical Sciences Building Room 5-14 Department of Cell Biology University of Alberta

department: Cell Biology

country: Canada

institute: University of Alberta

description: wild-type larvae, biological rep3

hyb_protocol: 10ug of the fragmented biotin-modified aRNA was hybridized to the microarray. Affymetrix GeneChip Drosophila Genome 2.0 (P/N 520087) arrays were hybridized for 16 hours at 45°C with the rotation of the oven set to 60 rpm (GeneChip Hybridization Oven 640- Affymetrix). 20x eukaryotic hybridization controls were added to the hybridization cocktail.  Arrays were washed and stained  (GeneChip Fluidics Station 450- Affymetrix) (GeneChip Hybridization, Wash and Stain Kit – P/N 901241-Affymetrix)

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 7G

data_processing: Data were MAS 5.0 normalized using and then further analyzed in Cytoscape using the David and ClueGO plugins.

source_name: wild-type larvae

label_protocol: 100 ng of the total RNA was labelled with the GeneChip 3’ IVT Express Kit (Affymetrix- Part No. 901229). Poly-A RNA controls were added to the sample (“exogenous positive controls to monitor the entire eukaryotic target labelling process”* Affymetrix manual)- 4th dilution for 100ng of the total RNA. The size of the biotin-modified aRNA with IVT labelling was evaluated using an Agilent 2100 Bioanalyzer RNA nano LabChip Kit ( most aRNA between 600-1200 nt)

growth_protocol: Heterozygous l(3)70Das4868/TM3, P{ActGFP}JMR2, Ser1 parents were allowed to lay embryos on apple juice agar plates for 30 minutes at 25°C. The plates were then supplemented with yeast paste, and the embryos were allowed to develop for 48 hours at 25°C and 70% humidity. Hatched larvae were then hand sorted under a SX61 fluorescence stereomicroscope (Olympus) to select homozygous l(3)70Das4868 larvae, i.e. those lacking GFP. Care was taken to select only larvae judged clearly to be alive as evidenced by their movement. Corresponding wild-type siblings were isolated from w1118/TM3, P{ActGFP}JMR2, Ser1 parents.

extract_protocol: Total mRNA from 200 mg samples was isolated using Trizol (Invitrogen) and purified using RNeasy.

value: larvae

tag: genotype

value: w1118/TM3, P{ActGFP}JMR2, Ser1 parents

value: freshly hatched


title: female_normal_diet_plus_resveratrol_rep1


title: Drosophila_wt-1

description: wild-type larvae, biological rep1


title: female_normal_diet_rep2


title: Drosophila_wt-2

description: wild-type larvae, biological rep2


title: female_restricted_diet_rep2


title: Drosophila_sa mutant testis_replicate 3

status: Public on Jul 15 2011

city: Stanford

first: Margaret T.

last: Fuller

address: Beckman Center B300, 279  Campus Drive

department: Departments of Developmental Biology and Genetics

institute: Stanford University School of Medicine

hyb_protocol: Approximately 4 μg of total RNA from each biological replicate were used to generate labeling probes to hybridize with the Affymetix GeneChip Drosophila Genome 2.0 Array according to the Affymetrix protocol. Three biological replicates were performed for each genotype. Microarray hybridization was processed at the Core Facility at the Stanford University School of Medicine.

scan_protocol: Scanning was performed with the Affymetrix GeneChip scanner using default settings.

data_processing: The raw data were exported from the Affymetrix Microarray Suite (MAS). The CEL files were used for signal normalization with RMA as part of the limma package from the Bioconductor R packages (http://www.bioconductor.org).

source_name: sa mutant testis, replicate 3

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

growth_protocol: All fly stocks were grown in a 25 °C incubator with standard medium.

extract_protocol: Total RNA from approximately 200 pairs of fly testes was extracted using TRIzol (Invitrogen, #15596-018, Carlsbad, CA, USA) following the manufacturer's instructions. The genomic DNA was degraded using 2 Units of DNase I (Fermentas, #EN0521, Glen Burnie, MD, USA) at 37°C for 20 minutes. RNA integrity was checked by gel electrophoresis (1% agarose).

treatment_protocol: sa mutant testes were dissected in DEPC-treated 1× PBS buffer in 20 min interval, followed by immediate snap freezing in liquid nitrogen.

tag: strain

value: sa1/sa2 mutant fly.

tag: time point

value: 1 day old.


title: Drosophila_pex1-2

description: pex1 homozygous mutant larvae, biological rep2

source_name: pex1 homozygous mutant larvae

value: Heterozygous l(3)70Das4868/TM3, P{ActGFP}JMR2, Ser1 parents


title: Drosophila_pex1-3

description: pex1 homozygous mutant larvae, biological rep3


title: Drosophila_yw mutant testis_replicate 1

source_name: yw mutant testis, replicate 1

treatment_protocol: yw mutant testes were dissected in DEPC-treated 1× PBS buffer in 20 min interval, followed by immediate snap freezing in liquid nitrogen.

value: y,w mutant fly.


title: female_normal_diet_rep1


title: Drosophila_aly mutant testis_replicate 3

source_name: aly mutant testis, replicate 3

treatment_protocol: aly mutant testes were dissected in DEPC-treated 1× PBS buffer in 20 min interval, followed by immediate snap freezing in liquid nitrogen.

value: aly2/aly5P mutant fly.


title: Drosophila_yw mutant testis_replicate 3

source_name: yw mutant testis, replicate 3


title: Drosophila_sa mutant testis_replicate 2

source_name: sa mutant testis, replicate 2


title: Drosophila_aly mutant testis_replicate 2

source_name: aly mutant testis, replicate 2

value: 1 day old


title: Drosophila_yw mutant testis_replicate 2

source_name: yw mutant testis, replicate 2


title: Drosophila_sa mutant testis_replicate 1

source_name: sa mutant testis, replicate 1


title: Drosophila_pex1-1

description: pex1 homozygous mutant larvae, biological rep1


title: Drosophila_bam mutant testis_replicate 3

source_name: bam mutant testis, replicate 3

treatment_protocol: bam mutant testes were dissected in DEPC-treated 1× PBS buffer in 20 min interval, followed by immediate snap freezing in liquid nitrogen.

value: bam1/bamΔ86 mutant fly.


title: mid-L3_12 hour high sugar fed_biological rep 1

status: Public on Jun 21 2011

first: Thomas

middle: John

last: Baranski

address: 660 S. Euclid Ave. Box 8127

institute: Washington University School of Medicine

description:
14079
Gene expression data from actively feeding, mid-L3 larvae.

hyb_protocol: 15 ug of biotinylated cRNAs were hybridized to Affymetrix Drosophila 2.0 oligonucleotide arrays.

scan_protocol: Gene chips were scanned using the GeneChip GS3000.

data_processing: The data were analyzed with dChip (2006 version) and precise match/mismatch probe intensity was used as normalization method.

source_name: whole male Canton-S Drosophila mid-third instar larvae

label_protocol: Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Canton S were reared at 25C on Bloomington Semi-Defined Food with sucrose substituted for glucose (0.15M). High sugar food contained 1M sucrose instead of 0.15M.

extract_protocol: Tripure extraction of total RNA was performed according to the manufacturer's instructions; RNA was DNase-treated and then cleaned on a Qiagen RNeasy column and eluted in RNase-free H2O.

treatment_protocol: Animals harvested as wandering L3 were fed control or high sucrose Semi-Defined food from embryo hatch. Animals harvested as mid-L3 were fed control food from embryo hatch, then transferred to fresh control or high sucrose as early L3 and aged 12 hours before harvest.

value: whole larva

value: Canton-S

value: mid-third instar

value: male

tag: agent

value: high sugar


title: mid-L3_12 hour control fed_biological rep 2

description:
14077
Gene expression data from actively feeding, mid-L3 larvae.

value: control


title: mid-L3_12 hour high sugar fed_biological rep 3

description:
14081
Gene expression data from actively feeding, mid-L3 larvae.


title: Drosophila_aly mutant testis_replicate 1

source_name: aly mutant testis, replicate 1


title: wandering L3_high sugar reared_biological rep 1

description:
14073
Gene expression data from wandering L3 larvae, after feeding has ceased but before pupariation.

source_name: whole male Canton-S Drosophila wandering third instar larvae

value: wandering third instar


title: wandering L3_high sugar reared_biological rep 2

description:
14074
Gene expression data from wandering L3 larvae, after feeding has ceased but before pupariation.


title: wandering L3_control reared_biological rep 2

description:
14071
Gene expression data from wandering L3 larvae, after feeding has ceased but before pupariation.


title: wandering L3_control reared_biological rep 1

description:
14070
Gene expression data from wandering L3 larvae, after feeding has ceased but before pupariation.


title: wandering L3_high sugar reared_biological rep 3

description:
14075
Gene expression data from wandering L3 larvae, after feeding has ceased but before pupariation.


title: Drosophila_bam mutant testis_replicate 1

hyb_protocol: Approximately 4 μg of total RNA from each biological replicate were used to generate labeling probes to hybridize with the Affymetix GeneChip Drosophila Genome 2.0 Array according to the Affymetrix protocol. Three biological replicates were performed for each genotype. Microarray hybridization was processed at the Core Facility at the Stanford University School of Medicine

source_name: bam mutant testis, replicate 1


title: mid-L3_12 hour control fed_biological rep 3

description:
14078
Gene expression data from actively feeding, mid-L3 larvae.


title: mid-L3_12 hour control fed_biological rep 1

description:
14076
Gene expression data from actively feeding, mid-L3 larvae.


title: mid-L3_12 hour high sugar fed_biological rep 2

description:
14080
Gene expression data from actively feeding, mid-L3 larvae.


title: Drosophila_bam mutant testis_replicate 2

source_name: bam mutant testis, replicate 2


title: wandering L3_control reared_biological rep 3

description:
14072
Gene expression data from wandering L3 larvae, after feeding has ceased but before pupariation.


title: Young 0-2

status: Public on Jun 19 2011

city: Changhua

first: Shih-Feng

last: Fu

state: Changhua

address: No.1 Jin-De Road

country: Taiwan

institute: National Changhua University of Education

description: Gene expression data from 7-day-old hypocotyls without auxin treatment biological rep 2

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: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix GeneChip assay were performed by the Affymetrix Gene Expression Service Lab (http://ipmb.sinica.edu.tw/affy/), supported by Academia Sinica, Taiwan. The CEL files were imported into GeneSpring and normalized by the RMA algorithm.

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: 7-day-old seedlings or 35-day-old plants in full-strength MS

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Either with or without auxin treatment for 1 day

value: hypocotyls

tag: ecotype


title: Mature 1-3

description: Gene expression data from 35-day-old hypocotyls with auxin treatment for 1 day biological rep 3


title: Young 0-1

description: Gene expression data from 7-day-old hypocotyls without auxin treatment biological rep 1


title: Mature 0-2

description: Gene expression data from 35-day-old hypocotyls without auxin treatment biological rep 2


title: Young 1-3

description: Gene expression data from 7-day-old hypocotyls with auxin treatment for 1 day biological rep 3


title: Mature 0-1

description: Gene expression data from 35-day-old hypocotyls without auxin treatment biological rep 1


title: Young 0-3

description: Gene expression data from 7-day-old hypocotyls without auxin treatment biological rep 3


title: Mature 1-1

description: Gene expression data from 35-day-old hypocotyls with auxin treatment for 1 day biological rep 1


title: Mature 1-2

description: Gene expression data from 35-day-old hypocotyls with auxin treatment for 1 day biological rep 2


title: Mature 0-3

description: Gene expression data from 35-day-old hypocotyls without auxin treatment biological rep 3


title: Control-pxt^EY03052-S12-Rep1

status: Public on Jun 09 2011

city: Iowa City

first: Tina

last: Tootle

state: IA

address: 51 Newton Rd, 1-500BSB

department: Anatomy and Cell Biology

institute: University of Iowa

hyb_protocol: Performed by Johns Hopkins Microarray Faciltiy - affymetrix Drosohila Genechip 2.0

data_processing: MAS5 data processing

source_name: stage12 follicle

label_protocol: Performed by Johns Hopkins Microarray Faciltiy - 10ug RNA used to generate probe, no amplification

growth_protocol: 2-4 day old female flies were fed wet yeast for at least 36 hours prior to follicle dissections.

extract_protocol: Trizol

treatment_protocol: Follicles of the stages and genotypes indicated were dissected in Grace's media.

value: follicle

value: female


title: Control-pxt^EY03052-S12-Rep2

scan_protocol: Performed by Johns Hopkins Microarray Faciltiy


title: Control-pxt^EY03052-S14-Rep2

source_name: stage14 follicle


title: Control-pxt^EY03052-S14-Rep1


title: Young 1-1

description: Gene expression data from 7-day-old hypocotyls with auxin treatment for 1 day biological rep 1


title: Control-pxt^EY03052-S10B-Rep2

source_name: stage10B follicle


title: Control-pxt^f01000-S14-Rep2


title: Control-pxt^EY03052-S10B-Rep1


title: Control-pxt^f01000-S14-Rep1


title: Control-pxt^f01000-S12-Rep1


title: Control-yw-S12-Rep2

value: yw


title: Control-pxt^f01000-S12-Rep2


title: Control-pxt^f01000-S10B-Rep2


title: Control-yw-S12-Rep1


title: Control-yw-S14-Rep1


title: Control-yw-S10B-Rep4


title: Control-yw-S10B-Rep2


title: Control-yw-S10B-Rep3


title: Control-pxt^f01000-S10B-Rep1


title: Control-yw-S14-Rep2


title: Control-yw-S10B-Rep1


title: Control-yw-S9/10A-Rep1

source_name: stage9/10A follicle


title: Control-yw-S9/10A-Rep2


title: seedlings +5AC rep3

status: Public on Jun 03 2011

city: West Lafayette

first: Karen

middle: A

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

institute: USDA-ARS

description: Gene expression data from 10day old seedlings treated with 5-AC

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: Data for the matrix was normalized using the threestep method from Bioconductor: GCRMA background correction, scaling normalization, and median polish for summarization, for all probes on the array.

source_name: seedlings + 20mg/L 5-aza-2’deoxycytidine

label_protocol: According to Affymetrix protocol

growth_protocol: Plants were germinated in liquid 0.5X MS media with 1% sucrose in 15cm petri plates in constant light at 21C.

extract_protocol: 10 days after germination, RNA was extracted from whole seedlings using the Qiagen Plant Rneasy kit.

treatment_protocol: After 24 hours, 5-AC (20mg/L)  and TSA (2.5mg/L) in DMSO were added to chemically-treated samples, control and ddm1 seedlings received DMSO alone.  After 5 days, media was drained and fresh media including supplements was added.

value: 10-day old whole seedling

value: wildtype

value: Ws


title: seedlings + TSA rep1

description: Gene expression data from 10day old seedlings treated with TSA

source_name: seedlings + 2.5 mg/L trichostatin A


title: seedlings + TSA rep3


title: seedlings +5AC rep1


title: control seedlings rep2

description: Gene expression data from 10day old Ws seedlings grown in contiuous light in 0.5X MS + sucrose.

source_name: untreated, wild-type seedlings


title: control seedlings rep3