title: INP Tim-Dcr ZT15

description: INP sample from Tim-Dcr flies, ZT15


title: T+S I BEAS2b_ML06C

status: Public on Aug 31 2009

type: RNA

city: Toronto

first: Claudia

middle: Chimisso

last: dos Santos

state: ON

address: 30, Bond Street, room 4-011

department: University of Toronto

country: Canada

institute: Saint Michaels Hospital

description: Gene expression data from cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133plus2.0 chips . 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: Probe based analysis, background reduction, and quantile data normalization was performed in MeV 4.0 of TM4 using Robust Multi-array Average (RMA).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: BEAS-2B - mechanical stretch plus TNF-α

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

growth_protocol: Cells were grown in DMEM with 5% FBS. Cells were seeded at 2 x 10E+5 in 6 well Flexercell plates - silicon elastic plates coated with Type I collagen (Flexercell International, McKeesport, PA)

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

treatment_protocol: Human Bronchial Epithelial Cells (Beas-B2)  were exposed to six regiments for 4 h: 1) control (static, [control]); 2) mechanical stretch (25 PKa, 30 cycles per min, [stretch]); 3) LPS (1 mcg/ml [LPS]); 4) TNF-α (20 ng/ml; [TNF]); 5) mechanical stretch plus LPS [LPS+S], and 6) mechanical stretch plus TNF-α [TNF+S].

tag: cell line

value: Human Bronchial Epithelial Cells Beas-B2

tag: cell type

value: Transformed Pulmonary distal (small) airway cell


title: TNF II BEAS 2b_ML03

description: Gene expression data from cells

source_name: BEAS-2B - TNF-α


title: Control I BEAS2b_ML01C

description: Gene expression data from cells

source_name: BEAS-2B - control


title: IP ZT19, replica 2

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

country: USA

institute: Janelia Research Campus

description: IP sample, ZT19

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hrs at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G7

data_processing: The data were processed with GCRMA algorithm in the Bioconductor with default settings

organism: Drosophila melanogaster

source_name: fly head

label_protocol: RNA was utilized to prepare cDNA and cRNA using the Affymetrix IVT labeling Kit

growth_protocol: Flies were grown under standard conditions in 12hs light and 12hs dark cycles

extract_protocol: Heads were collected and RNA extracted using TRIZOL

tag: time point

tag: replicate

tag: tissue

value: head

tag: developmental stage

value: adult


title: IP ZT15, replica 1

description: IP sample, ZT15


title: LPS I BEAS2b_ML03C

description: Gene expression data from cells

source_name: BEAS-2B - LPS


title: Stretch II BEAS 2b_ML04

description: Gene expression data from cells

source_name: BEAS-2B - mechanical stretch


title: Control II BEAS2b_ML01

description: Gene expression data from cells


title: LPS II BEAS 2b_ML02

description: Gene expression data from cells


title: TNF I BEAS2b_ML05C

description: Gene expression data from cells


title: IP ZT7, replica 2

description: IP sample, ZT7


title: IP ZT23, replica 2

description: IP sample, ZT23


title: IP ZT11, replica 2

description: IP sample, ZT11


title: IP ZT11, replica 1

description: IP sample, ZT11


title: IP ZT3, replica 1

description: IP sample, ZT2


title: INPUT ZT23, replica 1

description: INP sample, ZT23


title: INPUT ZT23, replica 2

description: INP sample, ZT23


title: INPUT ZT19, replica 2

description: INP sample, ZT19


title: INPUT ZT15, replica 1

description: INP sample, ZT15


title: INPUT ZT15, replica 2

description: INP sample, ZT15


title: INPUT ZT19, replica 1

description: INP sample, ZT19


title: IP ZT3, replica 2

description: IP sample, ZT3


title: INPUT ZT11, replica 1

description: INP sample, ZT11


title: INPUT ZT3, replica 1

description: INP sample, ZT3


title: Mock 4h, biological rep1

city: Sheffield

first: Martin

last: Zeidler

address: Western Bank

department: Dept of Biomedical Science

country: United Kingdom

institute: University of Sheffield

description: Mock 4h, biological rep1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: The data were analyzed using the PUMA package available on the Bioconductor webpage

source_name: Drosophila Kc167 cells treated with Mock for 30 min and total RNA extracted after 4h

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

growth_protocol: Kc167 cells were grown in Schneider's Drosophila medium

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. A second cleanup of total RNA was performed as suggested by Affymetrix. After the ethanol precipitation in the Trizol procedure, a cleanup using QIAGEN Rneasy Mini Kit was performed

treatment_protocol: 5 million Kc167 cells were distributed in individual wells of a 6-well tissue culture plate and treated with UPD or Mock condtioned media for 30 min, the conditioned media was then replaced by Schneider's Drosophila media and total RNA extracted 2, 4 or 10h after initial addition of conditioned media. Biological duplicates were generated for each condition and time point resulting in a total of 12 samples

value: Kc167 cell line

tag: treatment

value: Mock

tag: time


title: INPUT ZT7, replica 1

description: INP sample, ZT7


title: UPD 10h, biological rep1

description: UPD 10h, biological rep1

source_name: Drosophila Kc167 cells treated with UPD for 30 min and total RNA extracted after 10h

value: UPD


title: UPD 2h, biological rep1

description: UPD 2h, biological rep1

source_name: Drosophila Kc167 cells treated with UPD for 30 min and total RNA extracted after 2h


title: UPD 10h, biological rep2

description: UPD 10h, biological rep2


title: Mock 4h, biological rep2

description: Mock 4h, biological rep2


title: Mock 2h, biological rep1

description: Mock 2h, biological rep1

source_name: Drosophila Kc167 cells treated with Mock for 30 min and total RNA extracted after 2h


title: INPUT ZT11, replica 2

description: INP sample, ZT11


title: Mock 2h, biological rep2

description: Mock 2h, biological rep2


title: IP ZT7, replica 1

description: IP sample, ZT7


title: Mock 10h, biological rep1

description: Mock 10h, biological rep1

source_name: Drosophila Kc167 cells treated with Mock for 30 min and total RNA extracted after 10h


title: INPUT ZT7, replica 2

description: INP sample, ZT7


title: UPD 4h, biological rep2

description: UPD 4h, biological rep2

source_name: Drosophila Kc167 cells treated with UPD for 30 min and total RNA extracted after 4h


title: UPD 4h, biological rep1

description: UPD 4h, biological rep1


title: Mock 10h, biological rep2

description: Mock 10h, biological rep2


title: UPD 2h, biological rep2

description: UPD 2h, biological rep2


title: Col-0_37C_rep1

status: Public on Aug 28 2009

city: Taipei

first: Yee-yung

last: Charng

address: 128, Academia Rd. Sec. 2

department: Agric. Biotech. Res. Center

country: Taiwan

institute: Academia Sinica

description: seedling, heat shock

hyb_protocol: According to standard Affymetrix protocols.

data_processing: GCOS; normalized by global scaling

organism: Arabidopsis thaliana

source_name: Col-0 seedlings heat stress rep1

extract_protocol: Qiagen RNA extraction kit

tag: Seven days old seedlings of Arabidopsis wild type ecotype Columbia were used


title: til1-1_22C_rep1

description: seedling, heat shock control

scan_protocol: According to standard Affymetrix protocols.

source_name: til1-1 seedlings control condition rep1

tag: Seven days old seedlings of Arabidopsis mutant of til1-1 ecotype Columbia were used


title: Col-0_37C_rep2

description: seedling, heat shock

source_name: Col-0 seedlings heat stress rep2

label_protocol: According to standard Affymetrix protocols.


title: Stretch I BEAS2b_ML02C

description: Gene expression data from cells


title: til1-1_22C_rep2

description: seedling, heat shock, control

source_name: til1-1 seedlings control condition rep2


title: Col-0_22C_rep1

description: seedling, heat shock, control

source_name: Col-0 seedlings control condition rep1


title: til1-1_37C_rep1

description: seedling, heat shock

source_name: til1-1 seedlings heat stress rep1


title: til1-1_37C_rep2

description: seedling, heat shock

source_name: til1-1 seedlings heat stress rep2


title: Col-0_22C_rep2

description: seedling, heat shock, control

source_name: Col-0 seedlings control condition rep2


title: small airways, smoker 264

status: Public on Aug 27 2009

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: small airways, smoker 264

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: airway epithelial cells obtained by bronchoscopy and brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: age

tag: sex

value: M

tag: ethnic group

value: black

tag: smoking status

value: smoker, 11 pack-years


title: MCF7-V(2)

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: vehicle treated MCF-7, biological rep2

hyb_protocol: Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS

data_processing: MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100

source_name: MCF-7, vehicle treated

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)

growth_protocol: MCF-7/BUS cell culture was maintained in high-glucose, phenol red-free DMEM (PF-DMEM) and supplemented with 5% fetal calf serum.

extract_protocol: QIAGEN RNeasy protocol and reagents for extraction of total RNA

treatment_protocol: Vehicle (0.1% ethanol = 1000X working stock solution) was added directly to cell culture (10 microliter for a 10-cm dish containing 10 ml medium). Cells were incubated for 48 hours, and their total RNA was isolated for transcriptomal analysis.

value: cancer cell culture

value: vehicle


title: small airways, non-smoker 141

description: small airways, non-smoker 141

value: non-smoker


title: small airways, smoker 241

description: small airways, smoker 241

value: smoker, 45 pack-years


title: MCF7-V(1)

description: vehicle treated MCF-7, biological rep1


title: MCF7-F(1)

description: Fulvestrant treated MCF-7, biological rep1

source_name: MCF-7, fulvestrant treated

treatment_protocol: Fulvestrant (0.1 mM in ethanol = 1000X working stock solution) was added directly to cell culture (10 microliter for a 10-cm dish containing 10 ml medium). Cells were incubated for 48 hours, and their total RNA was isolated for transcriptomal analysis.

value: fulvestrant


title: MCF7-V(3)

description: vehicle treated MCF-7, biological rep3


title: small airways, non-smoker 124

description: small airways, non-smoker 124

value: F


title: MCF7-F(2)

description: Fulvestrant treated MCF-7, biological rep2


title: trachea, smoker 177

value: Afr

value: smoker, 38 pack-years


title: MCF7-F(3)

description: Fulvestrant treated MCF-7, biological rep3


title: small airways, non-smoker 138

description: small airways, non-smoker 138


title: trachea, smoker 203

value: smoker, 24.5 pack-years


title: trachea, smoker 179

value: smoker, 40 pack-years


title: trachea, smoker 188

value: smoker, 17.5 pack-years


title: trachea, smoker 250

value: smoker, 22 pack-years


title: trachea, smoker 219

value: smoker, 24 pack-years


title: trachea, smoker 169

value: smoker, 47 pack-years


title: trachea, smoker 176

value: M

value: smoker, 33 pack-years


title: trachea, smoker 225

value: smoker, 16.4 pack-years


title: trachea, smoker 114

value: black


title: trachea, smoker 215

value: Eur

value: smoker, 26 pack-years


title: trachea, smoker 214

value: smoker, 10 pack-years


title: trachea, non-smoker 095

value: white

value: non-smoker


title: trachea, smoker 220

value: Afr

value: smoker, 9.25 pack-years


title: trachea, non-smoker 083

value: F


title: trachea, non-smoker 074


title: trachea, non-smoker 045


title: trachea, non-smoker 065


title: trachea, non-smoker 060


title: small airways, non-smoker 110


title: small airways, smoker 246

value: smoker, 26.5 pack-years


title: trachea, non-smoker 059_089


title: trachea, non-smoker 064_094


title: trachea, non-smoker 061


title: small airways, non-smoker 118


title: trachea, non-smoker 088


title: trachea, non-smoker 042


title: trachea, non-smoker 066


title: small airways, smoker 208

value: smoker, 46 pack-years


title: trachea, smoker 164

value: smoker, 44.3 pack-years


title: trachea, smoker 130

value: smoker, 12 pack-years


title: trachea, smoker 186

value: smoker, 23.5 pack-years


title: trachea, smoker 058

value: M

value: smoker, 80 pack-years


title: trachea, non-smoker 050

value: hispanic


title: trachea, smoker 120

value: black

value: smoker, 30 pack-years


title: trachea, non-smoker 048


title: trachea, non-smoker 023


title: trachea, smoker 152

value: smoker, 16 pack-years


title: trachea, non-smoker 021


title: trachea, non-smoker 059


title: trachea, non-smoker 047


title: trachea, non-smoker 029


title: trachea, non-smoker 039


title: trachea, non-smoker 022


title: trachea, non-smoker 036


title: trachea, non-smoker 004


title: trachea, non-smoker 005


title: trachea, non-smoker 011


title: trachea, non-smoker 015


title: IXB_induced_Rep1

city: Sherbrooke

first: Nathalie

last: Beaudoin

state: Quebec

address: 2500, Blvd Universite

department: Faculte des Sciences

institute: Universite de Sherbrooke

description: Control CEL files are the same as for the TA treatment.

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Fluidics protocol EukGE_WS2v5_450

scan_protocol: GeneChip scanner

data_processing: Robust Multichip Average (RMA) via FlexArray software package (http://genomequebec.mcgill.ca/FlexArray).  Data for IXB treatment were processed separately from TA treatment.

source_name: 100mL suspension cells, 100nM IXB, 6h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana ecotype Landsberg erecta suspension cultured cells were grown in Murashige and Skoog (MS) medium (pH 5.7, 0.6 g L-1 MES) supplemented with B5 vitamins and 1 mg L-1 2,4-D. Cells were maintained in the dark under continuous shaking (gyratory shaker) at 120 rpm at 21ºC. Suspensions of 100 mL were sub-cultured weekly in 250mL flasks using 3:7 dilution.

extract_protocol: Cells were vacuum-filtered. Then 500 mg were ground in liquid N2 and mixed vigorously with hot extraction buffer consisting in one part of RNA buffer (100 mM Tris pH 8, 10 mM EDTA, 100 mM LiCl, 1% SDS) and one part of equilibrated phenol heated at 80°C. Samples were extracted with chloroform/isoamyl alcohol (24:1) and RNA was precipitated from the supernatant with 4 M LiCl. Pellets were resuspended in DEPC-treated water and extracted with phenol/chloroform/isoamyl alcohol (25:24:1). RNA was precipitated from the aqueous phase with 3 M sodium acetate and ethanol. RNA pellets were dissolved in DEPC-treated water.

treatment_protocol: IXB (1 mM in methanol; Crescent Chemicals Co., Inc., Islandia, NY, USA) was added at a final concentration of 100 nM. The same volume of methanol (20 µL) was added to all cells. Treatments were carried out the third day after sub-culture, at the beginning of the exponential phase. Samples consisted of four replicates for each condition, and each replicate was the combination of two 250 mL flasks containing 100 mL of cells pooled together before freezing in liquid N2 after 6 h of contact with the inhibitor.

tag: agent

value: 100nM IXB

tag: genotype

value: Ecotype Landsberg erecta

value: Suspension cells

value: Third day after subculture


title: Methanol_Rep4, IXB

source_name: 100mL suspension cells, 20µL methanol, 6h

value: 20µL methanol


title: IXB_induced_Rep2


title: Methanol_Rep2, IXB


title: TA_induced_Rep2

description: Control CEL files are the same as for the IXB treatment.

data_processing: Robust Multichip Average (RMA) via FlexArray software package (http://genomequebec.mcgill.ca/FlexArray). Data for TA treatment were processed separately from IXB treatment.

source_name: 100mL suspension cells, 2µM TA, 6h

treatment_protocol: TA diluted in methanol (10 mM) was added to Arabidopsis cell suspensions at a final concentration of 2 µM. The same volume of methanol (20 µL) was added to all cells. Treatments were carried out the third day after sub-culture, at the beginning of the exponential phase. Samples consisted of four replicates for each condition, and each replicate was the combination of two 250 mL flasks containing 100 mL of cells pooled together before freezing in liquid N2 after 6 h of contact with the inhibitor.

value: 2µM TA


title: IXB_induced_Rep3


title: TA_induced_Rep4


title: TA_induced_Rep3


title: Methanol_Rep2, TA


title: Methanol_Rep3, IXB


title: IXB_induced_Rep4


title: Methanol_Rep3, TA


title: Methanol_Rep1, IXB


title: Methanol_Rep4, TA


title: TA_induced_Rep1


title: Human trunk neural crest cell line N3

status: Public on Aug 26 2009

city: Marseille

first: Heather

middle: C

last: Etchevers

address: 27 boulevard Jean Moulin

department: INSERM U1251

country: France

institute: INSERM/Aix-Marseille Univ

description: Human trunk neural crest cell line N3

hyb_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, Calif.

data_processing: GC-RMA normalization

source_name: migrated neural crest cells from trunk level of Carnegie stage 12 embryonic neural tube

growth_protocol: 8h clean neural tube in film of medium on collagen I-coated plastic. Add 1ml medium in 35mm dish to promote cell migration for 8-16 subsequent hours. Remove neural tube with fire-rounded glass filament, leaving neural crest cells. Detach with trypsin and reseed all regularly and sparsely in new 35mm dish. Medium: 12% fetal calf serum, 8.5% BGjb medium, 25.5% DMEM, 51% F12 medium, 1x penicillin/streptomycin, 2 mM glutamine, 10 mM HEPES, 0.1 ug/ml hydrocortisone, 10 µg/ml transferrin, 0.4 ng/ml T3 (3,3,5-thio-iodo-thyronine), 10 pg/ml glucagon, 100 pg/ml EGF, 1 ng/ml insulin, 200pg/ml FGF2

extract_protocol: Qiagen RNA mini columns with on-column DNase treatment. RNA integrity number >9.9 on Agilent Bioanalyzer.

treatment_protocol: Dissociate mesoderm (including notochord), ectoderm and endoderm from neural tube segment corresponding to somites 6-18 with brief incubation in PBS-diluted pancreatin. Stop reaction with serum-containing PBS and transfer to clean PBS to finish cleaning neural tube.

tag: Gender

value: Male

tag: Karyotype

tag: Developmental stage

value: Carnegie stage 12

tag: Cell type

value: Enriched trunk neural crest cells


title: ARPE-19 42h-2

city: Kisarazu

first: Rui

last: Ose

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Department of Human Genome Research

country: Japan

institute: Kazusa DNA Research Institute

description: ARPE-19 42h-2

hyb_protocol: Refer to the Affymetrix Expression Analysis Technical Manual

label: Biotin

source_name: ARPE-19 treated with TGF and TNF for 42 hour

label_protocol: IVT labeling Kit

extract_protocol: Qiagen RNeasy Mini Kit


title: ARPE-19 42h-0

description: ARPE-19 42h-0

scan_protocol: Refer to the Affymetrix Expression Analysis Technical Manual

tag: ARPE-19 treated with TGF and TNF for 42 hour


title: Human trunk neural crest cell line N5

description: Human trunk neural crest cell line N5

scan_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, Calif.

source_name: migrated neural crest cells from trunk level of Carnegie stage 13 embryonic neural tube

value: Female

value: Carnegie stage 13

value: Enriched human trunk neural crest cells


title: Human trunk neural crest cell line N1

description: Human trunk neural crest cell line N1

label_protocol: According to Affymetrix Gene-Chip expression analysis technical manual, Affymetrix, Santa Clara, Calif.

value: Enriched neural crest cells


title: ARPE-19 24h-2

description: ARPE-19 24h-2

source_name: ARPE-19 treated with TGF and TNF for 24 hour


title: ARPE-19 42h-1

description: ARPE-19 42h-1


title: Human trunk neural crest cell line N4

description: Human trunk neural crest cell line N4


title: ARPE-19 24h-0

description: ARPE-19 24h-0

tag: ARPE-19 treated with TGF and TNF for 24 hour


title: ARPE-19 60h-1

description: ARPE-19 60h-1

source_name: ARPE-19 treated with TGF and TNF for 60 hour


title: ARPE-19 16h-1

description: ARPE-19 16h-1

source_name: ARPE-19 treated with TGF and TNF for 16 hour


title: ARPE-19 16h-0

description: ARPE-19 16h-0

tag: ARPE-19 treated with TGF and TNF for 16 hour


title: ARPE-19 60h-0

description: ARPE-19 60h-0

tag: ARPE-19 treated with TGF and TNF for 60 hour


title: Human trunk neural crest cell line N2

description: Human trunk neural crest cell line N2


title: ARPE-19 24h-1

description: ARPE-19 24h-1


title: ARPE-19 6h-2

description: ARPE-19 6h-2

source_name: ARPE-19 treated with TGF and TNF for 6 hour


title: ARPE-19 1h-1

description: ARPE-19 1h-1

source_name: ARPE-19 treated with TGF and TNF for 1 hour


title: ARPE-19 16h-2

description: ARPE-19 16h-2


title: ARPE-19 6h-0

description: ARPE-19 6h-0

tag: ARPE-19 treated with TGF and TNF for 6 hour


title: ARPE-19 0h-2

description: ARPE-19 0h-2


title: ARPE-19 0h-1

description: ARPE-19 0h-1


title: ARPE-19 6h-1

description: ARPE-19 6h-1


title: ARPE-19 1h-0

description: ARPE-19 1h-0

tag: ARPE-19 treated with TGF and TNF for 1 hour


title: ARPE-19 0h-0

description: ARPE-19 0h-0


title: VEGF + 8CPT

status: Public on Aug 25 2009

city: Chicago

first: Robert

last: Doebele

state: IL

address: 5841 S. Maryland Ave. MC 2115

department: Medicine

institute: University of Chicago

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on Affy U133A + 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Pooled primary dermal human microvascular endothelial cells

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

growth_protocol: 10^6 HMVEC were starved overnight in EBM2 media supplemented with 0.1% BSA followed by treatment as indicated

extract_protocol: Total RNA was extracted from cells using the Qiagen Rneasy kit according to manufacturer's instructions

treatment_protocol: Cells were mock treated (control) or treated for 4 hours with either VEGF (100pg/ml), VEGF + 8CPT (100 micromolar), or VEGF + ET [5 micrograms/ml protective antigen (PA) + 1 microgram/ml edema factor (EF)]

tag: treatment

value: VEGF + 8CPT

tag: cell type


title: VEGF + ET

value: VEGF + ET

value: primary dermal human microvascular endothelial cell


title: Untreated control

value: Untreated


title: VEGF

value: VEGF


title: P32/10mg/kg/W0

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

description: Response to infliximab was defined as endoscopic and histologic healing at week 8

hyb_protocol: Following fragmentation, 11 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GCOS 1.4 (GeneChip Operating System) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: colonic biopsy; WK8RSPHM: No

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

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

value: No


title: P14/5mg/kg/W0

source_name: colonic biopsy; WK8RSPHM: Yes

value: Yes


title: P24/10mg/kg/W0


title: P16/5mg/kg/W0


title: P33/5mg/kg/W0


title: P13/5mg/kg/W0 P111633


title: P17/10mg/kg/W0


title: P27/10mg/kg/W0


title: P47/5mg/kg/W0


title: P36/10mg/kg/W0


title: P45/5mg/kg/W0


title: P28/10mg/kg/W0


title: P19/10mg/kg/W0


title: P15/10mg/kg/W0


title: P29/5mg/kg/W0


title: P34/10mg/kg/W0


title: P13/5mg/kg/W0 P111632


title: P12/5mg/kg/W0


title: P9/5mg/kg/W0


title: P5/10mg/kg/W0


title: Infected pft1 leaf, rep1

status: Public on Aug 24 2009

city: St Lucia

first: Brendan

last: Kidd

state: QLD

address: 306 Carmody Road

department: Plant Industry

country: Australia

institute: CSIRO

description: Expression data from pft1 leaves harvested 48 hours after inoculation with F. oxysporum.

hyb_protocol: The RNA was labelled, hybridized, washed and scanned by the AGRF (Australian Genome Research Facility - http://www.agrf.org.au) according to Affymetrix requirements.

data_processing: The data was analyzed using GenespringGX 7.3.1. The raw CEL files were pre-processed using the RMA algorithm and the resulting expression values were normalized per chip to the median across all chips.

source_name: pft1 leaves, inoculation with F. oxysporum

growth_protocol: Plants were grown under short day conditions (8hrs light, 24C and 21C day night cycle) in plastic trays (30 cells 5cmx5cm) with two plants per cell for 4 weeks before treatment.

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

treatment_protocol: Treatment involved gently uprooting the plants from the soil, rinsing the roots with distilled water to remove excess soil and then incubating in either a F. oxysporum spore suspension (1 million spores/ml resuspended in water) or distilled water (mock) for 15 seconds before replanting in soil. Plants were moved to hotter, long day conditions (16hr light, 28C and 21C day night cycle) to promote infection and harvested 48 hours after treatment.

value: pft1 mutant

tag: tissue

value: leaf

value: F. oxysporum


title: P2/10mg/kg/W0


title: Infected pft1 leaf, rep2

scan_protocol: The RNA was labelled, hybridized, washed and scanned by the AGRF (Australian Genome Research Facility - http://www.agrf.org.au) according to Affymetrix requirements.


title: P3/5mg/kg/W0


title: P10/10mg/kg/W0


title: Infected pft1 leaf, rep4

label_protocol: The RNA was labelled, hybridized, washed and scanned by the AGRF (Australian Genome Research Facility - http://www.agrf.org.au) according to Affymetrix requirements.


title: Infected Col-0 leaf, rep4

description: Expression data from Col-0 leaves harvested 48 hours after inoculation with F. oxysporum.

source_name: Col-0 leaves, inoculation with F. oxysporum

value: WT


title: Infected pft1 leaf, rep3


title: Infected Col-0 leaf, rep2


title: Infected Col-0 leaf, rep3


title: Infected Col-0 leaf, rep1


title: Mock pft1 leaf, rep4

description: Expression data from pft1 leaves harvested 48 hours after the Mock treatment.

source_name: pft1 leaves, mock treatment

value: water


title: Mock pft1 leaf, rep1


title: Mock Col-0 leaf, rep3

description: Expression data from Col-0 leaves harvested 48 hours after the Mock treatment.

source_name: Col-0 leaves, mock treatment


title: Mock Col-0 leaf, rep4


title: Mock Col-0 leaf, rep2


title: Mock pft1 leaf, rep2


title: Mock pft1 leaf, rep3


title: pKLO beta-catenin shRNA,, biological rep2

first: Daniel

middle: Ruben

last: Carrasco

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

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.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Data were further process by the PLIER method.

source_name: Cultured MM1S cell line, treated (maternal transcripts)

growth_protocol: Cell were grown and maintained in a 37oC incubator with 5% CO2.

extract_protocol: RNA was extracted according to the manufacturer's protocol, purified using RNeasy kit (Qiagen)

treatment_protocol: 5x10^6 MM1.S cells lentivirally infected with control shRNA or beta-catenin shRNA vectors and sorted for GFP positive populations were cultured in triplicate, washed in PBS and then resuspended in Trizol reagent (invitrogen).

tag: cell line

value: Multiple myeloma line MM1.S

tag: protocol

value: beta-catenin knockdown


title: Mock Col-0 leaf, rep1


title: pKLO GFP control, biological rep3

value: control


title: pKLO beta-catenin shRNA,, biological rep1


title: pKLO beta-catenin shRNA,, biological rep3


title: CLL with 1mM VPA, biological rep13

city: Bruxelles

first: Basile

last: Stamatopoulos

address: Bd de Waterloo n°121

department: Experimental Hematology

country: Belgium

institute: Jules Bordet Institute

description: Gene expression data from CLL treated or not with 1mM VPA during 4hrs

hyb_protocol: Following fragmentation, 16 µg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Geneship Fluidics Station 450 regarding Affymetrix protocol (www.affymetrix.com)

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

data_processing: Image analysis and probe quantification were done with Affymetrix software, which produced raw probe intensity data in the Affymetrix CEL files. Normalization was done with the RMA method, which processed a group of CEL files simultaneously using BRB arrays tools.

source_name: CLL with 1mM VPA, biological rep13

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (www.affymetrix.com)

growth_protocol: Peripheral Blood Mononuclear Cells (PBMC) were obtained from blood of Chronic lymphocytic leukemia patients and were plated with 1mM VPA during 4hrs (for all VPA sample)

extract_protocol: Total RNA was extracted from purified B cells in a single step using TriPure Isolation Reagent

treatment_protocol: PBMC were isolated by density-gradient centrifugation and B cells were purified negatively with magnetic-bead system.

tag: sex

value: M

tag: age

tag: binet stage

value: A

tag: mutational status


title: CLL without VPA, biological rep11

source_name: CLL without VPA, biological rep11

growth_protocol: Peripheral Blood Mononuclear Cells (PBMC) were obtained from blood of Chronic lymphocytic leukemia patients and were plated without VPA during 4hrs (for all control sample)

value: B


title: pKLO GFP control, biological rep2


title: CLL without VPA, biological rep12

source_name: CLL without VPA, biological rep12

value: F


title: CLL without VPA, biological rep14

source_name: CLL without VPA, biological rep14


title: CLL without VPA, biological rep13

source_name: CLL without VPA, biological rep13


title: CLL with 1mM VPA, biological rep10

source_name: CLL with 1mM VPA, biological rep10


title: pKLO GFP control, biological rep1


title: CLL with 1mM VPA, biological rep12

source_name: CLL with 1mM VPA, biological rep12


title: CLL without VPA, biological rep9

source_name: CLL without VPA, biological rep9


title: CLL without VPA, biological rep10

source_name: CLL without VPA, biological rep10


title: CLL with 1mM VPA, biological rep14

source_name: CLL with 1mM VPA, biological rep14


title: CLL with 1mM VPA, biological rep11

source_name: CLL with 1mM VPA, biological rep11


title: CLL with 1mM VPA, biological rep8

source_name: CLL with 1mM VPA, biological rep8

value: UM; ZAP70 -; LPL - ; CD38 +


title: CLL with 1mM VPA, biological rep7

source_name: CLL with 1mM VPA, biological rep7

value: UM; ZAP70 +; LPL - ; CD38 +


title: CLL with 1mM VPA, biological rep9

source_name: CLL with 1mM VPA, biological rep9


title: CLL with 1mM VPA, biological rep5

source_name: CLL with 1mM VPA, biological rep5

value: UM; ZAP70 +; LPL +; CD38 +


title: CLL with 1mM VPA, biological rep6

source_name: CLL with 1mM VPA, biological rep6

value: UM; ZAP70 +; LPL +; CD38 -


title: CLL without VPA, biological rep6

source_name: CLL without VPA, biological rep6


title: CLL with 1mM VPA, biological rep2

source_name: CLL with 1mM VPA, biological rep2


title: CLL without VPA, biological rep7

source_name: CLL without VPA, biological rep7


title: ARPE-19 60h-2

description: ARPE-19 60h-2

source_name: ARPE-19 treated with TGF and TNF for 60 hour


title: CLL with 1mM VPA, biological rep3

source_name: CLL with 1mM VPA, biological rep3


title: CLL with 1mM VPA, biological rep4

source_name: CLL with 1mM VPA, biological rep4


title: CLL without VPA, biological rep8

source_name: CLL without VPA, biological rep8


title: CLL without VPA, biological rep4

source_name: CLL without VPA, biological rep4


title: CLL without VPA, biological rep2

source_name: CLL without VPA, biological rep2


title: CLL without VPA, biological rep5

source_name: CLL without VPA, biological rep5


title: CLL without VPA, biological rep1

source_name: CLL without VPA, biological rep1

value: C


title: CLL without VPA, biological rep3

source_name: CLL without VPA, biological rep3


title: CLL with 1mM VPA, biological rep1

source_name: CLL with 1mM VPA, biological rep1


title: wild type dark repA

status: Public on Aug 19 2009

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

description: Seedlings were kept in the dark for 3 days after germination

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

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

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

source_name: plant seedlings

label_protocol: 100ng of total RNA were amplified and labeled using the Message Amp II-biotin Enhanced reagents (Ambion; catalog #AM1791). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (www.affymetrix.com).

growth_protocol: Seedlings were grown as described previously (Duek et al., 2004, Curr Biol, 14, 2296-2301). All mutants were in the Columbia background (Col) and the pif4pif5 double mutant has been described previously (Lorrain et al., 2008, Plant J, 53, 312-323).

extract_protocol: Seedlings were flash-frozen in liquid nitrogen, ground using a tissulyser (Qiagen) 2 times 30s, 30Hz without extraction buffer, then twice again in the presence of RLT extraction buffer (Qiagen). RNAs were extracted using the RNeasy plant mini kit (Qiagen) following the manufacturer’s recommendations except that 3 washes were done with the RLP buffer instead of 2.

treatment_protocol: Approximately 100 seeds were plated on half MS and kept in the dark and cold for 3 days. Germination was induced by a 3 hours red light (50µmol/m2/s) and seedlings were kept in the dark for 3 days before being subjected to 1 or 24 hrs of 0.5 or 5µmol.m2.s1 of FR light.

tag: growth stage

value: seedling

tag: genotype

value: wild type


title: pif4pif5 mut dark repA


title: wild type 1h FR repC

description: Seedlings were kept in the dark for 3 days after germination  before being subjected to 1 hr of 0.5µmol.m2.s1 of FR light


title: pif4pif5 mut dark repC


title: pif4pif5 mut 1h FR repB


title: wild type 24h FR repB

description: Seedlings were kept in the dark for 3 days after germination  before being subjected to 24 hrs of 5µmol.m2.s1 of FR light


title: pif4pif5 mut 24h FR repC


title: wild type 24h FR repC


title: wild type 1h FR repB


title: pif4pif5 mut dark repB


title: pif4pif5 mut 24h FR repA


title: wild type dark repC


title: wild type 1h FR repA


title: wild type 24h FR repA


title: pif4pif5 mut 1h FR repA


title: pif4pif5 mut 24h FR repB


title: SPS1 dsRNA treated cell at day 1, biological rep 5

status: Public on Aug 18 2009

city: Seoul

first: Byeong

middle: Jae

last: Lee

address: 599 Gwanak-ro, Gwanak-gu,

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: Gene expression data from SPS1 dsRNA treated cell at day1(biological replication 5)

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45℃ on Gene Chip Drosophila Genome 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Acuty 4.0 (Axon instrument) using a RMA (Robuster Multichip Analysis) as following 3step;background correction, normalization between chip using quantile normalization method, summerization using median polish method.

source_name: Drosophila SL2 cell of 1day after SPS1 dsRNA treatment

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

growth_protocol: Drosophila Schneider cell line 2 (SL2) was cultured at 25℃ using HyQ SFX-Insect media

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. The RNA quality was checked with Experion (Applied Biosystems) according to the manufacturer’s instructions.

treatment_protocol: 0.25×106 cells were plated on a 24-well plate in 0.5ml of HyQ SFX-Insect media. 4 mg of dsRNAs were added directly to the cells and incubated for 24 hrs and split into appropriate culture dishes for further incubation


title: No treatment control cell at day 3, biological rep 2

description: Gene expression data from no treated cell at day3 (biological replication 2)

source_name: Drosophila SL2 cell of 3day after no treatment


title: No treatment control cell at day 5, biological rep 1

description: Gene expression data from no treated cell at day5 (biological replication 1)

source_name: Drosophila SL2 cell of 5day after no treatment


title: SPS1 dsRNA treated cell at day 3, biological rep 1

description: Gene expression data from SPS1 dsRNA treated cell at day3 (biological replication 1)

source_name: Drosophila SL2 cell of 3day after SPS1 dsRNA treatment


title: No treatment control cell at day 3, technical rep 2

description: Gene expression data from no treated cell at day3 (technical replication 2)


title: SPS1 dsRNA treated cell at day 3, technical rep 2

description: Gene expression data from SPS1 dsRNA treated cell at day3 (technical replication 2)


title: No treatment control cell at day 3, biological rep 1

description: Gene expression data from no treated cell at day3 (biological replication 1)


title: SPS1 dsRNA treated cell at day 5, biological rep 2

description: Gene expression data from SPS1 dsRNA treated cell at day5 (biological replication 2)


title: SPS1 dsRNA treated cell at day 5, biological rep 1

description: Gene expression data from SPS1 dsRNA treated cell at day5 (biological replication 1)


title: SPS1 dsRNA treated cell at day 1, biological rep 4

description: Gene expression data from SPS1 dsRNA treated cell at day1(biological replication 4)


title: No treatment control cell at day 5, biological rep 2

description: Gene expression data from no treated cell at day5 (biological replication 2)


title: SPS1 dsRNA treated cell at day 3, biological rep 2

description: Gene expression data from SPS1 dsRNA treated cell at day3 (biological replication 2)


title: pif4pif5 mut 1h FR repC


title: SPS1 dsRNA treated cell at day 1, biological rep 1

description: Gene expression data from SPS1 dsRNA treated cell at day1(biological replication 1)


title: SPS1 dsRNA treated cell at day 1, biological rep 3

description: Gene expression data from SPS1 dsRNA treated cell at day1(biological replication 3)


title: No treatment control cell at day 1, biological rep 4

description: Gene expression data from no treated cell at day1 (biological replication 4)

source_name: Drosophila SL2 cell of 1day after no treatment


title: No treatment control cell at day 1, biological rep 1

description: Gene expression data from no treated cell at day1 (biological replication 1)


title: No treatment control cell at day 1, biological rep 3

description: Gene expression data from no treated cell at day1 (biological replication 3)


title: No treatment control cell at day 1, biological rep 5

description: Gene expression data from no treated cell at day1 (biological replication 5)


title: wild-type plants, biological rep1

status: Public on Aug 17 2009

city: pohang

first: Lee

last: Sookjin

address: san 31, POSTECH, hyojadong, namgu

department: POSTECH

institute: inhwan Hwang

description: Gene expression data from wild-type plants

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 GenomeArray. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The normalized data were log-transformed with base 2. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: wild-type plants grown for 10 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual Rev. 3, 2005, Affymetrix).

growth_protocol: plants were grown on MSagar plates for xx days with 16h/8h light/dark cycle at 70% relative humidity at 20C in a growth chamber.

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

treatment_protocol: No special treatment was given.

value: whole plant

value: wild-type

tag: time

value: 10 days


title: wild-type plants, biological rep2


title: No treatment control cell at day 1, biological rep 2

description: Gene expression data from no treated cell at day1 (biological replication 2)


title: SPS1 dsRNA treated cell at day 1, biological rep 2

description: Gene expression data from SPS1 dsRNA treated cell at day1(biological replication 2)


title: female_larvae_roX1roX2 mutant_1

status: Public on Aug 03 2009

city: Detroit

first: Ying

last: Kong

state: MI

address: 5047 Gullen Mall

department: Department of Biological Sciences

institute: Wayne State University

description: Total RNA was prepared from roX1- roX2- female third instar larvae. SMC17A was used for the roX1 mutant, which is described in Deng et al., 2005.

hyb_protocol: Affymetrix GeneChip® Expression Analysis Technical Manual

data_processing: RMA

source_name: Larvae

extract_protocol: TRIzol standard protocol; RNeasy kit (Qiagen).

tag: Gender

value: female

tag: Stage

value: third instar larvae

tag: Genotype


title: female_larvae_roX1roX2 mutant_2

scan_protocol: Affymetrix GeneChip® Expression Analysis Technical Manual


title: ppi2 plants, biological rep1

description: Gene expression data from ppi2 plants

source_name: ppi2 plants grown for 20 days

value: ppi2 mutant

value: 20 days


title: female_larvae_roX1roX2 mutant_3

label_protocol: Affymetrix GeneChip® Expression Analysis Technical Manual


title: female_larvae_control_3

description: Total RNA was prepared from roX1SMC17ADf(1)52; [w+44.3]; [hsp83-roX1+] female third instar larvae. It was used as the wildtype control.


title: female_larvae_control_2


title: female_larvae_control_1


title: ppi2 plants, biological rep2

description: Gene expression data from ppi2 plants


title: larvae_msl2_mutant_1

first: Satya

middle: Kiran

last: Koya

address: 5047, Gullen Mall

department: Biological Sciences

description: Total RNA was prepared from msl21 male third instar larvae. msl21 is an EMS-induced mutation that has been previously described (Zhou et al., 1995)

data_processing: The Chip Image was analysed using GCOS 1.4 from Affymetrix. Gene expression data was background corrected, normalized and summarized into a one expression value per sample and probeset using the RMA (robust multi-array average) algorithm.

source_name: Larvae, msl2 mutant

extract_protocol: TRIzol standard protocol

value: male


title: larvae_msl2_mutant_2


title: larvae_wt_control_2

description: Total RNA was prepared from msl21 msl2+ male third instar larvae. msl21 msl2+ male was used for the wildtype control. msl21 is an EMS-induced mutation that has been previously described (Zhou et al., 1995)

source_name: Larvae, wildtype


title: larvae_wt_control_3


title: larvae_msl2_mutant_3


title: larvae_wt_control_1


title: Mid-third_instar_larval_eye_disc_GMR-upd_rep3

status: Public on Aug 01 2009

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

description: Gene expression data from a single Drosophila mid-third instar larval eye disc

hyb_protocol: 9 mcg of amplified and biotin-labeled control (yw) and GMR-upd aRNA were separately 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 MBEI algorithm using dChip program. No further adjustments were made to the data in the table.

source_name: Total RNA, single Drosophila mid-third instar larval eye disc, GMR-upd

label_protocol: Labeled anti-sense RNA (aRNA) was synthesized from the resulting cDNA using the ENZO BioArrayTM High Yield RNA Transcript Labeling Kit.

extract_protocol: Arcturus Isolation kit (PicoPure RNA Isolation Kit) was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Arcturus Amplification kit (RiboAmp® RNA Amplification Kit)

treatment_protocol: single Drosophila mid-third instar larval eye disc were dissected from equally aged larvae (2-hr time collections)

value: Glass multiple reporter unpaired (GMR-upd)


title: Mid-third_instar_larval_eye_disc_GMR-upd_rep5

value: Arcturus Isolation kit (PicoPure RNA Isolation Kit)


title: Mid-third_instar_larval_eye_disc_GMR-upd_rep2


title: Mid-third_instar_larval_eye_disc_GMR-upd_rep4


title: Mid-third_instar_larval_eye_disc_GMR-upd_rep1


title: Mid-third_instar_larval_eye_disc_yw_rep3

source_name: Total RNA, single Drosophila mid-third instar larval eye disc, yw

value: yellow white (yw)


title: Mid-third_instar_larval_eye_disc_yw_rep5


title: Mid-third_instar_larval_eye_disc_yw_rep1


title: DKO, HB-Bmi1, rep2

city: Chiba

first: Tetsuhiro

last: Chiba

address: 1-8-1 Inohana, Chuo-ku

institute: Graduate School of Medicine, Chiba University

description: Bmi1-overexpressing Ink4a-Arf-null hepatoblasts at day 28 of culture

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Softwere version 1.4 (GCOS1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared from the purified total RNA equivalent to 10,000 cells with a Two-Cycle cDNA Synthesis Kit and 3'-Amplification Reagents for IVT Labeling (Affymetrix).

growth_protocol: Dlk-positive hepatoblasts were sorted by magnetic activated cell sorting (MACS) and plated on collagen type IV-coated 6-well plates (Beckton Dickinson). Sorted cells were transduced with EGFP or Bmi1 after 12-18 hours of pre-incubation. The cells were cultured in medium supplemented with 50 ng/ml of hepatocyte growth factor (HGF) (Peprotech) and 20 ng/ml of epidermal growth factor (EGF) (Peprotech).

treatment_protocol: Ink4a-Arf-null Dlk-positive hepatoblasts transduced with EGFP or Bmi1 at day 28 of culture were purified using flow cytometry.

value: Liver

tag: developmental stage

value: Embryonic day (ED) 14.5

value: hepatoblast


title: DKO, HB-Control, rep4

description: Control Ink4a-Arf-null hepatoblasts (expressing EGFP) at day 28 of culture

source_name: Control Ink4a-Arf-null hepatoblasts


title: DKO, HB-Control, rep1


title: DKO, HB-Control, rep3


title: Mid-third_instar_larval_eye_disc_yw_rep4


title: DKO, HB-Bmi1, rep3


title: DKO, HB-Bmi1, rep4


title: Mid-third_instar_larval_eye_disc_yw_rep2


title: DKO, HB-Bmi1, rep1


title: DKO, HB-Control, rep2


title: GVGdvl4dex3

city: Columbia

first: Clayton

middle: T

last: Larue

state: MO

address: 304 Life Sciences Bldg

department: Dept of Biological Sciences

institute: University of Missouri, Columbia

description: Plants were grown in artificial greenhouse potting media in standard growth chambers at 22C and 16hr days. Plants were treated when they reached the six expanded rosette leaf stage (vegetative) with mock treatment or 30um dex in water. At 10hrs post-treatment, the largest rosette leaf was collected from 20 plants. These leaves were pooled and were considered one biological replicate.

hyb_protocol: Hybridization was completed according to chip manufacturer's instructions (Affymetrix) using an Affymetrix GeneChip Hybridization Oven 640 and GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned and data acquired using an Affymetrix GeneChip Scanner 3000 driven by GCOS 1.2 software (Affymetrix).

data_processing: Data were processed using dChip software (www.dchip.org).

source_name: Arabidopsis rosette leaves.

label_protocol: cDNA synthesis and labeling was completed according to chip manufacturer's instructions (Affymetrix).

extract_protocol: Total RNA was isolated from the leaf samples using TRIzol reagent (Invitrogen) and purified using the RNeasy Midi Kit (Qiagen) according to manufacturer's instructions.

tag: Material was derived from dex treated fully expanded Arabidopsis rosette leaves 10hrs post-treatment.


title: GVGdvl4mock3

tag: Material was derived from mock treated fully expanded Arabidopsis rosette leaves 10hrs post-treatment.


title: GVGdvl4mock2


title: GVGdvl4dex2


title: emptyvectordex3


title: Geminating pollen with pollen tube_1

city: Okazaki

first: Mitsuyasu

last: Hasebe

state: Aichi

address: Nishigounaka 38

institute: National Institute for Basic Biology

description: Pollen germination rate was about 80%.

hyb_protocol: Followed Affymetrix experimental procedure. 200 micro liter of hybrization solution was used for 16 hrs hybridization at 45°C.

scan_protocol: GCOS/Microarray Suite

data_processing: MAS 5.0, normalized with Microarray suite using seedling data as a baseline

source_name: Germinating pollen with pollen tube

label_protocol: Followed Affymetrix experimental procedure. One cycle cDNA sysnthesis with 10 micro gram of Total RNA was used.

extract_protocol:
6hrs after the inoculation on the pollen tube media at 25°C (13.5% sucrose, 10 mM CaCl2, 0.4 mM boric acid, 1 mM KCl, 0.001% myo-inositol, and 0.6% agarose), germinating pollen was collected
(1)Grinded in the mortar (2) Extracted with Isogene (Nippone gene) (3) LiCl percipitaiton (4) RNeasy purification (Qiagen)

tag: Germinating pollen with pollen tube


title: Seedlings

description: Plants were grown at 18L (22°C) and 6D (18°C) growth condition.

scan_protocol: GCOS/Microarray suite

data_processing: MAS 5.0, normalized with germinating pollen with pollen tube in Microarray suite. This seedling data was used as a baseline probe set.

source_name: Seedlings

label_protocol: Followed Affymetrix instructions, using one cycle cDNA labeling with 10 micro gram of Total RNA.

extract_protocol:
Arabidopsis seedlings with one rosette leave
(1)Grinded in the mortar (2) Extracted with Isogene (Nippone Gene) (3) RNesy purification (Qiagen)


title: emptyvectordex2


title: GVGdvl4dex1


title: GVGdvl4mock1


title: C2C12-control-day0

status: Public on Jul 31 2009

city: Setagaya

first: Hiroshi

last: Asahara

state: Tokyo

department: Department of Systems BioMedicine

institute: National Research Institute for Child Health and Development

description: Gene expression data from C2C12 culture treated stable control sh at day0

hyb_protocol: Hybridization to Affymetrix® GeneChip® Mouse Genome 430 2.0 arrays was carried out following standard Affymetrix® protocols. 10 ug cRNA used.

scan_protocol: GeneChips® were scanned using GeneChip Scanner 3000

data_processing: Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Operating Software version 1.1 using default parameters. We used the Bioconductor 'affy' software package for further data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation.

source_name: mouse C2C12 culture treated control LacZ vector at day0

label_protocol: Biotinylated cRNA were prepared from total RNA following standard Affymetrix® protocols

growth_protocol: C2C12 murine skeletal muscle cells were purchased from American Type culture Collection (ATCC). These cells were maintained in GM (DMEM supplemented with 10% FBS). Cells were grown in GM and after reaching confluence, the medium was switched to DM (DMEM supplemented with 2% hourse serum) and further incubated. The medium was changed every 2 days. Culture was performed by using within five passages cells.

extract_protocol: RNA of the culture was extracted using ISOGEN (NIPPONGENE).

treatment_protocol: For the experiment of shRNA for Rp58, transfection was performed by using Lipofectamin 2000 (Invitrogen). Stable transfectants were obtained by selection of the transfected C2C12 cells by G418 (500 μg/ml, GIBCO) for two weeks.


title: emptyvectordex1


title: C2C12-day2

description: Gene expression data from C2C12 culture at day2, i.e.  2 day after  change to DM.

source_name: mouse C2C12 culture at Differentiation day2


title: C2C12-day4

description: Gene expression data from C2C12 culture at day4, i.e.  4 day after  change to DM.

source_name: mouse C2C12 culture at Differentiation day4


title: C2C12-day0

description: Gene expression data from C2C12 culture at day0, i.e. just after change to DM.

source_name: mouse C2C12 culture at Differentiation day0


title: Geminating pollen with pollen tube_2

description: Pollen germination rate was about 80%.

data_processing: MAS 5.0, normalized with Microarray Suite using seedling data as a baseline

extract_protocol:
6hrs after the inoculation on the pollen tube media at 25°C (13.5% sucrose, 10mM CaCl2, 0.4 mM boric acid , 1 mM KCl, 0.001% myo-inositol, and 0.6% agarose), germianting pollen was collected.
(1)Grinded in the mortar (2) Extracted with Isogene (Nippone gene) (3) LiCl percipitaiton (4) RNeasy purification (Qiagen)


title: C2C12-GM

description: Gene expression data from C2C12 culture in GM, i.e. before change to DM.

source_name: mouse C2C12 culture in Growth Medium


title: CXCR5_Negative_Rep1

status: Public on Jul 28 2009

city: San Diego

first: Shane

last: Crotty

state: CA

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Allergy and Immunology

description: Gene expression data from CXCR5+CD4+ T follicular helper cells

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

source_name: mouse CXCR5+ CD4 T cells

label_protocol: RNA quality of all samples was confirmed by BioAnalyzer Nano gel (Agilent), then probes were generated from 30ng total RNA by single round linear amplification using the Ovation Pico system (Nugen).

growth_protocol: All infections were done by intraperitoneal injection of 1-2 x 10^5 plaque-forming units (PFU) of LCMV Armstrong per mouse. 6,000 naïve SMtg (SMARTA LCMV-specific TCR transgenic) CD4 T cells were transferred per mouse, prior to LCMV infection.  Spleens were harvested 8 days after LCMV infection.

extract_protocol: RNA was isolated using Qiagen RNAeasy Mini spin columns (Qiagen), including QiaShredder and on-column digestion of genomic DNA. Some RNA samples were then concentrated using MinElute spin columns (Qiagen).

treatment_protocol: Splenocytes were isolated and antigen-specific CD4 T cells were enriched using anti-CD45.1-FITC and magnetic bead purification (Miltenyi). Virus-specific SMtg CD4+CD45.1+TCRβ+CD19-7AAD- cells were then sorted into TFH and non-TFH populations on the basis of CXCR5 expression using a FACSAria (BD Biosciences).

tag: strain

value: C57BL6/J Mice

tag: cell type

value: CD4 T cells


title: CXCR5_Positive_Rep1

description: Gene expression data from CXCR5-CD4+ T cells

source_name: mouse CXCR5- CD4 T cells


title: CXCR5_Positive_Rep2

description: Gene expression data from CXCR5-CD4+ T follicular helper cells


title: CXCR5_Negative_Rep2


title: Naïve

description: Gene expression data from naïve CD4+ T Cells. (CD44low CD62Lhigh CD4 T cells from uninfected mice)

source_name: mouse naive CD4 T cells


title: SIVPT, biological rep1

city: Tucson

first: RAVISHANKAR

last: PALANIVELU

state: AZ

address: 1140 E. South Campus Drive P.O. Box 210036

department: Plant Sciences

institute: University of Arizona

description: Gene expression data from semi in vivo-grown pollen tubes.

hyb_protocol: For each pollen condition, labeled cRNA was fragmented and 15 µg of fragmented cRNA (25-200nt as per Agilent 2100 Bioanalyzer RNA 6000 Nano Chip Series II Assay, Agilent Technologies, Waldbronn, Germany) was hybridized to the GeneChip® Arabidopsis ATH1 genome arrays (http://www.affymetrix.com) for 20 hours at 45oC. Standard washing and staining procedures were performed using the GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: The arrays were then scanned using the GeneChip Scanner 3000 with 7G upgrade (Affymetrix, Santa Clara, CA).

data_processing: Signal intensities from each of the 15 arrays were converted to raw expression data (with Present, "P", Absent, "A" and Marginal, "M" scores) using GeneChip Operating Software (GCOS) (Affymetrix, Santa Clara, CA).

source_name: Arabidopsis pollen tubes grown through the stigma and style pistil tissues

label_protocol: After first and second strand cDNA synthesis with total RNA, the cDNAs were used to generate cRNA labeled with biotin in an in vitro transcription reaction.

growth_protocol: Arabidopsis plants (Col-0 accession) were grown in chambers at 21°C under illumination (100 µmol m-2 s-1 with a 16-hour photoperiod). Wild-type pollen obtained from these plants were used to grow in vitro or semi in vivo pollen tubes which were then used for microarray experiments.

extract_protocol: Total RNA was extracted from dry pollen, 0.5h PT, 4h PT and SIV PT using the Qiagen RNeasy kit (http://www.qiagen.com). Total RNA (5 µg, dry pollen, 0.5h PT and 4h PT) and 2 µg (SIV PT) was prepared for microarray experiment as per the Affymetrix GeneChip Expression Analysis protocol (Part#701071, Rev 5, Affymetrix, Santa Clara, CA).

treatment_protocol: Pollen tubes grown through the stigma and style were collected by a semi in vivo procedure. Pollinated pistils were placed vertically on solid pollen growth medium for one hour (establish growth into the pistil) before they were laid horizontally; tubes emerged from cut pistils after three hours of growth and were harvested as bundles after three hours of growth on the media surface. Bundles were excised at the point of emergence from the cut pistil and collected into liquid nitrogen-frozen microfuge tubes. Eight hundred pollen tube bundles (obtained from 800 cut pistil explants) were used for each of the three replicate RNA isolations. Pollen tube bundles were confirmed to be free of pistil tissue contamination by microscopy.

tag: tissue

value: Semi in vivo-grown pollen tubes

value: Columbia

value: Pollen tubes grown for 3 hours in an Arabidopsis pistil and then 5 hours in solid pollen tube growth medium


title: SIVPT, biological rep3


title: 4hPT, biological rep2

description: Gene expression data from in vitro-grown pollen tubes for 4 hours.

source_name: Arabidopsis pollen grown in vitro for 4 hours in pollen growth medium

treatment_protocol: Dry pollen grains were collected by a vacuum method into microfuge tubes containing 250 µl liquid pollen growth medium and incubated for 4 hours in a 24°C growth chamber to produce in vitro pollen tubes. Pollen tubes were centrifuged at 4,000 rpm for 5 minutes, the supernatant was removed and the microfuge tubes were frozen in liquid nitrogen and stored in -80°C until RNA isolation. Aliquots of pollen tube suspensions were observed under microscope to determine % pollen germination and pollen tube length. Pollen grains with emerging tubes equal to or longer than their diameters were considered germinated. After 4 hours of growth, 58.3±6.0% of the pollen grains germinated and formed tubes (average length of 383.8±32.1 µm).

value: in vitro-grown pollen tubes

value: Pollen tubes grown for 4 hours in liquid pollen tube growth medium


title: wild type dark repB

description: Seedlings were kept in the dark for 3 days after germination

source_name: plant seedlings

value: seedling

value: wild type


title: 4hPT, biological rep3


title: 4hPT, biological rep4


title: 0.5hPT, biological rep4

description: Gene expression data from in vitro-grown pollen tubes for 0.5 hours.

source_name: Arabidopsis pollen grown in vitro for 0.5h in pollen growth medium

treatment_protocol: Dry pollen grains were collected by a vacuum method into microfuge tubes containing 250 µl liquid pollen growth medium and incubated for 0.5 in a 24°C growth chamber to produce in vitro pollen tubes. Pollen tubes were centrifuged at 4,000 rpm for 5 minutes, the supernatant was removed and the microfuge tubes were frozen in liquid nitrogen and stored in -80°C until RNA isolation. Aliquots of pollen tube suspensions were observed under microscope to determine % pollen germination and pollen tube length. Pollen grains with emerging tubes equal to or longer than their diameters were considered germinated.

value: Pollen tubes grown for 0.5 hours in liquid pollen tube growth medium


title: 0.5PT, biological rep3


title: drypollen, biological rep3

description: Gene expression data from dessicated, mature pollen.

source_name: Dry pollen from Arabidopsis mature flowers

treatment_protocol: Dry pollen grains were collected by a vacuum method from stage 14-15 flowers and frozen in liquid nitrogen until RNA isolation.

value: pollen

value: mature, dessicated pollen from stage 14-15 flowers


title: 4hPT, biological rep1


title: C2C12-shRp58-day0

description: Gene expression data from C2C12 culture treated stable shRp58 at day0

source_name: mouse C2C12 culture treated shRp58 vector at day0


title: 0.5PT, biological rep2


title: drypollen, biological rep1


title: 0.5PT, biological rep1


title: drypollen, biological rep2


title: Fat CD4 Tconv cells, repl. 1

status: Public on Jul 27 2009

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Per Joslin Diabetes Center microarray core facility.

source_name: Abdominal adipose tissue Tconv

label_protocol: BioArray High Yield RNA Transcript Labeling T7 Kit (Enzo Life Sciences)

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

tag: Male C57Bl/6 (retired breeders 25-35 weeks old)  purchased from the Jackson Laboratory. Abdominal (epidydimal) adipose tissue was cut into small pieces and digested for about 40 minutes with collagease type II. Cell suspensions were then filtered through a sieve and stromovascular fraction (SVF) was harvested after spinning.

tag: Genetic background

value: Male C57Bl/6;

tag: Age

value: 25-35 weeks old;

tag: Number of mice per chip

tag: Tissue

value: Abdominal (epidydimal) adipose tissue;

tag: Sorting


title: DBA control (201msn)

status: Public on Jul 24 2009

city: Bethesda

first: Ke

last: Zhang

state: MD

address: 37 Convent Dr.

institute: NCI

description: no additional information

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse genome 430 2.0 array chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Genechip Scanner 3000.

data_processing:
The data were analyzed with GeneChip® Operating Software (GCOS) using MAS5 Statistical algorithm.
The data in the matrix table are normalized by global scaling, and the mean target signal was set to 500.

source_name: DBA mouse untreated control

label_protocol: Labeled aRNA prepared from 1 µg of RNA using MessageAmpII aRNA Amplification kit ( Ambion) following manufactory instruction.

extract_protocol: total RNA was extracted from mesentery of experimental/control animals, using TRIzol (Invitrogen), and followed by a cleanup using Qiagen Rneasy kit.

treatment_protocol: Using institutionally approved animal protocols, mice were given 0.5 ml TMPD intraperitoneally, and grow for 3 and 18 days. Animals untreated were prepared at the same time and used as the control

tag: agent

value: control

value: DBA

value: mesentery


title: Fat CD4 Tconv cells, repl. 3

scan_protocol: Per Joslin Diabetes Center microarray core facility.

source_name: Abdominal adipose tissue Tconv cells


title: Fat CD4 Treg cells,  repl. 3

source_name: Abdominal adipose tissue Treg cells


title: Fat CD4 Tconv cells, repl. 2


title: CDF1-c (197msn)

description: no additional information

source_name: BALB/DBA F1 mouse untreated control

value: BALB/DBA F1 hybrid


title: Fat CD4 Treg cells,  repl. 2


title: TregLN, rep1

source_name: Treg cells isolated from LN

value: LN (cervical, inguinal, mesenteric)

tag: Sort


title: CDF1-p3 (179msn)

description: no additional information

source_name: BALB/DBA F1 mouse treated with pristane for 3 days

value: pristane

tag: time

value: 3 days


title: DBA d3 (184msn)

description: no additional information

source_name: DBA mouse treated with pristane for 3 days


title: drypollen, biological rep4

value: Columbia

tag: age


title: DBA control (202msn)

description: no additional information


title: CDF1-p3 (178msn)

description: no additional information


title: TconvLN, rep1

source_name: Tconv cells isolated from LN


title: TconvThy, rep1

source_name: Tconv cells isolated from the thymus

value: 4-6 wks

value: Thymus

value: (pre-sort depletion of CD8a by MACS) B220-, CD11b-, CD8a-, CD4+, CD25-


title: BALB/c control (198msn)

description: no additional information

source_name: BALB/c mouse untreated control

value: BALB/c


title: BALB/c control (199msn)

description: no additional information


title: DBA d3 (185msn)

description: no additional information


title: BALB/c d3 (191msn)

description: no additional information

source_name: BALB/c mouse treated with pristine for 3 days


title: BALB/c d3 (187msn)

description: no additional information


title: DBA d3 (183msn)

description: no additional information


title: DBA control (203msn)

description: no additional information


title: TregThy, rep1

source_name: Treg cells isolated from the thymus

value: (pre-sort depletion of CD8a by MACS) B220-, CD11b-, CD8a-, CD4+, CD25+


title: CDF1-c (196msn)

description: no additional information


title: SIVPT, biological rep2

source_name: Arabidopsis pollen tubes grown through the stigma and style pistil tissues

value: Semi in vivo-grown pollen tubes

value: Pollen tubes grown for 3 hours in an Arabidopsis pistil and then 5 hours in solid pollen tube growth medium


title: CDF1-c (195msn)

description: no additional information


title: CDF1-p3 (177msn)

description: no additional information


title: DBA control (124-5msn)

description: no additional information


title: DBA control (122msn)

description: no additional information


title: BALB/c d3 (190msn)

description: no additional information


title: Fat CD4 Treg cells,  repl. 1

source_name: adipose Treg cells

value: Male C57Bl/6;

value: 25-35 weeks old;


title: BALB/c control (bmsnmix9)

description: no additional information

value: control


title: BALB/c d18 (bmsnmix1)

description: no additional information

source_name: BALB/c mouse treated with pristane for 18 days

value: 18 days


title: BALB/c control (bmsnmix8)

description: no additional information

value: mesentery


title: DBA d18 (119msn)

description: no additional information

source_name: DBA mouse treated with pristane for 18 days

value: DBA


title: BALB/c control (bmsnmix6)

description: no additional information


title: BALB/c d18 (bmsnmix2)

description: no additional information


title: DBA control (121msn)

description: no additional information


title: DBA d18 (123msn)

description: no additional information


title: DBA d18 (120msn)

description: no additional information


title: BALB/c control (bmsnmix7)

description: no additional information


title: BALB/c d18 (bmsnmix4)

description: no additional information


title: BALB/c d18 (bmsnmix3)

description: no additional information


title: Glyphosate EC50 biological rep3

status: Public on Jul 22 2009

city: Corvallis

first: Malay

last: Das

state: OR

address: 200 SW 35th STreet

department: EEB

institute: National Research Council, US-EPA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip scanner 3000 at 570 nm.

data_processing: Intensities of the fluorescence emission were captured and array image was visually screened for signal artifacts

source_name: Leaf, Glyphosate, 24h post tretment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds of A. thaliana, col 0 were stratified at 3-4C for 2-4 days and then grown under 22-23C, 16h photoperiod and 175-210 micromol per sec light intensity

extract_protocol: Triazol extraction of total RNA and subsequent purification with Rneasy mini spin columns

treatment_protocol: 14 days old plants were sprayed with surfactant and herbicide solutions in a RIC spray chamber (RC-5000-100EP)

tag: No visible symptoms of injury observed


title: Glyphosate EC50 biological rep1


title: Triazolopyrimidine EC50 biological rep3

source_name: Leaf, Triazolopyrimidine, 24h post tretment

treatment_protocol: 14 days old plants were sprayed with surfectant and herbicide solutions in a RIC spray chamber (RC-5000-100EP)


title: Triazolopyrimidine EC50 biological rep1


title: Triazolopyrimidine EC50 biological rep2


title: Glyphosate EC50 biological rep2


title: Carrier biological rep3 (Glyphosate)

source_name: Leaf, surfactant (preference, 0.25%) 24h post tretment


title: Carrier biological rep1 (Glyphosate)


title: Carrier biological rep2 (Glyphosate)


title: Imidazolinone EC50 biological rep2

source_name: Leaf, Imidazolinone, 24h post tretment


title: Primisulfuron EC50 biological rep2

source_name: Leaf, Primisulfuron, 24h post tretment


title: Sulfometuron EC50 biological rep2

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip scanner 3000 at 570 nm..

source_name: Leaf, sulfometuron methyl, 24h post tretment


title: Imidazolinone EC50 biological rep3


title: Imidazolinone EC50 biological rep1


title: Carrier biological rep3 (primisulfuron)

source_name: Leaf, surfectant (preference, 0.25%) 24h post tretment


title: hepatic gene expression at "6 hr" (rep3)

status: Public on Jul 21 2009

city: HangZhou

first: Dong Cheng

last: Liu

address: Qingchun Road 79, Hangzhou, Zhejiang 310003, China

country: China

institute: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, affiliated to Zhejiang University

description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "6hr" (rep3)

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures using GeneChip® Scanner 3000.

data_processing: Affymetrix® Microarray Suite Version 5.0

source_name: 8- to 10-week-old male balb/c mice. tissue: whole liver

label_protocol: standard Affymetrix procedures

extract_protocol: Liver samples from each mouse were ground into a fine powder in a mortar cooled by liquid nitrogen, and 100 mg was added to 1 ml prechilled Trizol reagent (Invitrogen, Carlsbad, CA). Total RNA extractions were performed according to the manufacturer’s directions, and the RNA was further puri-fied by passage through RNeasy mini-columns (QIAGEN, Valencia, CA) according to the manufacturer’s protocols for RNA clean-up. Final RNA preparations were resuspended in RNase-free water and stored at –80°C. The RNA samples were quantified spectrophotometrically, and purity and integrity were assessed by agarose gel electrophoresis. All samples exhib-ited 260/280 absorbance ratios of approximately 2.0, and all showed intact ribosomal 28S and 18S RNA bands in an approximate ratio of 2:1 as visu-alized by ethidium bromide staining.

value: ConA

tag: time point

value: 6 hr

tag: replicate

value: 8- to 10-week-old

tag: gender

value: male

value: Balb/c

value: whole liver


title: Primisulfuron EC50 biological rep1


title: Carrier biological rep2


title: Carrier biological rep2 (primisulfuron)


title: Sulfometuron EC50 biological rep1


title: hepatic gene expression at "6 hr" (rep2)

description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "6hr" (rep2)

tag: strain


title: Primisulfuron EC50 biological rep3


title: Sulfometuron EC50 biological rep3


title: Carrier biological rep1 (primisulfuron)


title: Carrier biological rep1


title: Carrier biological rep3


description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "3 hr" (rep1)

value: 3 hr


description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "3 hr" (rep3)


title: hepatic gene expression at "0 hr", rep3

description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "0 hr" (rep3)

value: untreated

value: 0 hr


title: hepatic gene expression at "0 hr", rep2

description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "0 hr" (rep2)


description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "6 hr" (rep1)


title: hepatic gene expression at "1 hr", rep3

description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "1hr" (rep3)

value: 1 hr


title: hepatic gene expression at "1 hr", rep2

description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "1 hr" (rep2)


title: hepatic gene expression at "3 hr" (rep2)

description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "3hr" (rep2)


title: BALB/c control (200msn)

description: no additional information

value: BALB/c


title: hepatic gene expression at "0 hr", rep1

description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "0 hr" (rep1)


title: hepatic gene expression at "1 hr", rep1

description: a time series of ConA injections was administered and  20 mg/kg ConA was injected through the mouse caudal vein at one of 4 time points (0 hr, 1 hr, 3 hr, 6 hr),here is  hepatic gene expression at "1 hr" (rep1)


title: BDntTS4

status: Public on Jul 17 2009

city: Tokyo

first: Mayumi

last: Oda

address: 35 Shinanomachi, Shinjuku

institute: Keio University

description: TS cell lines were established from E3.5 blastocysts according to previously published report (Tanaka et al. Science (1988) 282:2072-2075).

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5

source_name: Trophoblast stem cell, BDF1 background

label_protocol: standard Affymetrix protocol

growth_protocol: Cultured in proliferation medium for TS cells (RPMI1640 + 20%FBS + 1 mM Sodium Pyruvate + 2 mM L-glutamine + penicillin/storeptmycin + 25ng/ml bFGF +  heparin)(Tanaka et al. Science (1988) 282:2072-2075)

extract_protocol: standard Affymetrix protocol

treatment_protocol: Day 4 in proliferation medium.

tag: cell line

value: TS cell line derived from somatic cell nuclear transferred blastocyst (BDF1 background)


title: BDntTS5


title: BDntTS2


title: GFPntTS3

source_name: Trophoblast stem cell, CD-1, EGFP Tg.

value: TS cell line derived from somatic cell nuclear transferred blastocyst (EGFP-Tg CD-1 background)


title: GFPntTS5


title: GFPTS2

value: TS cell line derived from EGFP-Tg CD-1 native blastocyst


title: GFPTS1


title: BDTS2

value: TS cell line derived from B6D2F1 native blastocyst


title: BDTS1

source_name: Trophoblast stem cell, BDF1 background.


title: Expression profiling of WT littermate dorsal skin_rep1

city: Irvine

first: Kevin

middle: K

last: Lin

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

description: Hair cycle staging: telogen

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Drosophila Genome Array using manufacturer's standard protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: WT dorsal skin at P23, biological replicate 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 11 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

value: postnatal day 23

tag: Gender

value: female

value: dorsal skin


title: WT dorsal skin at D17, biological replicate 2

description: Hair cycle phase: early anagen

source_name: Mouse dorsal skin at 17 days after depilation, early anagen

tag: Strain

value: at least postnatal day 50

value: Female


title: WT dorsal skin at D12, biological replicate 1

description: Hair cycle phase: early anagen

source_name: Mouse dorsal skin at 12 days after depilation, early anagen


title: WT dorsal skin at D5, biological replicate 1

description: Hair cycle phase: early anagen

source_name: Mouse dorsal skin at 5 days after depilation, early anagen


title: WT dorsal skin at P44, biological replicate 2

description: Hair cycle phase: early anagen

source_name: Mouse dorsal skin at postnatal day 44, early anagen

value: postnatal day 44

value: Male


title: WT dorsal skin at D3, biological replicate 2

description: Hair cycle phase: early anagen

source_name: Mouse dorsal skin at 3 days after depilation, early anagen


title: Expression profiling of Clock mutant dorsal skin_rep2

description: Hair cycle staging: telogen

source_name: Clock mutant dorsal skin at P23, biological replicate 2


title: WT dorsal skin at D17, biological replicate 1

description: Hair cycle phase: early anagen


title: WT dorsal skin at D8, biological replicate 1

description: Hair cycle phase: early anagen

source_name: Mouse dorsal skin at 8 days after depilation, early anagen


title: Expression profiling of WT littermate dorsal skin_rep2

description: Hair cycle staging: telogen

source_name: WT dorsal skin at P23, biological replicate 2


title: WT dorsal skin at D3, biological replicate 1

description: Hair cycle phase: early anagen


title: Expression profiling of WT littermate dorsal skin_rep3

description: Hair cycle staging: telogen

source_name: WT dorsal skin at P23, biological replicate 3


title: WT dorsal skin at P44, biological replicate 3

description: Hair cycle phase: early anagen


title: Expression profiling of Clock mutant dorsal skin_rep1

description: Hair cycle staging: telogen

source_name: Clock mutant dorsal skin at P23, biological replicate 1

value: male


title: WT dorsal skin at D8, biological replicate 2

description: Hair cycle phase: early anagen


title: WT dorsal skin at D5, biological replicate 2

description: Hair cycle phase: early anagen


title: WT dorsal skin at D12, biological replicate 2

description: Hair cycle phase: early anagen


title: WT dorsal skin at P44, biological replicate 1

description: Hair cycle phase: early anagen


title: WT dorsal skin at P41, biological replicate 3

description: Hair cycle phase: early anagen

source_name: Mouse dorsal skin at postnatal day 41, early anagen

value: postnatal day 41


title: WT dorsal skin at P41, biological replicate 2

description: Hair cycle phase: early anagen


title: WT dorsal skin at P39, biological replicate 3

description: Hair cycle phase: early catagen

source_name: Mouse dorsal skin at postnatal day 39, early catagen

value: postnatal day 39


title: WT dorsal skin at P29, biological replicate 2

description: Hair cycle phase: late anagen

source_name: Mouse dorsal skin at postnatal day 29, late anagen

value: postnatal day 29


title: WT dorsal skin at P37, biological replicate 2

description: Hair cycle phase: early catagen

source_name: Mouse dorsal skin at postnatal day 37, early catagen

value: postnatal day 37


title: WT dorsal skin at P37, biological replicate 1

description: Hair cycle phase: early catagen


title: WT dorsal skin at P29, biological replicate 3

description: Hair cycle phase: late anagen


title: WT dorsal skin at P34, biological replicate 1

description: Hair cycle phase: late anagen

source_name: Mouse dorsal skin at postnatal day 34, late anagen

value: postnatal day 34


title: WT dorsal skin at P37, biological replicate 3

description: Hair cycle phase: early catagen


title: WT dorsal skin at P39, biological replicate 1

description: Hair cycle phase: early catagen


title: WT dorsal skin at P29, biological replicate 1

description: Hair cycle phase: late anagen


title: WT dorsal skin at P25, biological replicate 2

description: Hair cycle phase: early anagen

source_name: Mouse dorsal skin at postnatal day 25, early anagen

value: postnatal day 25


title: WT dorsal skin at P25, biological replicate 1

description: Hair cycle phase: early anagen


title: WT dorsal skin at P27, biological replicate 1

description: Hair cycle phase: mid anagen

source_name: Mouse dorsal skin at postnatal day 27, mid anagen

value: postnatal day 27


title: WT dorsal skin at P27, biological replicate 3

description: Hair cycle phase: mid anagen


title: WT dorsal skin at P23, biological replicate 1

description: Hair cycle phase: early anagen

source_name: Mouse dorsal skin at postnatal day 23, early anagen


title: WT dorsal skin at P23, biological replicate 2

description: Hair cycle phase: early anagen


title: NIH3T3_LatB_90min_rep7

status: Public on Jul 15 2009

city: Martinsried

first: Guido

last: Posern

address: Am Klopferspitz 18

department: Dept. Molecular Biology

country: Germany

institute: Max-Planck-Institute of Biochemistry

description: translation inhibited by cycloheximide

hyb_protocol: cRNA was hybridized on Affymetrix Murine Genome 430 2.0 Array according to manufacturers instruction. Arrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Affymetrix GeneArray Scanner.

data_processing: The raw data were acquired with Microarray Suite version 5.0. Data were processed and analysed with R and Bioconductor, as described (van Erp et al., 2006). Cel files were normalized with GC-RMA as implemented in the gcrma package (Wu and Irizarry, 2005).

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

growth_protocol: Cells were cultured in TC dishes in DMEM and serum-starved prior to treatment.

extract_protocol: Extraction of total RNA using RNeasy kit (Qiagen) according to manufacturers protocol

treatment_protocol: All conditions treated with cycloheximide (3 µg/ml, 2 hours) to inhibit translation. When indicated, treated with cytochalasin D (2 µM, 90 min) and latrunculin B (5 µM, 90 min).

value: latrunculin B and cytochalasin D

value: 90 minutes

tag: f-actin state

value: depolymerized


title: WT dorsal skin at P27, biological replicate 2

description: Hair cycle phase: mid anagen

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

tag: Age


title: NIH3T3_CytoD_90min_rep7

description: translation inhibited by cycloheximide

value: cytochalasin D


title: NIH3T3_CytoD_90min_rep1

description: translation inhibited by cycloheximide


title: NIH3T3_ctrl_rep7

description: translation inhibited by cycloheximide

value: control

value: normal


title: NIH3T3_LatB_90min_rep3

description: translation inhibited by cycloheximide


title: NIH3T3_CytoD_90min_rep3

description: translation inhibited by cycloheximide


title: WT dorsal skin at P41, biological replicate 1

description: Hair cycle phase: early anagen

value: Female


title: NIH3T3_LatB_90min_rep1

description: translation inhibited by cycloheximide


title: Murine Lung Endothelial Cells KO3

city: Philadelphia

first: Nicolas

last: Skuli

address: 421 Curie Boulevard

institute: HHMI

description:
Experimental Conditions: Hypoxia
Gene expression data from murine endothelial cells
Endothelial cells were isolated from lungs of VE-Cadherin-Cre HIF-2a floxed/WT mice for control cells and VE-Cadherin-Cre HIF-2a floxed/floxed mice for KO cells.
Endothelial cells were selected several times with specific endothelial cell markers and characterized  by flow cytometry.

hyb_protocol: 3.5 ug of cDNA was hybridized on the Affymetrix Mouse Genome 430 2.0 Chip following standard protocols.

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

data_processing: The data were extracted with Microarray Suite version 5.0 (MAS 5.0) and normalized with the GC-RMA algorithm in Array Assist Lite 3.4

source_name: mRNA from murine lung endothelial cells

label_protocol: Nugen Ovation version 2 was used for amplification, labeling and fragmentation

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, with additional purification with Qiagen Rneasy columns

tag: cell type

value: lung endothelial cells

tag: genotype

value: Hif-2a knockout


title: Murine Lung Endothelial Cells KO2


title: Murine Lung Endothelial Cells KO1


title: Murine Lung Endothelial Cells Cnt3

value: wild type control


title: Murine Lung Endothelial Cells Cnt2


title: ESC like cells 1

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

description: GSCs were established from Oct4-GFP transgenic mice as previously described (Kanatsu-Shinohara et al., 2003) with modifications.

hyb_protocol: Affymetrix arrays were prehybridized with 200 μl MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 μg of labeled cRNA in 200 μl MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Hierarchical clustering of samples was done with the functions “pdis”, “linkage” and “cluster” of the Statistical toolbox of Matlab®. Scatter plots were performed using in-house developed functions in Matlab®.

source_name: ESC-like cells

label_protocol: Probe preparation was with 1 μg RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

growth_protocol: ESC-like cells from post natal day (PND) 0-2 testis were provided by Dr. Shinohara and grown under standard ESC conditions on MEF feeder plus murine leukemia inhibitory factor (LIF). See Kanatsu-Shinohara et al. (PMID: 15620358) for further details.

extract_protocol: Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

tag: ESC-like cells from neonatal mouse testis


title: Germline pluripotent stem cells (gPSC_5) sample_5

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

hyb_protocol: Affymetrix arrays were prehybridized with 200 ml MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 ml MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

source_name: Germline pluripotent stem cells (gPS cells, gPSCs) derived from germline stem cells (GSCs) by in-vitro culture

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

growth_protocol: To expand the gPS cells, the gPS cells colonies were enzymatically dissociated into single cells and cultured under ESC culture conditions at 37°C in an atmosphere of 5% CO2 in air.

treatment_protocol: To obtain embryonic stem cell (ESC)-like cells, approximately 1,000 GSCs were plated per well in 24-well plates containing mouse embryonic fibroblast MEFs. Cultures were maintained in GSC culture medium without subculturing. Within 3 to 4 weeks, colonies with high green fluorescent protein (GFP) intensity and a morphology distinct from typical GSC colonies appeared; the GFP-positive colonies were round-shaped, while GSC colonies appear irregular. To expand the ESC-like cells, colonies were isolated mechanically, dissociated by trypsinisation, and plated onto MEFs in ESC medium.

value: Oct4-GFP transgenic mice (B6;CBA-Tg[Pou5f1-EGFP]2Mnn/J) referred to as OG2 mice.


title: ESC like cells 2


title: Mouse embryonic fibroblasts (MEF_3) sample_3

source_name: Mouse embryonic fibroblasts (MEFs)

treatment_protocol: Mouse embryonic fibroblast were prepared from C3H mice at day E12.5 and cultured under standard conditions.

value: C3H mice


title: NIH3T3_ctrl_rep1

description: translation inhibited by cycloheximide

tag: agent


title: Murine Lung Endothelial Cells Cnt1


title: ESC like cells 3


title: NIH3T3_ctrl_rep3

description: translation inhibited by cycloheximide


title: Neural stem cells (NSC_2) sample_2

source_name: Neural stem cells (NSCs)

treatment_protocol: NSCs were derived from Olig2-GFP ESCs according to Conti et al., (PLoS Biology, 2005) with modifications (Jeong Beom Kim, unpublished)

tag: Neural stem cells (NSCs) derived from embryonic stem cells (ESCs); Strain

value: Olig2-GFP ESC-derived NSCs


title: Embryonic stem cells (ESC_1) sample_1

source_name: Embryonic stem cells (ESCs)

treatment_protocol: Embryonic stem cells (ESCs, RW4 line, ATCC collection SCRC-1037) grown under standard conditions on MEF feeder plus murine leukemia inhibitory factor (LIF).

value: Embryonic stem cells (ESCs, RW4 cell line, ATCC collection SCRC-1037)


title: Neural stem cells (NSC_3) sample_3


title: Germline pluripotent stem cells (gPSC_3) sample_3


title: Germline pluripotent stem cells (gPSC_2) sample_2


title: Neural stem cells (NSC_1) sample_1


title: Embryonic stem cells (ESC_3) sample_3


title: Germline pluripotent stem cells (gPSC_4) sample_4


title: Embryonic stem cells (ESC_2) sample_2