title: control mouse 2 liver 5hmC profile (7d)

description: normal whole liver genomic DNA

value: M

tag: antibody

tag: antibody manufacturer

value: Active Motif

value: control

tag: tissue

value: liver


title: 165N

status: Public on Nov 09 2012

type: RNA

city: Brussels

first: Gil

last: Tomas

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description:
patient-matched nontumor control
165N-Plus.CEL

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were normalized with RMA using the affy Bioconductor package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: patient-matched non-tumor control

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted from thyroid tissues using Trizol reagent (Invitrogen), followed by purification on RNeasy columns (Qiagen). The RNA concentration was spectrophotometrically quantified, and its integrity was verified using an automated gel electrophoresis system (Experion, Biorad).

tag: pathological diagnostic

value: patient-matched non-tumor control

tag: tissue type

value: patient-matched non-tumor


title: 1486N

description:
patient-matched nontumor control
1486N-25-Plus.CEL


title: Mouse embryo, 44 hours, Nanog MO-injected, biological rep 2

city: Stanford

first: Kin Fai

last: Au

address: James H. Clark Center, 1st Floor East, 318 Campus Drive,

department: Statistics

country: USA

institute: Stanford

description:
Gene expression data
Mouse_44h_NN_R2

hyb_protocol: The arrays were hybridized in an Affymetrix GeneChip Hybridization Oven 640 for 40 hours.

scan_protocol: The arrays were scanned using a Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were processed using dChip.

label: Biotin

organism: Mus musculus

source_name: Preimplantation embryos (Nanog MO-injected) collected at 44 hours post-injection

label_protocol: The RNA was reverse transcribed and amplified using the WT-Ovation One-Direct Amplification System (NuGEN). The cDNA was then fragmented and labelled using the FL-Ovation cDNA Biotin Module (NuGEN).

growth_protocol: Embryos were cultured in drops of Human Tubal Fluid with 10% serum supplement (SAGE In-Vitro Fertilization Inc.) under mineral oil (Sigma) in 5% CO2 at 37oC.

extract_protocol: RNA was extracted using the PicoPure RNA Isolation Kit (Arcturus) according to manufacturer's instructions.

treatment_protocol: Embryos were injected with either a morpholino targeting Oct4, Sall4, or Nanog or a control morpholino targeting a sequence that does not exist in the mouse genome or transcriptome.

tag: strain

tag: developmental stage

value: preimplantation embryo

tag: condition

value: Nanog

tag: time (post-injection)

value: 44 hours


title: 242N

description:
patient-matched nontumor control
242N-Plus.CEL


title: Mouse embryo, 44 hours, Sall4 MO-injected, biological rep 3

description:
Gene expression data
Mouse_44h_S4_R3

source_name: Preimplantation embryos (Sall4 MO-injected) collected at 44 hours post-injection


title: 145N

description:
patient-matched nontumor control
145N-Plus.CEL


title: Mouse embryo, 44 hours, Sall4 MO-injected, biological rep 2

description:
Gene expression data
Mouse_44h_S4_R2


title: 144N

description:
patient-matched nontumor control
144N-Plus.CEL


title: Mouse embryo, 44 hours, Oct4 MO-injected, biological rep 2

description:
Gene expression data
Mouse_44h_O4_R2

source_name: Preimplantation embryos (Oct4 MO-injected) collected at 44 hours post-injection


title: Mouse embryo, 44 hours, Oct4 MO-injected, biological rep 3

description:
Gene expression data
Mouse_44h_O4_R3


title: 1367N

description:
patient-matched nontumor control
1367N-21-Plus.CEL


title: b148

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description: Gene expression data from human colon biopsies; non-inflammatory control

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: The data were analyzed with Bioconductor tools in R (http://www.r-project.org) using GC-RMA as normalization method. Next we employ a conservative probe-filtering step excluding those probe sets not reaching a log2 expression values of 5 in at least 1 sample.

source_name: Human colon biopsies from non-inflammatory control

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

extract_protocol: Total RNA was extracted by Rneasy Kit (Qiagen) according to the manufacturer's instructions.

tag: gender

value: male

tag: age (years)

tag: evolution time (years)

tag: disease extension

tag: treatment


title: Mouse embryo, 44 hours, Sall4 MO-injected, biological rep 1

description:
Gene expression data
Mouse_44h_S4_R1


title: 1337N

description:
patient-matched nontumor control
1337N-19-Plus.CEL


title: 1426N

description:
patient-matched nontumor control
1426N-23-Plus.CEL


title: Mouse embryo, 44 hours, uninjected (for Nanog experiment), biological rep 1

description:
Gene expression data
Mouse_44h_UI(NN)_R1

source_name: Preimplantation embryos (uninjected) collected at 44 hours post-injection

value: Uninjected


title: Mouse embryo, 44 hours, control-injected (for Oct4 and Sall4 experiment), biological rep 3

description:
Gene expression data
Mouse_44h_HG(O4S4)_R3

source_name: Preimplantation embryos (control-injected) collected at 44 hours post-injection

value: Control (HG)


title: Mouse embryo, 44 hours, uninjected (for Oct4 and Sall4 experiment), biological rep 2

description:
Gene expression data
Mouse_44h_UI(O4S4)_R2


title: 130N

description:
patient-matched nontumor control
130N-Plus.CEL


title: 1224N

description:
patient-matched nontumor control
1224N-11-Plus.CEL


title: 1190N

description:
patient-matched nontumor control
1190N-7-Plus.CEL


title: 1243N

description:
patient-matched nontumor control
1243N-13-Plus.CEL


title: 1328N

description:
patient-matched nontumor control
1328N-17-Plus.CEL


title: Mouse embryo, 44 hours, uninjected (for Oct4 and Sall4 experiment), biological rep 1

description:
Gene expression data
Mouse_44h_UI(O4S4)_R1


title: Mouse embryo, 44 hours, control-injected (for Oct4 and Sall4 experiment), biological rep 1

description:
Gene expression data
Mouse_44h_HG(O4S4)_R1


title: 1208N

description:
patient-matched nontumor control
1208N-9-Plus.CEL


title: 1247N

description:
patient-matched nontumor control
1247N-15-Plus.CEL


title: Mouse embryo, 44 hours, control-injected (for Oct4 and Sall4 experiment), biological rep 2

description:
Gene expression data
Mouse_44h_HG(O4S4)_R2


title: 1144N

description:
patient-matched nontumor control
1144N-1-Plus.CEL


title: Mouse embryo, 20 hours, Nanog MO-injected, biological rep 2

description:
Gene expression data
Mouse_20h_NN_R2

source_name: Preimplantation embryos (Nanog MO-injected) collected at 20 hours post-injection

value: 20 hours


title: Mouse embryo, 44 hours, uninjected (for Oct4 and Sall4 experiment), biological rep 3

description:
Gene expression data
Mouse_44h_UI(O4S4)_R3


title: 1053N

description:
patient-matched nontumor control
1053N-31-Plus.CEL


title: Mouse embryo, 44 hours, Oct4 MO-injected, biological rep 1

description:
Gene expression data
Mouse_44h_O4_R1


title: 1319N

description:
patient-matched nontumor control
1319N-27-Plus.CEL


title: Mouse embryo, 20 hours, Nanog MO-injected, biological rep 1

description:
Gene expression data
Mouse_20h_NN_R1


title: Mouse embryo, 20 hours, Nanog MO-injected, biological rep 3

description:
Gene expression data
Mouse_20h_NN_R3


title: Mouse embryo, 20 hours, control-injected (for Nanog experiment), biological rep 3

description:
Gene expression data
Mouse_20h_HG(NN)_R3

source_name: Preimplantation embryos (control-injected) collected at 20 hours post-injection


title: 103N

description:
patient-matched nontumor control
103N_Plus.CEL


title: 1030N

description:
patient-matched nontumor control
1030N-Plus.CEL


title: Mouse embryo, 20 hours, control-injected (for Nanog experiment), biological rep 1

description:
Gene expression data
Mouse_20h_HG(NN)_R1


title: Mouse embryo, 20 hours, uninjected (for Nanog experiment), biological rep 2

description:
Gene expression data
Mouse_20h_UI(NN)_R2

source_name: Preimplantation embryos (uninjected) collected at 20 hours post-injection


title: Mouse embryo, 20 hours, control-injected (for Nanog experiment), biological rep 2

description:
Gene expression data
Mouse_20h_HG(NN)_R2


title: 964T

description:
papillary thyroid carcinoma
964T-Plus.CEL

source_name: tumour

value: papillary thyroid carcinoma (PTC)

value: tumour


title: Mouse embryo, 20 hours, uninjected (for Nanog experiment), biological rep 3

description:
Gene expression data
Mouse_20h_UI(NN)_R3


title: Mouse embryo, 20 hours, uninjected (for Nanog experiment), biological rep 1

description:
Gene expression data
Mouse_20h_UI(NN)_R1


title: 1175N

description:
patient-matched nontumor control
1175N-3-Plus.CEL


title: Mouse embryo, 20 hours, Sall4 MO-injected, biological rep 1

description:
Gene expression data
Mouse_20h_S4_R1

source_name: Preimplantation embryos (Sall4 MO-injected) collected at 20 hours post-injection


title: Mouse embryo, 20 hours, Sall4 MO-injected, biological rep 3

description:
Gene expression data
Mouse_20h_S4_R3


title: 905T

description:
papillary thyroid carcinoma
905T-40-Plus.CEL


title: 886T

description:
papillary thyroid carcinoma
886T-38-plus.CEL


title: Mouse embryo, 20 hours, Sall4 MO-injected, biological rep 2

description:
Gene expression data
Mouse_20h_S4_R2


title: 954T

description:
papillary thyroid carcinoma
954T-42-Plus.CEL


title: 939T

description:
papillary thyroid carcinoma
939T-Plus.CEL


title: Mouse embryo, 20 hours, uninjected (for Sall4 experiment), biological rep 3

description:
Gene expression data
Mouse_20h_UI(S4)_R3


title: Mouse embryo, 20 hours, uninjected (for Sall4 experiment), biological rep 2

description:
Gene expression data
Mouse_20h_UI(S4)_R2


title: Mouse embryo, 20 hours, uninjected (for Sall4 experiment), biological rep 1

description:
Gene expression data
Mouse_20h_UI(S4)_R1


title: 771T

description:
papillary thyroid carcinoma
771T-36-Plus.CEL


title: 758T

description:
papillary thyroid carcinoma
758T-34-Plus.CEL


title: Mouse embryo, 20 hours, Oct4 MO-injected, biological rep 3

description:
Gene expression data
Mouse_20h_O4_R3

source_name: Preimplantation embryos (Oct4 MO-injected) collected at 20 hours post-injection


title: 752T

description:
papillary thyroid carcinoma
752T-Plus.CEL


title: 686T

description:
papillary thyroid carcinoma
686T-Plus.CEL


title: 601T

description:
papillary thyroid carcinoma
601T-Plus.CEL


title: 710T

description:
papillary thyroid carcinoma
710T-Plus.CEL


title: 615T

description:
papillary thyroid carcinoma
615Tbis-Plus.CEL


title: Mouse embryo, 20 hours, uninjected (for Oct4 experiment), biological rep 3

description:
Gene expression data
Mouse_20h_UI(O4)_R3


title: Mouse embryo, 20 hours, uninjected (for Oct4 experiment), biological rep 2

description:
Gene expression data
Mouse_20h_UI(O4)_R2


title: Mouse embryo, 20 hours, uninjected (for Oct4 experiment), biological rep 1

description:
Gene expression data
Mouse_20h_UI(O4)_R1


title: 574T

description:
papillary thyroid carcinoma
574T-Plus.CEL


title: 557T

description:
papillary thyroid carcinoma
557T-Plus.CEL


title: Mouse embryo, 20 hours, Oct4 MO-injected, biological rep 1

description:
Gene expression data
Mouse_20h_O4_R1


title: 501T

description:
papillary thyroid carcinoma
501T-48-Plus.CEL


title: Mouse embryo, 20 hours, Oct4 MO-injected, biological rep 2

description:
Gene expression data
Mouse_20h_O4_R2


title: 607T

description:
papillary thyroid carcinoma
607T-Plus.CEL


title: 446T

description:
papillary thyroid carcinoma
446T-Plus.CEL


title: 465T

description:
papillary thyroid carcinoma
465T-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi EP_rep2_2

city: Winnipeg

first: Sarah

middle: Jean

last: Medina

state: Manitoba

address: 1015 Arlington Street

department: Molecular PathoBiology

country: Canada

institute: Public Health Agency of Canada

description:
NML_251486812086_RML_2_555_PBS_2_647_dpi EP_ca1_1_4
RML = Rocky Mountain Laboratory scrapie strain

hyb_protocol: Hybridization and washing was performed according to the Two-Color Microarray-Based Gene Expression Analysis protocol for a 4x44K microarray format (Agilent technologies) following manufacturer's instructions.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner system with surescan technology (v.6.3) following the scan settings for a 4x44K microarray format according to manufacturer's instructions.

data_processing: The .TIFF images were uploaded into Feature Extraction (Agilent technologies, G2567AA FE software, v.10.5), the spots were identified, and the grids constructed using the GE2-v5_95_Feb07 & GE2_105_Dec08 protocol and the 014868_D_20060807 grid file for the whole mouse genome 4x44K expression arrays which were downloaded from the Agilent technologies website. Background calculations were performed by the feature extraction software using spatial and multiplicative detrending and normalization was performed using linear and lowess. The p-value to determine differential expression was 0.01 and the resulting log10 ratios from the feature extraction software were provided as the red (AlexaFlour 647)/green (AlexaFlour 555) channel.

label: AlexaFluor 555

source_name: CA1 cells_RML

label_protocol: Production of aRNA from total RNA was accomplished using the MessageAmpII kit (Ambion) following manufacturer's instructions. Upon 2 rounds of amplification, each aRNA was split into two samples (for dye-swapping) and labeled each with AlexaFluor 555 carboxylic acid, succinimidyl ester dye (Invitrogen) or AlexaFluor 647 (Invitrogen).

extract_protocol: Total RNA extracted using the RNAqueous® Micro kit (Ambion cat.# AM1931) following manufacturer's instructions.

tag: cell type

value: CA1 (cornu ammonis area 1 of the hippocampus)

tag: dpi

value: 183 (end point)

label: AlexaFluor 647

source_name: CA1 cells_PBS


title: CA1 cells_RML_vs_PBS_dpi EP_rep1_1

description:
NML_251486812086_PBS_1_555_RML_1_647_dpi EP_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain

value: 163 (end point)


title: 515T

description:
papillary thyroid carcinoma
515T-46-Plus.CEL


title: 502T

description:
papillary thyroid carcinoma
502Tbis-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 130_rep4_1

description:
NML_251486817567_PBS_4_555_RML_4_647_dpi_130_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi EP_rep1_2

description:
NML_251486812086_RML_1_555_PBS_1_647_dpi EP_ca1_1_2
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi EP_rep2_1

description:
NML_251486812086_PBS_2_555_RML_2_647_dpi EP_ca1_1_3
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 130_rep3_2

description:
NML_251486817567_RML_3_555_PBS_3_647_dpi_130_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 130_rep2_2

description:
NML_251486812083_RML_2_555_PBS_2_647_dpi 130_ca1_1_4
RML = Rocky Mountain Laboratory scrapie strain


title: 307T

description:
papillary thyroid carcinoma
307T-Plus.CEL


title: 366T

description:
papillary thyroid carcinoma
366T-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 130_rep4_2

description:
NML_251486817567_RML_4_555_PBS_4_647_dpi_130_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: 249T

description:
papillary thyroid carcinoma
249T-44-Plus.CEL


title: 411T

description:
papillary thyroid carcinoma
411T-Plus.CEL


title: 343T

description:
papillary thyroid carcinoma
343T-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 130_rep2_1

description:
NML_251486812083_PBS_2_555_RML_2_647_dpi 130_ca1_1_3
RML = Rocky Mountain Laboratory scrapie strain


title: 243T

description:
papillary thyroid carcinoma
243T-Plus.CEL


title: 242T

description:
papillary thyroid carcinoma
242T-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 130_rep1_1

description:
NML_251486812083_PBS_1_555_RML_1_647_dpi 130_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: 165T

description:
papillary thyroid carcinoma
165T-Plus.CEL


title: 1502T

description:
papillary thyroid carcinoma
1502T-6-Plus.CEL


title: 1486T

description:
papillary thyroid carcinoma
1486T-26-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 130_rep3_1

description:
NML_251486817567_PBS_3_555_RML_3_647_dpi_130_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 110_rep2_1

description:
NML_251486812143_PBS_2_555_RML_2_647_dpi 110_ca1_1_3
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 130_rep1_2

description:
NML_251486812083_RML_1_555_PBS_1_647_dpi 130_ca1_1_2
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 110_rep2_2

description:
NML_251486812143_RML_2_555_PBS_2_647_dpi 110_ca1_1_4
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 110_rep1_2

description:
NML_251486812143_RML_1_555_PBS_1_647_dpi110_ca1_1_2
RML = Rocky Mountain Laboratory scrapie strain


title: 144T

description:
papillary thyroid carcinoma
144T-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 100_rep2_1

description:
NML_251486817566_PBS_2_555_RML_2_647_dpi_100_ca1_1_3
RML = Rocky Mountain Laboratory scrapie strain


title: 145T

description:
papillary thyroid carcinoma
145T-Plus.CEL


title: 1426T

description:
papillary thyroid carcinoma
1426T-24-Plus.CEL


title: 1367T

description:
papillary thyroid carcinoma
1367T-22-Plus.CEL


title: 1328T

description:
papillary thyroid carcinoma
1328T-18-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 100_rep1_1

description:
NML_251486817566_PBS_1_555_RML_1_647_dpi_100_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: 1319T

description:
papillary thyroid carcinoma
1319T-28-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 90_rep3_1

description:
NML_251486812085_PBS_3_555_RML_3_647_dpi_90_ca1_1_3
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 110_rep1_1

description:
NML_251486812143_PBS_1_555_RML_1_647_dpi 110_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: 147T

description:
papillary thyroid carcinoma
147T-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 90_rep2_1

description:
NML_251486812085_PBS_2_555_RML_2_647_dpi_90_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: 130T

description:
papillary thyroid carcinoma
130T-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 100_rep1_2

description:
NML_251486817566_RML_1_555_PBS_1_647_dpi_100_ca1_1_2
RML = Rocky Mountain Laboratory scrapie strain


title: 1337T

description:
papillary thyroid carcinoma
1337T-20-Plus.CEL


title: 1247T

description:
papillary thyroid carcinoma
1247T-16-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 90_rep3_2

description:
NML_251486812085_RML_3_555_PBS_3_647_dpi_90_ca1_1_4
RML = Rocky Mountain Laboratory scrapie strain


title: 1243T

description:
papillary thyroid carcinoma
1243T-14-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 90_rep2_2

description:
NML_251486812085_RML_2_555_PBS_2_647_dpi_90_ca1_1_2
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 70_rep4_2

description:
NML_251486828124_RML_4_555_PBS_4_647_dpi_70_ca1_1_4
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 90_rep1_2

description:
NML_251486812101_RML_1_555_PBS_1_647_dpi 90_ca1_1_2
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 90_rep1_1

description:
NML_251486812101_PBS_1_555_RML_1_647_dpi 90_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 100_rep2_2

description:
NML_251486817566_RML_2_555_PBS_2_647_dpi_100_ca1_1_4
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 70_rep3_2

description:
NML_251486828124_RML_3_555_PBS_3_647_dpi_70_ca1_1_2
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 70_rep3_1

description:
NML_251486828124_PBS_3_555_RML_3_647_dpi_70_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 70_rep4_1

description:
NML_251486828124_PBS_4_555_RML_4_647_dpi_70_ca1_1_3
RML = Rocky Mountain Laboratory scrapie strain


title: 1208T

description:
papillary thyroid carcinoma
1208T-10-Plus.CEL


title: 1175T

description:
papillary thyroid carcinoma
1175T-4-Plus.CEL


title: 1144T

description:
papillary thyroid carcinoma
1144T-2-Plus.CEL


title: 1190T

description:
papillary thyroid carcinoma
1190T-8-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 70_rep2_2

description:
NML_251486812084_RML_2_555_PBS_2_647_dpi 70_ca1_1_4
RML = Rocky Mountain Laboratory scrapie strain


title: 1224T

description:
papillary thyroid carcinoma
1224T-12.CEL


title: 1030T

description:
papillary thyroid carcinoma
1030T-Plus.CEL


title: 1053T

description:
papillary thyroid carcinoma
1053T-32-Plus.CEL


title: 103T

description:
papillary thyroid carcinoma
103T_Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 70_rep1_1

description:
NML_251486812084_PBS_1_555_RML_1_647_dpi 70_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 40_rep5_1

description:
NML_251486817531_PBS_5_555_RML_5_647_dpi_40_ca1_1_1
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 70_rep2_1

description:
NML_251486812084_PBS_2_555_RML_2_647_dpi 70_ca1_1_3
RML = Rocky Mountain Laboratory scrapie strain


title: CA1 cells_RML_vs_PBS_dpi 70_rep1_2

description:
NML_251486812084_RML_1_555_PBS_1_647_dpi 70_ca1_1_2
RML = Rocky Mountain Laboratory scrapie strain


title: ATC17

description:
anaplastic thyroid carcinoma
7-ATC17-Plus.CEL

value: anaplastic thyroid carcinoma (ATC)


title: CA1 cells_RML_vs_PBS_dpi 40_rep6_2

description:
NML_251486817531_RML_6_555_PBS_6_647_dpi_40_ca1_1_4
RML = Rocky Mountain Laboratory scrapie strain


title: ATC15

description:
anaplastic thyroid carcinoma
5-ATC15-Plus.CEL


title: E.coli_polyphenols_repB_t2

city: Legnaro

first: Lisa

last: Carraro

state: Padova

address: Viale dell'Università 16, Agripolis

department: Department of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5.1 and quantile normalized using R2.6.1 statistical software

organism: Escherichia coli K-12

source_name: E.coli, culture with VWPE extract diluted in ethanol 20%, 20 minutes (t2) after treatment, replicate B

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: E.coli K12 was cultured in LB and grown at 37°C

extract_protocol: RNA extracted according to QiAgen RNeasy MiniKit protocol for bacterial samples

treatment_protocol: 1 ml of VWPE extract (1 mg/ml), 1 ml of ethanol 20% and 1 ml of LB broth were added when the OD600 of each culture reached 0.4

tag: agent

value: polyphenols (1 ml of OVWPE diluted in ethanol 20% added)

tag: time

value: 20 minutes (t2) after treatment


title: E.coli_polyphenols_repB_t3

source_name: E.coli, culture with VWPE extract diluted in ethanol 20%, 40 minutes (t3) after treatment, replicate B

value: 40 minutes (t3) after treatment


title: CA1 cells_RML_vs_PBS_dpi 40_rep6_1

description:
NML_251486817531_PBS_6_555_RML_6_647_dpi_40_ca1_1_3
RML = Rocky Mountain Laboratory scrapie strain


title: ATC14

description:
anaplastic thyroid carcinoma
4-ATC14-Plus.CEL


title: E.coli_polyphenols_repC_t3

source_name: E.coli, culture with VWPE extract diluted in ethanol 20%, 40 minutes (t3) after treatment, replicate C


title: E.coli_polyphenols_repC_t2

source_name: E.coli, culture with VWPE extract diluted in ethanol 20%, 20 minutes (t2) after treatment, replicate C


title: ATC12

description:
anaplastic thyroid carcinoma
2-ATC12-Plus.CEL


title: ATC22

description:
anaplastic thyroid carcinoma
9-ATC22-Plus.CEL


title: ATC21

description:
anaplastic thyroid carcinoma
8-ATC21-Plus.CEL


title: CA1 cells_RML_vs_PBS_dpi 40_rep5_2

description:
NML_251486817531_RML_5_555_PBS_5_647_dpi_40_ca1_1_2
RML = Rocky Mountain Laboratory scrapie strain


title: ATC16

description:
anaplastic thyroid carcinoma
6-ATC16-Plus.CEL


title: E.coli_polyphenols_repC_t1

source_name: E.coli, culture with VWPE extract diluted in ethanol 20%, at the time of treatment (t1), replicate C

value: at time of treatment (t1)


title: E.coli_polyphenols_repA_t2

source_name: E.coli, culture with VWPE extract diluted in ethanol 20%, 20 minutes (t2) after treatment, replicate A


title: ATC13

description:
anaplastic thyroid carcinoma
3-ATC13-Plus.CEL


title: E.coli_polyphenols_repA_t3

source_name: E.coli, culture with VWPE extract diluted in ethanol 20%, 40 minutes (t3) after treatment, replicate A


title: ATC23

description:
anaplastic thyroid carcinoma
10-ATC23-Plus.CEL


title: E.coli_ethanol_repC_t1

source_name: E.coli, culture with ethanol 20%, at the time of treatment (t1), replicate C

value: ethanol (1 ml of ethanol 20% added)


title: E.coli_polyphenols_repA_t1

source_name: E.coli, culture with VWPE extract diluted in ethanol 20%, at the time of treatment (t1), replicate A


title: ATC24

description:
anaplastic thyroid carcinoma
11-ATC24-Plus.CEL


title: E.coli_polyphenols_repB_t1

source_name: E.coli, culture with VWPE extract diluted in ethanol 20%, at the time of treatment (t1), replicate B


title: E.coli_ethanol_repC_t2

source_name: E.coli, culture with ethanol 20%, 20 minutes (t2) after treatment, replicate C


title: E.coli_ethanol_repC_t3

source_name: E.coli, culture with ethanol 20%, 40 minutes (t3) after treatment, replicate C


title: E.coli_ethanol_repB_t3

source_name: E.coli, culture with ethanol 20%, 40 minutes (t3) after treatment, replicate B


title: E.coli_ethanol_repB_t1

source_name: E.coli, culture with ethanol 20%, at the time of treatment (t1), replicate B


title: E.coli_ethanol_repB_t2

source_name: E.coli, culture with ethanol 20%, 20 minutes (t2) after treatment, replicate B


title: E.coli_ethanol_repA_t2

source_name: E.coli, culture with ethanol 20%, 20 minutes (t2) after treatment, replicate A


title: E.coli_ethanol_repA_t3

source_name: E.coli, culture with ethanol 20%, 40 minutes (t3) after treatment, replicate A


title: E.coli_control_repC_t2

source_name: E.coli, control culture, 20 minutes (t2) after treatment, replicate C

value: control (1 ml of LB broth added)


title: E.coli_control_repC_t1

source_name: E.coli, control culture, at the time of treatment (t1), replicate C


title: E.coli_ethanol_repA_t1

source_name: E.coli, culture with ethanol 20%, at the time of treatment (t1), replicate A


title: E.coli_control_repB_t1

source_name: E.coli, control culture, at the time of treatment (t1), replicate B


title: Array11.Slide10051 Clean

city: Guelph

first: Derek

last: Toms

state: Ontario

address: 50 Stone Road East

department: Animal and Poultry Science

institute: University of Guelph

description: LG oocytes treated with GDNF, pool 2

hyb_protocol: Hybridization of microarray slides with the Agilent Gene Expression Hybridization Kit 60-mer oligo microarray protocol version 4.0. 825 ng of each Cy3 and Cy5 labelled aRNA plus 2.75 μl of labelled Agilent spike (0.01X) was hybridized for 17 hours at 65°C rotating at 10 rpm in an oven.

scan_protocol: GenePix 4200 Autoloader by Molecular Devices. Software is GenePix Pro, Acuity 4.0

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. FlexArray software was used.

organism: Sus scrofa

source_name: REF (consists of oocytes pooled from all of the treatment groups and acts as an average of expression values to which the other samples are compared)

label_protocol: For each sample, total oocyte RNA was amplified using the RiboAmp HS kit (Molecular Devices, Sunnyvale, USA) following manufacturer instructions, and consisted of oligo(dT) priming, followed by two rounds of in vitro transcription. Amplified antisense RNA was labelled using the Universal Linkage System (ULS; Kreatech, Amsterdam, The Netherlands) with either ULS-linked Cy5 or Cy3 dyes.

growth_protocol: Protocol for in vitro maturation of porcine oocytes. Oocytes were matured for 44 hours in TCM199 with 10% porcine follicular fluid, LH, FSH and EGF. Oocytes were denuded with hyaluronidase and aspirated by glass pipette.

extract_protocol: Total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.

tag: sample type

tag: breed (swine)

value: crossbred

tag: compound added

tag: number per pool

tag: in vitro production

value: Yes

tag: reproductive status (swine)

value: Prepubertal gilts

tag: tissue or cell type

value: oocyte

value: GDNF


title: E.coli_control_repC_t3

source_name: E.coli, control culture, 40 minutes (t3) after treatment, replicate C


title: Array10.Slide10050 Clean

description: LG oocytes treated with GDNF, pool 1


title: Array04.Slide10052

description: SM control oocytes, pool 3


title: Array03.Slide10051

description: SM control oocytes, pool 2


title: E.coli_control_repB_t2

source_name: E.coli, control culture, 20 minutes (t2) after treatment, replicate B


title: E.coli_control_repA_t3

source_name: E.coli, control culture, 40 minutes (t3) after treatment, replicate A


title: Array08.Slide10052

description: LG control oocytes, pool 2


title: Array05.Slide10052

description: SM oocytes treated with GDNF, pool 2


title: E.coli_control_repA_t2

source_name: E.coli, control culture, 20 minutes (t2) after treatment, replicate A


title: Array09.Slide10051

description: LG control oocytes, pool 3


title: Array12.Slide10052

description: LG oocytes treated with GDNF, pool 3


title: E.coli_control_repB_t3

source_name: E.coli, control culture, 40 minutes (t3) after treatment, replicate B


title: Array07.Slide10050

description: LG control oocytes, pool 1


title: Array02.Slide10050

description: SM oocytes treated with GDNF, pool 1


title: Array01.Slide10050

description: SM control oocytes, pool 1


title: primary breast tumor 4

city: Montreal

first: Sean

last: Cory

state: QC

address: 3649 Promenade Sir William Osler

department: Bioinformatics

institute: McGill University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Microarray data were extracted using Feature Extraction Software v. 9.5.3.1 (Agilent Technologies). The arrays were normalized using normexp background correction, loess within array and quantile between array normalization.

source_name: PRIMARY 4

label_protocol: The profiles of resulting amplified RNA (aRNA) were assessed using a 2100 Bioanalyzer (Agilent Technologies). The aRNA samples (5μg) were conjugated to Cy3 dye using an Arcturus Turbo Labeling Kit (Cat. #: KIT0609, Applied Biosystems). Universal human reference RNA (Stratagene) was amplified using the same procedure and labeled with Cy5 dye (CAT # KIT0619, Applied Biosystems).

growth_protocol: Histological sections of primary breast tumors or bone metastases were H&E stained and examined by a clinical pathologist to identify regions within each section suitable for Laser Capture Microdissection (LCM).

extract_protocol: Total RNA (1-2.5ng) from microdissected material was subjected to two rounds of linear amplification using a RiboAmp HSPlus Amplification Kit (Cat. #: KIT0525, Applied Biosystems) following the manufacturer’s protocol.

tag: tissue

value: Primary Breast Tumor

tag: disease state

value: breast cancer

source_name: Universal Human Refence RNA

value: Stratagene Universal Human Refence RNA


title: primary breast tumor 5

source_name: PRIMARY 5


title: bone biopsy 3

source_name: BONE 3

value: Bone trephine

value: breast cancer bone metastasis


title: bone biopsy 2

source_name: BONE 2


title: primary breast tumor 1

source_name: PRIMARY 1


title: primary breast tumor 3

source_name: PRIMARY 3


title: Array06.Slide10051

description: SM oocytes treated with GDNF, pool 3


title: primary breast tumor 2

source_name: PRIMARY 2


title: bone biopsy 5

source_name: BONE 5


title: bone biopsy 4

source_name: BONE 4


title: bone biopsy 1

source_name: BONE 1


title: SW480

city: Oslo

first: Lina

last: Cekaite

state: Norge (+47)

address: Ullernchausseen 70

department: Molecular Oncology

country: Norway

institute: Oslo University Hospital, Radiumhospitalet

description:
MSS
colon cancer cell line

hyb_protocol: Biotin labeled samples were mixed with the eukaryotic hybridization controls (Affymetrix) and hybridized to Affymetrix miRNA arrays. Arrays were subsequently washed and stained in the GeneChip fluidics station 450 (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RMA normalization and probe summarization
program-name = Expression Console

source_name: untreated SW480

label_protocol: Samples were spiked with RNA spike control oligos (Genisphere) and labeled according to the Genisphere solution using the Genisphere FlashTag™ Biotin RNA Labeling Kit

growth_protocol: The cell lines were obtained from American Type Culture Collection (ATCC) and cultured according to their recommendations

extract_protocol: TRIzol Reagent (Invitrogen by Life Technologies, Carlsbad, CA, USA)

tag: cell line


title: E.coli_control_repA_t1

source_name: E.coli, control culture, at the time of treatment (t1), replicate A


title: HT-29

description:
MSS
colon cancer cell line

source_name: untreated HT-29


title: PLZF lu/lu gammadelta NKT cells

city: Boston

first: Michael

last: Gleimer

state: MA

address: SM736, 450 Brookline Ave

department: CIA

institute: DFCI

hyb_protocol: Hybridization was performed at 45C overnight

scan_protocol: Samples were washed using a microfluidics Affymetrix FS450 device and scanned using the Affymetrix GCS3000

data_processing:
Data processing and analysis was performed using the GenePattern v3.21 package using ExpressionFileCreator, MultiplotPreprocess and Multiplot modules
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Luxoid homozygote thymic gd NKT cells

label_protocol: Samples were enzymatically sheared and biotin end-labeled using the Affymetrix WT terminal labeling kit

growth_protocol: Ex vivo gd NKT cells sorted from adult thymi (3-4 weeks of age)

extract_protocol: Cells were FACsorted directly into TriZOL followed by Rneasy cleanup (Qiagen)

tag: genotype

value: PLZF lu/lu

value: gammadelta NKT cells

tag: age

value: adult

tag: gender

value: female

tag: genetic background


title: HCT116

description:
MSI
colon cancer cell line

source_name: untreated HCT116


title: Peripheral Blood, MI 3, 14hrs fasting , rep 1

city: Bangalore

first: prathima

last: arvind

address: #258/A, Bommasandra Industrial Area, Anekal Taluk

department: Functional Genomics

country: India

institute: Thrombosis Research Institute

description: Gene expression in case samples

hyb_protocol: 5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1ul of 25x Agilent fragmentation buffer and 5ul of 10x Agilent blocking agent following the manufacturer’s instructions. 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent G4851A , human genome G3 Hmn GE 8X60K microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505-64250) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20101102) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral Blood, case, 14hrs fasting , replicate 1

label_protocol: cDNA was synthesized from 200ng of total RNA, and cRNA was synthesized from cDNA and incorporated with Cy3-dUTP through in vitro transcription of the cDNA. Labeled probes were purified using RNAeasy mini kit (Qiagen, USA) and Dye incorporation and cRNA yield were verified with the NanoDrop ND-1000 Spectrophotometer and concentrated to the desired volume

extract_protocol: A total of 3ml of peripheral blood was collected in EDTA coated tubes from each participant after overnight fast. Total RNA was extracted from the blood samples using QIAamp RNA Blood mini kit (Qiagen, USA) using the protocol recommended by the manufacturer.  For the microarray experiment, the extracted RNA was cleaned up using the RNeasy Mini Elute cleanup kit (Qiagen, USA). RNA was quantified by NanoDrop ND-1000 Spectrophotometer (NanoDrop,Wilmington,DE, USA) , while the quality was determined using a Bioanalyzer 2100 (Agilent Technologies, CA, USA).

value: whole blood

value: male

tag: age (y)

value: coronary artery disease


title: PLZF +/lu gammadelta NKT cells

source_name: Luxoid heterozygote thymic gd NKT cells

value: PLZF +/lu

tag: cell type


title: Peripheral Blood, MI 4, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, SA 2, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, MI 1, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, control 10, 14hrs fasting , rep 1

description: Gene expression in control samples

source_name: Peripheral Blood, control, 14hrs fasting , replicate 1

value: control


title: Peripheral Blood, SA 4, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, SA 6, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, SA 3, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, control 6, 14hrs fasting , rep 1

description: Gene expression in control samples


title: Peripheral Blood, MI 6, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, control 7, 14hrs fasting , rep 1

description: Gene expression in control samples


title: Peripheral Blood, control 4, 14hrs fasting , rep 1

description: Gene expression in control samples


title: Peripheral Blood, control 5, 14hrs fasting , rep 1

description: Gene expression in control samples


title: Peripheral Blood, SA 1, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Col-0_Compost_3

first: guillem

last: segarra

address: Diagonal 643

department: Plant Biology

institute: Universitat de Barcelona

description: Col-0 plants grown in compost made from olive marc and olive tree leaves

hyb_protocol: Each sample was hybridized to a GeneChip Arabidopsis ATH1 Genome Array (Affymetrix).

scan_protocol: Arrays were scanned in a GeneChip Scanner 3000 (Affymetrix). CEL files were generated from DAT files using GCOS software (Affymetrix).

data_processing: CEL files were generated from DAT files using GCOS software (Affymetrix). To generate the log2 expression estimates, overall array intensity was  normalized between arrays and the probe intensity of all probes in a probe set summarized to a single value using RMA (Robust Multichip Average) algorithm

organism: Arabidopsis thaliana

source_name: leaves of 5-week-old plants grown in compost

label_protocol: cDNA library preparation and amplification were performed from 25ng total RNA using WTA2 (Sigma-Aldrich) with 17cycles of amplification. 8µg cDNA were subsequently fragmented by DNAseI and biotinylated by terminal transferase obtained from GeneChip Mapping 10Kv2 Assay Kit (Affymetrix).

growth_protocol: Arabidopsis thaliana Col-0 plants were grown in perlite trays in a growth chamber at 22ºC, 70% RH and 8 h/day of 110 µmol m-2 s-1 PPFD. 17 days later, plants were transplanted to individual 60-mL pots containing either OMC or perlite and were maintained until they were 5 weeks old. The plants were watered with half-strength Hoagland solution every other day.

extract_protocol: RNA was extracted from samples ground under liquid nitrogen using SpeedTools Total RNA Extraction kit (Biotools, Madrid, Spain), according to the manufacturer’s instructions.

treatment_protocol: Perlite and olive marc compost (OMC) were used as substrates. OMC was produced at the University of Seville (Spain) starting from a 1:1.125 mixture of olive marc and olive tree leaves composted in piles for 19 weeks and then matured for one year.

tag: ecotype


title: Peripheral Blood, MI 2, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, control 8, 14hrs fasting , rep 1

description: Gene expression in control samples


title: Peripheral Blood, control 9, 14hrs fasting , rep 1

description: Gene expression in control samples


title: PLZF +/+ gammadelta NKT cells

source_name: Wild-type thymic gd NKT cells

value: PLZF +/+


title: Peripheral Blood, control 3, 14hrs fasting , rep 1

description: Gene expression in control samples


title: Peripheral Blood, SA 7, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, SA 5, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, control 11, 14hrs fasting , rep 1

description: Gene expression in control samples


title: Peripheral Blood, MI 5, 14hrs fasting , rep 1

description: Gene expression in case samples


title: Peripheral Blood, control 2, 14hrs fasting , rep 1

description: Gene expression in control samples


title: Col-0_Compost_2


title: Sen1-S16C

type: genomic

city: Milan

first: Rodrigo

last: Bermejo

state: Lombardy

address: Via Adamello 16

institute: IFOM-IEO-Campus

description: Sen1-FLAG wt CY8511 S 16C GLU

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: BAR files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: IP fraction of Sen1-FLAG wt CY8511 S 16C GLU

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol

growth_protocol: Cells were grown in YPD

extract_protocol: Extracton was performed as described in Bermejo et al., 2011. Antibodies used are: Monoclonal ANTI-FLAG M2, SIGMA-ALDRICH, F1804-1MG, Batch: 080M6035 and anti-BrdU, Medical&Biological Laboratories (MBL), MI-11-3, Batch: 052

treatment_protocol: G1 synchronization was performed by α−factor treatment (2 μg/ml), S synchronization release from factor block in 200 mM HU, G2 synchronization released from alpha factor block in nocodazole 15 μg/ml, S 16C synchronization release from factor block at 16C

tag: strain

tag: phase

value: S

tag: treatment

value: GLU 16C

source_name: SUP of Sen1-FLAG wt CY8511 S 16C GLU

tag: sample type

value: IP

tag: genotype/variation

value: SUP


title: Sen1-HU-disars607

description: Sen1-FLAG CY9003 S GLU

source_name: IP fraction of Sen1-FLAG CY9003 S GLU

value: GLU

source_name: SUP of Sen1-FLAG CY9003 S GLU


title: Col-0_Perlite_1

description: Col-0 plants grown in perlite

source_name: leaves of 5-week-old plants grown in perlite


title: rpb1-1 37C G2

description: Sen1-FLAG rpb1-1 CY10399 G2 37C GLU

source_name: IP fraction of Sen1-FLAG rpb1-1 CY10399 G2 37C GLU

value: GLU 37C

source_name: SUP of Sen1-FLAG rpb1-1 CY10399 G2 37C GLU


title: BrdU-16C

description: Brdu wt SY2201 S 16C GLU

source_name: IP fraction of Brdu wt SY2201 S 16C GLU

source_name: SUP of Brdu wt SY2201 S 16C GLU

value: Brdu-Brdu


title: wt 37C G2

description: Sen1-FLAG wt CY8511 G2 37C GLU

source_name: IP fraction of Sen1-FLAG wt CY8511 G2 37C GLU

source_name: SUP of Sen1-FLAG wt CY8511 G2 37C GLU


title: Col-0_Perlite_2

description: Col-0 plants grown in perlite


title: CD4 T cells, WT, biological rep3

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

institute: University of Chicago

description: Gene expression data from WT activated CD4 T cell

hyb_protocol: Performed according to the manufacturer's instructions.

data_processing: Data was normalized with robust multi-array analysis (RMA) normalization using the 'affy' Bioconductor package in R. Gene level expression was summarized from mean probe set level intensities using Mouse430A 2 Annotations, Release 31. log2(gene expression change) was calculated using the WT expression level as reference. All log gene expression changes were centered with mean log2(expression change) and normalized to have unit variance. This normalization resulted in a simple Z-transformation of log2(gene expression change).

source_name: CD4+ T cells from spleen and lymph nodes

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

growth_protocol: CD4 T cells were isolated using CD4 dynabeads (Invitrogen) according to the manufacture's instructions.

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

treatment_protocol: CD4 T cells were activated upon culture in the presence of 1ug/mL CD3 and CD28 antibodies in 20U/mL IL-2 for 3 days at 37oC, 5% CO2.

value: WT

value: CD4+ T cells [activated]


title: 14286351 - Ctrl-TuYV_BR1 vs Ctrl-LMV_BR1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: transcriptome analysis of Arabidopsis Companion cells after infection by plants viruses

hyb_protocol: Ctrl-LMV_BR1 Cy5 / Ctrl-TuYV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0 Cy3: pmt voltage 532nm,480V,laser power 35% Cy5: 635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: protoplast, rosette; media=soil, hygrometry=50%, temperature=20°C, light=8h-16h

extract_protocol: Ctrl-LMV_BR1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name: Ctrl-LMV - infection - infection, mock infection:time 27day. All leaves from 42 days old plants were infected by hand-rubbing with buffer. For the Ctrl we infiltred all leaves with agrobacteria containing the empty vector. We used 20 plants for each condition. Then, 26 days after infection, we made protoplasts with 50 leaves from all mock plants.

value: mutant (c24) expressing GFP under the control of a companion cell specific promoter

tag: dev.stage (boyes et al. plant cell 2001)

value: boyes 3.70

value: FACS-sorted companion cell protoplasts

extract_protocol: Ctrl-TuYV_BR1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name: Ctrl-TuYV - inoculation - inoculation, mock infection:time 29day. All leaves from 42 days old plants were infected by hand-rubbing with buffer. For the Ctrl we infiltred all leaves with agrobacteria containing the empty vector. We used 20 plants for each condition. Then, 28 days after infection, we made protoplasts with 50 leaves from all mock plants.


title: Roots-control_Roots-Trichoderma_24h_rep2

city: Potsdam

first: Yariv

last: Brotman

address: Am Mühlenberg 1

country: Germany

institute: Max-Planck-Institute of Molecular Plant Physiology

description:
R2-T2
Arabidopsis roots treated with Trichoderma for 24 hours versus control roots not treated with Trichoderma at the same time point (dye swap).

hyb_protocol: Hybridization was performed in the Microarrays Unit of the Weizmann Institute of Science according to Agilent's instructions.

scan_protocol: An Agilent scanner was used and image feature quantification was performed using Agilent Feature Extraction Software.

data_processing: Limma bioconductor R package was used to process the raw files. normexp, robustsplit, and quantile methods were used for background correction, normalization within arrays, and normalization between arrays, respectively. Other parameters were set to default.

source_name: Root, non-treated with Trichoderma (control)

label_protocol: Labeling was performed in the Microarrays Unit of the Weizmann Institute of Science according to Agilent's instructions.

growth_protocol: Arabidopsis (Col-O) plants were grown 25 days under a long day regime (16 hours light), on rock-wool placed over a 5 L tank supplemented with Arabidopsis hydroponic solution (Brotman et al. 2012).

extract_protocol: Total RNA was purified using the RNeasy Mini Kit (Qiagen, http://www.qiagen.com).

treatment_protocol: Trichoderma asperelloides (T203) inoculum was added to the root system, resulting in a concentration of 105 germinated spores mL–1. Roots were collected at 24 hours post inoculation.

value: root

source_name: Root, 24 hours after treatment with Trichoderma

value: Trichoderma asperelloides (T203) inoculation


title: Roots-Trichoderma_Roots-control_24h_rep1

description:
T1-R1
Arabidopsis roots treated with Trichoderma for 24 hours versus control roots not treated with Trichoderma at the same time point


title: CD4 T cells, 155KO, biological rep1

description: Gene expression data from 155KO activated CD4 T cell

scan_protocol: Performed according to the manufacturer's instructions.

value: miR-155 KO


title: 14286350 - Ctrl-LMV_BR1 vs Ctrl-TuYV_BR1

hyb_protocol: Ctrl-TuYV_BR1 Cy5 / Ctrl-LMV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14286330 - Ctrl-TuYV_BR3 vs TuYV_BR3

hyb_protocol: TuYV_BR3 Cy5 / Ctrl-TuYV_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: TuYV_BR3:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name: TuYV - inoculation - inoculation, infection with symbiotic bacteria,tuyv:time 29day . All leaves from 42 days old plants were infected by agro-inoculation. We infiltred all leaves with agrobacteria containing the pBIN vector with the whole sequence of the TuYV. We used 20 plants for each condition. Then, 29 days after infection, we made protoplasts with 50 leaves from all infected or mock plants.

extract_protocol: Ctrl-TuYV_BR3:10ug. (Qiagen_RNeasy.pdf)


title: 14286331 - TuYV_BR3 vs Ctrl-TuYV_BR3

hyb_protocol: Ctrl-TuYV_BR3 Cy5 / TuYV_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CD4 T cells, WT, biological rep2


title: CD4 T cells, WT, biological rep1


title: 14286370 - Ctrl-LMV_BR1 vs TuYV_BR1

hyb_protocol: TuYV_BR1 Cy5 / Ctrl-LMV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: TuYV_BR1:10ug. (Qiagen_RNeasy.pdf)


title: 14286371 - TuYV_BR1 vs Ctrl-LMV_BR1

hyb_protocol: Ctrl-LMV_BR1 Cy5 / TuYV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14268907 - TuYV_BR2 vs Ctrl-TuYV_BR2

hyb_protocol: Ctrl-TuYV_BR2 Cy5 / TuYV_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Ctrl-TuYV_BR2:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: TuYV_BR2:10ug. (Qiagen_RNeasy.pdf)


title: BrdU-HU

description: Brdu wt SY2201 S

source_name: IP fraction of Brdu wt SY2201 S

source_name: SUP of Brdu wt SY2201 S


title: 14286328 - LMV_BR3 vs Ctrl-LMV_BR3

hyb_protocol: Ctrl-LMV_BR3 Cy5 / LMV_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Ctrl-LMV_BR3:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: LMV_BR3:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name: LMV - pathogen - pathogen infection, lmv:time 27day. All leaves from 42 days old plants were infected by hand-rubbing with ground LMV infected leaves. We used 20 plants for each condition. Then, 27 days after infection, we made protoplasts with 50 leaves from all infected or mock plants.


title: 14268903 - Ctrl-TuYV_BR2 vs TuYV_BR2

hyb_protocol: TuYV_BR2 Cy5 / Ctrl-TuYV_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14268900 - LMV_BR2 vs Ctrl-LMV_BR2

hyb_protocol: Ctrl-LMV_BR2 Cy5 / LMV_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Ctrl-LMV_BR2:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: LMV_BR2:10ug. (Qiagen_RNeasy.pdf)


title: 14268909 - TuYV_BR2 vs LMV_BR2

hyb_protocol: LMV_BR2 Cy5 / TuYV_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14268908 - LMV_BR2 vs TuYV_BR2

hyb_protocol: TuYV_BR2 Cy5 / LMV_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CD4 T cells, 155KO, biological rep3


title: 14269117 - Ctrl-LMV_BR3 vs LMV_BR3

hyb_protocol: LMV_BR3 Cy5 / Ctrl-LMV_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Nrd1-G2

description: Nrd1-FLAG wt CY1112 G2 GLU

source_name: IP fraction of Nrd1-FLAG wt CY1112 G2 GLU

source_name: SUP of Nrd1-FLAG wt CY1112 G2 GLU


title: CD4 T cells, 155KO, biological rep2


title: Nrd1-HU

description: Nrd1-FLAG wt CY1112 S GLU

source_name: IP fraction of Nrd1-FLAG wt CY1112 S GLU

source_name: SUP of Nrd1-FLAG wt CY1112 S GLU


title: Nrd1-G1

description: Nrd1-FLAG wt CY1112 G1 GLU

source_name: IP fraction of Nrd1-FLAG wt CY1112 G1 GLU

source_name: SUP of Nrd1-FLAG wt CY1112 G1 GLU


title: 14268898 - Ctrl-LMV_BR2 vs LMV_BR2

hyb_protocol: LMV_BR2 Cy5 / Ctrl-LMV_BR2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Sen1-G2

description: Sen1-FLAG wt CY8511 G2 GLU

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

source_name: IP fraction of Sen1-FLAG wt CY8511 G2 GLU

source_name: SUP of Sen1-FLAG wt CY8511 G2 GLU


title: Sen1-HU

description: Sen1-FLAG wt CY8511 S GLU

source_name: IP fraction of Sen1-FLAG wt CY8511 S GLU

source_name: SUP of Sen1-FLAG wt CY8511 S GLU


title: 14178754 - TuYV_BR1 vs LMV_BR1

hyb_protocol: LMV_BR1 Cy5 / TuYV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: LMV_BR1:10ug. (Qiagen_RNeasy.pdf)


title: Sen1-G1

description: Sen1-FLAG wt CY8511 G1 GLU

source_name: IP fraction of Sen1-FLAG wt CY8511 G1 GLU

source_name: SUP of Sen1-FLAG wt CY8511 G1 GLU


title: Peripheral Blood, control 1, 14hrs fasting , rep 1

description: Gene expression in control samples

hyb_protocol: 5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1ul of 25x Agilent fragmentation buffer and 5ul of 10x Agilent blocking agent following the manufacturer’s instructions. 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent G4851A , human genome G3 Hmn GE 8X60K microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

source_name: Peripheral Blood, control, 14hrs fasting , replicate 1

extract_protocol: A total of 3ml of peripheral blood was collected in EDTA coated tubes from each participant after overnight fast. Total RNA was extracted from the blood samples using QIAamp RNA Blood mini kit (Qiagen, USA) using the protocol recommended by the manufacturer.  For the microarray experiment, the extracted RNA was cleaned up using the RNeasy Mini Elute cleanup kit (Qiagen, USA). RNA was quantified by NanoDrop ND-1000 Spectrophotometer (NanoDrop,Wilmington,DE, USA) , while the quality was determined using a Bioanalyzer 2100 (Agilent Technologies, CA, USA).

value: whole blood

value: male

value: control


title: 14178751 - LMV_BR1 vs Ctrl-LMV_BR1

hyb_protocol: Ctrl-LMV_BR1 Cy5 / LMV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178753 - LMV_BR1 vs TuYV_BR1

hyb_protocol: TuYV_BR1 Cy5 / LMV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178749 - Ctrl-LMV_BR1 vs LMV_BR1

hyb_protocol: LMV_BR1 Cy5 / Ctrl-LMV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178752 - TuYV_BR1 vs Ctrl-TuYV_BR1

hyb_protocol: Ctrl-TuYV_BR1 Cy5 / TuYV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178750 - Ctrl-TuYV_BR1 vs TuYV_BR1

hyb_protocol: TuYV_BR1 Cy5 / Ctrl-TuYV_BR1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CM1748 replicate 1

status: Public on Nov 08 2012

city: Cambridge

middle: Michael

last: Carroll

address: Biological Laboratories, Room 3084, 16 Divinity Ave

department: Organismic and Evolutionary Biology

institute: Harvard University

description:
One of eight replicate populations founded from EM and evolved on methanol for 600 generations
Marx lab 2012, Harvard University, custom Agilent 60-mer array with 15K features for Methylobacterium extorquens AM1 based on GPL6262

hyb_protocol: standard Agilent protocol by MOgene, LC

scan_protocol: standard Agilent protocol by MOgene, LC

data_processing: standard Agilent protocol by MOgene, LC

organism: Methylorubrum extorquens AM1

source_name: Mid-exponential phase batch cultures grown on 15 mM methanol

label_protocol: standard Agilent protocol by MOgene, LC

growth_protocol: Growth experiments were initiated by inoculating 10 μL of freezer stock into 9.6 mL Hypho in a 50 mL Erlenmeyer flask containing 10 mM methanol and 1.75 mM succinate plus 50 mg/mL kanamycin. Flasks were grown at 225 rpm in a 30 °C shaker-incubator until reaching stationary phase (2-4 days). A second acclimation cycle was accomplished by transferring 150 μL of saturated culture into 9.45 mL fresh medium with 0.5x kanamycin plus the carbon substrate to be tested; then transferred again into the same conditions for experimental (measured) growth. A 1:64 dilution of cultures with the given substrate concentrations allowed for ~ 26 doublings per growth cycle.

extract_protocol: Total RNA extraction was performed using the RNeasy kit (Qiagen, Valencia, CA), genomic DNA was removed using the TURBO DNA-free kit (Ambion, Austin, TX), and the RNA samples were concentrated using Amicon Ultra centrifugal filters (Millipore, Billerica, MA).

treatment_protocol: Triplicate cultures of strains were grown to half-maximal OD600 in 15 mM methanol before harvesting and RNA

tag: isolate

value: Isolate gen. 600 population F8 (F8)


title: CM1748 replicate 2

value: One of eight replicate populations founded from EM and evolved on methanol for 600 generations


title: CM1745 replicate 2

value: Isolate gen. 600 population F7 (F7)


title: CM1748 replicate 3


title: CM1745 replicate 1


title: CM1742 replicate 3

value: Isolate gen. 600 population F6 (F6)


title: CM1742 replicate 2


title: CM1745 replicate 3


title: CM1742 replicate 1


title: CM1739 replicate 2

value: Isolate gen. 600 population F5 (F5)


title: CM1739 replicate 3


title: CM1145 replicate 3

value: Isolate gen. 600 population F4 (F4)


title: CM1739 replicate 1


title: CM1145 replicate 2


title: CM1139 replicate 3

value: Isolate gen. 600 population F3 (F3)


title: CM1145 replicate 1


title: CM1139 replicate 1


title: CM1139 replicate 2


title: DSS CX3CR1int Ly6Chi

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description: SAMPLE 7

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G plus scanner

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

source_name: sorted cells from the lamina propria of the colon at day 4 of Dextran Sodium Sulphate colitis model

growth_protocol: All mice were maintained under specific pathogen-free conditions and handled according to protocols approved by the Weizmann Institute and the Institute Pasteur Animal Care Committee as per international guidelines.

extract_protocol: Total RNA was extracted with the miRNeasy Mini Kit (Qiagen). RNA purity was assessed with ND-1000 Nanodrop (Peqlab) and BioAnalyzer 2100 (Agilent).

treatment_protocol: Cells were sorted from the digested tissue and were sorted using a FACSAria machine (BD).

tag: strain background

tag: tissue

value: Colon

tag: condition

value: inflammatory (Dextran Sodium Sulphate induced colitis model)


title: DSS splenic Ly6Chi monocytes

description: SAMPLE 8

hyb_protocol: According to Affymetrix standard protocols

source_name: sorted cells from the spleen at day 4 of Dextran Sodium Sulphate colitis model

value: Spleen


title: Steady state splenic Ly6Chi monocytes

description: SAMPLE 3

source_name: sorted cells from the spleen in steady state conditions

label_protocol: According to Affymetrix standard protocols

value: female

value: steady state


title: CM1730 replicate 3

value: Isolate gen. 600 population F2 (F2)


title: Steady state CX3CR1hi monocyte-reconstituted resident MFs

description: SAMPLE 2

source_name: sorted cells from the lamina propria of the colon in steady state conditions


title: DSS CX3CR1int Ly6Clo

description: SAMPLE 6


title: CM1730 replicate 2


title: DSS CX3CR1hi F4/80hi

description: SAMPLE 5


title: Steady state CX3CR1hi F4/80hi

description: SAMPLE 4

source_name: sorted cells from the lamina propria of the colon at steady state conditions


title: CM1727 replicate 2

value: Isolate gen. 600 population F1 (F1)


title: CM701 replicate 2

description:
Engineered, GSH-based C1-metabolism
Marx lab 2012, Harvard University, custom Agilent 60-mer array with 15K features for Methylobacterium extorquens AM1 based on GPL6262

value: Engineered Methylobacterium (EM)

value: Engineered, GSH-based C1-metabolism


title: CM1727 replicate 3


title: CM1727 replicate 1


title: CM701 replicate 1


title: CM1730 replicate 1


title: CM701 replicate 3


title: Steady state CX3CR1hi resident MFs

description: SAMPLE 1


title: CM501 replicate 1

description:
Wild-type C1-metabolism
Marx lab 2012, Harvard University, custom Agilent 60-mer array with 15K features for Methylobacterium extorquens AM1 based on GPL6262

value: wild-type (WT)

value: Wild-type C1-metabolism


title: CM501 replicate 2


title: FoxO6 -/- (Mutant) Before Learning (Basal) biological replicate 5

first: Anne

last: Brunet

state: California

address: 300 Pasteur Drive,

department: Genetics

institute: Stanford University

description: Gene expression data from adult hippocampus from FoxO6 mutant mice before learning task

hyb_protocol: Followed the 169 Format array requirements. GeneChip Hybridization Oven 640, GeneChip Fluidics station 450.

scan_protocol: GeneChip Scanner 3000 7G.

data_processing: The data were adjusted for background and then normalized using Robust Multiarray Analysis (RMA).

source_name: adult hippocampus, FoxO6 mutant, basal

label_protocol: Biotinylated single-stranded DNA was prepared according to Affymetrix Whole Transcript Sense Targeting Labeling Assay protocol.

extract_protocol: RNAqueous (Ambion) using the manufacturer's protocol.

treatment_protocol: The cohort of basal mice were housed individually for at least 3 days prior to tissue harvesting. The mice used to collect hippocampal samples after the object learning task were handled daily  in the procedure room, prior to the object learning task. 24 hours before the object learning task, each mouse was individually habituated to the empty novel object arena for 10 min. On the days of the novel object learning task and the empty arena habituation, the mice were transferred to the procedure room and acclimatized for 60 min. For the novel object learning task, the mice were allowed to explore two identical and novel objects for 10 min in a 70 x 70 x 70 cm black plastic arena with a white PVC vinyl material on the base. After the object exploration, mice were transferred to an empty cage, and were euthanized after 60 min. The brains were dissected and incubated in ice-cold RNAlater (Ambion) for 24 hours at 4ºC. The brains were then rapidly frozen in O.C.T. Tissue-Tek (Sakura) at -80ºC. Coronal brain sections (300 µm) were made using a microtome (Microm), the hippocampus was finely dissected and collected into ‘RNA lysis buffer’ (Ambion), and homogenized for 30 sec using a rotar-stat homogenizer.

value: male

value: C57BL/6J-129sv mixed background

value: FoxO6 null

tag: time point

value: Before learning


title: FoxO6 +/+ (WT) Before Learning (Basal) biological replicate 2

description: Gene expression data from adult hippocampus from Wild Type mice before learning task

source_name: adult hippocampus, Wild Type, basal

tag: age

value: Wild Type FoxO6


title: FoxO6 +/+ (WT) Before Learning (Basal) biological replicate 1

tag: gender


title: FoxO6 -/- (Mutant) Before Learning (Basal) biological replicate 2


title: FoxO6 +/+ (WT) Before Learning (Basal) biological replicate 4


title: FoxO6 -/- (Mutant) Before Learning (Basal) biological replicate 6


title: FoxO6 +/+ (WT) Before Learning (Basal) biological replicate 5


title: manR overexpression rep1

city: Noda City

first: Masahiro

last: Ogawa

state: Chiba

address: 399 Noda

country: Japan

institute: Noda Institute for Scientific Research

description: Konjac glucomannan, 6h induction

hyb_protocol: Labeled cRNAs were hybridized with NISR Aspergillus oryzae 24K v.2.0. using Gene Expression Hybridization Kit (Agilent Technologies). Then, the array slides were washed with Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: The array slides were scanned with an Agilent Microarray Scanner G2505B (Agilent Technologies).

data_processing: Raw microarray image files were processed using Feature Extraction Software version 9.5.1(Agilent Technologies). In this process, linear and lowess normalizations were carried out to remove the dye-biases of the data.

organism: Aspergillus oryzae RIB40

source_name: control

label_protocol: Cyanine-3 (Cy-3) or Cyanine-5 (Cy-5) were used to label 500 ng of total RNA sample, using a Low RNA Input Linear Amplification/Labeling Kit Plus, Two colors (Agilent Technologies).

growth_protocol: For microarrays, conidia of the manR disruptant, manR-overexpressing strain and A. oryzae RkuptrP2-1∆AF/P (used as a control) were inoculated into 60 mL of minimal medium (1.0 g KCl, 0.5 g KH2PO4, 2.0 g NaNO3, 0.5 g MgSO4·7H2O, 10 mg FeSO4 per 1 L; pH 6.0) containing 3.0% trisodium citrate and 0.2% polypeptone as the carbon sources, and incubated at 30°C for 18 h with shaking at 150 rpm. After germination of the conidia, the mycelia were collected by filtration and transferred into 20 mL minimal medium containing 1.0% konjac glucomannan as the sole carbon source before being incubated at 30°C for 6 h with shaking at 150 rpm.

extract_protocol: Total RNA was extracted from the samples with ISOGEN RNA Extraction Reagent (Nippon Gene, Tokyo, Japan). To remove the contamination of genomic DNA, RNA samples were treated with DNase I (TakaraBio), and these samples were further purified using an RNeasy Mini Kit (QIAGEN). The RNA quality was verified using an RNA 6000 LabChip Kit and an Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA). The quantity of the RNA sample was determined using an UV–visible spectrophotometer, Gene Spec III (Hitachi, Tokyo, Japan).

treatment_protocol: The mycelia were collected by filtration, and the samples were frozen and ground in liquid nitrogen using a mortar and pestle.

value: A. oryzae RkuptrP2-1∆AF/P, △ku70, △aflatoxin cluster, pyrG+

tag: incubated with

value: 1.0% konjac glucomannan for 6hr

value: mycelia

source_name: manR Overexpression

value: A. oryzae TEF1 promoter-manR, △ku70, △aflatoxin cluster


title: FoxO6 +/+ (WT) After Learning biological replicate 6

description: Gene expression data from adult hippocampus from Wild Type mice after learning task

source_name: adult hippocampus, Wild Type, object learning task

value: After learning


title: FoxO6 -/- (Mutant) Before Learning (Basal) biological replicate 1


title: FoxO6 -/- (Mutant) Before Learning (Basal) biological replicate 3


title: FoxO6 -/- (Mutant) Before Learning (Basal) biological replicate 4


title: manR overexpression rep3

description: Konjac glucomannan, 6h induction


title: FoxO6 -/- (Mutant) After Learning biological replicate 5

description: Gene expression data from adult hippocampus from FoxO6 mutant mice after learning task

source_name: adult hippocampus, FoxO6 mutant, object learning task


title: manR disruption rep3

description: Konjac glucomannan, 6h induction

source_name: manR disruptant

value: A. oryzae △manR, △ku70, △aflatoxin cluster


title: manR overexpression rep2

description: Konjac glucomannan, 6h induction


title: manR disruption rep1

description: Konjac glucomannan, 6h induction


title: FoxO6 +/+ (WT) After Learning biological replicate 4


title: FoxO6 +/+ (WT) Before Learning (Basal) biological replicate 3


title: manR disruption rep2

description: Konjac glucomannan, 6h induction


title: FoxO6 -/- (Mutant) After Learning biological replicate 6


title: FoxO6 +/+ (WT) After Learning biological replicate 5


title: AP3 null mutant perturbation 15

city: Zurich

first: Samuel

middle: Elias

last: Wuest

address: Winterthurerstrasse 190

department: Institute of Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

description: Biological Replicate 1: several plants (approx 20-25) pooled per replicate and genotype

hyb_protocol: Fragmentation buffer and Hybridization Buffer HI-RPM (Agilent Gene Expression Hybridization Kit) were added and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized for 16 hrs at 65 °C. After hybridization, slides were washed sequentially according to the manufacturer's instruction.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (v 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization

label_protocol: 500ng of total RNA were primed with 0.6 µl of T7 DNA primer at 65 °C for 10 min, then reverse transcribed at 40 °C  for 2 hrs in the presence of 300 U MMLV Reverse Transcriptase and 10mM dNTP mix, with Cy3-label and Cy5- label.

growth_protocol: Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees (16 degrees for plants used for temperature-sensitive perturbation experiments) under constant illumination with cool white fluorescent light

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich), according to the manufacturer's instructions

treatment_protocol: For all experiments,  ~4 week-old plants were used. For experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in  Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.

value: 5 days after Dexamethasone treatment

tag: developmental stage

value: early-intermediate floral stage ~ stage 5-6 flowers

tag: genotype

value: FIS (ap1 cal AP1-GR); ap3-3 homozygous

tag: temperature

value: 20 degrees (constant)

value: FIS (ap1 cal AP1-GR); ap3-3 heterozygous


title: FoxO6 -/- (Mutant) After Learning biological replicate 4

city: Stanford

tag: strain


title: manR disruption rep4

description: Konjac glucomannan, 6h induction


title: AP3 null mutant perturbation 14

value: 2.5 days after Dexamethasone treatment

value: early floral stages ~ stage 3-4 flowers


title: FoxO6 +/+ (WT) After Learning biological replicate 3

value: male

value: C57BL/6J-129sv mixed background


title: FoxO6 +/+ (WT) Before Learning (Basal) biological replicate 6

value: Before learning


title: Col-0_Compost_1

city: Barcelona

hyb_protocol: Each sample was hybridized to a GeneChip Arabidopsis ATH1 Genome Array (Affymetrix).

source_name: leaves of 5-week-old plants grown in compost

extract_protocol: RNA was extracted from samples ground under liquid nitrogen using SpeedTools Total RNA Extraction kit (Biotools, Madrid, Spain), according to the manufacturer’s instructions.

tag: ecotype


title: VPI7943

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

hyb_protocol: Labeled DNA was hybridized with microarrays at 42 degrees C for 16 hours.

scan_protocol: Arrays were scanned with a GenePix 4000B.

data_processing: The log10 (average 635 nm median signal intensity for triplicate probes/average signal intensity for all empty spots on the array) was determined. Normalization was not performed.

organism: Clostridium botulinum

source_name: VPI7943, type F

label_protocol: Genomic DNA was labeled with Klenow fragment and Cy5-labeled random primers at 37 degrees C for 2 hours.

growth_protocol: Bacteria were grown under anaerobic conditions at 35 degrees C for 24-48 hours prior to genomic DNA extraction.

extract_protocol: DNA was isolated using the PureLink Genomic DNA kit (Life Technologies, Grand Island, NY).

tag: group

value: II

tag: strain type

value: F

tag: source

value: venison jerky

tag: geographical location

value: California


title: 17B

source_name: 17B, type B

value: B

value: marine sediment

value: Pacific coast, US


title: CDC706

source_name: CDC706, type B

value: fermented salmon brine

value: Alaska


title: KA173

source_name: KA173, type F

value: salmon

value: Columbia River, US


title: CDC38597

source_name: CDC38597, type B

value: blood sausage

value: Iceland


title: CDC30592

source_name: CDC30592, type B

value: gastric fluid


title: CDC66177

data_processing: The log10 (average 635 nm mean signal intensity for triplicate probes/average signal intensity for all empty spots on the array) was determined. Normalization was not performed.

source_name: CDC66177, type E

value: E

value: soil

value: Argentina


title: AP3 null mutant perturbation 13

tag: treatment

value: no Dexamethasone treatment

value: undifferentiated meristematic tissue

value: FIS (ap1 cal AP1-GR); ap3-3 homozygous

value: 20 degrees (constant)

value: FIS (ap1 cal AP1-GR); ap3-3 heterozygous