title: IBS_35

city: Los Angeles

first: Chang

state: CA

address: 10833 Le Conte Avenue, CHS 47-122

department: Medicine

institute: University of California, Los Angeles

hyb_protocol: The fragmented single-stranded cDNA was combined with hybridization controls from  Affymetrix and hybridized in the HTA 2.0 array overnight for 16-18 hours in the Affymetrix Genechip Hybridization Oven 645

scan_protocol: Arrays were stained and washed in the Affymetrix GeneChip Fluidics Station 450.  Mircoarrays were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Raw data was extracted and preprocessed using Expression Console from Affymetrix. CEL files were generated by the scanner.

label_protocol: After Purification, single-stranded cDNA was fragmented and labeled using the GeneChip WT Terminal Labeling kit from Affymetrix (900671)

extract_protocol: PBMCs were extracted from blood using standard protocols. RNA was isolated using the Qiagen  RNeasy mini Kit (cat 74104).  Column based.

tag: disease status

value: IBS

value: blood

tag: cell type

value: peripheral blood mononuclear cells


title: patient 15, tumoral sample1, array 2

status: Public on Dec 31 2016

type: RNA

city: Catania

first: Daniele

middle: F

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

hyb_protocol: Fragmented and labeled target (Sense Strand-cDNA  5.2-5.5 µg) was used for hybridization to the “GeneChip Human Transcriptome Array 2.0” according to the protocol supplied by the manufacturer was used for  hybridization step. The hybridization has been performed in an hybridization oven at 45°C for 16 hours with rotation at 60 rpm.

scan_protocol: Scanning was performed using the  Affymetrix Scanner GCS3000 7G.

data_processing: Data analysis was performed using Affymetrix® Expression Console™ software (v.1.4). Expression level analysis was obtained using the normalization method based on the processing algorithm Robust Multi-array Average (RMA).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: colon adenocarcinoma

label_protocol: Biotinylated fragmented sense strand cDNA were prepared according to the protocol supplied by the Affymetrix for Human Transcriptome Array 2.0 (HTA).

growth_protocol: Caco-2 and HT29 cell lines have been cultured in D-MEM medium (Dulbecco's Modified Eagle Medium 1X; GIBCO, COD:31965-023 containing 4.5g/L of  D-glucose), supplemented with 10% FBS (Fetal Bovine Serum) and 100 U/ml of antibiotics (Penicillin-Streptomycin). HCT116 cell line was cultured in McCoy 5A+ (McCoy’s 5A Medium 1X GIBCO, COD: 36600021 containing 3 g/L of D-glucose) supplemented with 10%FBS (Fetal Bovine Serum), 1.5 mM L-glutamine and 2200 mg/L of sodium bicarbonate. Cell lines were incubated at 37 °C in humidified atmosphere with 5% of CO2  and 95% of air. The culture medium was changed twice a week, then RNA was extracted using RNeasy Mini Kit- (Qiagen, Milan-Italy).

extract_protocol: Total RNA (100 ng) was extracted from frozen tissue and cell cultures using RNeasy Mini Kit (Qiagen, Milan - Italy) according to the manufacturer’s instructions. The concentration and the quality of  RNA were determined using a ND-1000 spectrophotometer (NanoDrop, Thermo Scientific, USA).

tag: tissue

value: colon adenocarcinoma

tag: tissue preparation

value: frozen sample

tag: anatomical site

value: right colon

tag: gender

value: male

tag: patient age

tag: tumor stage

value: tumor stage 3


title: patient 11, tumoral sample1,  single array

value: left colon

value: female


title: patient 19, tumoral sample1, single array

value: tumor stage 2


title: patient AA1, tumoral sample1, single array

value: sigmoid colon

value: tumor stage 4


title: patient 37, tumoral sample3, array 1

value: transverse colon


title: IBS_33

last: Lin

country: USA


title: IBS_21


title: IBS_34


title: IBS_32


title: IBS_30


title: IBS_27


title: IBS_15


title: IBS_26


title: IBS_31


title: IBS_24


title: IBS_23


title: IBS_22


title: IBS_25


title: IBS_17


title: IBS_20


title: IBS_18


title: IBS_28


title: IBS_19


title: IBS_29


title: IBS_7


title: IBS_5


title: IBS_13


title: IBS_11


title: IBS_16


title: IBS_12


title: IBS_9


title: IBS_14


title: IBS_3


title: IBS_6


title: IBS_10


title: PBMCs_healthy_control_31

value: healthy


title: DS#48

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: tumoral sample 48

hyb_protocol: Samples were hybridized over 16 h at 56°C onto miRNA microarray (Exiqon, v.11.0-hsa, mmu & rho) according to the manufacturer’s instructions using miRCURY LNATM microRNA Array kit (Exiqon).

scan_protocol: The slides were scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

data_processing:
Fluorescence intensities on scanned one-color images were quantified using Feature Extraction v9.5 software (Agilent Technologies) using the modified Exiqon protocol. Background correction was carried out, and raw data were normalized by quantiles.
Raw data were normalized by quantiles and probes belonging to the same microRNA gene were merged by median.

source_name: tumor tissue

label_protocol: RNA was labeled with Hy3 fluorescent dye according to the manufacturer’s instructions using miRCURY LNATM microRNA Array kit (Exiqon).

extract_protocol: Total RNA was obtained following the manufacturer’s instructions using the TriReagent kit (MRC, Cincinnati, OH, USA).

tag: tissue type

value: medullary thyroid carcinoma


title: DS#47

description: tumoral sample 47


title: IBS_8


title: PBMCs_healthy_control_27


title: PBMCs_healthy_control_29


title: IBS_1


title: PBMCs_healthy_control_30


title: DS#45

description: tumoral sample 45


title: PBMCs_healthy_control_25


title: DS#44

description: tumoral sample 44


title: DS#43

description: tumoral sample 43


title: PBMCs_healthy_control_28


title: IBS_4


title: DS#42

description: tumoral sample 42


title: DS#46

description: tumoral sample 46


title: IBS_2


title: PBMCs_healthy_control_32


title: DS#39

description: tumoral sample 39


title: DS#37

description: tumoral sample 37


title: DS#36

description: tumoral sample 36


title: PBMCs_healthy_control_26


title: DS#35

description: tumoral sample 35


title: DS#34

description: tumoral sample 34


title: PBMCs_healthy_control_24


title: PBMCs_healthy_control_23


title: DS#24

description: tumoral sample 24


title: DS#23

description: tumoral sample 23


title: DS#22

description: tumoral sample 22


title: PBMCs_healthy_control_21


title: PBMCs_healthy_control_22


title: PBMCs_healthy_control_19


title: DS#19

description: tumoral sample 19


title: DS#18

description: tumoral sample 18


title: PBMCs_healthy_control_18


title: PBMCs_healthy_control_17


title: PBMCs_healthy_control_14


title: PBMCs_healthy_control_16


title: DS#17

description: tumoral sample 17


title: PBMCs_healthy_control_20


title: PBMCs_healthy_control_15


title: DS#15

description: tumoral sample 15


title: PBMCs_healthy_control_13


title: DS#12

description: tumoral sample 12


title: PBMCs_healthy_control_12


title: DS#16

description: tumoral sample 16


title: DS#20

description: tumoral sample 20


title: DS#10

description: tumoral sample 10


title: DS#9

description: tumoral sample 9


title: DS#8

description: tumoral sample 8


title: PBMCs_healthy_control_11


title: DS#6

description: tumoral sample 6


title: PBMCs_healthy_control_10


title: DS#1

description: tumoral sample 1


title: DS#13

description: tumoral sample 13


title: DS#7

description: tumoral sample 7


title: PBMCs_healthy_control_9


title: PBMCs_healthy_control_8


title: DS#11

description: tumoral sample 11


title: PBMCs_healthy_control_5


title: PBMCs_healthy_control_7


title: PBMCs_healthy_control_6


title: PBMCs_healthy_control_4


title: DS#4

description: tumoral sample 4


title: PBMCs_healthy_control_3


title: PBMCs_healthy_control_1


title: PBMCs_healthy_control_2


title: Treatment80_rep2

city: Delhi

first: Atish

last: Ray

state: Delhi

address: North Campus - in front of VP Chest Institute

department: Zoology

country: India

institute: University of Delhi

description:
Gene expression after 80ppb arsenic exposure for 30 days
Pool of 80-1+80-2+80-3

hyb_protocol: Samples that pass the QC for specific activity were taken for hybridization. 600ng of labeled cRNA were hybridized on the array (AMADID: 64074) using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent)

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift method.

organism: Danio rerio

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0442). 500ng of pooled total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: Following removal of head and fins the fish body was cut into small pieces and snap frozen in liquid nitrogen. The total RNA was extracted from each fish using Tri Reagent following chloroform extraction and isopropanol precipitation method according to the manufacturer’s (Sigma Tri Reagent T-944) guideline. The RNA samples were treated with RNase free DNase I and the yield and purity evaluated using Nanodrop Spectrophotometer (Thermo Scientific; 1000) and Bioanalyzer (Agilent; 2100) respectively. RNA quality was checked based on the 260 to 280 ratio values, rRNA 28S to 18S ratios and RNA integrity number (RIN). The RNA obtained from 3 fish were pooled and used for single array.

treatment_protocol: Adult wild type zebrafish of 4 to 5 months old obtained from the single stock were acclimatized in reversed osmosis (RO) water in glass tank for 15 days and exposed to three environmentally relevant concentration of arsenic trioxide (eg 20ppb, 40ppb, 80ppb) for 30 days. At the end three individuals were randomly selected from each group for each replicates and sacrificed with excess of MS222

value: Whole body


title: Treatment40_rep1

description:
Gene expression after 40ppb arsenic exposure for 30 days
Pool of 40-1+40-2+40-3


title: Treatment40_rep2


title: Treatment20_rep2

description:
Gene expression after 80ppb arsenic exposure for 30 days
Pool of 20-1+20-2+20-3


title: Treatment80_rep1


title: 4968473028_H

city: Callaghan

first: Nikola

last: Bowden

state: NSW

address: University Dr

department: School of Medicine and Public Health

country: Australia

institute: University of Newcastle

description: SAMPLE 141

hyb_protocol: Whole genome gene expression analysis was performed using the FFPE optimised Illumina cDNA-mediated Annealing, Selection, extension, and Ligation (DASL) assay and WGGEX V3 beadarrays

scan_protocol: Beadarrays were scanned and images acquired using an Illumina Bead Array Reader

data_processing: Data was cubic spline normalised using GenomeStudio V2011.1

source_name: melanoma

extract_protocol: Hematoxylin and eosin (H&E) stained slides for each block were examined to identify the area with the highest concentration of tumour tissue and minimal stromal and lymphocytic infiltration. A 2mm punch biopsy was taken through the block and de-paraffinised using xylene. RNA was extracted using Life Technologies RNA extraction kit as per manufacturer’s instructions.

value: M

tag: kinase mutation

value: KIT L576P

tag: braf/nras/wt

value: WT

tag: primary/metastatic

value: Primary

tag: age at diagosis

tag: age at death

tag: overall survival (weeks)

tag: solar elastosis score

tag: likely sun exposure score

tag: breslow depth


title: 4968473028_C

description: SAMPLE 137

label_protocol: Whole genome gene expression analysis was performed using the FFPE optimised Illumina cDNA-mediated Annealing, Selection, extension, and Ligation (DASL) assay and WGGEX V3 beadarrays

value: F

value: Metastatic


title: 4968473028_A

description: SAMPLE 135

value: BRAF V600R

value: BRAF


title: 4968473017_C

description: SAMPLE 130

value: NRAS Q61K

value: NRAS


title: Treatment20_rep1

description:
Gene expression after 20ppb arsenic exposure for 30 days
Pool of 20-1+20-2+20-3


title: 4968473017_B

description: SAMPLE 129

value: NRAS Q61K, MET R988C


title: 4968473028_F

description: SAMPLE 139

value: NRAS Q61R


title: Control_rep2

description:
Gene expression in control zebrafish
Pool of C1+C2+C3


title: 4968473017_H

description: SAMPLE 134


title: 4968473017_G

description: SAMPLE 133

value: BRAF V600E, MET T1010I


title: 4968473017_F

description: SAMPLE 132


title: 4968473028_B

description: SAMPLE 136


title: 4569624074_H

description: SAMPLE 126


title: 4968473028_G

description: SAMPLE 140

value: BRAF V600E


title: 4569624074_G

description: SAMPLE 125


title: 4569624074_F

description: SAMPLE 124


title: 4569624074_D

description: SAMPLE 122


title: 4968473017_A

description: SAMPLE 128

value: CTNNB1 S45F


title: 4569624074_E

description: SAMPLE 123

value: NRAS Q61L, MET R988C


title: 4569624084_D

description: SAMPLE 127


title: 4968473017_E

description: SAMPLE 131


title: 4569624061_E

description: SAMPLE 119


title: 4569624061_H

description: SAMPLE 121


title: 4569624061_G

description: SAMPLE 120

value: NRAS Q61L


title: Control_rep1

value: Whole body


title: 4569624061_B

description: SAMPLE 117

value: M


title: 4569624053_C

description: SAMPLE 111


title: 4569624053_E

description: SAMPLE 113


title: 4569624053_D

description: SAMPLE 112


title: 4569624053_F

description: SAMPLE 114

value: WT


title: 4569624030_H

description: SAMPLE 104

value: Primary


title: 4569624061_D

description: SAMPLE 118

value: F


title: 4569624053_G

description: SAMPLE 115

value: KRAS G12A

value: Metastatic


title: 4569624053_H

description: SAMPLE 116


title: 4569624029_F

description: SAMPLE 100

value: MET T1010I


title: 4968473028_D

description: SAMPLE 138

value: BRAF


title: 4569624031_C

description: SAMPLE 107


title: 4569624031_D

description: SAMPLE 108

value: BRAF V600R


title: 4569624030_D

description: SAMPLE 103

value: NRAS Q61K

value: NRAS


title: 4569624029_B

description: SAMPLE 96


title: 4569624014_G

description: SAMPLE 94


title: 4569624029_H

description: SAMPLE 101

value: NRAS Q61R


title: 4569624031_B

description: SAMPLE 106

value: BRAF V600E


title: 4569624030_B

description: SAMPLE 102

value: BRAF V600E, MET R988C


title: 4569624031_F

description: SAMPLE 109


title: 4569624031_A

description: SAMPLE 105


title: 4569624029_D

description: SAMPLE 98


title: 4569624053_B

description: SAMPLE 110


title: 4569624029_A

description: SAMPLE 95


title: 4569624029_E

description: SAMPLE 99


title: 4569624029_C

description: SAMPLE 97


title: 4569624014_E

description: SAMPLE 93


title: 4569624014_D

description: SAMPLE 92


title: 4569624014_B

description: SAMPLE 90

value: NRAS  Q61K


title: 4569624014_A

description: SAMPLE 89

value: NRAS Q61L


title: 4569624013_F

description: SAMPLE 86


title: 4569624013_H

description: SAMPLE 88

value: KIT D572G


title: 4569624013_E

description: SAMPLE 85

value: M


title: 4569624013_C

description: SAMPLE 83

value: WT


title: 4569624013_G

description: SAMPLE 87


title: 4569624014_C

description: SAMPLE 91


title: 4569624013_B

description: SAMPLE 82

value: Primary


title: 4569624006_D

description: SAMPLE 80


title: 4569624006_E

description: SAMPLE 81


title: 4569624006_B

description: SAMPLE 78


title: 4569624013_D

description: SAMPLE 84

value: F


title: 4569624005_H

description: SAMPLE 76

value: BRAF V600E, NRAS Q61K


title: 4569624006_A

description: SAMPLE 77

value: Metastatic


title: 4569624005_G

description: SAMPLE 75


title: 4569624005_F

description: SAMPLE 74


title: 4569624005_C

description: SAMPLE 71


title: 4569624006_C

description: SAMPLE 79


title: 4569624005_A

description: SAMPLE 69


title: 4569624005_B

description: SAMPLE 70

value: NRAS G13D


title: 4569624005_E

description: SAMPLE 73


title: 4569624004_H

description: SAMPLE 68

value: BRAF


title: 4569624004_E

description: SAMPLE 65


title: 4569624004_G

description: SAMPLE 67


title: 4569624004_F

description: SAMPLE 66


title: 4569624004_C

description: SAMPLE 63


title: 4569624004_B

description: SAMPLE 62


title: 4531335118_H

description: SAMPLE 60

value: KIT N822I


title: 4569624004_D

description: SAMPLE 64


title: 4569624004_A

description: SAMPLE 61


title: BX12m0029_1

city: Stanford

first: Li

last: Li

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

hyb_protocol: Hybriziation was performed by following Affymetrix standard procedure.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Exon-level raw data was processed by quantile-quantile normalization
MoEx-1_0-st-v1.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: 12 mos biopsy post-txp

label_protocol: ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to the first batch of samples starting with approximately 100ng of total RNA to generate biotin-labeled RNA fragments for hybridization to the chip.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from percutaneous allograft biopsy samples obtained at 12 month after transplantation using All prep kit (QIAGEN-ALLprep kit, Valencia, CA USA). RNA quality was assessed using Bioanalyzer 2100 (Agilent Technologies)

treatment_protocol: not applicable

tag: chronic allograft injury (cai)

value: non-CAI


title: 4531335118_G

description: SAMPLE 59


title: 4569624005_D

description: SAMPLE 72


title: 4531335118_F

description: SAMPLE 58

value: NRAS


title: BX12m0023_1


title: 4531335118_C

description: SAMPLE 55


title: BX12m0022_1


title: 4531335118_D

description: SAMPLE 56


title: 4531335118_E

description: SAMPLE 57

value: KIT K642E


title: BX12m0024_0


title: 4531335118_A

description: SAMPLE 53


title: 4531335118_B

description: SAMPLE 54


title: 4531335117_H

description: SAMPLE 52

value: NRAS Q61R


title: 4531335117_G

description: SAMPLE 51

value: BRAF V600E


title: 4531335117_E

description: SAMPLE 49


title: 4531335117_D

description: SAMPLE 48


title: 4531335117_F

description: SAMPLE 50

value: NRAS G12C


title: 4531335117_C

description: SAMPLE 47


title: 4531335116_D

description: SAMPLE 42


title: 4531335116_C

description: SAMPLE 41


title: 4531335116_F

description: SAMPLE 44


title: BX12m0018_1


title: 4531335116_G

description: SAMPLE 45


title: 4531335115_G

description: SAMPLE 39

value: MET R988C


title: 4531335115_F

description: SAMPLE 38


title: 4531335115_D

description: SAMPLE 36

value: MET T1010I


title: 4531335116_A

description: SAMPLE 40

value: M


title: 4531335117_A

description: SAMPLE 46

value: WT


title: 4531335116_E

description: SAMPLE 43

value: Primary


title: BX12m0011_1


title: 4531335115_E

description: SAMPLE 37


title: BX12m0019_4

value: CAI


title: 4531335115_C

description: SAMPLE 35

value: F

value: NRAS Q61H


title: BX12m0017_4


title: BX12m0010_1


title: BX12m0007_0


title: 4531335115_B

description: SAMPLE 34

value: NRAS G13R

value: Metastatic


title: BX12m0025_1


title: 4531335114_D

description: SAMPLE 30

value: NRAS Q61H, MET T1010I


title: 4531335114_C

description: SAMPLE 29

value: BRAF


title: BX12m0012_0

value: non-CAI


title: 4531335097_H

description: SAMPLE 26


title: 4531335114_G

description: SAMPLE 33

value: KIT G498S


title: BX12m0009_1


title: 4531335097_E

description: SAMPLE 23


title: 4531335097_F

description: SAMPLE 24


title: 4531335114_B

description: SAMPLE 28

value: KIT V654M


title: 4531335097_C

description: SAMPLE 21

value: BRAF V600E, MET T1010I


title: BX12m0008_0


title: 4531335097_B

description: SAMPLE 20

value: BRAF V600E


title: 4531335097_D

description: SAMPLE 22


title: 4531335114_A

description: SAMPLE 27

value: NRAS Q61L

value: NRAS


title: 4531335114_E

description: SAMPLE 31


title: 4531335090_G

description: SAMPLE 18

value: M


title: BX12m0016_5


title: 4531335090_D

description: SAMPLE 17

value: WT


title: 4531335114_F

description: SAMPLE 32

value: Primary


title: BX12m0005_4

value: CAI


title: 4531335097_G

description: SAMPLE 25

value: F


title: BX12m0021_1


title: BX12m0006_1


title: 4531335090_C

description: SAMPLE 16


title: BX12m0004_0


title: 4531335090_A

description: SAMPLE 15


title: 4531335097_A

description: SAMPLE 19


title: 4531335089_D

description: SAMPLE 12


title: 4531335087_F

description: SAMPLE 6

value: KRAS G12C


title: 4531335087_B

description: SAMPLE 2


title: 4531335087_C

description: SAMPLE 3


title: 4531335087_A

description: SAMPLE 1


title: 4531335087_E

description: SAMPLE 5


title: BX12m0003_4


title: 4531335089_B

description: SAMPLE 10


title: BX12m0001_7


title: 4531335089_A

description: SAMPLE 9


title: 48hNaB (Cy3) vs. Undiff (Cy5)

city: Kolkata

first: Santasabuj

last: Das

state: West Bengal

address: P-33,CIT Road

department: Clinical Medicine

institute: National Institute of cholera & Enteric Diseases

hyb_protocol: The labeled cRNA samples were hybridized on to a Whole Genome Human 4x44k (AMADID: 14850).825ng of cy3 and cy5 labeled samples were pooled, fragmented and hybridized and data from these channels were used for comparison to test hybridizations of respective channels.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.Data extraction from Images was done using Feature Extraction software v 9.5 of Agilent.

data_processing: Normalization of the data was done using GeneSpring GX by applying Lowess normalization.  Genes showing ≥2 fold change (log2 (Butyrate treated/Untreated) = -1 or +1) in the test sample compared to the control were compiled as differentially regulated genes.

source_name: HT-29 colorectal adenocarcinoma_NaB_48h

label_protocol: The samples for Gene expression were labeled using Agilent Low RNA Input Linear amplification Kit (Part number:5184-3523).  Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 42°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dyes Cy5 CTP(Agilent) for control samples and Cy3 CTP(Agilent) for test samples were incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: HT-29 cells were grown in DMEM media with 10% FBS.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies).

treatment_protocol: Cells were serum-starved for 16 hours followed by 24 hours or  48 hours butyrate treatment

tag: cell line

value: HT-29 (ATCC® HTB-38™)

tag: cell type

value: colorectal adenocarcinoma


title: 4531335087_G

description: SAMPLE 7

value: NRAS Q61R

value: Metastatic


title: 4531335087_H

description: SAMPLE 8

value: BRAF


title: 24hNaB (Cy3) vs. Undiff (Cy5)

source_name: HT-29 colorectal adenocarcinoma_NaB_24h


title: 48h_NaB(12) (Cy3) vs. Undiff(10) (Cy5)


title: human fetal arteria endothelial cells_rep1

city: Cantanhede

first: Helena

last: Vazão

address: Nucleo 4, Lote 4

department: Tissue Engeneering

country: Portugal

institute: Biocant

description: Gene expression after 2 days in culture with endothelial cell medium

hyb_protocol: 30µg Cy3-labelled cRNA  was mixed with Agilent 10× blocking agent and Fragmentation Buffer  and incubated at 60ºC for exactly 30 min to fragment RNA. To stop de fragmentation reaction, 2x GEx Hybridization Buffer was added. After a short spin-down, the labelled cRNA mixture was applied to a microarray slide, assembled in a SureHyb Hybridization Chamber fitted with a gasket slide (Agilent), and incubated for 18 h at 65ºC in a hybridization oven, with 10 rpm rotation speed. Slides were washed as described in the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. Afterwards, the microarray and gasket slide were briefly disassembled inside a staining dish containing GE Wash Buffer 1 and the slides (up to 4 slides) were washed in fresh GE Wash Buffer 1 solution at room temperature, during 1 min, with gentle agitation from a magnetic stirrer. A second wash step was carried out by immersing the slides in GE Wash Buffer 2 solution, previously warmed to 37ºC, during 1 min, also with gentle magnetic stirring. Finally, slides were dried by centrifugation at 800 rpm for 3 min.

scan_protocol: Microarrays were scanned in the Agilent B Scanner using specific scanning protocols for gene expression microarrays and the format 4×44K. Agilent Feature Extraction Image Analysis Sofware (Version 10.7.3.1) was used to obtain fluorescence intensities from raw microarray image files.

data_processing: Analysis of raw data was performed using BRB-ArrayTools v3.4.0. BRB-Array Each gene’s measured intensity was median normalized to correct for differences in the labelling efficiency between samples. This analysis provided a median normalized dataset.

source_name: primary cells, umbilical cord, replicate 1

label_protocol: Before labeling, a mixture of ten in vitro synthesized RNAs were added to total RNA to allow for hybridization quality control and normalization of the microarrays. The RNA was amplified and labeled according to the One-Color Microarray-Based Gene Expression Analysis (Agilent). The efficiency of cRNA synyhesis and dye incorporation was measured using NanoDrop ND-1000 UV-VIS spectrophotometer and samples with neither a yield below 1.65 µg nor a specific activity (pmol Cy3 per ug cRNA) below 6 were not considered for hybridization.

growth_protocol: all cell samples were grown in T75 flasks coated with gelatin at 1x10^6 cells per flask,, culture medium was endothelial cell medium. Cells at passage 4, without any type of treatement were tripsinized and collected for RNA isolation.

extract_protocol: hESC-derived EC, HUAEC or AEC (adult aortic endothelial cells) were homogenized in Trizol reagent (Invitrogen) and total RNA was extracted by using the RNeasy Mini Kit (Qiagen, Valencia, USA), according to manufacturer’s instructions.  The quality of the RNA was assessed in the Agilent 2100 Bioanalyser (G2943CA) using the RNA 6000 Pico Kit (5067-1513).

treatment_protocol: There was no treatement added to the samples

value: HUAEC

tag: tissue

value: umbilical arteria


title: 4531335089_H

description: SAMPLE 14

tag: gender

value: KIT V559I


title: human hESC derived arterial cells_rep3

source_name: derived from hESC, replicate 3

value: hESC-derived EC

value: derived form stem cells


title: 4531335089_C

description: SAMPLE 11


title: human arterial adult cells_rep2

source_name: primary cells, aorta, replicate 2

value: AEC

value: arterial


title: human fetal arteria endothelial cells_rep3

source_name: primary cells, umbilical cord, replicate 3


title: BX12m0002_0

value: non-CAI


title: 4531335089_G

description: SAMPLE 13

value: WT


title: human hESC derived arterial cells_rep2

source_name: derived from hESC, replicate 2


title: D6F_rep3

city: La Jolla

first: Tianxu

last: Han

address: 9500 Gilman Dr

institute: UCSD

description:
10012449079_B
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The sample probe files of all samples were collected using Illumina’s GenomeStudio sorftware

organism: Mus musculus

source_name: ES-derived cells

label_protocol: Standard label protocol

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: ES-derived mesodermal/endothelium cells

tag: sorting strategy


title: BCL6 ChIP-chip in FL primary sample, FL_19

type: genomic

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: BCL6 ChIP-chip in FL primary sample - FL_19.

hyb_protocol: Described in www.nimblegen.com.

scan_protocol: Described in www.nimblegen.com.

data_processing: Take all the probes in the promoter region and perform log2 transformation of IP/Input (Cy5/Cy3). Then use the maximal summary of three connected probes as the bound intensity of the promoter. The detailed analysis method (script) was published in Ci et al. Blood. 2009 May 28;113(22):5536-48 (PMID 19307668).

molecule: genomic DNA

source_name: follicular lymphoma, input

label_protocol: Described in www.nimblegen.com.

extract_protocol: Sonicated genomic DNA, then purified by Qiagen column.

value: primary follicular lymphoma

tag: chip antibody

source_name: follicular lymphoma, BCL6 ChIP

extract_protocol: Chromatin immunoprecipitation to isolate genomic regions bound by BCL6, then purify by Qiagen column.

tag: sample identifier

value: anti-BCL6 antibody (N3)

tag: antibody vendor

value: Santa Cruz Biotechnology (Santa Cruz, CA)

tag: antibody catalog number

tag: antibody lot number


title: D20LKS_rep3

description:
10012449079_D
replicate 3

value: ES-derived hematopoietic progenitor cells


title: 24h_NaB(11) (Cy3) vs. Undiff(10) (Cy5)

value: HT-29 (ATCC® HTB-38™)

value: colorectal adenocarcinoma


title: BCL6 ChIP-chip in FL primary sample, FL_15

description: BCL6 ChIP-chip in FL primary sample - FL_15.


title: ESC_rep2

description:
3999926035_A
replicate 2

source_name: ESC

value: ESC


title: D20LS_rep2

description:
3999926035_E
replicate 2

value: ES-derived non-hematopoietic and differentiated cells


title: D20LK_rep2

description:
3999926035_F
replicate 2

value: ES-derived hematopoietic cells


title: D6F_rep2

description:
3999926035_B
replicate 2


title: D20LKS_rep2

description:
3999926035_D
replicate 2


title: D6C_rep1

description:
3999926028_C
replicate 1

value: ES-derived endodermal cells


title: human hESC derived arterial cells_rep1

source_name: derived from hESC, replicate 1

value: hESC-derived EC


title: D20LK_rep3

description:
10012449079_F
replicate 3


title: D6C_rep2

description:
3999926035_C
replicate 2


title: D20LS_rep3

description:
10012449079_E
replicate 3


title: D6F_rep1

description:
3999926028_B
replicate 1


title: ESC_rep1

description:
3999926028_A
replicate 1


title: human arterial adult cells_rep1

source_name: primary cells, aorta, replicate 1


title: human fetal arteria endothelial cells_rep2

source_name: primary cells, umbilical cord, replicate 2

value: HUAEC

value: umbilical arteria


title: D6C_rep3

description:
10012449079_C
replicate 3


title: ESC_rep3

description:
10012449079_A
replicate 3


title: D20LK_rep1

description:
3999926028_F
replicate 1


title: D20LKS_rep1

description:
3999926028_D
replicate 1


title: 9379087022_F

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing: The raw data were exported from Genome Studio without applying any normalization or background correction and imported into a R using the read.ilmn function of the limma package (version 3.22.1).  Background correction and quantile normalization were done using the limma function neqc (Shi et al., 2010, Nucleic Acids Research 38, e204). Probes with a detection p value < 0.05 in more than 4 arrays were discarded and not considered in any downstream analysis.

source_name: Atg7 FF (Olig1 Control)

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp Premier RNA Amplification Kit.

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted with the Trizol reagent, followed by a DNase I and proteinase K treatment and another phenol chloroform extraction. The RNA was recovered by ethanol precipitation, and column treated with the QIagen miRNeasy kit according to the manufacturers instructions. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol: Not applicable.

value: liver

tag: genotype

value: control

tag: age

value: 2 months

value: female


title: BCL6 ChIP-chip in FL primary sample, FL_17

description: BCL6 ChIP-chip in FL primary sample - FL_17.

value: primary follicular lymphoma


title: D20LS_rep1

description:
3999926028_E
replicate 2


title: BCL6 ChIP-chip in FL primary sample, FL_16

description: BCL6 ChIP-chip in FL primary sample - FL_16.

value: anti-BCL6 antibody (N3)


title: 9379087022_E

source_name: Atg7 FF (Alb Control)


title: 9379087005_E

value: male


title: 9379087005_D

source_name: Olig1-Cre:Atg7 FF

value: Atg7 cKO


title: 4531335087_D

description: SAMPLE 4

source_name: melanoma

value: M

tag: braf/nras/wt

value: WT

tag: primary/metastatic

value: Primary

tag: age at diagosis

tag: age at death

tag: overall survival (weeks)


title: 9379087022_C


title: 9379087022_B

source_name: Alb-Cre:Atg7 FF


title: 9379087005_F


title: HeLa_Dox_2

city: Ube

first: Eiichi

last: Takaki

state: Yamaguchi

address: minami-kogushi, 1-1-1

country: Japan

institute: Yamaguchi university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HeLa Dox 2

label_protocol: Biotinylated cDNA were prepared from 200 ng total RNA with the Ambion WT Expression Kit (Ambion) and Affimetrix GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: DMEM containing 10% fetal boviine serum at 37C

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).

treatment_protocol: HeLa cells were infected with Ad-sh-hHSF1-KD (1 x 107 pfu/ml) for 2 h and maintained in normal medium for 22 h. They were then infected with Ad-hHSF1,  Ad-hHSF1-T20A or GFP (2 x 106 pfu/ml) for 2 h and maintained with normal medium for a further 46 h. HeLa cells were treated with with  0.5 μM doxorubicine for 16 h,

tag: treatment

value: Doxorubicine


title: 9379087022_A


title: AI29

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: transgenic d16HER2-positive cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

tag: cell line

tag: cell type

value: mammary tumor cell line

tag: genotype/variation

value: transgenic d16HER2-positive


title: AI22


title: 9379087005_C

tag: tissue

tag: gender


title: 9379087022_D


title: HeLa_Dox_3

source_name: HeLa Dox 3


title: AI46

source_name: transgenic WT HER2-positive cell line

value: transgenic WT HER2-positive


title: AI32


title: HeLa_cont_2

source_name: HeLa cont 2


title: AI33


title: 9379087005_A


title: HeLa_cont_1

source_name: HeLa cont 1


title: AI31


title: HeLa_Dox_1

source_name: HeLa Dox 1


title: HeLa_cont_3

source_name: HeLa cont 3


title: AI34


title: AI21


title: AI23


title: AI28


title: HeLa+reHSF1-T20A_3

source_name: HeLa+reHSF1-T20A 3

value: HSF1 knockdown +  HSF1-T20A


title: AI47


title: AI44


title: AI35


title: AI30


title: 9379087005_B


title: AI45


title: JQ1 and nanaomycin treatment replicate 2

city: Sydney

first: Tao

last: Liu

address: C25 Lowy Cancer Research Center Gate 9 High St UNSW

department: Histone Modifications

institute: Children's Cancer Institute

description: Gene expression data from neuroblastoma cells treated with 500nM JQ1 and 125nM nanaomycin

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix HuGene-1_0-st-v1 Arrays. GeneChips were washed and stained.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner.

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

source_name: neuroblastoma BE(2)-C cells treated with JQ1 and nanaomycin -2

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

growth_protocol: BE(2)-C neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum.

extract_protocol: RNA was extracted from the cells six hours after treatment with RNeasy mini kit (Qiagen, Hamburg, Germany).

treatment_protocol: BE(2)-C neuroblastoma cells were treated with vehicle control, 500nM JQ1, 125nM nanaomycin, or combination of JQ1 and nanomycin for 6 hours.

value: peripheral nervous system tumour cell

value: MYCN-amplified neuroblastoma cells

value: BE(2)-C cells

tag: drug treatment

value: 500nM JQ1 and 125nM nanaomycin


title: Control vehicle treatment replicate 2

description: Gene expression data from control neuroblastoma cells

source_name: neuroblastoma BE(2)-C cells treated with vehicle control -2

value: vehicle control


title: JQ1 and nanaomycin treatment replicate 1

source_name: neuroblastoma BE(2)-C cells treated with JQ1 and nanaomycin -1


title: Leukocytes_non_athlete, biological rep5

city: Shanghai

first: Dongmei

address: Henren Road, #188

department: Sports Rehabilitation

country: China

institute: Shanghai University of Sport

hyb_protocol: Labeled and fragmented cDNA was hybridized onto human gene 1.1 ST array strips (Affymetrix, Inc, Santa Clara, CA).

scan_protocol: The reactions of hybridization, staining, scanning and imaging were performed on the Affymetrix Gene Atlas instrument according to the manufacturer’s protocol.

data_processing: Microarray hybridizations were analyzed on the software platform R 3.1.0 with Bioconductor 2.14.0 (10). Initially, the expression data from all chips were background corrected, quantile normalized and summarized with RMA (Robust Multichip Average)

source_name: Blood leukocytes in non-athlete

label_protocol: Total RNA (250 ng) from each sample was reverse transcribed to complementary DNA (cDNA), followed by overnight in vitro transcription to generate complementary RNA (cRNA).  Then, cRNA was reverse transcribed, and the 7.5 μg of sense cDNA were fragmented and labeled with Biotinylated.

extract_protocol: Total RNA from blood samples of all subjects was isolated using PaxGene Blood RNA Kit (Qiagen) according to the manufacturer protocols.

value: blood leukocytes

value: young


title: Nanaomycin treatment replicate 2

description: Gene expression data from neuroblastoma cells treated with 125nM nanaomycin

source_name: neuroblastoma BE(2)-C cells treated with nanaomycin -2

value: 125nM nanaomycin


title: Nanaomycin treatment replicate 1

source_name: neuroblastoma BE(2)-C cells treated with nanaomycin -1


title: HeLa+reHSF1-T20A_2

source_name: HeLa+reHSF1-T20A 2


title: HeLa+reHSF1_1

source_name: HeLa+reHSF1 1

value: HSF1 knockdown + Wild-type HSF1


title: Leukocytes_non_athlete, biological rep9


title: HeLa+SCR_1

source_name: HeLa+SCR 1

value: scramble + GFP


title: HeLa+reHSF1_2

source_name: HeLa+reHSF1 2


title: HeLa+hHSF1-KD_3

source_name: HeLa+hHSF1-KD 3

value: HSF1 knockdown + GFP


title: HeLa+SCR_2

source_name: HeLa+SCR 2


title: HeLa+reHSF1-T20A_1

source_name: HeLa+reHSF1-T20A 1


title: HeLa+hHSF1-KD_2

source_name: HeLa+hHSF1-KD 2


title: HeLa+SCR_3

source_name: HeLa+SCR 3


title: HeLa+reHSF1_3

source_name: HeLa+reHSF1 3


title: Leukocytes_non_athlete, biological rep11


title: Control vehicle treatment replicate 1

source_name: neuroblastoma BE(2)-C cells treated with vehicle control -1


title: Leukocytes_non_athlete, biological rep2


title: Leukocytes_non_athlete, biological rep8


title: Leukocytes_non_athlete, biological rep4


title: Leukocytes_non_athlete, biological rep3


title: Leukocytes_non_athlete, biological rep7


title: Leukocytes_non_athlete, biological rep6


title: JQ1 treatment replicate 2

description: Gene expression data from neuroblastoma cells treated with 500nM JQ1

source_name: neuroblastoma BE(2)-C cells treated with JQ1 -2

value: 500nM JQ1


title: JQ1 treatment replicate 1

source_name: neuroblastoma BE(2)-C cells treated with JQ1 -1


title: HeLa+hHSF1-KD_1

source_name: HeLa+hHSF1-KD 1


title: Leukocytes_athlete, biological rep11

source_name: Blood leukocytes in athlete


title: Leukocytes_athlete, biological rep9


title: Leukocytes_athlete, biological rep3


title: Leukocytes_non_athlete, biological rep10

source_name: Blood leukocytes in non-athlete


title: Leukocytes_athlete, biological rep12


title: Leukocytes_athlete, biological rep6


title: Leukocytes_athlete, biological rep4


title: Leukocytes_athlete, biological rep10


title: Leukocytes_athlete, biological rep7


title: Leukocytes_athlete, biological rep5


title: tumor sample P7 at t3, biological replicate 1

city: Oeiras

first: Joana

last: Cardoso

address: Instituto Gulbenkian de Ciência, 6

institute: Instituto Gulbenkian de Ciência

description:
Gene expression data from tumor sample at t3
Hs_P7_3rd_A927_sbraga_IGC_JL_(HuGene-1_0-st-v1)

hyb_protocol: Biotinilated cRNA was hybridized to the Human Gene 1.0 ST v1 array according to Affymetrix instructions. Liquid handling steps were performed with GeneChip Fluidics Station 45.

scan_protocol: Array was scanned with GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA) using Command Console v1.1.

data_processing: Raw data was pre-processed using aroma.affymetrix v2.4.0 package (http://aroma-project.org/) using the RMA algorithm; expression values were log2 transformed.

source_name: tumor sample at t3

label_protocol: Total RNA (100 ng) was used to generate cDNA with the Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays 12, (Applied Biosystems, Carlsbad, CA). Biotin labeled cRNAs, produced with the Affymetrix GeneChip WT Terminal Labeling kit according to Affymetrix instructions.

extract_protocol: RNA was extracted and purified from snap-frozen breast cancer samples using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as according to manufacturer’s instructions. The quantity and quality of the RNA was assessed on a nanodrop and with an Agilent Bioanalyzer.

tag: disease state

value: BC

tag: patient

value: sunitinib and docetaxel combined treatment

tag: timepoint

tag: neosu_response (neoadjuvant treatment with sunitinib_response)

value: bad


title: Leukocytes_non_athlete, biological rep1

tag: age


title: Leukocytes_athlete, biological rep2


title: tumor sample P9 at t3, biological replicate 2

description:
Gene expression data from tumor sample at t3
Hs_P9_3rd_b_A944_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: Leukocytes_athlete, biological rep1


title: Leukocytes_athlete, biological rep8


city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

description: Gene expression profiles of 3T3-L1 adipocytes in response to GDE5 siRNA transfection

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).

source_name: control

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: Mouse 3T3-L1 preadipocytes were cultured in a maintenance medium (10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin in Dulbecco’s modified medium) .

extract_protocol: Total RNAs of 3T3-L1 cells were extracted using QIAzol following manufacturer's instructions.

treatment_protocol: Stealth siRNA duplex oligoribonucleotides against mouse GDE5 were synthesized by Invitrogen. The sequences were as follows: mouse GDE5, sense 5′-CAGUGUGUUGUGGAAAGCAGUGAUU-3, antisense 5′-AAUCACUGCUUUCCACAACACACUG-3′ . 3T3-L1 cells were transfected with siRNAs in a final concentration of 20 nM using LipofectAMINE RNAimax (Invitrogen).

value: 3T3-L1 adipocyte cell line

tag: protocol

value: control

source_name: GDE5 siRNA

value: GDE5 siRNA


title: tumor sample P7 at t1(diagnosis), biological replicate 2

description:
Gene expression data from tumor sample at diagnosis
Hs_P7_1st_b_A940_sbraga_IGC_JL_(HuGene-1_0-st-v1)

source_name: tumor sample at diagnosis

value: prior to any treatment


title: AI20

source_name: transgenic d16HER2-positive cell line

value: mammary tumor cell line

value: transgenic d16HER2-positive


title: UnDiff_rep4

city: Cambridge

first: Zuzana

last: Keckesova

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

hyb_protocol: Agilent expression arrays were hybridized according to  manufacturer instructions and scanned using an Agilent DNA microarray scanner.

scan_protocol: Arrays were scanned using an Agilent scanner and the data was extracted using Agilent’s Feature Extraction software.

data_processing: Arrays were quantile normalized using limma (v 3.4.5) from Bioconductor in R.

source_name: skeletal muscle

label_protocol: Standard Agilent protocol

growth_protocol: C2C12 mouse myoblast cells (ATCC) were cultured in DMEM+15%FBS. Human progenitor muscle cells (Cell Applications 151-25a) were grown according to manufacturer’s protocol using their growth media supplied with these cells.

extract_protocol: 2 biological replicates of un-differentiated and differentiated mouse muscle cells (differentiated for 5 days in vitro), and 3 biological replicates of un-differentiated (one collected at 4 days after thawing, the remaining two collected at 12 days after thawing) and differentiated (for 8 days in vitro) human muscle cells were harvested and RNA extracted using RNeasy Plus Mini kit (Qiagen # 74136).

treatment_protocol: For differentiation of C2C12 cells media were changed to DMEM+2% horse serum. Media was changed every 3 days and differentiation occurred around days 4-6. Human progenitor muscle cells were differentiated according to manufacturer’s protocol using their differentiation media provided with the cells.

tag: Stage

value: Un-differentiated

value: Differentiated


title: tumor sample P7 at t2, biological replicate 1

description:
Gene expression data from tumor sample at t2
Hs_P7_2nd_A922_sbraga_IGC_JL_(HuGene-1_0-st-v1)

source_name: tumor sample at t2

value: sunitinib


title: tumor sample P9 at t3, biological replicate 1

description:
Gene expression data from tumor sample at t3
Hs_P9_3rd_A928_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P7 at t1(diagnosis), biological replicate 1

description:
Gene expression data from tumor sample at diagnosis
Hs_P7_1st_A917_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P6 at t1(diagnosis), biological replicate 2

description:
Gene expression data from tumor sample at diagnosis
Hs_P6_1st_b_A939_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P6 at t3, biological replicate 1

description:
Gene expression data from tumor sample at t3
Hs_P6_3rd_A926_sbraga_IGC_JL_(HuGene-1_0-st-v1)

value: good


title: tumor sample P7 at t2, biological replicate 2

description:
Gene expression data from tumor sample at t2
Hs_P7_2nd_b_A933_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P7 at t3, biological replicate 2

description:
Gene expression data from tumor sample at t3
Hs_P7_3rd_b_A943_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P6 at t1(diagnosis), biological replicate 1

description:
Gene expression data from tumor sample at diagnosis
Hs_P6_1st_A916_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: UnDiff_rep2


title: UnDiff_rep3


title: pmr1∆ 5mM CaCl2 rep 3

city: Sevilla

first: Ralf

middle: Erik

last: Wellinger

state: Sevilla

address: Avd Americo Vespucio SN

department: Molecular Biology

institute: CABIMER_Universidad de Sevilla

hyb_protocol: Following fragmentation, 5.5 ug of single-stranded cDNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix GCOS software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package (oneChannelGUI interface) of R/Bioconductor project.

organism: Saccharomyces cerevisiae

source_name: Mutant pmr1∆_YPD+5mM CaCl2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA Labeling Protocol (GeneChip® 3' IVT Express Kit User Manual, Affymetrix, 2008-2010).

growth_protocol: Each strain was grown to mid-log phase in liquid YPAD medium supplemented with 5mM CaCl2.

extract_protocol: Rneasy mini Kit (Qiagen) of total RNA was performed according to the manufacturer's instruction.

tag: strain background

tag: strain

value: pmr1∆ ; BY4741 pmr1Δ::kann

tag: growth phase

value: exponential phase


title: pmr1∆ 5mM CaCl2 rep 2


title: tumor sample P5 at t1(diagnosis), biological replicate 2

description:
Gene expression data from tumor sample at diagnosis
Hs_P5_2nd_b_A932_sbraga_IGC_JL_(HuGene-1_0-st-v1)

tag: treatment


title: pmr1∆ 5mM CaCl2 rep 1


title: UnDiff_rep1

tag: cell line


title: tumor sample P4 at t1(diagnosis), biological replicate 2

description:
Gene expression data from tumor sample at diagnosis
Hs_P4_1st_b_A937_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: BY 5mM CaCl2 rep 3

source_name: Wild type BY4147_YPD+5mM CaCl2

value: WT; MAT a ura3Δ0 leu2Δ0 his3Δ0 met15Δ0


title: tumor sample P5 at t2, biological replicate 2

description:
Gene expression data from tumor sample at t2
Hs_P5_1st_b_A938_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P4 at t1(diagnosis), biological replicate 1

description:
Gene expression data from tumor sample at diagnosis
Hs_P4_1st_A914_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: BY 5mM CaCl2 rep 1


title: tumor sample P12 at t3, biological replicate 2

description:
Gene expression data from tumor sample at t3
Hs_P12_3rd_b_A947_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P5 at t2, biological replicate 1

description:
Gene expression data from tumor sample at t2
Hs_P5_1st_A915_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P11 at t1(diagnosis), biological replicate 2

description:
Gene expression data from tumor sample at diagnosis
Hs_P11_st_b_A942_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P5 at t1(diagnosis), biological replicate 1

description:
Gene expression data from tumor sample at diagnosis
Hs_P5_2nd_A921_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: BY 5mM CaCl2 rep 2


title: tumor sample P12 at t2, biological replicate 1

description:
Gene expression data from tumor sample at t2
Hs_P12_2nd_A925_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P4 at t2, biological replicate 1

description:
Gene expression data from tumor sample at t2
Hs_P4_2nd_A920_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: TET2 KO clone 1.1

city: Baltimore

first: Stephen

middle: B

last: Baylin

state: MD

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University SOM

description: Biological replicate KO1.1/Con1

hyb_protocol: 0.75 microgram of samples labeled with Cy3 or Cy5 were mixed with control targets (Agilent Technologies), assembled on Oligo Microarray, hybridized, and processed according to the Agilent microarray protocol.

scan_protocol: Scanning was performed with the Agilent Technologies Scanner G2505B US2250258 under the default settings recommended by Agilent Technologies.

data_processing: Raw data was processed in Bioconductor running on R and LOWESS normalized (package Limma) without background correction.

source_name: A2780 TET2 KO clone

label_protocol: Sample amplification and labeling procedures were carried out using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturer's instructions. The labeled cRNA was purified using the RNeasy mini kit (Qiagen).

growth_protocol: A2780 cells were maintained in RPMI-1640 medium containing 10% FBS.

extract_protocol: Total RNA extracted using RNeasy mini kit following manufacturer's instructions

treatment_protocol: A2780 cells were infected with either Control or LentiCRISPR virus against TET2 genes for 2 days, followed by puromycin selection. Single clones were selected and validated after ~8 weeks selection in puromycin.

tag: infected with

value: LentiCRISPR virus against TET2 genes

value: chronic stable TET2 KO

tag: clone id

value: A2780 TET2 KO clone 1.1

source_name: A2780 control clone 1

value: Control virus

value: control clone generated in parallel with TET2 KO clones

value: A2780 control clone


title: TET2 KO clone 1.36

description: Biological replicate KO1.36/Con2

tag: genotype/variation

value: A2780 TET2 KO clone 1.36

source_name: A2780 control clone 2


title: tumor sample P12 at t3, biological replicate 1

description:
Gene expression data from tumor sample at t3
Hs_P12_3rd_A931_sbraga_IGC_JL_(HuGene-1_0-st-v1)

value: BC

value: sunitinib and docetaxel combined treatment


title: TET2 KO clone 2.32

description: Biological replicate KO2.32/Con2

value: A2780 TET2 KO clone 2.32


title: MHCC-97L cell

city: Hefei

first: Peng

last: Chen

state: Anhui province

address: Jixi road

institute: liver

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bitt. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: hepatocellular carcinoma

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: hepatocellular carcinoma cell line MHCC-97L

value: control


title: tumor sample P11 at t3, biological replicate 1

description:
Gene expression data from tumor sample at t3
Hs_P11_3rd_A930_sbraga_IGC_JL_(HuGene-1_0-st-v1)


title: tumor sample P12 at t2, biological replicate 2

description:
Gene expression data from tumor sample at t2
Hs_P12_2nd_b_A936_sbraga_IGC_JL_(HuGene-1_0-st-v1)

value: sunitinib


title: tumor sample P11 at t3, biological replicate 2

description:
Gene expression data from tumor sample at t3
Hs_P11_3rd_b_A946_sbraga_IGC_JL_(HuGene-1_0-st-v1)

value: good


title: tumor sample P10 at t3, biological replicate 2

description:
Gene expression data from tumor sample at t3
Hs_P10_3rd_b_A945_sbraga_IGC_JL_(HuGene-1_0-st-v1)

value: bad


title: sh-Talin-1 MHCC-97L cell

value: Talin-1 knockdown


title: Control_transgenic_plant_Replicate2_vs_Double_knockdown_transgenic_plant_Replicate2

city: Tsukuba

first: Naoki

last: Kishimoto

state: Ibaraki

address: 2-1-2 Kannondai

department: Agrogenomics Research Center

institute: National Institute of Agrobiological Sciences

description: Control biological replicate 2 vs Knockdown biological replicate 2

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2505B, software G2565BA

data_processing: Data was analyzed by Fearure Extraction software (version 9.1, Agilent)

organism: Oryza sativa

source_name: Young leaves of a control transgenic plant

label_protocol: Low RNA inout Lineat Amplification/Labeling Lit (Agilent)

growth_protocol:
The OsMOM1a/b double knockdown transgenic line "641-1" harbors two hairpin RNA-producing (double-stranded RNA-producing) constructs derived from OsMOM1a and OsMOM1b genes, based on GATEWAY™-compatible binary T-DNA destination vector. The double knockdown line was produced with the GATEWAY technology as follows: sequences of transcribed regions of OsMOM1a and OsMOM1b were used to make entry clones for each gene using BP reaction with a donor vector; then hairpin RNA-producing clones for each gene were obtained using LR reaction with each entry clone and a destination vector, p*7GWIWG2(I)-hpt; each construct was separately introduced into Agrobacterium tumefaciens (strain EHA105); transfected A. tumefaciens lines were allowed to infect primary callus derived from scutellum tissue and transgenic plants were generated according to an Agrobacterium-mediated transformation method of rice (Plant Molecular Biology Reporter 15 (1), 1997); single knockdown plants were selected from plants regenerated from primarily-transformed calli; a double knockdown plant was identified in the progeny of a sexual inter-strain cross between single knockdown lines for each gene. Double knockdown plants used in this study, OMAB8-A and OMAB8-B, are sibling individuals in the double knockdown line "641-1".    The control transgenic line "631-1" was produced with the same methods described above, except the use of A. tumefaciens transfected with only the destination vector. Control transgenic plants pHI-3 and pHI-6 are sibling individuals in the control transgenic line "631-1".
Plants were raised in green house for about 2 months in a room of greenhouse.

extract_protocol: Total RNA was extracted from young leaves by using Trizol (Invitrogen).

treatment_protocol: Young leaves were sampled before the boot stage. Cut leaves were frozen using liquid nitrogen immediately after sampling.

value: a control transgenic line, 631-1

tag: genetic background/cultivar

value: Nipponbare

tag: indivisual id

tag: tissue

value: young leaves

source_name: Young leaves of a knockdown transgenic plant

value: a double knockdown line of OsMOM1a & OsMOM1b, 641-1


title: Double_knockdown_transgenic_plant_Replicate1_vs_Control_transgenic_plant_Replicate1

description: Control biological replicate 1 vs Knockdown biological replicate 1 (the dye-swap experiment)


title: Double_knockdown_transgenic_plant_Replicate2_vs_Control_transgenic_plant_Replicate2

description: Control biological replicate 2 vs Knockdown biological replicate 2 (the dye-swap experiment)


title: Control_transgenic_plant_Replicate1_vs_Double_knockdown_transgenic_plant_Replicate1

description: Control biological replicate 1 vs Knockdown biological replicate 1


title: tumor sample P11 at t2, biological replicate 1

description:
Gene expression data from tumor sample at t2
Hs_P11_2nd_A924_sbraga_IGC_JL_(HuGene-1_0-st-v1)

tag: disease state

tag: patient


title: UnDiff_12days_rep4

tag: cell type

value: Primary muscle progenitor

value: Un-differentiated

value: Differentiated


title: TMK1PD-2

city: yufu

first: yuka

last: hirashita

institute: Oita University

description: IC50 of MEK inhibition by PD0325901 was more than 10 µM in TMK1

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing:
Feature Extraction software (Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed with GeneSpring GX software(Aglrent).
For cmoparison among multiple arrays, probr set data were median-normalized per chip. The probes were filterd based on signal intensity and flagged velues. Differentially  expressed genes between sensitive cell lines (HSC57 and SNU719) and resistant cell lines (SH10TC and TMK1) at 3h PD0325901 treatment.

source_name: PD1μM, 3H

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from cells treated with DMSO or MEK inhibitor (1μM), using an RNeasy mini kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s instructions.

tag: cell lines

tag: sensitivity

value: resistant


title: TMK1PD-3


title: tumor sample P10 at t3, biological replicate 1

description:
Gene expression data from tumor sample at t3
Hs_P10_3rd_A929_sbraga_IGC_JL_(HuGene-1_0-st-v1)

value: BC

tag: timepoint

tag: age

tag: neosu_response (neoadjuvant treatment with sunitinib_response)


title: tumor sample P11 at t1(diagnosis), biological replicate 1

description:
Gene expression data from tumor sample at diagnosis
Hs_P11_1st_A919_sbraga_IGC_JL_(HuGene-1_0-st-v1)

value: prior to any treatment


title: UnDiff_12days_rep3

tag: Stage


title: tumor sample P10 at t1(diagnosis), biological replicate 1

description:
Gene expression data from tumor sample at diagnosis
Hs_P10_1st_b_A941_sbraga_IGC_JL_(HuGene-1_0-st-v1)

tag: treatment


title: TMK1PD-1


title: TMK1mock-3

source_name: mock, 3h


title: Normal Blood Macrophage High

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Gene expression data from mouse blood

hyb_protocol: Hybridization cocktails containing 5.5 μg of fragmented, end-labeled cDNA were prepared and applied to GeneChip Mouse Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned at 5-m resolution using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.

data_processing: Quality assessment and statistical analysis of gene expression data were performed using the R/Bioconductor packages. To ensure the quality of the microarray assay, a set of quality assessment steps implemented in Bioconductor package “AffyExpress” were applied to the data. Raw intensity measurements of all probe sets were converted into expression measurements using the “RMA” method.

label: Biotin

source_name: Normal Blood Macrophage High

label_protocol: cRNA was generated using 10ng total RNA according to the manufacturer's protocol by using Affymetrix's GeneChip Whole Transcript Sense Target Labeling Assay in the first cycle of amplification.

growth_protocol: 7-week C57BL/6J mice were implanted with GL261 glioma cells, then sacrificed after 2 weeks.

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

treatment_protocol: FACS sorted cells were collected and total RNA was isolated using TRIzol (Invitrogen).

value: Blood

tag: strain

value: Normal


title: Normal Brain Microglia

description: Gene expression data from mouse brain

source_name: Normal Brain Microglia

value: Brain


title: Normal Blood Macrophage Low

description: Gene expression data from mouse blood

source_name: Normal Blood Macrophage Low


title: Tumor Brain Microglia

description: Gene expression data from mouse brain

source_name: Tumor Brain Microglia

value: Tumor


title: TMK1mock-2


title: UnDiff_4days_rep3


title: Tumor Blood Gr-1 Negative

description: Gene expression data from mouse blood

source_name: Tumor Blood Gr-1 Negative


title: Normal Brain Macrophage

description: Gene expression data from mouse brain

source_name: Normal Brain Macrophage


title: UnDiff_4days_rep4

source_name: skeletal muscle


title: UnDiff_12days_rep2


title: SNU719PD-3

description: IC50 of MEK inhibition by PD0325901 was less than 0.01µM in SNU719

value: sensitive


title: Tumor Brain Macrophage

description: Gene expression data from mouse brain

source_name: Tumor Brain Macrophage


title: TMK1mock-1


title: Tumor Blood Gr-1 Positive

description: Gene expression data from mouse blood

source_name: Tumor Blood Gr-1 Positive


title: Tumor Blood Macrophage Low

description: Gene expression data from mouse blood

source_name: Tumor Blood Macrophage Low


title: UnDiff_4days_rep2


title: tumor sample P11 at t2, biological replicate 2

description:
Gene expression data from tumor sample at t2
Hs_P11_2nd_b_A935_sbraga_IGC_JL_(HuGene-1_0-st-v1)

source_name: tumor sample at t2

value: sunitinib

value: good


title: UnDiff_4days_rep1


title: Tumor Blood Macrophage High

description: Gene expression data from mouse blood

source_name: Tumor Blood Macrophage High


title: SNU719PD-2


title: Tumor Brain Gr-1 Positive

description: Gene expression data from mouse brain

source_name: Tumor Brain Gr-1 Positive


title: SNU719PD-1


title: SNU719mock-2


title: SINET-32

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

description: Gene expression of SI-NET liver metastasis

hyb_protocol: Labeled samples were hybridized to 4x44K Whole Human Genome Microarrays (G4112F, Design ID: 014850, Agilent Technologies)

scan_protocol: Arrays were scanned using Agilent’s Microarray Scanner G2565BA (Agilent Technologies). Images were read and processed using Feature extraction version 10.7.1.1 (Agilent Technologies).

data_processing: The microarrays were background corrected using the normexp method and normalized using the quantile-quantile method.

source_name: liver metastasis

label_protocol: cDNA synthesis, labeling and hybridization were performed according to the One-Color Microarray-Based Gene Expression Analysis protocol v5.7

extract_protocol: RNA was isolated from fresh-frozen specimens using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

value: liver metastasis

tag: genetics


title: SNU719mock-3


title: K14-CreER;Ctnnb1 cKO digit,  biological rep3

first: Makoto

last: Takeo

address: 522 First Ave.

institute: New York University School of Medicine

hyb_protocol: We used AffymertixGeneChip 3 IVT Express Kit for hybridization according to manufacture's protocol.

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

data_processing: The data were analyzed with GeneSpring GX using Affymetrix default analysis settings and global scaling as normalization method.

source_name: 8 weeks old K14-CreER;Ctnnb1 cKO mouse, intact digit

label_protocol: We used AffymertixGeneChip 3 IVT Express Kit for labeling according to manufacture's protocol.

value: 8 weeks old

value: K14-CreER;Ctnnb1 cKO

value: whole digit


title: SINET-33

description: Gene expression of SI-NET primary tumor

source_name: primary tumor

value: primary tumor


title: K14-CreER;Ctnnb1 cKO digit,  biological rep2


title: SNU719mock-1

source_name: mock, 3h


title: control digit, biological rep3

source_name: 8 weeks old wildtype mouse, intact digit

value: wildtype


title: K14-CreER;Ctnnb1 cKO digit,  biological rep1


title: SH10TCPD-3

description: IC50 of MEK inhibition by PD0325901 was more than 10 µM in SH-10-TC

source_name: PD1μM, 3H


title: Sample 593/7, knockout DC stimulated with swollen conidia

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description:
593/7
Gene expression from calcineurin knock-out bone marrow-derived dendritic cells stimulated with swollen conidia.

hyb_protocol: Fragmented ssDNAs were hybridized to the standard arrays for 17h at 45°C; the arrays were then washed and stained using the Fluidics Station.

scan_protocol: The arrays were scanned using GeneChip Scanner 3000. The images were analyzed using Command Console and comparison analyses were carried out according to the instructions provided by Affymetrix.

data_processing: CEL files were processed in Bioconductor using the affy package. Expression data was summarized at the transcript level and normalized using RMA. Log2 transformation was applied to the expression data.

source_name: Calcineurin knock-out bone marrow-derived dendritic cells stimulated with swollen conidia

label_protocol: ssDNA was prepared, fragmented and labelled according to the Affymetrix protocol.

growth_protocol: Bone marrow cells from CD11c-cre Cnb-flow and from littermate controls were cultured in IMDM (containing 10ng/ml GM-CSF, 10% heat-inactivated FCS (Life Technologies), streptomycin 100mg/ml and penicillin 100U/ml) at 5x10^5cells/ml. Day 6 cells were harvested and re-stimulated with Aspergillus fumigatus morphotypes.

extract_protocol: Total RNA was extracted following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizolitrogen) followed by a Qiagen RNeasy clean-up procedure. RNA purity was assessed by spectrophotometer (NanoDrop): 260/280 and 260/230 ratios were evaluated. If the 260/280 and 260/230 ratios are < of 1.8, RNA samples are ethanol precipitated. Total RNA integrity was assessed by Agilent Bioanalyzer and the RNA Integrity Number (RIN) was calculated and RIN greater than 9, were used for microarray analysis.

treatment_protocol: Bone marrow-derived dendritic cells were harvested (day 6) and re-stimulated with panel A. fumigatus morphotypes (conidia, swollen conidia and hyphae). Depletion of contaminating Gr-1 positive cells was performed prior to the DCs stimulation using AutoMACS (Miltenyi Biotec).

value: calcineurin knock-out

value: bone marrow-derived dendritic cells

tag: stimulation

value: Aspergillus fumigatus swollen conidia


title: control digit, biological rep2

tag: genotype/variation


title: SH10TCPD-2

value: resistant


title: SINET-28

description: Gene expression of SI-NET lymph node metastasis

source_name: lymph node metastasis

value: lymph node metastasis


title: SINET-29


title: Sample 592/8, knockout DC stimulated with hyphae

description:
592/8
Gene expression from calcineurin knock-out bone marrow-derived dendritic cells stimulated with hyphae.

source_name: Calcineurin knock-out bone marrow-derived dendritic cells stimulated with hyphae

value: Aspergillus fumigatus hyphae


title: Sample 593/8, knockout DC stimulated with hyphae

description:
593/8
Gene expression from calcineurin knock-out bone marrow-derived dendritic cells stimulated with hyphae.


title: SINET-30

description: Gene expression of SI-NET primary tumor


title: Sample 593/6, knockout DC stimulated with conidia

description:
593/6
Gene expression from calcineurin knock-out bone marrow-derived dendritic cells stimulated with conidia.

source_name: Calcineurin knock-out bone marrow-derived dendritic cells stimulated with conidia

value: Aspergillus fumigatus conidia


title: control digit, biological rep1


title: Sample 592/6, knockout DC stimulated with conidia

description:
592/6
Gene expression from calcineurin knock-out bone marrow-derived dendritic cells stimulated with conidia.


title: SH10TCPD-1


title: Sample 592/7, knockout DC stimulated with swollen conidia

description:
592/7
Gene expression from calcineurin knock-out bone marrow-derived dendritic cells stimulated with swollen conidia.


title: SH10TCmock-3


title: SH10TCmock-2


title: SINET-27


title: SINET-31


title: SINET-26


title: SH10TCmock-1


title: Sample 586/7, wild type DC stimulated with swollen conidia

description:
586/7
Gene expression from wild type bone marrow-derived dendritic cells stimulated with swollen conidia.

source_name: Wild type bone marrow-derived dendritic cells stimulated with swollen conidia


title: HSC57PD-3

description: IC50 of MEK inhibition by PD0325901 was less than 0.01µM in HSC57


title: Sample 591/6, knockout DC stimulated with conidia

description:
591/6
Gene expression from calcineurin knock-out bone marrow-derived dendritic cells stimulated with conidia.


title: Sample 591/7, knockout DC stimulated with swollen conidia

description:
591/7
Gene expression from calcineurin knock-out bone marrow-derived dendritic cells stimulated with swollen conidia.


title: Sample 586/6, wild type DC stimulated with conidia

description:
586/6
Gene expression from wild type bone marrow-derived dendritic cells stimulated with conidia.

source_name: Wild type bone marrow-derived dendritic cells stimulated with conidia


title: Sample 584/8, wild type DC stimulated with hyphae

description:
584/8
Gene expression from wild type bone marrow-derived dendritic cells stimulated with hyphae.

source_name: Wild type bone marrow-derived dendritic cells stimulated with hyphae


title: Sample 586/8, wild type DC stimulated with hyphae

description:
586/8
Gene expression from wild type bone marrow-derived dendritic cells stimulated with hyphae.


title: Tumor Brain Gr-1 Negative

description: Gene expression data from mouse brain

source_name: Tumor Brain Gr-1 Negative

value: Brain

value: Tumor


title: SINET-24


title: Sample 591/8, knockout DC stimulated with hyphae

description:
591/8
Gene expression from calcineurin knock-out bone marrow-derived dendritic cells stimulated with hyphae.


title: Sample 584/7, wild type DC stimulated with swollen conidia

description:
584/7
Gene expression from wild type bone marrow-derived dendritic cells stimulated with swollen conidia.


title: HSC57PD-2

value: sensitive


title: SImucosa-10

description: Gene expression of normal small intestine mucosa

source_name: normal small intestine mucosa

value: normal small intestine mucosa


title: Sample 584/6, wild type DC stimulated with conidia

description:
584/6
Gene expression from wild type bone marrow-derived dendritic cells stimulated with conidia.


title: SImucosa-9


title: HSC57mock-3


title: Sample 731/8, wild type DC stimulated with hyphae

description:
731/8
Gene expression from wild type bone marrow-derived dendritic cells stimulated with hyphae.


title: HSC57PD-1


title: Sample 731/6, wild type DC stimulated with conidia

description:
731/6
Gene expression from wild type bone marrow-derived dendritic cells stimulated with conidia.


title: SINET-23

description: Gene expression of SI-NET primary tumor


title: Sample 731/7, wild type DC stimulated with swollen conidia

description:
731/7
Gene expression from wild type bone marrow-derived dendritic cells stimulated with swollen conidia.


title: SINET-25

description: Gene expression of SI-NET liver metastasis

value: liver metastasis


title: SINET-22

description: Gene expression of SI-NET primary tumor


title: SPC-HA_lung_3

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

description: 12 week old female mouse

hyb_protocol: Samples were hybridized on the GeneChip® Mouse Gene 1.0 ST array (Affymetrix) according manufacurer's recommendations.

scan_protocol: Microarrays were scanned with an Affymetrix GCS 3000 scanner running with GCOS v1.1.1 software.

data_processing: The microarray data were analyzed using the GeneSpring GX software (Agilent). The data were summarized, log2 transformed and normalized with the Robust Multi-array Analysis (RMA) algorithm. Only probe sets with signal intensities above the 20th percentile in at least one of the 6 microarrays performed were retained, whereas all other probe sets were excluded from further analyses. Subsequently, the signal intensities of the replicate microarrays performed for each mouse group (SPC-HAxTCR-HA, SPC-HA) were averaged and the fold changes were calculated in reference to the data from the SPC-HA group. Only probe sets with a fold change greater than or equal to ±2 were retained. All other probe sets were excluded from further analyses. Finally, 378 transcripts were found to be differentially expressed in SPC-HAxTCR-HA vs. SPC-HA lungs. 326 of those were up-regulated and 52 were down-regulated.

source_name: SPC-HA lung

label_protocol: Synthesis, labeling and fragmentation of cRNA was performed using the GeneChip® 3’ IVT Express Kit (Affymetrix) according to manufacurer's protocols.

extract_protocol: RNA was isolated using RNeasy Midi Kit together with the RNase free DNase kit (both from Qiagen) for DNA-digestion according to manufacturer's instructions. RNA was photometrically quantified on a NanoDrop devive and RNA integrity was checked on an Agilent2100 Bioanalyzer (Agilent).

treatment_protocol: Sample preparation comprised perfusion of the lung with about 10 ml of sterile PBS and subsequent lysis of the tissue in RLT lysis-buffer (Qiagen) and a tissue homogenizer.

tag: mouse strain

value: SPC-HA

value: lung

tag: gender

value: female

value: 12 week old

tag: genetic background

value: BALB/c


title: HSC57mock-1


title: SPC-HA_lung_1

description: 12 week old female mouse

tag: tissue


title: SxT_lung_3

description: 12 week old female mouse

source_name: SPC-HAxTCR-HA lung

value: SPC-HAxTCR-HA


title: SxT_lung_1

description: 12 week old female mouse


title: SImucosa-7


title: HSC57mock-2


title: SINET-18

description: Gene expression of SI-NET primary tumor

value: primary tumor


title: NRCP2_ZT26

city: Lausanne

first: Jonathan

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

hyb_protocol: Affymetrix Mouse Gene 1.0 ST arrays were hybridized with 2.5μg of biotinylated target, at 45°C for 17 hours, and washed and stained according to the protocol described in Affymetrix GeneChip Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G, and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package.

data_processing: Affymerix Expression Console 1.1.2637.26569, RMA normalization.

source_name: liver, Bmal1 KO, ZT26

label_protocol: For each sample, 100ng of total RNA were amplified using the WT Expression kit (Invitrogen, Carlsbad, USA; catalogue no. 4411974); the resulting sense cDNA was fragmented using UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labelling kit (Affymetrix, Santa Clara, USA; catalogue no. 900671, Santa Clara, USA).

growth_protocol: Bmal1-KO male mice (9 to 11 weeks old) were housed in a 12h light/12h dark light regimen for 2 weeks with food and water available ad libitum during night and day.

extract_protocol: Trizol extraction of total RNA, followed by purification with the miRNeasy Mini Kit (Qiagen) following the manufacturer instructions. For each ZT, 500 ng of total RNA from each of the five mouse livers were pooled and hybridized to Mouse Gene 1.0 ST arrays (Affymetrix).

treatment_protocol: The mice were entrained with a 12h light/12h dark light regimen with food access between ZT12 and ZT24 for 7 days (ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off). At ZT02, ZT06, ZT10, ZT14, ZT18, ZT22 and ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 5 ml of PBS through the spleen and immediately collected. Up to 100 mg of liver was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The rest of the livers was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation.

tag: strain/background

value: Bmal1 KO

value: male

value: liver

tag: time point


title: SINET-20

description: Gene expression of SI-NET primary tumor


title: SINET-19

source_name: liver metastasis


title: SImucosa-8


title: SxT_lung_2

description: 12 week old female mouse


title: SINET-17


title: NRCP2_ZT10

source_name: liver, Bmal1 KO, ZT10


title: NRCP2_ZT18

source_name: liver, Bmal1 KO, ZT18


title: NRCP2_ZT14

source_name: liver, Bmal1 KO, ZT14


title: dmso_replicate2

city: Ankara

first: Ozlen

last: Konu

address: Bilkent University

department: Molecular Biology and Genetics

country: Turkey

institute: Bilkent University

description:
DMSO2_ZF4
ZF4 cells treated with equivalent DMSO.

hyb_protocol: Stained with streptavidin-phycoerythrin conjugate.

scan_protocol: Scanned with GeneChip scanner.

data_processing: Data was RMA normalized and analyzed with BRB ArrayTools software.

source_name: ZF4 cells, equivalent DMSO

label_protocol: Biotin-labeled cRNA was obtained using antisense RNA, 3' IVT Express Kit, (Affymetrix, Santa Clara, CA, USA).

growth_protocol: ZF4 (ATCC, CRL-2050) were cultured in DMEM/F-12 (1:1) containing 10% fetal bovine serum with 1% Streptomycin/Penicilin =at 28ºC.

extract_protocol: Total RNA was extracted with SV total RNA isolation kit (Promega). RIN values were calculated using Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: ZF4 cells were treated with 100nM final concentration of rapamycin (Calbiochem, 553210) and DMSO as control for 48h.

tag: cell line

value: equivalent DMSO


title: SPC-HA_lung_2

description: 12 week old female mouse


title: NRCP2_ZT22

source_name: liver, Bmal1 KO, ZT22


title: rap_replicate2

description:
RAPA2_ZF4
ZF4 cells treated with 100nM rapamycin.

source_name: ZF4 cells, 100nM rapamycin

value: 100nM rapamycin


title: rap_replicate3

description:
RAPA3_ZF4
ZF4 cells treated with 100nM rapamycin.


title: SoyGC-treated 3

city: saga city

first: Hiroshi

last: Kitagaki

address: 1, Honjo-cho

institute: Saga University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1. Quantile normalization of log2(probes) values using library(preprocessCore) in R 3.0.2 (www.r-project.org)

source_name: SoyGC-treated

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

extract_protocol: Hot phenol and quagen Rneasy


title: NRCP2_ZT06

source_name: liver, Bmal1 KO, ZT06


title: SoyGC-treated 2


title: NRCP2_ZT02

source_name: liver, Bmal1 KO, ZT02


title: SImucosa-6


title: dmso_replicate1

description:
DMSO1_ZF4
ZF4 cells treated with equivalent DMSO.


title: UnDiff_12days_rep1

source_name: skeletal muscle

tag: cell type

value: Primary muscle progenitor

value: Un-differentiated

value: Differentiated


title: NRCP1_ZT26


title: SINET-16

description: Gene expression of SI-NET primary tumor

source_name: primary tumor


title: SoyGC-treated 1


title: SINET-13

description: Gene expression of SI-NET primary tumor


title: NRCP1_ZT18


title: SINET-15

description: Gene expression of SI-NET primary tumor


title: NRCP1_ZT14


title: NRCP1_ZT22


title: er-105 control, biological replicate 2

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

institute: Institute of plant physiology & ecology, SIBS, CAS

description: Gene expression data of mutant er-105 leaves, grown at 21℃

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data were analyzed with Partek® Genomics Suite 6.5 using default analysis settings to get RMA data.

organism: Arabidopsis thaliana

source_name: er-105 control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol with GeneChip IVT Labeling Kit and Genechip Sample Cleanup Module (Affymetrix)

growth_protocol: Grown at 21℃

extract_protocol: Total RNA was extracted from the leaves using the Trizol method (Invitrogen) and purified with RNeasy MiniKit (Qiagen). cDNA was synthesized and purified with one-cycle cDNA Synthesis Kit (Affymetrix) and GeneChip Sample Cleanup Module (Affymetrix), respectively.

treatment_protocol: 40℃ for 6 hours, untreated as control

tag: ecotype

value: Columbia-0 (Col-0)

value: leaves

value: er-105 mutant

value: 2 week-old


title: NRCP1_ZT10


title: er-105 control, biological replicate 3

tag: age


title: SINET-14

description: Gene expression of SI-NET lymph node metastasis

source_name: lymph node metastasis

value: lymph node metastasis


title: HenGC-treated 3

source_name: HenGC-treated


title: HenGC-treated 2


title: NRCP1_ZT06


title: rap_replicate1

description:
RAPA1_ZF4
ZF4 cells treated with 100nM rapamycin.


title: SImucosa-5

source_name: normal small intestine mucosa

value: normal small intestine mucosa


title: WT2

city: Boston

first: Paul

last: Pilch

address: 72 E. Concord

department: Biochemistry

institute: Boston University

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45°C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed with Genepattern software modules. A GCT file was created by ExpressionfileCreator module settings as RMA, quantile normalization and background correction.

source_name: Adipose tissue from WT2

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

growth_protocol: The animals were maintained in a pathogen-free animal facility at 21°C under a 12-h light/12-h dark cycle with access to a standard rodent chow.

treatment_protocol: 6 hours fasting before taking adipose tissue from mice.

value: adipose

tag: genotype

value: WT

value: 10 weeks


title: er-105 control, biological replicate 1


title: Col-0 control, biological replicate 1

description: Gene expression data of wild type Columbia-0 leaves, grown at 21℃

source_name: Col-0 control

value: wild-type


title: Col-0 treated with 40℃ for 6 hours, biological replicate 3

description: Gene expression data of wild type Columbia-0 leaves, grown at 21℃, treated with 40℃ for 6 hours

source_name: Col-0 treated with 40℃ for 6 hours


title: vehicle control 3

source_name: vehicle control


title: vehicle control 1


title: HenGC-treated 1


title: vehicle control 2


title: SINET-21

description: Gene expression of SI-NET primary tumor

value: primary tumor


title: KO3

source_name: Adipose tissue from KO3

value: cavin-3 knockout


title: Col-0 control, biological replicate 3


title: er-105 treated with 40℃, biological replicate 3

description: Gene expression data of mutant er-105 leaves, grown at 21℃, treated with 40℃ for 6 hours

source_name: er-105 treated with 40℃ for 6 hours


title: er-105 treated with 40℃, biological replicate 2


title: WT1

source_name: Adipose tissue from WT1


title: SINET-8

source_name: liver metastasis

value: liver metastasis


title: er-105 treated with 40℃, biological replicate 1


title: Col-0 treated with 40℃ for 6 hours, biological replicate 1


title: SINET-7


title: NRCP1_ZT02

value: Bmal1 KO

value: male

value: liver


title: SImucosa-4


title: Col-0 treated with 40℃ for 6 hours, biological replicate 2


title: SINET-11


title: SINET-12


title: DS#47

city: Madrid

first: Mercedes

last: Robledo

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

institute: Spanish National Cancer Research Centre (CNIO)

description: tumoral tissue 47

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: tumoral tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: tissue type

value: medullary thyroid carcinoma


title: DS#48

description: tumoral tissue 48


title: KO2

source_name: Adipose tissue from KO2


title: DS#46

description: tumoral tissue 46


title: SImucosa-3


title: SINET-10


title: SINET-6


title: WT3

source_name: Adipose tissue from WT3


title: SImucosa-2


title: SINET-9


title: DS#45

description: tumoral tissue 45


title: Col-0 control, biological replicate 2

city: Shanghai

value: Columbia-0 (Col-0)


title: DS#44

description: tumoral tissue 44


title: SINET-2


title: Human Mammary Epithelial Cells_GFP_Transfected_9

city: Durham

first: David

last: Hsu

state: NC

address: 905 S. LaSalle St. Rm 3008

department: Medical Oncology

institute: Duke University

hyb_protocol: The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

data_processing: The data were analyzed using the R statistical platform with the Bioconductor affymetrix package [R version 2.13.1 (2011-07-08) and Bioconductor version 2.9].

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mammary epithelial cells were isolated from a breast reductive surgery at Duke University and grown at 37 degrees C in mammary epithelial cell growth medium (MEGM) containing a MEGM Bullet Kit, human transferrin and isopenterol.

extract_protocol: Total RNA was isolated using a Qiagen Rneasy kit.

treatment_protocol: Cells were brought to quisecence by serum starvation and treated with adenovirus to over-express the Rheb oncogene (10 replicates) or GFP (10 replicates).  Eighteen hours after infection, activation of oncogenes and secondary targets were confirmed by western blotting.

value: Human Mammary Epithelial cells (HMECs)

value: over-expressing GFP (control)


title: Human Mammary Epithelial Cells_GFP_Transfected_5


title: Human Mammary Epithelial Cells_GFP_Transfected_10


title: DS#43

description: tumoral tissue 43


title: SINET-4


title: DS#41

description: tumoral tissue 41


title: KO1

source_name: Adipose tissue from KO1


title: Human Mammary Epithelial Cells_GFP_Transfected_4


title: Human Mammary Epithelial Cells_GFP_Transfected_6


title: SINET-5


title: DS#40

description: tumoral tissue 40


title: DS#42

description: tumoral tissue 42


title: SINET-3


title: Human Mammary Epithelial Cells_GFP_Transfected_8


title: Human Mammary Epithelial Cells_GFP_Transfected_3


title: SINET-1


title: Human Mammary Epithelial Cells_GFP_Transfected_7


title: Human Mammary Epithelial Cells_GFP_Transfected_2


title: SImucosa-1


title: DS#38

description: tumoral tissue 38


title: Human Mammary Epithelial Cells_GFP_Transfected_1


title: DS#39

description: tumoral tissue 39


title: DS#37

description: tumoral tissue 37


title: Human Mammary Epithelial Cells_Rheb_transfected_9

value: over-expressing Rheb oncogene


title: Neutrophils_2

city: Suita

first: Takashi

last: Satoh

state: Osaka

address: 3-1 Yamada-oka

department: RIMD

institute: Osaka university

hyb_protocol: Following fragmentation,  cDNA were hybridized for 16 hr at 45C on GeneChip mouse genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using  Genechip Scanner.

data_processing: The data were analyzed by R

source_name: hematopoietic cells

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

growth_protocol: Mice were housed in individually ventilated cages in a temperature and light regulated room in a SPF facility and received food and water ad libitum. All studies received local ethics review board approval and were performed in accordance with the guidelines of the animal care and use committee of the Research Institute for Microbial Diseases at Osaka University.

extract_protocol: Total RNA was isolated from each cell sample using a RNA isolation kit (Roche) and further purified using a RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Cells were washed in ice-cold FACS buffer (2% FCS, 2 mM EDTA in PBS), then incubated with each antibody for 15 min and washed twice with FACS buffer. Then these cells were prepared by using FACS ARIA

value: 8 weeks old

value: spleen

value: Neutrophils


title: Human Mammary Epithelial Cells_Rheb_transfected_10


title: DS#35

description: tumoral tissue 35


title: Eosinophils_1

value: eosinophils


title: DS#36

description: tumoral tissue 36


title: DS#34

description: tumoral tissue 34


title: Human Mammary Epithelial Cells_Rheb_transfected_7


title: Human Mammary Epithelial Cells_Rheb_transfected_8


title: Basophils_2

value: basophils


title: Neutrophils_1


title: Eosinophils_2


title: Human Mammary Epithelial Cells_Rheb_transfected_5