title: blood C57BL/6 d21 p.i. mouse 5

status: Public on Sep 21 2017

city: Berlin

first: Teresa

last: Domaszewska

state: Berlin

address: Virchovweg 12

department: Immunology

country: Germany

description:
Gene expression after 21 day Mtb infection in C57BL/6 mouse blood
blood B5 d21

hyb_protocol: Quantity and labeling efficiency were verified before hybridization of the samples to SurePrint G3 Mouse GE 8x60K Microarray (Agilent Technologies, Product Number G4852A, Design ID 028005) according to manufacturer's instruction.

scan_protocol: Scanning of microarrays was performed with 3μm resolution using a high-resolution laser microarray scanner (Agilent Technologies G2565CA)

data_processing: Data analysis was performed in R version 3.2.3 (2015-12-10), and a script including all analysis steps is available upon request. The data sets have been analyzed with limma R package for differential expression analysis (Ritchie et al., 2015). The data sets were background corrected using the normexp method and quantile normalized. Limma lmFit function was used to fit linear models which included factors: stimulus type (TB, control) and time point. The p-values were calculated based on the moderated t-statistic and most differentially regulated genes were retrieved with topTable function.

source_name: blood C57BL/6 d21 p.i. mouse 5

label_protocol: RNA was labeled with the Low Input Quick Amp Labeling (Agilent Technologies) according to manufacturer’s instructions

growth_protocol: 129S2 (129SvPas) mice were bred and kept under specific pathogen-free (SPF) conditions at the Max Planck Institute for Infection Biology in Berlin, Germany. C57BL/6 animals were purchased from Charles Rivers Laboratories. 129S2 and C57BL/6 were matched for age and sex, and co-housed for at least two weeks under specific pathogen-free (SPF) conditions at the Max Planck Institute for Infection Biology in Berlin, Germany before beginning the experiments. At the time of infection, all mice were 9–12 weeks of age.

extract_protocol: Blood was drawn from the inferior vena cava of all mice at indicated time points using a 26G needle. 200 µl were directly transferred into 800 µl of TRIzol (Invitrogen). Total RNA extraction of all blood samples was performed according to the manufacturer’s instructions. The RNA yield and A260/280 ratio were measured with a NanoDrop ND 100 spectrometer (NanoDrop Technologies), and RNA integrity was verified using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Aerosol infection with Mtb strain H37Rv and enumeration of bacteria in lung tissue were performed as previously described (Dorhoi et al., 2013)

value: whole blood

tag: time point

value: day 21

tag: infection

value: Mtb


title: blood 129S2 d21 p.i. mouse 5

type: RNA

institute: Max Planck Institute for Infection Biology

description:
Gene expression after 21 day Mtb infection in 129S2 mouse blood
blood A5 d21

molecule: total RNA

organism: Mus musculus

source_name: blood 129S2 d21 p.i. mouse 5

tag: strain

tag: tissue


title: blood 129S2 d21 p.i. mouse 4

description:
Gene expression after 21 day Mtb infection in 129S2 mouse blood
blood A4 d21

source_name: blood 129S2 d21 p.i. mouse 4


title: blood 129S2 d21 p.i. mouse 2

description:
Gene expression after 21 day Mtb infection in 129S2 mouse blood
blood A2 d21

source_name: blood 129S2 d21 p.i. mouse 2


title: blood 129S2 d21 p.i. mouse 3

description:
Gene expression after 21 day Mtb infection in 129S2 mouse blood
blood A3 d21

source_name: blood 129S2 d21 p.i. mouse 3


title: blood C57BL/6 d21 p.i. mouse 3

description:
Gene expression after 21 day Mtb infection in C57BL/6 mouse blood
blood B3 d21

source_name: blood C57BL/6 d21 p.i. mouse 3


title: blood C57BL/6 naïve mouse 1

description:
Gene expression C57BL/6 mouse blood
blood B1 naive

source_name: blood C57BL/6 naïve mouse 1

value: day 0

value: Not infected


title: blood C57BL/6 naïve mouse 4

description:
Gene expression C57BL/6 mouse blood
blood B4 naive

source_name: blood C57BL/6 naïve mouse 4


title: blood C57BL/6 naïve mouse 3

description:
Gene expression C57BL/6 mouse blood
blood B3 naive

source_name: blood C57BL/6 naïve mouse 3


title: blood C57BL/6 naïve mouse 6

description:
Gene expression C57BL/6 mouse blood
blood B6 naive

source_name: blood C57BL/6 naïve mouse 6


title: blood 12S2 naïve mouse 7

description:
Gene expression 129S2 mouse blood
blood A7 naive

source_name: blood 12S2 naïve mouse 7


title: blood 12S2 naïve mouse 8

description:
Gene expression 129S2 mouse blood
blood A8 naive

source_name: blood 12S2 naïve mouse 8


title: blood 12S2 naïve mouse 1

description:
Gene expression 129S2 mouse blood
blood A1 naive

source_name: blood 12S2 naïve mouse 1


title: blood C57BL/6 d21 p.i. mouse 4

description:
Gene expression after 21 day Mtb infection in C57BL/6 mouse blood
blood B4 d21

source_name: blood C57BL/6 d21 p.i. mouse 4


title: blood C57BL/6 naïve mouse 7

description:
Gene expression C57BL/6 mouse blood
blood B7 naive

source_name: blood C57BL/6 naïve mouse 7


title: blood 12S2 naïve mouse 2

description:
Gene expression 129S2 mouse blood
blood A2 naive

source_name: blood 12S2 naïve mouse 2


title: blood C57BL/6 d14 p.i. mouse 5

description:
Gene expression after 14 day Mtb infection in C57BL/6 mouse blood
blood B5 d14

source_name: blood C57BL/6 d14 p.i. mouse 5

value: day 14


title: blood 12S2 naïve mouse 3

description:
Gene expression 129S2 mouse blood
blood A3 naive

source_name: blood 12S2 naïve mouse 3


title: blood C57BL/6 d21 p.i. mouse 2

description:
Gene expression after 21 day Mtb infection in C57BL/6 mouse blood
blood B2 d21

source_name: blood C57BL/6 d21 p.i. mouse 2


title: blood C57BL/6 d14 p.i. mouse 3

description:
Gene expression after 14 day Mtb infection in C57BL/6 mouse blood
blood B3 d14

source_name: blood C57BL/6 d14 p.i. mouse 3


title: blood 12S2 naïve mouse 5

description:
Gene expression 129S2 mouse blood
blood A5 naive

source_name: blood 12S2 naïve mouse 5


title: blood C57BL/6 d21 p.i. mouse 1

description:
Gene expression after 21 day Mtb infection in C57BL/6 mouse blood
blood B1 d21

source_name: blood C57BL/6 d21 p.i. mouse 1


title: blood 12S2 naïve mouse 4

description:
Gene expression 129S2 mouse blood
blood A4 naive

source_name: blood 12S2 naïve mouse 4


title: blood 129S2 d14 p.i. mouse 2

description:
Gene expression after 14 day Mtb infection in 129S2 mouse blood
blood A2 d14

source_name: blood 129S2 d14 p.i. mouse 2


title: blood C57BL/6 d14 p.i. mouse 4

description:
Gene expression after 14 day Mtb infection in C57BL/6 mouse blood
blood B4 d14

source_name: blood C57BL/6 d14 p.i. mouse 4


title: blood C57BL/6 d14 p.i. mouse 1

description:
Gene expression after 14 day Mtb infection in C57BL/6 mouse blood
blood B1 d14

source_name: blood C57BL/6 d14 p.i. mouse 1


title: blood C57BL/6 d14 p.i. mouse 2

description:
Gene expression after 14 day Mtb infection in C57BL/6 mouse blood
blood B2 d14

source_name: blood C57BL/6 d14 p.i. mouse 2


title: blood 12S2 naïve mouse 6

description:
Gene expression 129S2 mouse blood
blood A6 naive

source_name: blood 12S2 naïve mouse 6


title: blood 129S2 d14 p.i. mouse 5

description:
Gene expression after 14 day Mtb infection in 129S2 mouse blood
blood A5 d14

source_name: blood 129S2 d14 p.i. mouse 5


title: blood 129S2 d14 p.i. mouse 4

description:
Gene expression after 14 day Mtb infection in 129S2 mouse blood
blood A4 d14

source_name: blood 129S2 d14 p.i. mouse 4


title: blood 129S2 d14 p.i. mouse 3

description:
Gene expression after 14 day Mtb infection in 129S2 mouse blood
blood A3 d14

source_name: blood 129S2 d14 p.i. mouse 3


title: blood 129S2 d14 p.i. mouse 1

description:
Gene expression after 14 day Mtb infection in 129S2 mouse blood
blood A1 d14

source_name: blood 129S2 d14 p.i. mouse 1


title: blood C57BL/6 d7 p.i. mouse 3

description:
Gene expression after 7 day Mtb infection in C57BL/6 mouse blood
blood B3 d7

source_name: blood C57BL/6 d7 p.i. mouse 3


title: blood C57BL/6 d7 p.i. mouse 4

description:
Gene expression after 7 day Mtb infection in C57BL/6 mouse blood
blood B4 d7

source_name: blood C57BL/6 d7 p.i. mouse 4


title: blood 129S2 d7 p.i. mouse 5

description:
Gene expression after 7 day Mtb infection in 129S2 mouse blood
blood A5 d7

source_name: blood 129S2 d7 p.i. mouse 5


title: blood C57BL/6 d7 p.i. mouse 1

description:
Gene expression after 7 day Mtb infection in C57BL/6 mouse blood
blood B1 d7

source_name: blood C57BL/6 d7 p.i. mouse 1


title: blood 129S2 d7 p.i. mouse 4

description:
Gene expression after 7 day Mtb infection in 129S2 mouse blood
blood A4 d7

source_name: blood 129S2 d7 p.i. mouse 4


title: blood C57BL/6 d7 p.i. mouse 2

description:
Gene expression after 7 day Mtb infection in C57BL/6 mouse blood
blood B2 d7

source_name: blood C57BL/6 d7 p.i. mouse 2


title: blood 129S2 d7 p.i. mouse 2

description:
Gene expression after 7 day Mtb infection in 129S2 mouse blood
blood A2 d7

source_name: blood 129S2 d7 p.i. mouse 2


title: blood C57BL/6 d7 p.i. mouse 5

description:
Gene expression after 7 day Mtb infection in C57BL/6 mouse blood
blood B5 d7

source_name: blood C57BL/6 d7 p.i. mouse 5


title: blood 129S2 d7 p.i. mouse 3

description:
Gene expression after 7 day Mtb infection in 129S2 mouse blood
blood A3 d7

source_name: blood 129S2 d7 p.i. mouse 3


title: blood 129S2 d7 p.i. mouse 1

description:
Gene expression after 7 day Mtb infection in 129S2 mouse blood
blood A1 d7

source_name: blood 129S2 d7 p.i. mouse 1


title: blood 129S2 24h p.i. mouse 2

description:
Gene expression after 1 day Mtb infection in 129S2 mouse blood
blood A2 d1

source_name: blood 129S2 24h p.i. mouse 2

value: day 1


title: blood 129S2 24h p.i. mouse 3

description:
Gene expression after 1 day Mtb infection in 129S2 mouse blood
blood A3 d1

source_name: blood 129S2 24h p.i. mouse 3


title: THP1_1440_Mtb_1_1

description:
This sample failed quality control therefore no processed data are available for this sample.
Gene expression after 24hr in THP1 cells infected with Mtb

hyb_protocol: After quality control and labeling efficiency verification samples were hybridized to 4x44K Whole Human Genome Microarray kits (Agilent Technologies, Product Number G4112F, Design ID 014850).

scan_protocol: Scanning of microarrays was performed with 5μm resolution using a G2565CA high-resolution laser microarray scanner (Agilent Technologies) using extended dynamic range (XDR).

data_processing: Raw microarray data were extracted with the Agilent FE software V10.5.1.1. and GE1_105_Dec08 protocol using default settings. Data analysis was performed in R version 3.2.3 (2015-12-10), and a script including all analysis steps is available upon request. The data sets have been analyzed with limma R package for differential expression analysis (Ritchie et al., 2015). The data sets were background corrected using the normexp method and quantile normalized. Limma lmFit function was used to fit linear models which included factors: stimulus type (TB, control) and time point. The p-values were calculated based on the moderated t-statistic and most differentially regulated genes were retrieved with topTable function.

organism: Homo sapiens

source_name: THP1 cells

label_protocol: Total RNA of infected and uninfected THP-1 control cells was labeled with the Quick Amp Labeling (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: The human monocytic cell line THP-1 (ATCC TIB-202) was maintained in RPMI 1640 (Gibco), supplemented with 10% (v/v) heat-inactivated fetal calf serum (Gibco), 1% (v/v) penicillin–streptomycin (Gibco), 1% (v/v) L-glutamine (Gibco), 1% (v/v) HEPES buffer (Gibco) and 0.05 M 2-mercaptoethanol (Gibco).

extract_protocol: At 1, 6 and 24 hours following infection macrophages were lysed with 4M guanidine isothiocyanate solution (Invitrogen), eukaryotic RNA was stabilized in Trizol LS (Invitrogen) and extracted according to vendor’s instructions. The RNA yield was detected with a NanoDrop ND 100 spectrometer (NanoDrop Technologies), and RNA integrity was estimated using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Cells were differentiated into macrophages by treatment with 50 ng/ml of phorbol 12-myristate 13-acetate (PMA, Calbiochem). Subsequently they were rested for 48 hours and afterwards infected with single-bacterial suspensions of the virulent strain H37Rv, at a multiplicity of infection of 5.

tag: cell line

tag: time point (minutes)

tag: moi

tag: experiment

tag: replicate

tag: infection status


title: blood C57BL/6 24h p.i. mouse 5

description:
Gene expression after 1 day Mtb infection in C57BL/6 mouse blood
blood B5 d1

source_name: blood C57BL/6 24h p.i. mouse 5


title: blood C57BL/6 24h p.i. mouse 2

description:
Gene expression after 1 day Mtb infection in C57BL/6 mouse blood
blood B2 d1

source_name: blood C57BL/6 24h p.i. mouse 2


title: blood C57BL/6 24h p.i. mouse 1

description:
Gene expression after 1 day Mtb infection in C57BL/6 mouse blood
blood B1 d1

source_name: blood C57BL/6 24h p.i. mouse 1


title: blood C57BL/6 24h p.i. mouse 4

description:
Gene expression after 1 day Mtb infection in C57BL/6 mouse blood
blood B4 d1

source_name: blood C57BL/6 24h p.i. mouse 4


title: blood 129S2 24h p.i. mouse 5

description:
Gene expression after 1 day Mtb infection in 129S2 mouse blood
blood A5 d1

source_name: blood 129S2 24h p.i. mouse 5


title: blood 129S2 24h p.i. mouse 4

description:
Gene expression after 1 day Mtb infection in 129S2 mouse blood
blood A4 d1

source_name: blood 129S2 24h p.i. mouse 4


title: blood 129S2 24h p.i. mouse 1

description:
Gene expression after 1 day Mtb infection in 129S2 mouse blood
blood A1 d1

source_name: blood 129S2 24h p.i. mouse 1


title: THP1_1440_NI_3_3

description:
This sample failed quality control therefore no processed data are available for this sample.
Gene expression in unstimulated THP1 cells

value: no


title: THP1_1440_Mtb_1_2

description: Gene expression after 24hr in THP1 cells infected with Mtb


title: THP1_1440_Mtb_1_3


title: THP1_1440_Mtb_2_2


title: THP1_1440_Mtb_2_3


title: THP1_1440_Mtb_2_1


title: THP1_1440_NI_3_2

description: Gene expression in unstimulated THP1 cells


title: THP1_1440_NI_3_1


title: THP1_1440_NI_1_3


title: THP1_1440_Mtb_3_3


title: THP1_360_NI_3_3


title: THP1_1440_Mtb_3_1


title: THP1_1440_Mtb_3_2


title: THP1_1440_NI_2_2


title: THP1_1440_NI_2_3


title: THP1_1440_NI_2_1


title: THP1_1440_NI_1_2


title: THP1_1440_NI_1_1


title: THP1_360_NI_1_2


title: THP1_360_NI_3_2


title: THP1_360_NI_1_3


title: THP1_360_NI_3_1


title: THP1_360_NI_2_3


title: THP1_360_Mtb_2_3

description: Gene expression after 6hr in THP1 cells infected with Mtb


title: THP1_360_NI_2_1


title: THP1_360_NI_1_1


title: THP1_360_Mtb_3_2


title: THP1_360_Mtb_3_3


title: THP1_360_Mtb_2_2


title: blood C57BL/6 naïve mouse 8

description:
Gene expression C57BL/6 mouse blood
blood B8 naive

source_name: blood C57BL/6 naïve mouse 8


title: THP1_60_Mtb_5_3

description: Gene expression after 1hr in THP1 cells infected with Mtb


title: THP1_360_Mtb_2_1


title: THP1_360_Mtb_1_1


title: THP1_360_Mtb_1_2


title: THP1_60_Mtb_3_3


title: THP1_60_Mtb_1_3


title: THP1_60_Mtb_5_2


title: THP1_60_Mtb_4_3


title: THP1_60_Mtb_2_3


title: THP1_60_Mtb_4_2


title: THP1_60_Mtb_3_2


title: THP1_360_Mtb_3_1


title: THP1_60_Mtb_2_2


title: THP1_60_Mtb_4_1


title: THP1_60_Mtb_5_1


title: THP1_60_Mtb_2_1


title: THP1_0_NI_5_3


title: THP1_0_NI_2_2


title: THP1_60_Mtb_3_1


title: THP1_60_Mtb_1_1


title: THP1_0_NI_2_3


title: THP1_0_NI_3_3


title: THP1_0_NI_1_3


title: THP1_0_NI_4_2


title: THP1_0_NI_3_2


title: THP1_60_Mtb_1_2


title: THP1_0_NI_5_2


title: THP1_0_NI_4_3


title: THP1_0_NI_4_1


title: THP1_0_NI_1_2


title: THP1_0_NI_3_1


title: THP1_0_NI_2_1


title: THP1_0_NI_1_1


title: bronchial_d35_mouse76

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: Hybridization to Affymetrix HT MG-430 PM Array Plates was performed at the Microarray Department of the University of Amsterdam, the Netherlands according to Affymetrix protocols.

scan_protocol: Scanning was performed at the Microarray Department of the University of Amsterdam, the Netherlands according to Affymetrix protocols.

data_processing: Raw data (CEL files) were normalized by robust multichip average (RMA) using the MBNI custom CDF version 19.

label: biotin

source_name: PM - d35 - bronchial LN

label_protocol: Labeling was performed at the Microarray Department of the University of Amsterdam, the Netherlands according to Affymetrix protocols.

extract_protocol: RNA isolation was performed using a miRNeasy Mini Kit with DNAse treatment (Qiagen). RNA concentrations were determined using UV spectroscopy (Tech3 module, Synergy Mx, BioTek). RNA quality was determined using electrophoresis (RNA nano 6000 kit, 2100 Bioanalyzer, Agilent).

treatment_protocol: Female BALB/c mice (Harlan, The Netherlands), 8-week-old, were immunized with 1 ug total protein vaccine either pulmonary (PM) or subcutaneously (SC) on day 0 and 28. Non-immunized mice were used as controls. Mice were challenged under anestesia with 2x10^5 cfu of Bordetella pertussis.

value: BALB/c

tag: gender

value: female

tag: vaccination

value: pulmonary

tag: challenge

value: Bordetella pertussis

tag: time

value: 35 day challenge

value: bronchial lymph nodes


title: THP1_0_NI_5_1


title: Developmental time point for iSyTE 2.0 [Lens_P20_B]

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

country: USA

institute: University of Delaware

description:
Lens_P20_B
Lens, wild-type ICR mice.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using rank invariant normalisation method in R.

source_name: Lens tissue, 20 day

label_protocol: Standard protocol for Illumina arrays.

extract_protocol: Standard total RNA isolation protocol by RNeasy mini kit (Qiagen).

tag: strain/background

value: ICR

tag: genotype/variation

value: Wild-type

tag: age

value: 20 day

value: Lens


title: Whole, embryonic body control for iSyTE 2.0 [WB_10_11_12_A]

description:
WB_10_11_12_A
Whole body minus eye, wild-type ICR mice.

source_name: Whole body minus eye, pooled samples for embryonic 10, 11 and 12 day stage

value: embryonic 10, 11 and 12 day stage

value: Whole body minus eye


title: bronchial_d56_mouse79

source_name: PM - d56 - bronchial LN

value: 56 day challenge


title: bronchial_d56_mouse80


title: Developmental time point for iSyTE 2.0 [Lens_P20_A]

description:
Lens_P20_A
Lens, wild-type ICR mice.


title: bronchial_d14_mouse65

source_name: PM - d14 - bronchial LN

value: 14 day challenge


title: Developmental time point for iSyTE 2.0 [Lens_P12_A]

description:
Lens_P12_A
Lens, wild-type ICR mice.

source_name: Lens tissue, 12 day

value: 12 day


title: Developmental time point for iSyTE 2.0 [Lens_P52_B]

description:
Lens_P52_B
Lens, wild-type ICR mice.

source_name: Lens tissue, 52 day

value: 52 day


title: Developmental time point for iSyTE 2.0 [Lens_P42_A]

description:
Lens_P42_A
Lens, wild-type ICR mice.

source_name: Lens tissue, 42 day

value: 42 day


title: Developmental time point for iSyTE 2.0 [Lens_P12_B]

description:
Lens_P12_B
Lens, wild-type ICR mice.


title: bronchial_d28_mouse69

source_name: PM - d28 - bronchial LN

value: BALB/c

value: 28 day challenge


title: Developmental time point for iSyTE 2.0 [Lens_P42_B]

description:
Lens_P42_B
Lens, wild-type ICR mice.


title: bronchial_d14_mouse67

value: female

value: pulmonary


title: bronchial_d14_mouse68

value: Bordetella pertussis


title: bronchial_d56_mouse78

value: bronchial lymph nodes


title: Developmental time point for iSyTE 2.0 [Lens_P52_A]

description:
Lens_P52_A
Lens, wild-type ICR mice.

value: ICR


title: Developmental time point for iSyTE 2.0 [Lens_P8_B]

description:
Lens_P8_B
Lens, wild-type ICR mice.

source_name: Lens tissue, 8 day

value: Wild-type

value: 8 day


title: Whole, embryonic body control for iSyTE 2.0 [WB_10_11_12_B]

description:
WB_10_11_12_B
Whole body minus eye, wild-type ICR mice.


title: bronchial_d28_mouse70


title: bronchial_d35_mouse75

value: 35 day challenge


title: Developmental time point for iSyTE 2.0 [Lens_P8_A]

description:
Lens_P8_A
Lens, wild-type ICR mice.

value: Lens


title: bronchial_d7_mouse62

source_name: PM - d7 - bronchial LN

value: 7 day challenge


title: bronchial_d7_mouse61


title: bronchial_d28_mouse71


title: bronchial_d7_mouse64


title: bronchial_d35_mouse73


title: bronchial_d2_mouse57

source_name: PM - d2 - bronchial LN

value: 2 day challenge


title: bronchial_d2_mouse60


title: bronchial_d0-4h_mouse54

source_name: PM - d0-4h - bronchial LN

value: 4 hour challenge


title: bronchial_d0_mouse4

source_name: naive - d0 - bronchial LN

value: naive

value: control

value: 0 day challenge


title: bronchial_d0-4h_mouse55

value: BALB/c


title: bronchial_d0_mouse2


title: inguinal_d35_mouse28

source_name: SC - d35 - inguinal LN

value: subcutaneous

value: inguinal lymph nodes


title: inguinal_d35_mouse26

value: female


title: inguinal_d28_mouse24

source_name: SC - d28 - inguinal LN

value: Bordetella pertussis

value: 28 day challenge


title: bronchial_d0_mouse1

value: bronchial lymph nodes


title: bronchial_d2_mouse59

value: pulmonary


title: inguinal_d56_mouse29

source_name: SC - d56 - inguinal LN

value: 56 day challenge


title: bronchial_d0-4h_mouse56


title: inguinal_d56_mouse31


title: inguinal_d35_mouse25

value: 35 day challenge


title: THP1_360_Mtb_1_3

source_name: THP1 cells

value: Mtb


title: inguinal_d14_mouse19

source_name: SC - d14 - inguinal LN

value: 14 day challenge


title: inguinal_d56_mouse30


title: inguinal_d7_mouse16

source_name: SC - d7 - inguinal LN

value: 7 day challenge


title: inguinal_d7_mouse13


title: THP1_360_NI_2_2

value: no


title: inguinal_d2_mouse10

source_name: SC - d2 - inguinal LN

value: 2 day challenge


title: inguinal_d14_mouse17


title: inguinal_d0-4h_mouse8

source_name: SC - d0-4h - inguinal LN

value: 4 hour challenge


title: inguinal_d28_mouse21


title: inguinal_d14_mouse18


title: inguinal_d2_mouse11


title: inguinal_d28_mouse23


title: inguinal_d2_mouse9


title: inguinal_d7_mouse14


title: inguinal_d0-4h_mouse5


title: inguinal_d0_mouse4

source_name: naive - d0 - inguinal LN

value: naive

value: control

value: 0 day challenge


title: inguinal_d0-4h_mouse6

value: BALB/c

value: subcutaneous

value: inguinal lymph nodes


title: SC - 2 d - pool

source_name: SC - 2 d - lung

treatment_protocol: Female BALB/c mice (Harlan, The Netherlands), 8-week-old, were immunized with 1 ug total protein vaccine either pulmonary (PM) or subcutaneously (SC) on day 0 and 28. Non-immunized mice were used as controls. Mice were challenged under anesthesia with 2x10^5 cfu of Bordetella pertussis.

value: female

value: Bordetella pertussis

value: lung


title: PM - 28 d - mouse24

source_name: PM - 28 d - lung

value: pulmonary

value: 28 day challenge


title: PM - 28 d - mouse22


title: PM - 28 d - mouse21


title: SC - 28 d - pool

source_name: SC - 28 d - lung


title: SC - 7 d - pool

source_name: SC - 7 d - lung


title: inguinal_d0_mouse2


title: PM - 7 d - mouse13

source_name: PM - 7 d - lung


title: PM - 14 d - mouse17

source_name: PM - 14 d - lung


title: PM - 7 d - mouse16


title: PM - 14 d - mouse18


title: PM - 4 h - mouse8

source_name: PM - 4 h - lung


title: SC - 14 d - pool

source_name: SC - 14 d - lung


title: PM - 2 d - mouse11

source_name: PM - 2 d - lung


title: PM - 2 d - mouse12


title: PM - 4 h - mouse6


title: inguinal_d0_mouse3


title: SC - 4 h - pool

source_name: SC - 4 h - lung


title: PM - 4 h - mouse5


title: PM - 7 d - mouse15


title: PM - 14 d - mouse19


title: naive - 0 d - mouse4

source_name: naive - 0 d - lung


title: naive - 0 d - mouse3


title: PM - 2 d - mouse10


title: naive - 0 d - mouse2


title: GEP_00601

status: Public on Sep 20 2017

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

hyb_protocol: Following fragmentation, 5 µg of ST-cDNA were hybridized for 16-20 hours at 45°C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix Expression Console 1.1.2 using RMA Gene core analysis with default parameters.

label: Biotin

source_name: Bone marrow

label_protocol: According to manufacturer protocol

extract_protocol: Total RNA extraction was performed according to the manufacturer's instructions using kit: RLT+

tag: disease state

value: multiple myeloma

value: bone marrow

tag: cell type

value: purified CD138+ plasma cells

tag: death

tag: relapse


title: GEP_00600

tag: tissue


title: GEP_00599

description: Myeloma


title: GEP_00598


title: GEP_00596


title: GEP_00597


title: GEP_00593


title: GEP_00589

description: Myeloma


title: GEP_00602


title: GEP_00590

description: Myeloma


title: GEP_00591


title: GEP_00582


title: GEP_00583

description: Myeloma


title: GEP_00595

description: Myeloma


title: GEP_00587

description: Myeloma


title: GEP_00584


title: GEP_00592


title: GEP_00585


title: GEP_00581


title: GEP_00577


title: GEP_00573


title: GEP_00579

description: Myeloma


title: GEP_00575


title: GEP_00574


title: GEP_00571

description: Myeloma


title: GEP_00567


title: GEP_00580


title: GEP_00588

description: Myeloma


title: GEP_00569


title: GEP_00576


title: GEP_00568


title: GEP_00572

description: Myeloma


title: GEP_00565


title: GEP_00566


title: GEP_00586


title: GEP_00563


title: GEP_00594

description: Myeloma


title: GEP_00570


title: GEP_00578


title: GEP_00564


title: GEP_00561

description: Myeloma


title: GEP_00556

description: Myeloma


title: GEP_00555


title: GEP_00562


title: GEP_00554


title: GEP_00553


title: GEP_00548

description: Myeloma


title: GEP_00557


title: GEP_00558


title: GEP_00549


title: GEP_00541


title: GEP_00546


title: GEP_00547


title: GEP_00559

description: Myeloma


title: GEP_00560


title: GEP_00545


title: GEP_00538


title: GEP_00542


title: GEP_00543


title: GEP_00537


title: GEP_00544


title: GEP_00552


title: GEP_00540


title: GEP_00534


title: GEP_00533


title: GEP_00536


title: GEP_00530


title: GEP_00532


title: GEP_00539


title: GEP_00531


title: GEP_00551


title: GEP_00529


title: GEP_00535


title: GEP_00527


title: GEP_00528


title: GEP_00523


title: GEP_00525


title: GEP_00522


title: GEP_00524


title: GEP_00520


title: GEP_00515


title: GEP_00517


title: GEP_00521


title: GEP_00516


title: GEP_00526


title: GEP_00518


title: GEP_00514


title: GEP_00507


title: GEP_00513


title: GEP_00512


title: GEP_00508


title: GEP_00506


title: GEP_00501


title: GEP_00505


title: GEP_00519


title: GEP_00498


title: GEP_00509


title: GEP_00503


title: GEP_00499


title: GEP_00504


title: GEP_00510


title: GEP_00511


title: GEP_00550


title: GEP_00502


title: GEP_00500


title: GEP_00494


title: GEP_00497


title: GEP_00495


title: GEP_00492


title: GEP_00486


title: GEP_00491


title: GEP_00487


title: GEP_00485


title: GEP_00484


title: GEP_00493


title: GEP_00496


title: GEP_00490


title: GEP_00489


title: GEP_00488

description: Myeloma


title: GEP_00483


title: GEP_00482


title: GEP_00476


title: GEP_00481


title: GEP_00480


title: GEP_00472


title: GEP_00475


title: GEP_00474


title: GEP_00479


title: GEP_00477


title: GEP_00468


title: GEP_00471


title: GEP_00469


title: GEP_00470


title: GEP_00473


title: GEP_00467


title: GEP_00465


title: GEP_00460


title: GEP_00461


title: GEP_00462


title: GEP_00464


title: GEP_00454


title: GEP_00456


title: GEP_00463


title: GEP_00459


title: GEP_00466


title: GEP_00457


title: GEP_00455


title: GEP_00453


title: GEP_00458


title: GEP_00449


title: GEP_00451


title: GEP_00450


title: GEP_00452


title: GEP_00448


title: GEP_00447


title: GEP_00478


title: GEP_00440


title: GEP_00439


title: GEP_00446


title: GEP_00445


title: GEP_00441


title: GEP_00443


title: GEP_00444


title: GEP_00442


title: GEP_00438


title: GEP_00437


title: GEP_00434


title: GEP_00436


title: GEP_00430


title: GEP_00423


title: GEP_00431


title: GEP_00432


title: GEP_00435


title: GEP_00424


title: GEP_00426


title: GEP_00428


title: GEP_00429


title: GEP_00433


title: GEP_00421


title: GEP_00422


title: GEP_00425


title: GEP_00420


title: GEP_00419


title: GEP_00418


title: GEP_00414


title: GEP_00413


title: GEP_00416


title: GEP_00407


title: GEP_00396


title: GEP_00398


title: GEP_00412


title: GEP_00417


title: GEP_00397


title: GEP_00400


title: GEP_00395


title: GEP_00402


title: GEP_00408


title: GEP_00411


title: GEP_00393


title: GEP_00427


title: GEP_00409


title: GEP_00410


title: GEP_00404


title: GEP_00405


title: GEP_00391


title: GEP_00415


title: GEP_00406


title: GEP_00389


title: GEP_00403


title: GEP_00401


title: GEP_00390


title: GEP_00394


title: GEP_00392


title: GEP_00387


title: GEP_00386


title: GEP_00399


title: GEP_00388


title: GEP_00385


title: GEP_00381


title: GEP_00379


title: GEP_00377


title: GEP_00382


title: GEP_00380


title: GEP_00376


title: GEP_00371


title: GEP_00367


title: GEP_00370


title: GEP_00369


title: GEP_00363


title: GEP_00361


title: GEP_00366


title: GEP_00362


title: GEP_00372


title: GEP_00373


title: GEP_00364


title: GEP_00368


title: GEP_00375


title: GEP_00383


title: GEP_00365


title: GEP_00374


title: GEP_00355


title: GEP_00360


title: GEP_00378


title: GEP_00356


title: GEP_00384


title: GEP_00357


title: GEP_00358


title: GEP_00359


title: GEP_00354


title: GEP_00353


title: GEP_00352


title: GEP_00346


title: GEP_00351


title: GEP_00347


title: GEP_00345


title: GEP_00344


title: GEP_00348


title: GEP_00350


title: GEP_00349


title: GEP_00343


title: GEP_00341


title: GEP_00340


title: GEP_00337


title: GEP_00339


title: GEP_00335


title: GEP_00334


title: GEP_00330


title: GEP_00342


title: GEP_00328


title: GEP_00336


title: GEP_00338


title: GEP_00332


title: GEP_00333


title: GEP_00331


title: GEP_00329


title: GEP_00323


title: GEP_00322


title: GEP_00324


title: GEP_00321


title: GEP_00327


title: GEP_00326


title: GEP_00325


title: GEP_00317


title: GEP_00320


title: GEP_00312


title: GEP_00319


title: GEP_00307


title: GEP_00305


title: GEP_00318


title: GEP_00304


title: GEP_00302


title: GEP_00301


title: GEP_00316


title: GEP_00314


title: GEP_00313


title: GEP_00310


title: GEP_00306


title: GEP_00315


title: GEP_00311


title: GEP_00309


title: GEP_00308


title: GEP_00303


title: GEP_00295


title: GEP_00297


title: GEP_00294


title: GEP_00299


title: GEP_00300


title: GEP_00291


title: GEP_00287


title: GEP_00289


title: GEP_00293


title: GEP_00290


title: GEP_00288


title: GEP_00285


title: GEP_00282


title: GEP_00296


title: GEP_00284


title: GEP_00298


title: GEP_00283


title: GEP_00276


title: GEP_00292


title: GEP_00273


title: GEP_00286


title: GEP_00281


title: GEP_00279


title: GEP_00277


title: GEP_00272


title: GEP_00271


title: GEP_00269


title: GEP_00270


title: GEP_00278


title: GEP_00280


title: GEP_00275


title: GEP_00267


title: GEP_00274


title: GEP_00264


title: GEP_00266


title: GEP_00265


title: GEP_00260


title: GEP_00261


title: GEP_00268


title: GEP_00257


title: GEP_00262


title: GEP_00252


title: GEP_00255


title: GEP_00253


title: GEP_00263


title: GEP_00254


title: GEP_00259


title: GEP_00258


title: GEP_00249


title: GEP_00251


title: GEP_00256


title: GEP_00246


title: GEP_00250


title: GEP_00243


title: GEP_00245


title: GEP_00242


title: GEP_00241


title: GEP_00235


title: GEP_00238


title: GEP_00237


title: GEP_00240


title: GEP_00239


title: GEP_00236


title: GEP_00233


title: GEP_00226


title: GEP_00244


title: GEP_00230


title: GEP_00232


title: GEP_00229


title: GEP_00227


title: GEP_00222


title: GEP_00247


title: GEP_00225


title: GEP_00220


title: GEP_00223


title: GEP_00213


title: GEP_00228


title: GEP_00215


title: GEP_00224


title: GEP_00221


title: GEP_00219


title: GEP_00218


title: GEP_00234


title: GEP_00217


title: GEP_00210


title: GEP_00231


title: GEP_00214


title: GEP_00212


title: GEP_00208


title: GEP_00206


title: GEP_00203


title: GEP_00199


title: GEP_00209


title: GEP_00202


title: GEP_00198


title: GEP_00205


title: GEP_00194


title: GEP_00216


title: GEP_00197


title: GEP_00211


title: GEP_00195


title: GEP_00204


title: GEP_00201


title: GEP_00207


title: GEP_00196


title: GEP_00193


title: GEP_00200


title: GEP_00192


title: GEP_00187


title: GEP_00191


title: GEP_00189


title: GEP_00188


title: GEP_00190


title: GEP_00185


title: GEP_00184


title: GEP_00182


title: GEP_00179


title: GEP_00183


title: GEP_00175


title: genomic DNA from 293T-GFP

type: genomic

city: Seoul

first: Jin Hoe

last: Huh

address: Gwanak-gu

department: Dept Plant Science

country: South Korea

institute: Seoul National University

description: GFP

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
Illumina GenomeStudio v2011.1 (Methylation Module v1.9.0)
The non_normalized data matrix contains Unmethylated and methylated signal intensities

label: cy3, cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: GFP and DMEΔ were transfected in HEK-293T cells and the cells harvested 48 h after transfection. HEK-293T cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and a 1% antibiotic/antimycotic solution at 37°C in 5% CO2 humidity chamber.

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

tag: transfected with

value: GFP

tag: time point

value: 48 h after transfection


title: GEP_00186


title: GEP_00174


title: GEP_00181


title: GEP_00178


title: GEP_00173


title: GEP_00177


title: GEP_00169


title: GEP_00171


title: genomic DNA from 293T-DMEΔ

description: DME

value: plant-derived DNA demethylase DMEΔ


title: GEP_00167


title: GEP_00165


title: GEP_00180


title: GEP_00164


title: GEP_00172


title: GEP_00170


title: GEP_00166


title: GEP_00161


title: GEP_00163


title: GEP_00168


title: GEP_00155


title: GEP_00160


title: GEP_00176


title: GEP_00162


title: GEP_00157


title: GEP_00153


title: GEP_00146


title: GEP_00152


title: GEP_00150


title: GEP_00143


title: GEP_00145


title: GEP_00159


title: GEP_00154


title: GEP_00158


title: GEP_00144


title: GEP_00148


title: GEP_00138


title: GEP_00142


title: GEP_00147


title: GEP_00140


title: GEP_00149


title: GEP_00137


title: GEP_00139


title: GEP_00151


title: GEP_00136


title: GEP_00141


title: GEP_00134


title: GEP_00135


title: GEP_00131


title: GEP_00133


title: GEP_00132


title: GEP_00130


title: GEP_00156


title: GEP_00123


title: GEP_00127


title: GEP_00126


title: GEP_00124


title: GEP_00129


title: GEP_00119


title: GEP_00125


title: GEP_00128


title: GEP_00121


title: GEP_00122


title: GEP_00120


title: GEP_00118


title: GEP_00116


title: GEP_00114


title: GEP_00115


title: GEP_00110


title: GEP_00112


title: GEP_00107


title: GEP_00108


title: GEP_00111


title: GEP_00117


title: GEP_00113


title: GEP_00109


title: GEP_00106


title: GEP_00104


title: GEP_00105


title: GEP_00102


title: GEP_00101


title: GEP_00100


title: GEP_00103


title: GEP_00099


title: GEP_00098


title: GEP_00096


title: GEP_00097


title: GEP_00095


title: GEP_00093


title: GEP_00094


title: T84, P. jejuni (isolate CD3:33) rep1 (CTR 32 33 34)

city: Umeå

first: Marie-Louise

last: Hammarström

address: Peter Lestadius väg

department: Clinical Microbiology

country: Sweden

institute: Umeå universitet

description:
SAMPLE 7
6898376023_F

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background was first subtracted from the data and then normalized using Beadstudios cubic spline algorithm.

source_name: T84, P. jejuni (isolate CD3:33)

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

extract_protocol: Total RNA was extracted from T84 polarized tight monolayers by using the Qiagen RNeasy Mini Kit according to the manufacturer's instructions and dissolved in RNase-free water containing Promega rRNasin ribonuclease inhibitor. Quality control was performed with Agilent 2100 Bioanalyser and NanoDrop.

tag: cell line

value: colon carcinoma cell line T84

tag: treatment

value: P. jejuni (isolate CD3:33)


title: T84, P. melaninogenica (isolate CD3:34) rep1 (CTR 32 33 34)

description:
SAMPLE 10
6898376023_A

source_name: T84, P. melaninogenica (isolate CD3:34)

value: P. melaninogenica (isolate CD3:34)


title: T84, P. jejuni (isolate CD3:33) rep3 (CTR 32 33 34)

description:
SAMPLE 9
6898376023_D


title: T84, CTR rep2 (CTR 32 33 34)

description:
SAMPLE 2
6898376023_K

source_name: T84, CTR

value: CTR


title: T84, CTR rep1 (CTR 32 33 34)

description:
SAMPLE 1
6898376023_L


title: T84, P. melaninogenica (isolate CD3:34) rep3 (CTR 32 33 34)

description:
SAMPLE 12
6898376023_C


title: GEP_00092


title: GEP_00091


title: GEP_00089


title: T84, CTR rep3 (CTR 32 33 34)

description:
SAMPLE 3
6898376023_J


title: GEP_00090


title: GEP_00088


title: T84, P. histicola (isolate CD3:32) rep2 (CTR 32 33 34)

description:
SAMPLE 5
6898376023_H

source_name: T84, P. histicola (isolate CD3:32)

value: P. histicola (isolate CD3:32)


title: T84, P. histicola (isolate CD3:32) rep1 (CTR 32 33 34)

description:
SAMPLE 4
6898376023_I


title: T84, P. jejuni (isolate CD3:33) rep2 (CTR 32 33 34)

description:
SAMPLE 8
6898376023_E


title: T84, P. melaninogenica (isolate CD3:34) rep2 (CTR 32 33 34)

description:
SAMPLE 11
6898376023_B


title: GEP_00087


title: T84, P. histicola (isolate CD3:32) rep3 (CTR 32 33 34)

description:
SAMPLE 6
6898376023_G


title: GEP_00086


title: GEP_00085


title: GEP_00083


title: THP-1 infected by T.gondi replicate 2

city: Beijing

first: Feng

last: Xue

state: Beijing

address: No. 95, Yong'an Road

department: Department of Microbiology and Parasitology

country: China

institute: Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University

hyb_protocol: 750 ng cRNA per sample was hybridized to the BeadChip using Whole-Genome Expression Direct Hybridization kit

scan_protocol: Scanned with the Beadarray Reader (Illumina, Cambridge, United Kingdom).

data_processing:
The probe profile expression data were obtained and performed background adjustment with the Genomestudio software (Illumina, Cambridge, United Kingdom), then were normalized using the average normalization algorithm.
The differentially expressed genes were further analyzed using CapitalBio MAS (Molecule Annotation System, version 3.0).
The regulated genes with more than 2-fold (P<0.05) up-regulation or down-regulation were defined as significantly regulated genes in this report.

source_name: THP-1 infected by T.gondi

label_protocol: The cDNA were synthesized, and the cRNA were synthesized from the cDNA by in vitro transcription using Ambion® Illumina TotalPrep RNA amplification kit (Ambion, Austin, TX, USA).

growth_protocol: The THP-1 cells were cultivated respectively in RPMI-1640 mediums (Gibco-Invitrogen, Carlsbad, CA) supplemented with 10% (V/V) heat-inactivated fetal calf serum (FCS, Gibco-Invitrogen, Carlsbad, CA) with antibiotic, in a humidified 5% CO2 atmosphere at 37°C. The THP-1 cells were inoculated with T. gondii with a ratio of 1:1 (Parasite: cell) when the growth density of suspended cells reach 60%. The cell medium was renewed every day to maintain good growth state.

extract_protocol: The total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), then purified using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) with on-column DNase digestion (QIAGEN, Hilden, Germany) according to the RNeasy Mini handbook. RNA quantity and integrity were determined using an RNA 6000 Nano Laboratory-on-a-Chip kit and a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: The suspended THP-1 cells were treated with 5 nM phorbol myristate acetate (PMA; Sigma-Aldrich St. Louis, MO) for 24h; After differentiation, the cells were washed three times with autoclaved PBS, and rested for 24h in new cell medium to ensure that they reverted to a resting phenotype. The T. gondii RH tachyzoites were propagated in the differentiated cells and counted using a cell counting plate. Before infection or stimulation, the cells were washed by autoclaved PBS for three times, and the cell mediums were renewed as RPMI-1640 without FCS and antibiotics. 1×106 differentiated THP-1 cells were infected with 1×106 T. gondii RH tachyzoites or 1×106 EPEC, or stimulated with 0.5μg T. gondii surface and secreted proteins which were isolated from 1×106 T. gondii tachyzoites, respectively. Then the tissue culture flasks were centrifuged at 2500 g for 15 min to synchronize the infection. The 1×106 differentiated THP-1 cells not infected or stimulated were used as the negative controls.

value: peripheral blood monocyte THP-1

value: infected by T.gondi


title: THP-1 induced by isolated by surface T.gondi protein replicate 2

value: induced by isolated surface T.gondi protein


title: THP-1 infected by T.gondi replicate 1


title: THP-1 induced by isolated by surface T.gondi protein replicate 1


title: GEP_00080


title: GEP_00082


title: THP-1 infected by pathogenic E. coli replicate 2

source_name: THP-1 infected by pathogenic E. coli

value: infected by pathogenic E. coli


title: THP-1 infected by pathogenic E. coli replicate 1


title: GEP_00079


title: GEP_00081


title: GEP_00078


title: GEP_00074


title: GEP_00077


title: GEP_00075


title: GEP_00084


title: A375 dabrafenib treated

city: Macquarie University

first: Helen

last: Rizos

address: 2 Technology Place

country: Australia

institute: Macquarie University

description: SAMPLE 16

data_processing: Clustering using GenomeStudio (Illumina) confirmed that each replicate showed o1.2% variation. Gene expression data were normalized using the cubic spline function.

source_name: melanoma cell line_dabrafenib

label_protocol: Complementary RNA amplification and labelling with biotin were performed using the Illumina. TotalPrep RNA amplification kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions starting with 250 ng total RNA.

growth_protocol: Cells were grown in DMEM with 10% FCS and glutamine (Gibco BRL) and cultured in a 37 °C incubator with 5% CO2

extract_protocol: Total RNA was extracted in the presence of Trizol (LifeTechnologies, Carlsbad, CA, USA). Following homogenization, chloroform was added and the sample centrifuged. The upper phase was removed and mixed with 70% ethanol. The RNA was then isolated and purified with an RNeasy purification kit with DNase I digestion on the column (Qiagen, Valencia, CA, USA). The quality of the RNA preparations was assessed using a Agilent 2100 Bioanalyser

treatment_protocol: Stocks dabrafenib (supplied by Active Biochem, Maplewood, NJ, USA) and trametinib (Selleck Chemicals, Houston, TX, USA) were made in dimethyl sulfoxide. Cells were treated with 100nM dabrafenib ± 10nM trametinib for 24h

value: melanoma cell line

tag: treated with

value: 100nM dabrafenib


title: ME1042 control (DMSO-treated)

description: SAMPLE 21

source_name: melanoma cell line_DMSO

value: DMSO for 24h (control)


title: NM39 dabrafenib treated

description: SAMPLE 18


title: NM176 control (DMSO-treated)

description: SAMPLE 19


title: ME1042 dabrafenib treated

description: SAMPLE 22


title: NM39 control (DMSO-treated)

description: SAMPLE 17


title: NM176 dabrafenib treated

description: SAMPLE 20


title: A375 control (DMSO-treated)

description: SAMPLE 15


title: GEP_00076

value: multiple myeloma

value: bone marrow


title: NM16 dabrafenib treated

description: SAMPLE 14


title: THP-1 control replicate 2

source_name: THP-1 control

value: control


title: GEP_00071

value: purified CD138+ plasma cells


title: MM200 control (DMSO-treated)

description: SAMPLE 11


title: MM200 dabrafenib  treated

description: SAMPLE 12


title: GEP_00073


title: GEP_00070


title: GEP_00067


title: GEP_00072


title: GEP_00066


title: 033Mel control (DMSO-treated)

description: SAMPLE 7


title: 031Mel control (DMSO-treated)

description: SAMPLE 9


title: GEP_00069


title: GEP_00065


title: 031Mel dabrafenib+trametinib treated

description: SAMPLE 10

value: 100nM dabrafenib + 10nM trametinib for 24h


title: 033Mel dabrafenib+trametinib treated

description: SAMPLE 8


title: THP-1 control replicate 1


title: GEP_00062


title: GEP_00064


title: 501Mel dabrafenib treated

description: SAMPLE 6


title: GEP_00063


title: NM182c dabrafenib treated

description: SAMPLE 4


title: SKMel28 dabrafenib+trametinib treated

description: SAMPLE 2


title: NM182c control (DMSO-treated)

description: SAMPLE 3


title: NM16 control (DMSO-treated)

description: SAMPLE 13


title: GEP_00061


title: SKMel28 control (DMSO-treated)

description: SAMPLE 1


title: GEP_00057


title: GEP_00060


title: GEP_00052


title: GEP_00055


title: GEP_00058


title: GEP_00059


title: GEP_00051


title: GEP_00056


title: GEP_00053


title: GEP_00048


title: 501Mel control (DMSO-treated)

description: SAMPLE 5


title: GEP_00049


title: GEP_00040


title: GEP_00050


title: GEP_00047


title: GEP_00041


title: GEP_00042


title: GEP_00043


title: GEP_00044


title: GEP_00046


title: GEP_00039


title: GEP_00068


title: GEP_00036


title: GEP_00038


title: GEP_00054


title: GEP_00035


title: GEP_00034


title: GEP_00033


title: GEP_00045


title: GEP_00032


title: GEP_00037


title: GEP_00026


title: GEP_00029


title: GEP_00024


title: GEP_00030


title: GEP_00028


title: GEP_00027


title: GEP_00023


title: GEP_00018


title: GEP_00022


title: GEP_00020


title: GEP_00015


title: GEP_00021


title: GEP_00016


title: GEP_00017


title: GEP_00019


title: GEP_00014


title: GEP_00025


title: GEP_00011


title: GEP_00010


title: GEP_00012


title: GEP_00031


title: GEP_00006


title: GEP_00009


title: GEP_00007


title: GEP_00001


title: GEP_00004


title: GEP_00013


title: GEP_00008


title: Capan1_PF500μM_48h_Rep3

city: Guangzhou

first: Lili

last: Gong

state: Guangdong

address: Jinsui Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description:
Gene expression data from 500 μM paeoniflorin treated Capan-1 cells
PF3C

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human Gene Expression Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: Capan-1 cells were maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/ streptomycin.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Capan-1 cells cultured in 6-well plates were treated with 500 μM paeoniflorin or DMSO for 48 h

value: Capan1 pancreatic cancer cells

tag: agent

value: PF


title: Capan1_PF500μM_48h_Rep2

description:
Gene expression data from 500 μM paeoniflorin treated Capan-1 cells
PF2C


title: GEP_00005


title: Capan1_DMSO_48h_Rep1

description:
Gene expression data from DMSO treated control Capan-1 cells
CTL1C

source_name: DMSO treated control Capan-1 cells

value: DMSO


status: Public on Sep 19 2017

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Gene expression of PBMCs from KD patients 21 collected before and after IVIG treatment_dye-swap

hyb_protocol: Hybridization and rinsing were conducted using the Agilent Whole Human Genome Microarray (4x44K G4112F) according to the manufacturer’s protocol.

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.1.3.1 and LOWESS background subtraction and dye-normalization were used.

source_name: PBMCs from Kawasaki patient 21 before IVIG treatment

label_protocol: Total RNA (100 ng) isolated from the PBMCs of each KD patient were reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence, and the resulting cDNA was subjected to in vitro transcription using T7 RNA polymerase so that they were labeled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech). The Cy-labeled cRNAs (825 ng) of each patient were then mixed with the same amount of reverse color Cy-labeled cRNAs of each patient with a dye-swap approach.

extract_protocol: RNA was purified from human whole blood using the PAXgene Blood RNA Kit (Qiagen) according to the manufacture’s protocol. The quality of the RNA samples was examined using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) and an Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Inc., Palo Alto, CA).

treatment_protocol: Blood was collected in PAXgene blood RNA tubes

tag: gender

value: male

tag: age (y_m)

tag: state

value: Kawasaki

tag: ivig treatment

value: after  3days

source_name: PBMCs from Kawasaki patient 21 after 3 days

tag: age (y)

value: before IVIg treatment


description: Gene expression of PBMCs from KD patients 25 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 25 before IVIG treatment

source_name: PBMCs from Kawasaki patient 25 after 3 days


title: 295T-GFP rep3

description:
GFP-3
Gene expression data from 293T-GFP

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 ST Array. The 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 Micorarray Suite version 5 (MAS5) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

extract_protocol: Total RNA was extracted and purified using Qiagen RNeasy Kit according to standard instructions

value: GFP

value: 48 h after transfection


title: 293T-GFP rep1

description:
GFP-1
Gene expression data from 293T-GFP


title: Capan1_DMSO_48h_Rep3

description:
Gene expression data from DMSO treated control Capan-1 cells
CTL3C


title: Capan1_PF500μM_48h_Rep1

description:
Gene expression data from 500 μM paeoniflorin treated Capan-1 cells
PF1C


description: Gene expression of PBMCs from KD patients 19 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 19 before IVIG treatment

source_name: PBMCs from Kawasaki patient 19 after 3 days


title: 293T-DMEΔ rep3

description:
DME-3
Gene expression data from 293T-DMEΔ

value: plant-derived DNA demethylase DMEΔ


title: GEP_00002

source_name: Bone marrow


description: Gene expression of PBMCs from KD patients 22 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 22 before IVIG treatment

value: female

source_name: PBMCs from Kawasaki patient 22 after 3 days


description: Gene expression of PBMCs from KD patients 20 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 20 before IVIG treatment

source_name: PBMCs from Kawasaki patient 20 after 3 days


description: Gene expression of PBMCs from KD patients 24 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 24 before IVIG treatment

source_name: PBMCs from Kawasaki patient 24 after 3 days


description: Gene expression of PBMCs from KD patients 23 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 23 before IVIG treatment

source_name: PBMCs from Kawasaki patient 23 after 3 days


title: 293T-DMEΔ rep1

description:
DME-1
Gene expression data from 293T-DMEΔ


title: GEP_00003


title: 293T-DMEΔ rep2

description:
DME-2
Gene expression data from 293T-DMEΔ


description: Gene expression of PBMCs from KD patients 16 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 16 before IVIG treatment

value: after  4days

source_name: PBMCs from Kawasaki patient 16 after 4 days


title: Capan1_DMSO_48h_Rep2

description:
Gene expression data from DMSO treated control Capan-1 cells
CTL2C

source_name: DMSO treated control Capan-1 cells


title: 294T-GFP rep2

description:
GFP-2
Gene expression data from 293T-GFP


description: Gene expression of PBMCs from KD patients 14 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 14 before IVIG treatment

source_name: PBMCs from Kawasaki patient 14 after 3 days


description: Gene expression of PBMCs from KD patients 15 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 15 before IVIG treatment

source_name: PBMCs from Kawasaki patient 15 after 3 days


description: Gene expression of PBMCs from KD patients 11 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 11 before IVIG treatment

source_name: PBMCs from Kawasaki patient 11 after 3 days


description: Gene expression of PBMCs from KD patients 12 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 12 before IVIG treatment

source_name: PBMCs from Kawasaki patient 12 after 3 days


title: GEP_00248

source_name: Bone marrow

value: multiple myeloma


description: Gene expression of PBMCs from KD patients 5 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 5 before IVIG treatment

source_name: PBMCs from Kawasaki patient 5 after 3 days


description: Gene expression of PBMCs from KD patients 18 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 18 before IVIG treatment

source_name: PBMCs from Kawasaki patient 18 after 3 days


description: Gene expression of PBMCs from KD patients 4 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 4 before IVIG treatment

source_name: PBMCs from Kawasaki patient 4 after 3 days


description: Gene expression of PBMCs from KD patients 2 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 2 before IVIG treatment

source_name: PBMCs from Kawasaki patient 2 after 3 days


description: Gene expression of PBMCs from KD patients 24 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 24 before IVIG treatment

source_name: PBMCs from Kawasaki patient 24 after 3 days


description: Gene expression of PBMCs from KD patients 25 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 25 before IVIG treatment

source_name: PBMCs from Kawasaki patient 25 after 3 days


description: Gene expression of PBMCs from KD patients 3 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 3 before IVIG treatment

source_name: PBMCs from Kawasaki patient 3 after 3 days


description: Gene expression of PBMCs from KD patients 13 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 13 before IVIG treatment

source_name: PBMCs from Kawasaki patient 13 after 3 days


description: Gene expression of PBMCs from KD patients 20 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 20 before IVIG treatment

source_name: PBMCs from Kawasaki patient 20 after 3 days


description: Gene expression of PBMCs from KD patients 21 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 21 before IVIG treatment

source_name: PBMCs from Kawasaki patient 21 after 3 days


description: Gene expression of PBMCs from KD patients 1 collected before and after IVIG treatment_dye-swap

source_name: PBMCs from Kawasaki patient 1 before IVIG treatment

source_name: PBMCs from Kawasaki patient 1 after 3 days


description: Gene expression of PBMCs from KD patients 14 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 14 before IVIG treatment

source_name: PBMCs from Kawasaki patient 14 after 3 days


description: Gene expression of PBMCs from KD patients 16 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 16 before IVIG treatment

source_name: PBMCs from Kawasaki patient 16 after 4 days

value: after IVIg treatment


description: Gene expression of PBMCs from KD patients 12 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 12 before IVIG treatment

source_name: PBMCs from Kawasaki patient 12 after 3 days


description: Gene expression of PBMCs from KD patients 22 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 22 before IVIG treatment

source_name: PBMCs from Kawasaki patient 22 after 3 days


description: Gene expression of PBMCs from KD patients 19 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 19 before IVIG treatment

source_name: PBMCs from Kawasaki patient 19 after 3 days


description: Gene expression of PBMCs from KD patients 3 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 3 before IVIG treatment

source_name: PBMCs from Kawasaki patient 3 after 3 days


description: Gene expression of PBMCs from KD patients 18 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 18 before IVIG treatment

source_name: PBMCs from Kawasaki patient 18 after 3 days


description: Gene expression of PBMCs from KD patients 23 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 23 before IVIG treatment

source_name: PBMCs from Kawasaki patient 23 after 3 days


description: Gene expression of PBMCs from KD patients 1 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 1 before IVIG treatment

source_name: PBMCs from Kawasaki patient 1 after 3 days


description: Gene expression of PBMCs from KD patients 4 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 4 before IVIG treatment

source_name: PBMCs from Kawasaki patient 4 after 3 days


description: Gene expression of PBMCs from KD patients 15 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 15 before IVIG treatment

source_name: PBMCs from Kawasaki patient 15 after 3 days


description: Gene expression of PBMCs from KD patients 2 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 2 before IVIG treatment

source_name: PBMCs from Kawasaki patient 2 after 3 days


description: Gene expression of PBMCs from KD patients 11 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 11 before IVIG treatment

source_name: PBMCs from Kawasaki patient 11 after 3 days


title: Oligoendrocyte, biological rep3

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

hyb_protocol: For hybridization to a GeneChip Mouse Genome 430 2.0 Array (Affymetrix), 15 mg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA and 1x manufacturer-recommended hybridization buffer in a 45°C rotisserie oven for 16 h.

scan_protocol: Stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.

data_processing: RMA algorithm implemented background correction, normalization across arrays, and log2 transformation.

source_name: Primary Oligodendrocyte

label_protocol: cDNAs were labeled by in vitro transcription using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics).

extract_protocol: Total RNAs were purified using an RNeasy Mini kit (Qiagen), according to the manufacturer's instructions.

value: Primary Oligodendrocyte

tag: development stage


title: Astrocyte, biological rep3

source_name: Primary Astrocyte

value: Primary Astrocyte


description: Gene expression of PBMCs from KD patients 5 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 5 before IVIG treatment

source_name: PBMCs from Kawasaki patient 5 after 3 days


title: Oligoendrocyte, biological rep2


title: Astrocyte, biological rep2


title: E18.5 NS/PCs, biological rep2

source_name: NS/PCs isolated from Sox2-GFP mouse brain at Embryonic day 18


title: E14.5 NS/PCs, biological rep3

source_name: NS/PCs isolated from Sox2-GFP mouse brain at Embryonic day 14


title: Neuron, biological rep1

source_name: Primary Neuron

value: Primary Neuron


description: Gene expression of PBMCs from KD patients 13 collected before and after IVIG treatment

source_name: PBMCs from Kawasaki patient 13 before IVIG treatment

source_name: PBMCs from Kawasaki patient 13 after 3 days


title: E18.5 NS/PCs, biological rep3

value: NS/PCs isolated from Sox2-GFP mouse brain


title: E11.5 NS/PCs, biological rep2

source_name: NS/PCs isolated from Sox2-GFP mouse brain at Embryonic day 11


title: Neuron, biological rep2


title: E14.5 NS/PCs, biological rep2


title: E18.5 NS/PCs, biological rep1


title: E11.5 NS/PCs, biological rep1


title: Neuron, biological rep3


title: E11.5 NS/PCs, biological rep3


title: E14.5 NS/PCs, biological rep1


title: SVF cells from non-obese human adipose tissue JL32_SVF_1

city: Stockholm

first: Jurga

last: Laurencikiene

address: Hälsovägen 7

institute: Karolinska Institutet

hyb_protocol: Affymetrix standard protocol for hybridization of cartridge arrays

scan_protocol: Arrays were scanned in Affymetrix GeneChip Scanner 3000 7G

data_processing: CEL files were analyzed in Affymetrix Expression Console using RMA

source_name: Subcutaneous white adipose tissue

label_protocol: Affymetrix WT Plus protocol was used for 100ng total RNA input

extract_protocol: Adipose tissue samples were obtained from either liposuctions or  abdominoplasty. Adipose tissue were cut into small pieces and collagenase treated. Adipocytes and stromal vascular fractions were separated by centrifugation. SVF were further sorted using flow cytometry with CD45, CD34 and CD31 markers. CD45-/CD31- cells were called as Progenitors, CD45+/CD34 were called as Monocytes/Macrophages and CD45+/CD34 were called as Leukocytes.

value: SVF

tag: facs markers

value: Collagenase pellet

tag: weight status

value: Non-obese

tag: patient number

tag: Sex

value: Female


title: SVF cells from non-obese human adipose tissue JL34_SVF_3

tag: cell type


title: CD45+/CD14- cells from non-obese human adipose SVF JL30_P9_5

value: Leukocyte


title: Adipocytes from non-obese human adipose tissue JL42_M_5

value: Adipocyte

value: Collagenase float


title: Adipocytes from non-obese human adipose tissue JL40_M_3


title: Adipocytes from non-obese human adipose tissue JL39_M_2


title: CD45+/CD14- cells from non-obese human adipose SVF JL28_P9_3


title: SVF cells from non-obese human adipose tissue JL36_SVF_5


title: Adipocytes from non-obese human adipose tissue JL38_M_1


title: SVF cells from non-obese human adipose tissue JL37_SVF_6


title: Adipocytes from non-obese human adipose tissue JL43_M_6


title: SVF cells from non-obese human adipose tissue JL35_SVF_4


title: Adipocytes from non-obese human adipose tissue JL41_M_4


title: CD45+/CD14- cells from non-obese human adipose SVF JL26_P9_1


title: CD45+/CD14- cells from non-obese human adipose SVF JL29_P9_4


title: CD45+/CD14+ cells from non-obese human adipose SVF JL24_P8_5

value: Monocyte/Macrophage


title: CD45+/CD14+ cells from non-obese human adipose SVF JL21_P8_2


title: CD45+/CD14+ cells from non-obese human adipose SVF JL25_P8_6


title: CD45-/CD34+/CD31- cells from obese human adipose SVF JL17_P6_17

value: Progenitor

value: Obese


title: CD45-/CD34+/CD31- cells from obese human adipose SVF JL19_P6_19


title: CD45+/CD14+ cells from non-obese human adipose SVF JL23_P8_4


title: CD45-/CD34+/CD31- cells from obese human adipose SVF JL18_P6_18

value: Male


title: CD45+/CD14+ cells from non-obese human adipose SVF JL20_P8_1


title: SVF cells from non-obese human adipose tissue JL33_SVF_2


title: CD45+/CD14+ cells from non-obese human adipose SVF JL22_P8_3


title: CD45+/CD14- cells from non-obese human adipose SVF JL31_P9_6


title: CD45-/CD34+/CD31- cells from obese human adipose SVF JL16_P6_16


title: CD45+/CD14- cells from non-obese human adipose SVF JL27_P9_2


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL06_P6_6


title: CD45-/CD34+/CD31- cells from obese human adipose SVF JL14_P6_14


title: CD45-/CD34+/CD31- cells from obese human adipose SVF JL11_P6_11


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL09_P6_9


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL02_P6_2


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL07_P6_7


title: CD45-/CD34+/CD31- cells from obese human adipose SVF JL12_P6_12


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL10_P6_10


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL03_P6_3


title: CD45-/CD34+/CD31- cells from obese human adipose SVF JL13_P6_13


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL04_P6_4


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL05_P6_5


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL08_P6_8


title: CD45-/CD34+/CD31- cells from obese human adipose SVF JL15_P6_15


title: Astrocyte, biological rep1

tag: tissue


title: BMDMs-triple

status: Public on Sep 18 2017

city: kanazawa

first: Takamasa

last: Ishidome

state: Ishikawa

department: Medical sciences

institute: Kanazawa University

description: Gene expression 20hrs after adding triple

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Microarray Kit 8x60k (G4852A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37C°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: BMDMs, 20hrs, triple

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp labeling kit, one color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: BMDMs were obtained by culturing bone marrow cells isolated from the femurs and tibias of these mice for 4 - 6 days in high glucose DMEM supplemented with 10% FBS (Biowest), 1% penicillin/streptomycin and 10 units/ml macrophage colony-stimulating factor (M-CSF), which was prepared from the conditioned medium of mouse L929 cells transformed with a human M-CSF expression plasmid

extract_protocol: RNA was prepared using the RNeasy Plus Mini Kit (QIAGEN, Germany) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cultured BMDMs were treated with IFN-g, IL-10RB or CpG for 20hrs at 37 ºC in a humidified incubator with 5% CO2

tag: strain


title: BM104C3 PI 650 differentiated cells

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials: Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes; Transfer 200μl of hyb solution to each array, then tape holes; Hybridize 16 hours at 45° at 60rpm; Fluidics washing is FS450_00001

scan_protocol: Scanning was performed according to Affymetrix protocol - Affymetrix Gene Chip Scanner 3000 7G.

data_processing: CEL files were processed using Oligo Package in Bioconductor. Normalization was done employing RMA (Carvalho BS and Irizarry RA (2010). “A Framework for Oligonucleotide Microarray Preprocessing.” Bioinformatics, 26(19), pp. 2363-7. ISSN 1367-4803).

source_name: Bone marrow derived Mesenchymal Stem Cells

label_protocol: Samples were amplified and labelled using the GeneChip® WT PLUS Reagent Kit according to the manufacturers instructions.

growth_protocol: MSCs and fibroblasts were isolated after patient’s written consent using guidelines approved by the Ethic Committee of the University of Aachen (Permit number: EK163/07). Reprogramming has been performed as previously described (Willmann et al., Plos One 2013 May 29;8(5):e65324. doi: 10.1371/journal.pone.0065324. Culture medium consisted of iPS_Brew (Miltenyi Biotec) supplemented with 1% Penicillin/Streptomicin.  Cultures were maintained at 37 °C in a humidified atmosphere containing 5 % CO2 with medium changes every day.

extract_protocol: Total RNA was isolated with the NucleoSpin® RNA Isolation Kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: iPSCs were seeded on different substrates: non-structured polyimide  (PI flat) and nanogrooved polyimide (PI 650). Undifferentiated samples were cultured for 3 days in a iPS-Brew + 1% Pen/Strep, RNA was then harvested for gene expression analysis. Differentiated samples were cultured for 2 weeks in medium consisting of KO-DMEM 80%, serum replacement 20%, 2mM L-glutamine, 100 U/mL penicillin/streptomycin, non-essential amino-acids 1%, all reagents from Life Technologies then RNA was harvested for gene expression analysis.

tag: donor

value: Bone marrow donor 104

value: induced Pluripotent Stem Cells (iPSCs)

tag: seeded on

value: nanogrooved polyimide (PI 650) substrate

tag: differentiation status

value: differentiated cells


title: Oligoendrocyte, biological rep1

value: Primary Oligodendrocyte


title: BM104C3 PI 650 undifferentiated cells

value: undifferentiated cells


title: HFC6 PI flat undifferentiated cells

source_name: Fibroblasts obtained from foreskin

value: Human Fibroblasts donor A

value: non-structured polyimide (PI flat) substrate


title: BM102C2 PI flat differentiated cells

value: Bone marrow donor 102


title: BM104C3 PI flat undifferentiated cells


title: BM104C3 PI flat differentiated cells


title: BM102C2 PI 650 differentiated cells


title: HFC6 PI 650 undifferentiated cells


title: BMDMs-IFN-g+IL-10RB

description: Gene expression 20hrs after adding IFN-g+IL-10RB

source_name: BMDMs, 20hrs, IFN-g+IL-10RB


title: HFC6 PI flat differentiated cells


title: BM102C2 PI flat undifferentiated cells


title: BMDMs-CpG

description: Gene expression 20hrs after adding CpG

source_name: BMDMs, 20hrs, CpG


title: CD45-/CD34+/CD31- cells from non-obese human adipose SVF JL01_P6_1

value: Non-obese

value: Female


title: BM102C2 PI 650 undifferentiated cells


title: liver organization_30d_1000 mg/kg/d_replicate 2

city: jilin city

first: guangyu

last: xu

address: Binjiang Road 3999,jilin city,132013

institute: College of Pharmacy, Beihua University

description: Gene expression after 30d in mouse liver

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide.The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: liver organization,30d,1000 mg/kg/d

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 700μL RNA using the RNeasy Mini Kit (Qiagen p/n 74104) according to the manufacturer's instructions, followed by RNAeasy column purification. The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The total liver RNA was extracted with Trizol reagent (Invitrogen, Gaithersburg, MD, USA) and the mRNA was purified according to the instructions of RNeasy mini kit (Qiagen, Valencia, CA, USA). RNA samples were assessed for RNA integrity, inhibitor and DNA contamination by referring to the kit instructions. The quality of mRNA was detected by agarose gel electrophoresis, and the content was determined by UV spectrophotometer.

treatment_protocol: After they were acclimated to the laboratory environment for 3d, 20 male mice were randomly divided into 2 groups: model group (M), DECB group, 10 mice in each group.The DECB group was given DECB (1g/kg), and those in the M group (20 BW) were given normal saline (20mL/kg) intragastrically once daily continuously for 30d. At two hours after the last administration, mice in M and DECB groups were injected with 10% carbon tetrachloride blend oil (10mL/kg).

value: liver

value: male


title: liver organization_30d_1000 mg/kg/d_replicate 1


title: liver organization_1d_10 ml/kg_replicate 3

description: Gene expression after 1d in mouse liver

source_name: liver organization,1d,10 ml/kg


title: liver organization_30d_1000 mg/kg/d_replicate 3


title: 10ng/ml LPS + 20ug/ml Cystatin C Donor 4

city: Maaloev

first: Thomas

middle: Bovbjerg

last: Rasmussen

address: Novo Nordisk Park

country: Denmark

institute: Novo Nordisk A/S

description:
Gene expression data from treated monocytes
AneS_767

hyb_protocol: not provided

scan_protocol: Affymetrix GeneTitan

data_processing: Data were log2 transformed, quantile-normalized and then summarized using Tukeys mean polish.

source_name: Donor 4

label_protocol: Affymetrix 3' IVT PLUS

growth_protocol: Cells were maintained in RPMI1640 medium supplemented with 10% FCS and 1% penicillin + streptomycin, 37ºC in 5% CO2

extract_protocol: TriZol

treatment_protocol: 10 ng/mL LPS (E. coli, Santa Cruz, California, USA), 10 ng/mL LPS (E. coli, Santa Cruz, California, USA) and 20 µg/mL recombinant human Cystatin C (Biochrom AG, Berlin), or 20 µg/mL recombinant human Cystatin C (Biochrom AG, Berlin) for 20 hours

value: Monocytes


title: liver organization_1d_10 ml/kg_replicate 2

description: Gene expression after 1d in mouse liver


title: 10ng/ml LPS Donor 4

description:
Gene expression data from treated monocytes
AneS_766


title: Vehicle Donor 4

description:
Gene expression data from treated monocytes
AneS_765


title: 10ng/ml LPS + 20ug/ml Cystatin C Donor 3

description:
Gene expression data from treated monocytes
AneS_763

source_name: Donor 3


title: 20ug/ml Cystatin C Donor 3

description:
Gene expression data from treated monocytes
AneS_764


title: 10ng/ml LPS Donor 3

description:
Gene expression data from treated monocytes
AneS_762


title: 10ng/ml LPS Donor 2

description:
Gene expression data from treated monocytes
AneS_758

source_name: Donor 2


title: Vehicle Donor 2

description:
Gene expression data from treated monocytes
AneS_757


title: 20ug/ml Cystatin C Donor 2

description:
Gene expression data from treated monocytes
AneS_760


title: Vehicle Donor 3

description:
Gene expression data from treated monocytes
AneS_761


title: liver organization_1d_10 ml/kg_replicate 1

description: Gene expression after 1d in mouse liver


title: 10ng/ml LPS + 20ug/ml Cystatin C Donor 2

description:
Gene expression data from treated monocytes
AneS_759


title: HFC6 PI 650 differentiated cells


title: 20ug/ml Cystatin C Donor 1

description:
Gene expression data from treated monocytes
AneS_756

source_name: Donor 1


title: 10ng/ml LPS Donor 1

description:
Gene expression data from treated monocytes
AneS_754


title: Vehicle Donor 1

description:
Gene expression data from treated monocytes
AneS_753


title: 10ng/ml LPS + 20ug/ml Cystatin C Donor 1

description:
Gene expression data from treated monocytes
AneS_755


title: ZT8 KD24 LIVER

city: Irvine

first: Yu

last: Liu

state: California

address: UCI

department: Computer Science

institute: University of California, Irvine

description:
RNA level of mouse tissue at certain ZT under certain diet, all labeled
Mouse cell extracted at labeled ZT

hyb_protocol: Microarrays were erformed at the UCI Genomics High-throughput Facility, University of California, Irvine, as previously described(Eckel-Mahan et al., 2013).

data_processing:
Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.  The probe cell intensity files (.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (.CHP).
Data are expressed as mean ± SEM. The significance of differences was analyzed by Student’s t-test or two-way ANOVA and post hoc analysis for multiple group comparison. Expression levels time series were then used to determine circadian behaviors of transcripts using JTK-CYCLE and the results were corroborated using BIO_CYCLE, an improved circadian rhythm analysis software. Circadian behaviors include whether or not a transcript is circadian as well as its phase and amplitude. For JTK-CYCLE, a gene was considered circadian, if at least one of its transcripts passed a p-value cutoff of 0.01, while for BIO_CYCLE the p-value cutoff used was 0.05.

label: probe

source_name: LIVER ZT8 KD

growth_protocol: Eight week-old male C57BL/6J mice, maintained on a 12 hours light/ 12 hours dark cycle, were fed ad libitum to KD or CC for four weeks. The last week of feeding regimen, Fructose (4g/Kg) dissolved in PBS was administered to the mice through oral gavage (Volume = 200ul), once a day for seven days.

extract_protocol: Liver samples were homogenized in Trizol Lysis Reagent (Ambion 155696-018). Chloroform was added and the samples were shaken for 15 seconds. The samples were left at RT for 3 minutes and then centrifuged (12000g, 15 min, 4°C). The aqueous solution, containing RNA, was collected in a fresh tube and the RNA was precipitated by the addition of isopropanol. Samples were mixed by vortexing, left at RT for 10 minutes and then centrifuged (12000g, 10 min, 4°C). Supernatant was discarded and the RNA pellet was washed in 75% ethanol by centrifugation (7500g, 5 min, 4°C). Supernatant was discarded and the pellet was re-suspended in DEPC-treated water. To increase the purity of the RNA, RNA was purified using the RNeasy mini kit (Quiagen cat. N. 74106). Total RNA concentrations were determined by Nanodrop Spectrophotometer (Thermoscientific). RNA quality was analyzed via agarose gel electrophoresis (1 % agarose). Total RNA was reverse transcribed using Iscript reverse transcription Super mix (Biorad).

treatment_protocol: For sucrose experiments, mice were supplemented with 30% sucrose in drinking water ad libitum during the four weeks of dietary regimen. At the end of the 4th week animals were sacrificed via CO2 and cervical dislocation at ZT0 (light on) and ZT12 (light off). Liver and intestine were harvested and immediately frozen in liquid nitrogen.

value: LIVER

tag: diet

value: Ketogenic

tag: zt


title: ZT8 K26 IEC

scan_protocol: Microarrays were erformed at the UCI Genomics High-throughput Facility, University of California, Irvine, as previously described(Eckel-Mahan et al., 2013).

source_name: IEC ZT8 KD

value: INTESTINE (IEC)


title: ZT8 KD7 LIVER

label_protocol: Microarrays were erformed at the UCI Genomics High-throughput Facility, University of California, Irvine, as previously described(Eckel-Mahan et al., 2013).


title: ZT8 CC11 LIVER

source_name: LIVER ZT8 NC

value: Norma Chow


title: ZT8 CC12 LIVER


title: ZT8 KD8 LIVER


title: ZT8 K25 IEC


title: ZT8 K24 IEC


title: ZT8 C12 IEC

source_name: IEC ZT8 NC


title: ZT4 K20 IEC

source_name: IEC ZT4 KD


title: ZT4 KD20 LIVER

source_name: LIVER ZT4 KD


title: ZT8 C10 IEC


title: ZT4 KD3 LIVER


title: ZT4 K18 IEC


title: ZT4 KD4 LIVER


title: ZT4 C6 IEC

source_name: IEC ZT4 NC


title: ZT8 C11 IEC


title: ZT20 KD9 LIVER

source_name: LIVER ZT20 KD


title: ZT8 CC10 LIVER


title: ZT4 CC4 LIVER

source_name: LIVER ZT4 NC


title: ZT4 C24 IEC


title: ZT4 CC24 LIVER


title: ZT4 CC6 LIVER


title: ZT4 C25 IEC


title: ZT4 K19 IEC


title: ZT20 CC14 LIVER

source_name: LIVER ZT20 NC


title: ZT20 KD28 LIVER


title: ZT20 KD27 LIVER


title: ZT20 CC13 LIVER


title: ZT20 K29 IEC

source_name: IEC ZT20 KD


title: ZT20 C13 IEC

source_name: IEC ZT20 NC


title: ZT20 CC15 LIVER


title: 20ug/ml Cystatin C Donor 4

description:
Gene expression data from treated monocytes
AneS_768


title: ZT20 K10 IEC


title: ZT20 K27 IEC


title: ZT16 KD6 LIVER

source_name: LIVER ZT16 KD


title: ZT20 C31 IEC


title: ZT16 KD5 LIVER


title: ZT16 K23 IEC

source_name: IEC ZT16 KD


title: ZT16 CC8 LIVER

source_name: LIVER ZT16 NC


title: ZT16 KD22 LIVER


title: ZT16 C8 IEC

source_name: IEC ZT16 NC


title: ZT16 K22 IEC


title: ZT16 CC9 LIVER


title: ZT16 K6 IEC


title: ZT16 CC7 LIVER


title: ZT16 C26 IEC


title: ZT16 C7 IEC


title: ZT12 K11 IEC

source_name: IEC ZT12 KD


title: ZT12 KD30 LIVER

source_name: LIVER ZT12 KD


title: ZT12 K12 IEC


title: ZT12 K31 IEC


title: ZT12 CC18 LIVER

source_name: LIVER ZT12 NC


title: ZT12 C17 IEC

source_name: IEC ZT12 NC


title: ZT12 CC16 LIVER


title: ZT12 C18 IEC


title: ZT12 C32 IEC


title: ZT20 C30 IEC


title: ZT0 KD1 LIVER

source_name: LIVER ZT0 KD


title: ZT0 K2 IEC

source_name: IEC ZT0 KD


title: ZT12 CC17 LIVER


title: ZT0 KD15 LIVER


title: ZT0 K1 IEC


title: ZT0 CC22 LIVER

source_name: LIVER ZT0 NC


title: ZT0 K17 IEC


title: ZT0 C2 IEC

source_name: IEC ZT0 NC


title: ZT0 C22 IEC


title: ZT0 C23 IEC


title: ZT0 KD2 LIVER


title: ZT0 CC2 LIVER


title: ZT0 CC23 LIVER


title: DEA 24 h_rep 1

city: Aalborg East

first: Majken

last: Pagter

address: Fredrik Bajers Vej 7H

department: Chemistry and Bioscience

institute: Aalborg University

hyb_protocol: For hybridization the Affymetrix Wash and Stain Kit was used with the Command Console V3.2

scan_protocol: For scanning the Arabidopsis Gene 1.0 ST FS450_0002 protocol was used

data_processing: The raw Arabidopsis Gene 1.0 ST intensities were imported into the RobiNA software to perform quality assessment and data normalization and to identify genes differentially regulated between cold acclimated plants and plants subjected to different durations of deacclimation. Data normalization was performed using the RMA method. Statistical analysis of differential gene expression between cold acclimated and deacclimated or non-acclimated plants was carried out using a linear model-based approach, applying a 0.05 cut-off for P-values after Benjamini-Hochberg correction for multiple testing and log2 fold ratio greater than 1 and lower than -1.

organism: Arabidopsis thaliana

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 24 h replicate 1

label_protocol: For labeling and fragmentation the  NuGEN Encore Biotin Module was used according to the manusfacturer´s instructions

growth_protocol: Seeds from Arabidopsis thaliana Col-0 were sown in soil and grown in the greenhouse at 8-h day length with light supplementation to reach at least 200 µmol m-2 s-1 and a temperature of 20°C during the day, 18°C during the night. After three weeks of growth under these conditions plants were transferred to long days (16 h light/8 h dark), but otherwise similar growth conditions, for additionally one week of growth.

extract_protocol: Total RNA was isolated from a pool of rosettes from 10 different plants for each sample, using Trizol reagent (Invitrogen, Carlsbad, CA) and DNase treated with RapidOut DNA Removal Kit (Thermo Scientific, Waltham, MA). RNA quantity and quality were determined using a Nanodrop spectrophotomer (Nanodrop Technologies, Wilmington, DE), gel electrophoresis and a bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: For cold acclimation, plants were transferred to a 4°C growth cabinet at 16-h day length with 90 µmol m-2 s-1. for three days. For deacclimation, cold acclimated plants were transferred back to the greenhouse at 20°C/18°C day/night temperature and at least 200 µmol m-2 s-1 light as described previously. Complete rosettes of non-acclimated and cold acclimated plants and plants deacclimated for 2 h, 4 h, 6 h, 12 h and 24 h were harvested from 10 individual replicate plants for RNA extraction and hybridization on Affymetrix Genechip Arabidopsis Gene 1.0 ST Arrays.

tag: ecotype

value: Rosettes

tag: treatment

value: deacclimated for 24 h


title: DEA 24 h_rep 3

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 24 h replicate 3


title: DEA 24 h_rep 2

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 24 h replicate 2


title: DEA 12 h_rep 3

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 12 h replicate 3

value: deacclimated for 12 h


title: DEA 6h_rep 2

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 6 h replicate 2

value: deacclimated for 6 h


title: DEA 6h_rep 3

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 6 h replicate 3


title: DEA 6h_rep 1

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 6 h replicate 1


title: DEA 12 h_ rep2

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 12 h replicate 2


title: DEA 4h_rep 2

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 4 h replicate 2

value: deacclimated for 4 h


title: ZT12 KD12 LIVER


title: DEA 4h_rep 3

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 4 h replicate 3


title: DEA 2h_ rep 1

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 2 h replicate 1

value: deacclimated for 2 h


title: DEA 2h_ rep 2

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 2 h replicate 2


title: ZT12 KD11 LIVER

source_name: LIVER ZT12 KD


title: DEA 12 h_rep 1

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 12 h replicate 1


title: CA_rep 3

source_name: A. thaliana Col-0 cold acclimated for 3 d replicate 3

value: cold acclimated for 3 d


title: DEA 2h_rep 3

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 2 h replicate 3


title: CA_rep 2

source_name: A. thaliana Col-0 cold acclimated for 3 d replicate 2


title: NA_rep 3

source_name: A. thaliana Col-0 non-acclimated replicate 3

value: non-acclimated


title: CA_rep 1

source_name: A. thaliana Col-0 cold acclimated for 3 d replicate 1


title: DEA 4h_rep 1

source_name: Cold acclimated A. thaliana Col-0 deacclimated for 4 h replicate 1


title: NA_rep 1

source_name: A. thaliana Col-0 non-acclimated replicate 1


title: S1 SGC-7901_untreated_48h

city: hohhot

first: xuemin

last: Cao

address: 内蒙古呼和浩特市玉泉区

institute: Inner Mongolia University

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

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

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

label_protocol: standard Affymetrix protocol

growth_protocol: 37℃，5% CO2 cultured for 48h

extract_protocol: standard Affymetrix protocol

treatment_protocol: treat with GBK and cultured for 48h

tag: cell line

value: untreated


title: M2 MCF-7_untreated_48h


title: A549cont

city: Okinawa

first: Sayomi

last: Higa-Nakamine

address: 207 Uehara, Nishihara

department: Department of Biochemistry

institute: Graduate School of Medicine, University of the Ryukyus

description: SAMPLE 1

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.

source_name: A549 cell, DMSO 30min

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: A549 cells were grown on 60-mm Petri dishes in a culture medimum consisting DMEM and 0.45% glucose and 10% FCS.

extract_protocol: Total RNA was extracted using an Rneasy Mini Kit (Qiagen, MD) .

treatment_protocol: A549 cells were treated with 100 nM Bradykinin for 30 min in DMEM containing 0.1% FCS.

value: culltured lung alveolar epithelial cell

tag: treated with

value: DMSO (control)


title: S3 SGC-7901_GBK_48h

value: GBK


title: A549BK100nM30min

description: SAMPLE 2

source_name: A549 cell, 100 nM bradykinin 30min

value: 100 nM bradykinin for 30min


title: M9 MCF-7_GBK_48h


title: M4 MCF-7_GBK_48h


title: M7 MCF-7_untreated_48h


title: M1 MCF-7_untreated_48h


title: At_WOX5_3

city: Raleigh

first: Maria

middle: Angels

last: de Luis Balaguer

state: NC

address: 2115 Gardner Hall, Box 7612

department: Plant and Microbial Biology

institute: North Carolina State University

description: Gene expression data from QC sorted cells under standard conditions for 5 days

hyb_protocol: Standard Operating Procedure performed at the Duke Microarray Facility

data_processing: Mas5; target intensity of 250

source_name: WOX5::GFP sorted cells

label_protocol: Affy two-cycle labeling (raw 21-26) and one-cycle (everything else) labeling protocol

growth_protocol: Growth Media: Standard media for 5 days

extract_protocol: Affimetrix Kit

treatment_protocol: Seedling roots, 5 days after germination, either protoplasted cells or tissue

value: WOX5::GFP sorted cells (xylem)


title: At_TMO5_1

description: Gene expression data from xylem sorted cells under standard conditions for 5 days

scan_protocol: Standard Operating Procedure performed at the Duke Microarray Facility

source_name: pTMO5::GFP sorted cells

value: pTMO5::GFP sorted cells (QC)


title: At_WOX5_1


title: IMCD3_starved_rep2-1

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridisation and washing steps were carried out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 3000 ng of each labelled cRNA population were used for hybridisation.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565BA at two different photomultiplier tube (PMT) settings (100 % and 5 %) to increase the dynamic range of the measurement (extended dynamic range mode).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction software V9.5.3.1’ by using the extraction protocol file: GE2-v5_95_Feb07.xml.  Measurements of on-chip replicated features were averaged using the geometric mean of processed intensity values from both channels, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), separately to retrieve one resulting value per unique non-control probe. Single features were excluded from averaging if they i) were manually flagged, ii) were identified as outliers by the Feature Extraction software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or iv) showed a coefficient of variation of pixel intensities per feature that exceeded 0.5.  For inter-array normalisation, PS values were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th percentile value’ (targeted at 1500 for the whole series) by the 75th percentile of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalised PS values (nPS) for all samples (microarray data sets) were calculated by the following formula:   normalised PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold was defined as 1% of the reference 75th percentile value (= 15). All nPS values below this intensity cutoff were substituted by the surrogate value of 15.

source_name: IMCD3_starved_technical replicate of replicate2

label_protocol: Synthesis of Cy3- or Cy5-labelled cRNA was performed with the ‘Quick Amp Labeling kit, two color’ (#5190-0444, Agilent Technologies) according to the manufacturer’s recommendations using 500 ng of total RNA.

growth_protocol: IMCD3 cells (CRL-2123, ATCC) were grown in DMEM medium supplemented with 10% fetal calf serum (FCS; Biochrom), F12 (Invitrogen), 1x Glutamax (Gibco) and 1x Pen/Strep (Gibco) on 10 cm tissue culture dishes.

extract_protocol: Total RNA was extracted using the RNeasy Micro or Mini Kit (Qiagen) following the manufacturer’s instructions (including DNase digest). Total RNA was eluted in 40 µl H2O resulting in a concentration of 330 - 990 ng/µl.

treatment_protocol: Cells on two dishes were serum-starved in order to induce ciliogenesis by growing them for 48 h in medium lacking FCS before harvest (serum-starved IMCD3). Cells on two other dishes were split 1:10 the day before collection and did not reach confluency by the time of harvest (unstarved IMCD3).


title: At_TMO5_2


title: IMCD3_starved_rep2


title: IMCD3_starved_rep1-1

source_name: IMCD3_starved_technical replicate of replicate1


title: At_TMO5_3


title: IMCD3_rep1-1

source_name: IMCD3_technical replicate of replicate1