title: DKOG4_Flk1_long_DexPlus_48h_rep3

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 48hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 48hr, replicate 3

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences). The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 48 hours in the presence of 100 nM dexamethasone.


title: DKOG4_Flk1_long_DexPlus_48h_rep2

status: Public on Jun 24 2013

type: RNA

city: Kobe

first: Yuichi

last: Kumaki

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

hyb_protocol: 600 ng of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17 hours at 65 degrees C and 10 rpm according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 6.5).

scan_protocol: Slide scanning was performed using the Agilent DNA Microarray Scanner G2505C with 3 um resolution and 20-bit dynamic range.

data_processing: The scanned images were processed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028005_D_F_20110406) to generate background subtracted and spatially detrended green Processed Signal intensities. Normalize signal intensities were obtained by a) removal of data of control probes, b) log2 transformation, and c) quantile normalization, which was performed using the normalizeQuantiles function of the limma package of the R.

molecule: total RNA

organism: Mus musculus

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 48hr, replicate 2

label_protocol: Amplification and Cy3 labeling of RNA was prepared from 50 ng of RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions (G4140-90040 One-Color Microarray-Based Gene Expression Analysis Protocol Version 6.5). Purification of Cy3-labeled cRNA was performed using the RNeasy Mini Kit (Qiagen). Quantity, quality and dye incorporation of Cy3-labeled cRNA were checked using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

growth_protocol: ES cells were plated onto a 10-cm dish with confluent OP9 stromal cells in the differentiation medium (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 4 days.

extract_protocol: Total RNA was isolated by using the QIAshredder and the RNeasy Plus Micro Kit with gDNA Eliminator column (Qiagen) according to the manufacturer's protocols. RNA was quantified and quality controlled using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

tag: cell line

value: Line 16G4.3

tag: genotype/variation

value: Dnmt3a-/-Dnmt3b-/-, stably expressing Gata4-glucocorticoid receptor ligand binding domain fusion gene

tag: cell type

value: Flk1+/Ecad- mesoderm cells derived from embryonic stem (ES) cells, with further culture

tag: dexamethasone

value: yes

tag: time


title: DKOG4_Flk1_long_DexPlus_36h_rep3

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 36hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 36hr, replicate 3

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences). The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 36 hours in the presence of 100 nM dexamethasone.


title: TCD4_7H30_D001Gy_Ind5

city: Fontenay aux Roses Cedex

first: Gaetan

last: GRUEL

address: BP 17

department: Service de RadioBiologie et d'Epidemiologie

country: France

institute: Institut de Radioprotection et de Surete Nucleaire

description: Gene expression in Lymphocyte TCD4 450min post-exposure to 10mGy of human whole blood:IMDM (1:10)

hyb_protocol: 1.65 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 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565AA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um double pass, 16 bit Dye channel is set to Green and Green PMT is set to 100%, XDR set to 0.1).

data_processing: The scanned images were analyzed with Feature Extraction Software 7.5 (Agilent) using default parameters (protocol GE1-107_sep08 and Grid: 026652_D_F_20101031) to obtain raw signal intensities. Microarray raw data were analyzed, normalized and filtered with R software, limma and Agi4x44PreProcess package of the Bioconductor repository. Briefly, the mean signal intensity for each spot was used and a log base 2 transformation was performed. The normalization step was performed using the quantile method of the normalizeBetweenArrays function of the limma package. Agilent Feature Extraction Software flagged undetected spot and bad features allowing excluding them from the analysis. The filtering criteria consisted of removing a probe when it was undetected in at least 75% of the replicates. A total of 19,246 probes were selected after filtering step.

organism: Homo sapiens

source_name: Lymphocyte TCD4, 450min, 10mGy, Individual5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (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.

extract_protocol: Total RNA was extracted from lymphocyte T CD4+ using RNeasy Mini columns from the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: Human whole blood samples from 5 healthy donors were diluted in IMDM medium (1:10) and exposed to 500, 100, 50, 25, 10 and 5 mGy of Cobalt 60 gamma-rays. Gene expression alterations were measured 150, 300, 450 and 600 min post exposure after negative cell sorting of lymphocytes TCD4+ cells.

value: Lymphocyte TCD4

tag: gender

value: male


title: TCD4_10H_D001Gy_Ind3

description: Gene expression in Lymphocyte TCD4 600min post-exposure to 10mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 600min, 10mGy, Individual3


title: DKOG4_Flk1_long_DexPlus_72h_rep3

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 72hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 72hr, replicate 3

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences). The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 72 hours in the presence of 100 nM dexamethasone.


title: TCD4_7H30_D001Gy_Ind4

source_name: Lymphocyte TCD4, 450min, 10mGy, Individual4


title: TCD4_10H_D001Gy_Ind1

source_name: Lymphocyte TCD4, 600min, 10mGy, Individual1


title: TCD4_7H30_D001Gy_Ind3

source_name: Lymphocyte TCD4, 450min, 10mGy, Individual3


title: DKOG4_Flk1_long_DexPlus_48h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 48hr, replicate 1


title: TCD4_7H30_D001Gy_Ind2

source_name: Lymphocyte TCD4, 450min, 10mGy, Individual2


title: DKOG4_Flk1_long_DexPlus_36h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 36hr, replicate 2


title: DKOG4_Flk1_long_DexPlus_36h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 36hr, replicate 1


title: TCD4_5H_D001Gy_Ind5

description: Gene expression in Lymphocyte TCD4 300min post-exposure to 10mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 300min, 10mGy, Individual5


title: TCD4_7H30_D001Gy_Ind1

source_name: Lymphocyte TCD4, 450min, 10mGy, Individual1


title: TCD4_5H_D001Gy_Ind3

source_name: Lymphocyte TCD4, 300min, 10mGy, Individual3


title: TCD4_5H_D001Gy_Ind2

source_name: Lymphocyte TCD4, 300min, 10mGy, Individual2


title: TCD4_5H_D001Gy_Ind4

source_name: Lymphocyte TCD4, 300min, 10mGy, Individual4


title: DKOG4_Flk1_long_DexPlus_24h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 24hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 24hr, replicate 2

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences). The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 24 hours in the presence of 100 nM dexamethasone.


title: TCD4_2H30_D001Gy_Ind4

description: Gene expression in Lymphocyte TCD4 150min post-exposure to 10mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 150min, 10mGy, Individual4


title: DKOG4_Flk1_long_DexPlus_24h_rep3

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 24hr, replicate 3


title: TCD4_5H_D001Gy_Ind1

source_name: Lymphocyte TCD4, 300min, 10mGy, Individual1


title: DKOG4_Flk1_long_DexPlus_12h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 12hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 12hr, replicate 2

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences). The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 12 hours in the presence of 100 nM dexamethasone.


title: DKOG4_Flk1_long_DexPlus_12h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 12hr, replicate 1


title: DKOG4_Flk1_long_DexPlus_12h_rep3

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 12hr, replicate 3


title: TCD4_2H30_D001Gy_Ind2

source_name: Lymphocyte TCD4, 150min, 10mGy, Individual2


title: DKOG4_Flk1_long_DexPlus_24h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 24hr, replicate 1


title: TCD4_2H30_D001Gy_Ind3

source_name: Lymphocyte TCD4, 150min, 10mGy, Individual3


title: TCD4_10H_D0025Gy_Ind5

description: Gene expression in Lymphocyte TCD4 600min post-exposure to 25mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 600min, 25mGy, Individual5


title: TCD4_2H30_D001Gy_Ind1

source_name: Lymphocyte TCD4, 150min, 10mGy, Individual1


title: DKOG4_Flk1_long_DexMinus_48h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 48hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 48hr, replicate 2

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences).  The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 48 hours in the absence of dexamethasone.

value: no


title: TCD4_10H_D0025Gy_Ind3

source_name: Lymphocyte TCD4, 600min, 25mGy, Individual3


title: TCD4_10H_D0025Gy_Ind4

source_name: Lymphocyte TCD4, 600min, 25mGy, Individual4


title: TCD4_7H30_D0025Gy_Ind5

description: Gene expression in Lymphocyte TCD4 450min post-exposure to 25mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 450min, 25mGy, Individual5


title: DKOG4_Flk1_long_DexMinus_72h_rep1

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 72hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 72hr, replicate 1

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences).  The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 72 hours in the absence of dexamethasone.


title: DKOG4_Flk1_long_DexMinus_36h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 36hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 36hr, replicate 2

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences).  The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 36 hours in the absence of dexamethasone.


title: DKOG4_Flk1_long_DexMinus_72h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 72hr, replicate 2


title: DKOG4_Flk1_long_DexMinus_36h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 36hr, replicate 1


title: TCD4_7H30_D0025Gy_Ind4

source_name: Lymphocyte TCD4, 450min, 25mGy, Individual4


title: DKOG4_Flk1_long_DexMinus_12h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 12hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 12hr, replicate 2

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences).  The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 12 hours in the absence of dexamethasone.


title: DKOG4_Flk1_long_DexMinus_48h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 48hr, replicate 1


title: DKOG4_Flk1_long_DexMinus_24h_rep1

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with further 24hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 24hr, replicate 1

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences).  The cells were further cultured on type IV collagen-coated dishes in the differentiation medium  (alpha-MEM supplemented with 10% FCS and 50 uM 2-mercaptoethanol) for 24 hours in the absence of dexamethasone.


title: DKOG4_Flk1_long_DexMinus_24h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 24hr, replicate 2


title: TCD4_7H30_D0025Gy_Ind3

source_name: Lymphocyte TCD4, 450min, 25mGy, Individual3


title: DKOG4_Flk1_long_0h_rep3

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, replicate 3

treatment_protocol: The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences).

value: Flk1+/Ecad- mesoderm cells derived from embryonic stem (ES) cells


title: TCD4_5H_D0025Gy_Ind5

description: Gene expression in Lymphocyte TCD4 300min post-exposure to 25mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 300min, 25mGy, Individual5


title: TCD4_5H_D0025Gy_Ind4

source_name: Lymphocyte TCD4, 300min, 25mGy, Individual4


title: DKOG4_Flk1_long_0h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, replicate 2


title: DKOG4_Flk1_long_DexMinus_12h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, -Dex, 12hr, replicate 1


title: TCD4_7H30_D0025Gy_Ind1

source_name: Lymphocyte TCD4, 450min, 25mGy, Individual1


title: TCD4_10H_D0025Gy_Ind1

source_name: Lymphocyte TCD4, 600min, 25mGy, Individual1


title: TCD4_5H_D0025Gy_Ind1

source_name: Lymphocyte TCD4, 300min, 25mGy, Individual1


title: TCD4_7H30_D0025Gy_Ind2

source_name: Lymphocyte TCD4, 450min, 25mGy, Individual2


title: TCD4_2H30_D0025Gy_Ind5

description: Gene expression in Lymphocyte TCD4 150min post-exposure to 25mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 150min, 25mGy, Individual5


title: TCD4_5H_D0025Gy_Ind3

source_name: Lymphocyte TCD4, 300min, 25mGy, Individual3


title: DKOG4_Flk1_long_0h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, replicate 1


title: WTG4_Flk1_long_DexPlus_48h_rep3

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 48hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 48hr, replicate 3

value: Line J1G4.211

value: wild-type, stably expressing Gata4-glucocorticoid receptor ligand binding domain fusion gene


title: WTG4_Flk1_long_DexPlus_48h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 48hr, replicate 2


title: WTG4_Flk1_long_DexPlus_72h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 72hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 72hr, replicate 2


title: WTG4_Flk1_long_DexPlus_72h_rep3

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 72hr, replicate 3


title: WTG4_Flk1_long_DexPlus_36h_rep3

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 36hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 36hr, replicate 3


title: WTG4_Flk1_long_DexPlus_48h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 48hr, replicate 1


title: WTG4_Flk1_long_DexPlus_72h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 72hr, replicate 1


title: TCD4_2H30_D0025Gy_Ind2

source_name: Lymphocyte TCD4, 150min, 25mGy, Individual2


title: TCD4_7H30_D0005Gy_Ind1

description: Gene expression in Lymphocyte TCD4 450min post-exposure to 5mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 450min, 5mGy, Individual1


title: TCD4_10H00_D005Gy_Ind5

description: Gene expression in Lymphocyte TCD4 600min post-exposure to 50mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 600min, 50mGy, Individual5


title: WTG4_Flk1_long_DexPlus_36h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 36hr, replicate 1


title: TCD4_10H00_D005Gy_Ind4

source_name: Lymphocyte TCD4, 600min, 50mGy, Individual4


title: TCD4_2H30_D0025Gy_Ind4

source_name: Lymphocyte TCD4, 150min, 25mGy, Individual4


title: WTG4_Flk1_long_DexPlus_36h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 36hr, replicate 2


title: WTG4_Flk1_long_DexPlus_24h_rep3

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 24hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 24hr, replicate 3


title: WTG4_Flk1_long_DexPlus_24h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 24hr, replicate 2


title: TCD4_10H00_D005Gy_Ind1

source_name: Lymphocyte TCD4, 600min, 50mGy, Individual1


title: TCD4_7H30_D005Gy_Ind5

description: Gene expression in Lymphocyte TCD4 450min post-exposure to 50mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 450min, 50mGy, Individual5


title: TCD4_7H30_D005Gy_Ind4

source_name: Lymphocyte TCD4, 450min, 50mGy, Individual4


title: WTG4_Flk1_long_DexPlus_24h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 24hr, replicate 1


title: WTG4_Flk1_long_DexPlus_12h_rep1

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 12hr-culture in the presence of dexamethasone to activate Gata4GR transgene
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 12hr, replicate 1


title: TCD4_7H30_D005Gy_Ind3

source_name: Lymphocyte TCD4, 450min, 50mGy, Individual3


title: WTG4_Flk1_long_DexPlus_12h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 12hr, replicate 2


title: TCD4_7H30_D005Gy_Ind2

source_name: Lymphocyte TCD4, 450min, 50mGy, Individual2


title: WTG4_Flk1_long_DexMinus_72h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 72hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 72hr, replicate 2


title: TCD4_10H00_D005Gy_Ind3

source_name: Lymphocyte TCD4, 600min, 50mGy, Individual3


title: TCD4_5H_D005Gy_Ind4

description: Gene expression in Lymphocyte TCD4 300min post-exposure to 50mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 300min, 50mGy, Individual4


title: TCD4_7H30_D005Gy_Ind1

source_name: Lymphocyte TCD4, 450min, 50mGy, Individual1


title: WTG4_Flk1_long_DexMinus_72h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 72hr, replicate 1


title: WTG4_Flk1_long_DexPlus_12h_rep3

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 12hr, replicate 3


title: TCD4_5H_D005Gy_Ind1

source_name: Lymphocyte TCD4, 300min, 50mGy, Individual1


title: TCD4_10H_D01Gy_Ind5

description: Gene expression in Lymphocyte TCD4 600min post-exposure to 100mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 600min, 100mGy, Individual5


title: TCD4_10H_D01Gy_Ind3

source_name: Lymphocyte TCD4, 600min, 100mGy, Individual3


title: TCD4_2H30_D005Gy_Ind1

description: Gene expression in Lymphocyte TCD4 150min post-exposure to 50mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 150min, 50mGy, Individual1


title: TCD4_2H30_D005Gy_Ind5

source_name: Lymphocyte TCD4, 150min, 50mGy, Individual5


title: WTG4_Flk1_long_DexMinus_48h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 48hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 48hr, replicate 2


title: TCD4_5H_D005Gy_Ind3

source_name: Lymphocyte TCD4, 300min, 50mGy, Individual3


title: WTG4_Flk1_long_DexMinus_48h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 48hr, replicate 1


title: WTG4_Flk1_long_DexMinus_24h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 24hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 24hr, replicate 2


title: TCD4_2H30_D005Gy_Ind3

source_name: Lymphocyte TCD4, 150min, 50mGy, Individual3


title: TCD4_2H30_D005Gy_Ind2

source_name: Lymphocyte TCD4, 150min, 50mGy, Individual2


title: TCD4_10H_D01Gy_Ind4

source_name: Lymphocyte TCD4, 600min, 100mGy, Individual4


title: WTG4_Flk1_long_DexMinus_36h_rep1

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 36hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 36hr, replicate 1


title: WTG4_Flk1_long_DexMinus_12h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with further 12hr-culture in the absence of dexamethasone  (without Gata4GR induction)
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 12hr, replicate 2


title: TCD4_7H30_D01Gy_Ind4

description: Gene expression in Lymphocyte TCD4 450min post-exposure to 100mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 450min, 100mGy, Individual4


title: WTG4_Flk1_long_0h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, replicate 2


title: WTG4_Flk1_long_DexMinus_12h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 12hr, replicate 1


title: WTG4_Flk1_long_DexMinus_36h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 36hr, replicate 2


title: WTG4_Flk1_long_0h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, replicate 1


title: DKO_Flk1_short_DexPlus_3h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells, with 3hr-culture in the presence of dexamethasone before sorting
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

molecule: cytoplasmic RNA

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- (DKO) ES cells, +Dex, 3hr, replicate 2

extract_protocol: Cytoplasmic RNA was isolated by using the RNeasy Mini Kit (Qiagen) according to the manufacture's cytoplasmic RNA protocol with DNase digestion option. RNA was quantified and quality controlled using the NanoDrop ND-1000 Spectrophotometer (Thermo) and the 2100 Bioanalyzer (Agilent).

treatment_protocol: 3 hours before cell collection, 100 nM dexamethasone was added to the cells. The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences).

value: Line 16aabb


title: TCD4_2H30_D0025Gy_Ind3

description: Gene expression in Lymphocyte TCD4 150min post-exposure to 25mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 150min, 25mGy, Individual3


title: WTG4_Flk1_long_DexMinus_24h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, -Dex, 24hr, replicate 1


title: TCD4_7H30_D01Gy_Ind2

source_name: Lymphocyte TCD4, 450min, 100mGy, Individual2


title: TCD4_7H30_D01Gy_Ind3

source_name: Lymphocyte TCD4, 450min, 100mGy, Individual3


title: TCD4_7H30_D01Gy_Ind1

source_name: Lymphocyte TCD4, 450min, 100mGy, Individual1


title: TCD4_7H30_D01Gy_Ind5

source_name: Lymphocyte TCD4, 450min, 100mGy, Individual5


title: TCD4_10H_D01Gy_Ind1

source_name: Lymphocyte TCD4, 600min, 100mGy, Individual1


title: TCD4_2H30_D005Gy_Ind4

source_name: Lymphocyte TCD4, 150min, 50mGy, Individual4


title: TCD4_5H_D01Gy_Ind5

description: Gene expression in Lymphocyte TCD4 300min post-exposure to 100mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 300min, 100mGy, Individual5


title: DKO_Flk1_short_DexPlus_2h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells, with 2hr-culture in the presence of dexamethasone before sorting
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- (DKO) ES cells, +Dex, 2hr, replicate 2

treatment_protocol: 2 hours before cell collection, 100 nM dexamethasone was added to the cells. The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences).


title: DKO_Flk1_short_DexPlus_2h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- (DKO) ES cells, +Dex, 2hr, replicate 1


title: DKO_Flk1_short_DexPlus_3h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- (DKO) ES cells, +Dex, 3hr, replicate 1


title: DKO_Flk1_short_DexPlus_1h_rep1

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells, with 1hr-culture in the presence of dexamethasone before sorting
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- (DKO) ES cells, +Dex, 1hr, replicate 1

treatment_protocol: 1 hour before cell collection, 100 nM dexamethasone was added to the cells. The cells were collected using 0.25% trypsin-EDTA, and single cell suspensions were stained using APC-conjugated anti-Flk1, biotinylated anti-E-cadherin (Eccd2, Takara Bio or DECMA-1, eBioscience) antibodies, and PE-conjugated streptavidin. Flk1 positive/E-cadherin negative cells were sorted by FACS-Aria (BD Biosciences).


title: DKO_Flk1_short_0h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- ES cells
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- (DKO) ES cells, replicate 2


title: DKO_Flk1_short_DexPlus_1h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- (DKO) ES cells, +Dex, 1hr, replicate 2


title: TCD4_2H30_D01Gy_Ind5

description: Gene expression in Lymphocyte TCD4 150min post-exposure to 100mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 150min, 100mGy, Individual5


title: TCD4_5H_D01Gy_Ind4

source_name: Lymphocyte TCD4, 300min, 100mGy, Individual4


title: DKO_Flk1_short_0h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- (DKO) ES cells, replicate 1


title: DKOG4_Flk1_short_DexPlus_3h_rep1

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with 3hr-culture in the presence of dexamethasone to activate Gata4GR transgene before sorting
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 3hr, replicate 1


title: TCD4_5H_D01Gy_Ind2

source_name: Lymphocyte TCD4, 300min, 100mGy, Individual2


title: DKOG4_Flk1_short_DexPlus_3h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 3hr, replicate 2


title: DKOG4_Flk1_short_DexPlus_2h_rep1

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with 2hr-culture in the presence of dexamethasone to activate Gata4GR transgene before sorting
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 2hr, replicate 1


title: TCD4_2H30_D0025Gy_Ind1

source_name: Lymphocyte TCD4, 150min, 25mGy, Individual1


title: DKOG4_Flk1_short_DexPlus_2h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 2hr, replicate 2


title: DKOG4_Flk1_short_DexPlus_1h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells, with 1hr-culture in the presence of dexamethasone to activate Gata4GR transgene before sorting
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 1hr, replicate 2


title: TCD4_5H_D01Gy_Ind3

source_name: Lymphocyte TCD4, 300min, 100mGy, Individual3


title: TCD4_5H_D01Gy_Ind1

source_name: Lymphocyte TCD4, 300min, 100mGy, Individual1


title: TCD4_10H_D05Gy_Ind1

description: Gene expression in Lymphocyte TCD4 600min post-exposure to 500mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 600min, 500mGy, Individual1


title: DKOG4_Flk1_short_DexPlus_1h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, +Dex, 1hr, replicate 1


title: TCD4_10H_D05Gy_Ind4

source_name: Lymphocyte TCD4, 600min, 500mGy, Individual4


title: TCD4_2H30_D01Gy_Ind4

source_name: Lymphocyte TCD4, 150min, 100mGy, Individual4


title: TCD4_5H_D05Gy_Ind4

description: Gene expression in Lymphocyte TCD4 300min post-exposure to 500mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 300min, 500mGy, Individual4


title: DKOG4_Flk1_short_0h_rep1

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from Dnmt3a-/-Dnmt3b-/- Gata4GR ES cells
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, replicate 1


title: TCD4_7H30_D05Gy_Ind1

description: Gene expression in Lymphocyte TCD4 450min post-exposure to 500mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 450min, 500mGy, Individual1


title: TCD4_10H_D05Gy_Ind3

source_name: Lymphocyte TCD4, 600min, 500mGy, Individual3


title: TCD4_5H_D05Gy_Ind2

source_name: Lymphocyte TCD4, 300min, 500mGy, Individual2


title: TCD4_5H_D05Gy_Ind5

source_name: Lymphocyte TCD4, 300min, 500mGy, Individual5


title: WTG4_Flk1_short_DexPlus_2h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with 2hr-culture in the presence of dexamethasone to activate Gata4GR transgene before sorting
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 2hr, replicate 2


title: TCD4_2H30_D01Gy_Ind1

source_name: Lymphocyte TCD4, 150min, 100mGy, Individual1


title: WTG4_Flk1_short_DexPlus_3h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with 3hr-culture in the presence of dexamethasone to activate Gata4GR transgene before sorting
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 3hr, replicate 2


title: TCD4_7H30_D05Gy_Ind4

source_name: Lymphocyte TCD4, 450min, 500mGy, Individual4


title: TCD4_10H_D05Gy_Ind5

source_name: Lymphocyte TCD4, 600min, 500mGy, Individual5


title: WTG4_Flk1_short_DexPlus_2h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 2hr, replicate 1


title: TCD4_5H_D05Gy_Ind3

source_name: Lymphocyte TCD4, 300min, 500mGy, Individual3


title: TCD4_2H30_D05Gy_Ind5

description: Gene expression in Lymphocyte TCD4 150min post-exposure to 500mGy of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 150min, 500mGy, Individual5


title: WTG4_Flk1_short_DexPlus_3h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 3hr, replicate 1


title: TCD4_7H30_D05Gy_Ind5

source_name: Lymphocyte TCD4, 450min, 500mGy, Individual5


title: TCD4_2H30_D01Gy_Ind2

source_name: Lymphocyte TCD4, 150min, 100mGy, Individual2


title: WTG4_Flk1_short_DexPlus_1h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells, with 1hr-culture in the presence of dexamethasone to activate Gata4GR transgene before sorting
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 1hr, replicate 2


title: DKOG4_Flk1_short_0h_rep2

source_name: Flk1+/Ecad- mesoderm cells derived from mouse Dnmt3a-/-Dnmt3b-/- Gata4GR (DKOG4) ES cells, replicate 2


title: TCD4_2H30_D05Gy_Ind4

source_name: Lymphocyte TCD4, 150min, 500mGy, Individual4


title: TCD4_7H30_D05Gy_Ind2

source_name: Lymphocyte TCD4, 450min, 500mGy, Individual2


title: WTG4_Flk1_short_0h_rep2

description:
Gene expression data from Flk1+/Ecad- mesoderm cells derived from wild-type Gata4GR ES cells
'short' sample represents short time course experiment (0-3h). In this experiment, dexamethasone was added before FACS sorting.
'long' sample represents long time course experiment (0-72h). In this experiment, dexamethasone was added after FACS sorting.

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, replicate 2


title: WTG4_Flk1_short_0h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, replicate 1


title: WTG4_Flk1_long_0h_rep3

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, replicate 3


title: WTG4_Flk1_short_DexPlus_1h_rep1

source_name: Flk1+/Ecad- mesoderm cells derived from mouse wild-type Gata4GR (WTG4) ES cells, +Dex, 1hr, replicate 1


title: TCD4_2H30_D05Gy_Ind3

source_name: Lymphocyte TCD4, 150min, 500mGy, Individual3


title: TCD4_10H_D0Gy_Ind1

description: Gene expression in Lymphocyte TCD4 600min post-exposure to sham irradiation of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 600min, Sham, Individual1


title: TCD4_7H30_D0Gy_Ind3

description: Gene expression in Lymphocyte TCD4 450min post-exposure to sham irradiation of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 450min, Sham, Individual3


title: TCD4_2H30_D05Gy_Ind2

source_name: Lymphocyte TCD4, 150min, 500mGy, Individual2


title: TCD4_10H_D0Gy_Ind3

source_name: Lymphocyte TCD4, 600min, Sham, Individual3


title: TCD4_5H_D0Gy_Ind5

description: Gene expression in Lymphocyte TCD4 300min post-exposure to sham irradiation of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 300min, Sham, Individual5


title: TCD4_5H_D0Gy_Ind4

source_name: Lymphocyte TCD4, 300min, Sham, Individual4


title: TCD4_5H_D0Gy_Ind1

source_name: Lymphocyte TCD4, 300min, Sham, Individual1


title: TCD4_7H30_D0Gy_Ind4

source_name: Lymphocyte TCD4, 450min, Sham, Individual4


title: TCD4_7H30_D0Gy_Ind5

source_name: Lymphocyte TCD4, 450min, Sham, Individual5


title: TCD4_5H_D0Gy_Ind3

source_name: Lymphocyte TCD4, 300min, Sham, Individual3


title: TCD4_5H_D0Gy_Ind2

source_name: Lymphocyte TCD4, 300min, Sham, Individual2


title: TCD4_10H_D0Gy_Ind4

source_name: Lymphocyte TCD4, 600min, Sham, Individual4


title: TCD4_7H30_D0Gy_Ind1

source_name: Lymphocyte TCD4, 450min, Sham, Individual1


title: TCD4_2H30_D0Gy_Ind5

description: Gene expression in Lymphocyte TCD4 150min post-exposure to sham irradiation of human whole blood:IMDM (1:10)

source_name: Lymphocyte TCD4, 150min, Sham, Individual5


title: TCD4_2H30_D0Gy_Ind4

source_name: Lymphocyte TCD4, 150min, Sham, Individual4


title: TCD4_2H30_D0Gy_Ind3

source_name: Lymphocyte TCD4, 150min, Sham, Individual3


title: pBAD-RydC 2

type: mixed

city: Würzburg

first: Kai

last: Papenfort

state: Würzburg

address: Josef-Schneider Str.2/BAU D15

department: RNA Biology

country: Germany

institute: IMIB Würzburg

hyb_protocol: Labeled samples were mixed and hybridized to 8x15K custom-commercial microarrays overnight at 65ºC using 1x Hi hybridization buffer together with blocking buffer according to the supplier`s recommendations (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies). To compensate for unequal dye incorporation, data centering to zero was performed for each individual microarray on the slide separately. Microarray data were analysed using GeneSpring 7.3 (Agilent) and genes were considered to be differentially expressed if they displayed ≥2-fold changes in both replicates and were statistically significantly different

molecule: genomic DNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: SL1344 pBAD-RydC [genomic DNA]

label_protocol: total RNA was labelled with Cy3 using random hexamers and reverse transcriptase (Stratagene AffinityScript) while genomicDNA was labelled with Cy5 using the Invitrogen BioPrime DNA Labeling System

growth_protocol: Salmonella carrying pBAD-ctr or pBAD-RydC were grown in LB-media to OD=1.5.

extract_protocol: Total RNA was extracted using SV40 RNA isolation Kit (promega). GenomicDNA was extracted using the Qiagen 'Genomic DNA' Kit

treatment_protocol: At OD=1.5, 0.2% (final conc.) L-arabinose was added. Total RNA was isolated 10 min post treatment.

value: pBAD-RydC

source_name: SL1344 pBAD-RydC [total RNA]


title: TCD4_7H30_D0Gy_Ind2

source_name: Lymphocyte TCD4, 450min, Sham, Individual2


title: pBAD-RydC 1


title: TCD4_2H30_D0Gy_Ind1

source_name: Lymphocyte TCD4, 150min, Sham, Individual1


title: TCD4_10H_D0Gy_Ind2

source_name: Lymphocyte TCD4, 600min, Sham, Individual2


title: pBAD-ctr 2

source_name: SL1344 pBAD-ctr [genomic DNA]

value: pBAD-ctr

source_name: SL1344 pBAD-ctr [total RNA]


title: pBAD-ctr 1


title: Treg_CD4(cre)Raptor(fl/fl)_replicate_3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

country: USA

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 6 micrograms of cDNA was hybridized for 16 hr at 45C on an Affymetrix HT MG-430 PM array. Following hybridization, arrays were washed and stained using the GeneTitan system

scan_protocol: HT MG-430PM arrays were scanned using the Affymetrix GeneTitan system

data_processing: Probe signals were quantile normalized and summarized using the RMA algorithm

label: biotin

source_name: Regulatory T-cells from  CD4(cre)Raptor(fl/fl) mouse

label_protocol: Twelve nanograms of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Regulatory T cells were sorted based on surface markers (CD4+CD25+) and used for RNA extraction.

extract_protocol: RNA was extracted using Qiagen's RNAeasy kit, with on-column DNase digestion included.

treatment_protocol: Freshly isolated and sorted cells were used immediately, without treatment, for RNA extraction.

value: sorted regulatory T-cells from spleen and peripheral lymph nodes

tag: genotype

tag: genetic background


title: Treg_CD4(cre)Raptor(fl/fl)_replicate_1


title: FG-3019 + gemcitabine treated tumor, biological rep3

city: San Francisco

first: Mark

middle: D.

last: Sternlicht

state: CA

address: 409 Illinois Street

department: Molecular Biology

institute: FibroGen, Inc.

description: Tumoral gene expression data from FG-3019 + gemcitabine treated mouse MH8363, biological replicate 3

hyb_protocol: Following fragmentation, labeled cRNA were hybridized on Affymetrix mouse genome 430A 2.0 microarrays using the Affymetrix GeneChip Hybridization, Wash, and Stain kit (P/N 901241) and standard protocol. Hybridization was performed for 16hrs at 45°C, 60rpm in an Affymetrix GeneChip Hybridization Oven 640 and staining and washing were performed using an Affymetrix GeneChip Fluidics Station 450 using the manufacturer's recommended fluidics script for 430Av2 genechips (FS450_0002).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 7G. Scanning was performed using AGCC software and resulting CEL files were exported to GCOS v1.4.0.036 to generate CEL files compatible with Agilent GeneSpring GX 7.3.1 analysis software.

data_processing: CEL data were preprocessed using the GC content-based Robust Multi-Array (GCRMA) algorithm and imported into GeneSpring GX 7.3.1.  Between-group gene expression comparisons were performed on gene data normalized to the median of measurements in the IgG control samples V1-V7 using parametric t-tests without assuming equal variances or correcting for multiple comparisons.

source_name: PDA tumor, mouse MH8363, FG-3019 + gemcitabine, day 9

label_protocol: Biotinylated cRNA were prepared from 250ng total RNA using the Affymetrix GeneChip 3'IVT Express kit (P/N 901229) according the manufacturer's standard protocol.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Universal RNA purification kit per the manufacturer's recommended methods. RNA quantity and integrity were determined using a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano assay kit.

treatment_protocol: All animal procedures were carried out in accordance with institutional and national guidelines. For matching purposes, LSL-KrasG12D/+;LSL-Trp53R172H/+;Pdx1-Cre (KPC) mice (Hingorani et al. 2005 Cancer Cell 7:469-83.) were screened by high-resolution ultrasound using a Visual Sonics Vevo 2100 System with a MS250, 13-24MHz scanhead. Mice with tumor diameters of 6-9mm were randomized and enrolled into one of four treatment groups: IgG, gemcitabine/IgG, FG-3019, or FG-3019/gemcitabine. Gemcitabine (100mg/kg) was administered every 3-4 days by i.p. injection. Polyclonal human IgG or human monoclonal FG-3019 (30mg/kg) was administered by i.p. injection every 3 days. Tumor volumes were measured on days 4 and 7 by reconstructed 3D ultrasound using the Vevo 2100 software package. Mice were euthanized on day 9, 2h after the final gemcitabine dose, and perfused with PBS. Half of the tumor was fixed with 10% neutral buffered formalin, and the other half was divided into 4-6 pieces, some of which were snap frozen in liquid nitrogen and stored at -80°C, while those to be used for RNA extraction were stored for at least 24hrs in RNAlater (Ambion) at 4°C then snap frozen and stored at -80°C.

tag: tissue

value: pancreatic ductal adenocarcinoma

value: female

tag: strain

tag: treatment

value: FG-3019 + gemcitabine


title: IgG + gemcitabine treated tumor, biological rep2

description: Tumoral gene expression data from IgG + gemcitabine treated mouse MH7188, biological replicate 2

source_name: PDA tumor, mouse MH7188, IgG + gemcitabine, day 9

value: IgG + gemcitabine


title: FG-3019 + gemcitabine treated tumor, biological rep1

description: Tumoral gene expression data from FG-3019 + gemcitabine treated mouse MH8223, biological replicate 1

source_name: PDA tumor, mouse MH8223, FG-3019 + gemcitabine, day 9


title: FG-3019 + gemcitabine treated tumor, biological rep2

description: Tumoral gene expression data from FG-3019 + gemcitabine treated mouse MH8259, biological replicate 2

source_name: PDA tumor, mouse MH8259, FG-3019 + gemcitabine, day 9


title: FG-3019 + gemcitabine treated tumor, biological rep5

description: Tumoral gene expression data from FG-3019 + gemcitabine treated mouse MH9184, biological replicate 5

source_name: PDA tumor, mouse MH9184, FG-3019 + gemcitabine, day 9


title: Treg_WT_replicate_4

source_name: Regulatory T-cells from WT mouse

value: WT


title: Treg_CD4(cre)Raptor(fl/fl)_replicate_2


title: Treg_WT_replicate_1


title: IgG + gemcitabine treated tumor, biological rep4

description: Tumoral gene expression data from IgG + gemcitabine treated mouse MH6573, biological replicate 4

source_name: PDA tumor, mouse MH6573, IgG + gemcitabine, day 9


title: FG-3019 + gemcitabine treated tumor, biological rep4

description: Tumoral gene expression data from FG-3019 + gemcitabine treated mouse MH8524, biological replicate 4

source_name: PDA tumor, mouse MH8524, FG-3019 + gemcitabine, day 9


title: FG-3019 + gemcitabine treated tumor, biological rep6

description: Tumoral gene expression data from FG-3019 + gemcitabine treated mouse MH9523, biological replicate 6

source_name: PDA tumor, mouse MH9523, FG-3019 + gemcitabine, day 9


title: IgG + gemcitabine treated tumor, biological rep3

description: Tumoral gene expression data from IgG + gemcitabine treated mouse MH7874, biological replicate 3

source_name: PDA tumor, mouse MH7874, IgG + gemcitabine, day 9


title: FG-3019 treated tumor, biological rep2

description: Tumoral gene expression data from FG-3019 treated mouse MH9324, biological replicate 2

source_name: PDA tumor, mouse MH9324, FG-3019, day 9


title: FG-3019 treated tumor, biological rep5

description: Tumoral gene expression data from FG-3019 treated mouse MH9693, biological replicate 5

source_name: PDA tumor, mouse MH9693, FG-3019, day 9


title: IgG + gemcitabine treated tumor, biological rep6

description: Tumoral gene expression data from IgG + gemcitabine treated mouse MH7714, biological replicate 6

source_name: PDA tumor, mouse MH7714, IgG + gemcitabine, day 9


title: IgG + gemcitabine treated tumor, biological rep5

description: Tumoral gene expression data from IgG + gemcitabine treated mouse MH6658, biological replicate 5

source_name: PDA tumor, mouse MH6658, IgG + gemcitabine, day 9


title: FG-3019 treated tumor, biological rep4

description: Tumoral gene expression data from FG-3019 treated mouse MH9542, biological replicate 4

source_name: PDA tumor, mouse MH9542, FG-3019, day 9


title: Treg_WT_replicate_2


title: TBART control patient 36

city: Cape Town

last: Nicol

address: Anzio Road, Observatory,

country: South Africa

institute: University of Cape Town

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_36

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133+. 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 using the PLIER algorithm on ArrayAssist Lite using default analysis settings

source_name: TBART control patient, PBMC stimulated for 6 hours with heat-killed H37Rv

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

growth_protocol: fresh PBMC were plated at 1x10^6 cells per ml, 5ml per well, rested overnight

extract_protocol: RNA was extracted using RNeasy Mini Kit Spin protocol as per the manufacturer’s instructions

treatment_protocol: stimulated with heat killed kH37Rv (multiplicity of infection MOI = 1:1, H37Rv to PBMC) for 6 hours

tag: individual

value: HIV-infected patient placed on antiretroviral treatment

tag: case or control

value: Control

value: PBMC

tag: protocol


title: Treg_WT_replicate_3


title: IgG + gemcitabine treated tumor, biological rep1

description: Tumoral gene expression data from IgG + gemcitabine treated mouse MH7049, biological replicate 1

source_name: PDA tumor, mouse MH7049, IgG + gemcitabine, day 9

value: male


title: FG-3019 treated tumor, biological rep1

description: Tumoral gene expression data from FG-3019 treated mouse MH8720, biological replicate 1

source_name: PDA tumor, mouse MH8720, FG-3019, day 9


title: FG-3019 treated tumor, biological rep3

description: Tumoral gene expression data from FG-3019 treated mouse MH9525, biological replicate 3

source_name: PDA tumor, mouse MH9525, FG-3019, day 9


title: Treg_CD4(cre)Raptor(fl/fl)_replicate_4

source_name: Regulatory T-cells from  CD4(cre)Raptor(fl/fl) mouse


title: TBART control patient 37

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_37


title: TBART control patient 32

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_32


title: TBART control patient 35

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_35


title: TBART control patient 001_6

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_001_6

source_name: IRIS patient, PBMC stimulated for 6 hours with heat-killed H37Rv


title: IRIS patient 113

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_113_2

value: IRIS case


title: IRIS patient 48

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_048_2


title: TBART control patient 27

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_27


title: PG4P1_2

city: Houston

first: Merry

last: Ruan

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
Biological Replicate TG 2
SAMPLE 5

hyb_protocol: according to illumina protocols

scan_protocol: according to illumina protocols

data_processing: Data was quantile normalized and VST transformed with lumi package in R

source_name: superficial zone chondrocytes

label_protocol: according to illumina protocols

extract_protocol: Samples were frozen in Optimal cutting temperature compound, dehydrated using gradient ethanol and xylene.  After laser capture microdissection using arcturus microdissection system, samples were extracted according to manufacturer's protocol of Arcturus PicoPure Frozen RNA isolation kit

tag: age

value: FVB/N


title: WTP1_3

description:
Biological Replicate WT 3
SAMPLE 3


title: IgG treated tumor, biological rep7

description: Tumoral gene expression data from IgG treated mouse MH6670, biological replicate 7

source_name: PDA tumor, mouse MH6670, IgG, day 9

value: IgG


title: IRIS patient 44

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_044_2


title: IgG treated tumor, biological rep6

description: Tumoral gene expression data from IgG treated mouse MH8274, biological replicate 6

source_name: PDA tumor, mouse MH8274, IgG, day 9


title: IgG treated tumor, biological rep3

description: Tumoral gene expression data from IgG treated mouse MH7658, biological replicate 3

source_name: PDA tumor, mouse MH7658, IgG, day 9


title: IgG treated tumor, biological rep2

description: Tumoral gene expression data from IgG treated mouse MH6860, biological replicate 2

source_name: PDA tumor, mouse MH6860, IgG, day 9


title: IRIS patient 116

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_116_2


title: PG4P1_3

description:
Biological Replicate TG 3
SAMPLE 6


title: TBART control patient15_6

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
TBART_15_6


title: IgG treated tumor, biological rep5

description: Tumoral gene expression data from IgG treated mouse MH7942, biological replicate 5

source_name: PDA tumor, mouse MH7942, IgG, day 9


title: IgG treated tumor, biological rep4

description: Tumoral gene expression data from IgG treated mouse MH7776, biological replicate 4

source_name: PDA tumor, mouse MH7776, IgG, day 9


title: PG4P1_1

description:
Biological Replicate TG 1
SAMPLE 4


title: IgG treated tumor, biological rep1

description: Tumoral gene expression data from IgG treated mouse MH6042, biological replicate 1

source_name: PDA tumor, mouse MH6042, IgG, day 9


title: DMSO(1dpa)

city: Hsinchu

first: Yung-Jen

last: Chuang

state: Taiwan

address: No. 101, Sec. 2, Kuang Fu Road

department: Department of Medical Science

country: Taiwan

institute: National Tsing Hua University

description: Gene expression in DMSO-treated zebrafish ventricle at 1day post injury

hyb_protocol: 1.65 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Zebrafish Oligo V2 4×44K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: The three scanner output files were uploaded into GeneSpring program. Following the GeneSpring's online instruction, we obtained the output file as the gProcessedSignal (normalized signal by 75th percentile), and submitted the VALUEs without any further modification.

organism: Danio rerio

source_name: whole ventricle, DMSO-treated, 1 day after injury, replicate 1

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

extract_protocol: Total RNA were extracted by Trizol reagent (Invitrogen, USA) followed the standard protocol provided by the manufacturer and eventually dissolved in reagent grade water (Sigma-Aldrich, USA)

treatment_protocol: Zebrafish received ventricular amputation surgery were treated with 0.002%DMSO (vehicle control) or 0.25μM beclomethasone. Whole ventricles of sham operation, DMSO-treated, beclomethasone-treated were harvested at 1day post injury. Each sample group contained 10 individual ventricles pooled together.

value: whole ventricle

tag: time post injury

value: 24 hours after injury


title: Beclomethasone(1dpa)

description: Gene expression in beclomethasone-treated zebrafish ventricle at 1day post injury

source_name: whole ventricle, beclomethasone-treated, 1 day after injury, replicate 1

value: 0.25uM beclomethasone


title: WTP1_1

description:
Biological Replicate WT 1
SAMPLE 1


title: IRIS patient 24

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_024_2


title: WTP1_2

description:
Biological Replicate WT 2
SAMPLE 2


title: IRIS patient 22

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_022_2


title: sham operation

description: Gene expression in sham operation zebrafish ventricle

source_name: whole ventricle, sham operation, replicate 1

value: no injury, 24 hours after sham operation

value: sham operation


title: 10782

status: Public on Jun 23 2013

city: NY

first: Wasay

last: Hussain

state: NY

address: NY

institute: Signal Genetics

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol on the Affymetrix GeneChip Scanner 3000Dx V.2

data_processing: Probe intensities were MAS5-calculated using the Bioconductor 'AnnotationData' package, release 2.11 (http://www.bioconductor.org).

source_name: invasive breast carcinomas

label_protocol: standard Affymetrix protocol

extract_protocol: Extraction of RNA was done using the Prelude(tm) FFPE RNA Isolation Module from NuGEN according to the manufacturer's instructions.

tag: tumor stage

value: IA

tag: er status

tag: grade

tag: size (cm)


title: 10764


title: 7893


title: 5753


title: 5731

value: IB


title: 5789

value: IIA


title: 5009


title: 6729


title: IRIS patient 98

description:
Gene expression data from RNA extracted from PBMC stimulated for 6 hours with heat killed H37Rv
IRIS_098_2

tag: cell type


title: 4919


title: 11725


title: 9049

value: CT


title: 6097


title: 4586


title: 5263


title: 4184


title: 4309

value: PT


title: 3291


title: 3124


title: 4472


title: 4613


title: 3741


title: 1975


title: 2270


title: 4273


title: 4562


title: 981


title: 37280


title: 997


title: 1822


title: 38037


title: 36693


title: 37258


title: 35399


title: 37107


title: 659


title: 33104


title: 36389

value: IIB


title: 37454


title: 32011


title: 30454


title: 31214


title: 30958


title: 33386


title: 29960


title: 30019


title: 34067


title: 30563


title: 28128


title: 24734


title: 25281


title: 27715


title: 27177


title: 30451


title: 23605


title: 24450


title: 22770


title: 18559


title: 22220


title: 17043


title: 22788


title: 19141


title: 13279


title: 20451


title: 21252


title: 14178


title: 14017


title: 11715


title: 13074


title: 11007


title: 12273


title: 11420


title: 12163


title: 13066


title: 5155


title: 11694


title: 7806


title: 4681


title: 4906


title: 4376


title: 8077


title: 7388


title: 3114


title: 2799


title: 2759


title: 381


title: 1377


title: 1940


title: 748


title: 221


title: 36150


title: 36040


title: 33773


title: 34999


title: 32595


title: 32883


title: 33831


title: 30087


title: 30857


title: 28423


title: 29732


title: 31865


title: 29569


title: 24947


title: 5147


title: 24973


title: 26713


title: 30061


title: 24535


title: 24233


title: 22699


title: 23914


title: 22427


title: 26863


title: 23655


title: 22421


title: 20505


title: 20557


title: 20699


title: 23789


title: 17471


title: 19505


title: 21583


title: 18720


title: 19622


title: 20057


title: 18273


title: 17391


title: 17538


title: 17406


title: 18683


title: 28433


title: 15853


title: 19942


title: 20266


title: 18978


title: 17958


title: 20534


title: 14045


title: 13351


title: 14447


title: 11302


title: 9165


title: 9040


title: 11802


title: 15223


title: 9447


title: 12892


title: 12600


title: 6753


title: 5142


title: 2953


title: 8155


title: 9055


title: 9436


title: 2696


title: 4430


title: 6298


title: 4656


title: 10385


title: 4011


title: 4511


title: 6331


title: 8241


title: 12578


title: 2326


title: 1123


title: 38586


title: 675


title: 39183


title: 2075


title: 35073


title: 36074


title: 39026


title: 33135


title: 2191


title: 32528


title: 38410


title: 5205


title: 31535


title: 33801


title: 37871


title: 31869


title: 31321


title: 30204


title: 30827


title: 30996


title: 32648


title: 38698


title: 12482


title: 35511


title: 30534


title: 32982


title: 31229


title: 31295


title: 34551


title: 22130


title: 30067


title: 21568


title: 18449


title: 30065


title: 28610


title: 18411


title: 25466


title: 17127


title: 17904


title: 25941


title: 16896


title: 17924


title: 16095


title: 18069


title: 13563


title: 12525


title: 18197


title: 8518


title: 17113


title: 12817


title: 15791


title: 12626


title: 6135


title: 13089


title: 8261


title: 10485


title: 7981


title: 7961


title: 9058


title: 5337


title: 5227


title: 3912


title: 2899


title: 37603


title: 4288


title: 4301


title: 5047


title: 3942


title: 38735


title: 6266


title: 2966


title: 39976


title: 3652


title: 1427


title: 4943


title: FDC-induced myeloid cells (FDMCs)

city: Okayama-shi

first: Masaki

last: Magari

address: 3-1-1, Tsushima-naka, Kita-ku

institute: Okayama University

description: FDMCs were generated from lineage-negative c-kit+ splenocytes.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained under the Affymetrix Gene Chip Cpmmand Console Software (AGCC).

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

data_processing: The data were analyzed with Affymetrix Expression Console Software (Expression Console)  using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500 (TGT500).

source_name: Myeliod cells induced on FDC line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: FDMCs were induced from splenocyte on FDC line.

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

treatment_protocol: FDMCs were sparated by using FACS Aria.

value: BALB/c


title: 2808


title: M1, NS1 R227K 1

status: Public on Jun 22 2013

city: Ottawa

first: Earl

middle: Garnet

last: Brown

state: Ontario

address: 451 Smyth Rd

department: Biochemistry Microbiology and Immunology

country: Canada

institute: University of Ottawa

description: Affy#4487_1.0: biological replicate 1

hyb_protocol: Target cDNA were hybridized to the Mouse Gene 1.0 ST array according to Affymetrix standard protocol (Genechip WT Terminal Labeling and Hybridization Manual Rev.7, Affymetrix). 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: RMA normalization and scaling of data was performed with Affymetrix Expression Console v. 1.2

label: Biotin

label_protocol: Sense strand target cDNA were prepared using the Ambion WT Expression kit (Life Technologies cat# 4411973/4) from 300 ng of total RNA.  Fragmentation and labeling were performed according to the standard Affymetrix protocol from 5.5 ug of cDNA (Genechip WT Terminal Labeling and Hybridization Manual Rev.7, Affymetrix).

growth_protocol: M1 cells (Mouse kidney epithelium; ATCC, CRL-2038) were maintained in minimum essential medium (MEM).  MEM was supplemented with L-glutamine (2 mM), Penicillin (100 U/ml), Streptomycin (100 ug/ml) and fetal bovine serum (FBS) (10%). All cells were incubated at 37°C in the presence of 5% CO2.

extract_protocol: At 8 hpi, the cellular RNA was collected using manufacturer’s protocol (QIAGEN RNeasy mini-kit) quantified using a PowerWave XS2, Microplate Spectrophotometer  (BioTek Instruments, Inc. Winooski, VT, United States).

treatment_protocol: Confluent monolayers of 1.5E6 M1 cells in 35 mm dishes were infected with rHK-wt or rHK NS mutant viruses (MOI = 2) or mock-infected with PBS in triplicate for n=3 biological replicates before overflay with 3 ml  of MEM.

tag: cell line

value: immortal kidney epithilium


title: 38811


title: 5207


title: 36969


title: 1304


title: M1, NS1 V226I 3

description: Affy#4459_1.0: biological replicate 3


title: M1, NS1 R227K 3

description: Affy#4489_1.0: biological replicate 3


title: M1, NS1 V226I 2

description: Affy#4458_1.0: biological replicate 2


title: M1, NS1 V226I 1

description: Affy#4457_1.0: biological replicate 1


title: M1, NS1 V180A 1

description: Affy#4454_1.0: biological replicate 1


title: M1, NS1 R227K 2

description: Affy#4488_1.0: biological replicate 2


title: M1, NS1 V180A 3

description: Affy#4456_1.0: biological replicate 3


title: M1, NS1 M106V/M124I 1

description: Affy#4448_1.0: biological replicate 1


title: M1, NS1 V180A 2

description: Affy#4455_1.0: biological replicate 2


title: M1, NS1 M106V/M124I 3

description: Affy#4450_1.0: biological replicate 3


title: M1, NS1 V23A 2

description: Affy#4425_1.0: biological replicate 2

source_name: M1, NS1 V23A


title: M1, NS1 L98S/M106I 1

description: Affy#4430_1.0: biological replicate 1


title: M1, NS1 D125G 3

description: Affy#4453_1.0: biological replicate 3


title: M1, NS1 D125G 2

description: Affy#4452_1.0: biological replicate 2


title: M1, NS1 L98S/M106I 3

description: Affy#4432_1.0: biological replicate 3


title: M1, NS1 D125G 1

description: Affy#4451_1.0: biological replicate 1


title: M1, NS1 L98S 1

description: Affy#4427_1.0: biological replicate 1

source_name: M1, NS1 L98S


title: M1, NS1 M106V/M124I 2

description: Affy#4449_1.0: biological replicate 2


title: M1, NS1 L98S/M106I 2

description: Affy#4431_1.0: biological replicate 2


title: M1, NS1 V23A 1

description: Affy#4424_1.0: biological replicate 1


title: M1, NS1 V23A 3

description: Affy#4426_1.0: biological replicate 3


title: M1, NS1 L98S 3

description: Affy#4429_1.0: biological replicate 3


title: M1, NS1 L98S 2

description: Affy#4428_1.0: biological replicate 2


title: M1, NS1 D2N 3

description: Affy#4423_1.0: biological replicate 3

source_name: M1, NS1 D2N


title: M1, NS1 D2N 1

description: Affy#4421_1.0: biological replicate 1


title: M1, NS1 M106V 3

description: Affy#4444_1.0: biological replicate 3


title: M1, NS1 M106I 2

description: Affy#4482_1.0: biological replicate 2


title: M1, NS1 F103L 3

description: Affy#4435_1.0: biological replicate 3


title: M1, NS1 F103L/M106I 2

description: Affy#4485_1.0: biological replicate 2


title: M1, NS1 M106V 2

description: Affy#4443_1.0: biological replicate 2


title: M1, NS1 F103L/M106I 1

description: Affy#4484_1.0: biological replicate 1


title: M1, HK-NS1 WT 3

description: Affy#4480_1.0: biological replicate 3

source_name: M1, HK-NS1 WT


title: M1, NS1 F103L 1

description: Affy#4433_1.0: biological replicate 1


title: M1, NS1 M106I 3

description: Affy#4483_1.0: biological replicate 3


title: M1, NS1 M106V 1

description: Affy#4442_1.0: biological replicate 1


title: M1, HK-NS1 WT 2

description: Affy#4479_1.0: biological replicate 2


title: M1, HK-NS1 WT 1

description: Affy#4478_1.0: biological replicate 1


title: M1, NS1 M106I 1

description: Affy#4481_1.0: biological replicate 1


title: M1, NS1 D2N 2

description: Affy#4422_1.0: biological replicate 2


title: liver of NML-KO 3

first: Shohei

last: Oie

address: 1-1-1 tennodai

institute: Tsukuba university

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at 15,000 rpm for 1 minute.  • Transfer 80μl of hyb solution to each array, then tape holes. • Hybridize 17 hours at 45° at 60rpm

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneSpring software. Background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: liver of NML-KO

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse livers dissected from 12 weeks age of WT and NML-KO mice

extract_protocol: Liver tissues were homogenized in 1 ml of Sepazol and total RNA was extracted according to the manufacturer’s instructions (Nacalai tesque).

treatment_protocol: not applicable

value: 12 weeks

value: liver

tag: genotype/variation

value: NML-KO


title: liver of NML-KO 1


title: liver of NML-KO 4


title: M1, NS1 F103L/M106I 3

description: Affy#4486_1.0: biological replicate 3


title: M1, Control (Mock) 2

description: Affy#4476_1.0: biological replicate 2

source_name: M1, Control (Mock)


title: liver of WT4

source_name: liver of WT

value: WT


title: liver of WT3


title: M1, Control (Mock) 1

description: Affy#4475_1.0: biological replicate 1


title: M1, NS1 F103L 2

description: Affy#4434_1.0: biological replicate 2


title: A549, NS1 F103L/M106I 3

description: Affy#4359_1.0: biological replicate 3

hyb_protocol: Target cDNA were hybridized to the Human Gene 1.0 ST array according to Affymetrix standard protocol (Genechip WT Terminal Labeling and Hybridization Manual Rev.7, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

label_protocol: Sense strand target cDNA were prepared using the Ambion WT Expression kit (Life Technologies cat# 4411973/4) from 250 ng of total RNA.  Fragmentation and labeling were performed according to the standard Affymetrix protocol from 5.5 ug of cDNA (Genechip WT Terminal Labeling and Hybridization Manual Rev.7, Affymetrix).

growth_protocol: A549 cells (ATCC) were maintained in minimum essential medium (MEM).  MEM was supplemented with L-glutamine (2 mM), Penicillin (100 U/ml), Streptomycin (100 ug/ml) and fetal bovine serum (FBS) (10%). All cells were incubated at 37°C in the presence of 5% CO2.

treatment_protocol: Confluent monolayers of 1.5E6 A549 cells in 35 mm dishes were infected with rHK-wt or rHK NS mutant viruses (MOI = 2) or mock-infected with PBS in triplicate for n=3 biological replicates before overflay with 3 ml  of MEM fro 8 h at 37 C.

value: lung epithilium


title: liver of NML-KO 5


title: M1, Control (Mock) 3

description: Affy#4477_1.0: biological replicate 3


title: liver of NML-KO 2


title: A549, NS1 F103L/M106I 2

description: Affy#4358_1.0: biological replicate 2


title: liver of WT5


title: A549, NS1 F103L/M106I 1

description: Affy#4357_1.0: biological replicate 1


title: liver of WT1


title: A549, NS1 M106V 2

description: Affy#4355_1.0: biological replicate 2


title: A549, NS1 M106V 1

description: Affy#4354_1.0: biological replicate 1


title: A549, NS1 M106I 1

description: Affy#4351_1.0: biological replicate 1


title: liver of WT2


title: A549, NS1 M106I 2

description: Affy#4352_1.0: biological replicate 2


title: A549, NS1 M106V 3

description: Affy#4356_1.0: biological replicate 3


title: A549, Control (Mock) 3

description: Affy#4344_1.0: biological replicate 3

source_name: A549, Control (Mock)


title: A549, HK-NS1 WT 3

description: Affy#4347_1.0: biological replicate 3

source_name: A549, HK-NS1 WT


title: A549, HK-NS1 WT 1

description: Affy#4345_1.0: biological replicate 1


title: A549, NS1 F103L 1

description: Affy#4348_1.0: biological replicate 1


title: A549, NS1 F103L 3

description: Affy#4350_1.0: biological replicate 3


title: MDA-MB-231 taxol resistant (P-gp)

city: Thousand Oaks

first: Dan

last: Baker

address: 1 Amgen Center Drive

department: Molecular Sciences

institute: Amgen Inc.

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent Feature Extraction software protocol

source_name: taxol-resistant MDA-MB-231 cells

label_protocol: Agilent QuickAmp Low Input Labeling Kit

extract_protocol: Qiagen Rneasy Mini Kit

tag: phenotype

value: taxol resistant

source_name: MDA-MB-231 cells

value: not resistant


title: MDA-MB-231 parental


title: A549, Control (Mock) 2

description: Affy#4343_1.0: biological replicate 2


title: A549, HK-NS1 WT 2

description: Affy#4346_1.0: biological replicate 2


title: A549, NS1 F103L 2

description: Affy#4349_1.0: biological replicate 2


title: A549, Control (Mock) 1

description: Affy#4342_1.0: biological replicate 1


title: 15xG vs 1xG rep3

city: Derby

first: Nathaniel

middle: J

last: Szewczyk

address: Uttoxeter Road

department: MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research

country: United Kingdom

institute: University of Nottingham, Royal Derby Hospital

description:
Simple annotation: C. elegans, Increased gravity
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28574.gif
Physical Characteristics: 15g

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 1 to Channel 2

organism: Caenorhabditis elegans

source_name: mixed stage worms spun at 15 X G, 4d on 20G centrifuge

label_protocol: not provided

extract_protocol: not provided

treatment_protocol: Growing worms in centrifuge; The experiments were mixed stage C. elegans cultures grown in CeMM in tissue culture flasks. The control (red) channel for all three data sets is mixed stage C. elegans cultures. For the experimental channel (green) for all three data sets the experimental condition is G force. All worms were grown in CeMM in tissue culture flasks as mixed stage populations for 4 days. In the case of the control these worms were not placed on the long arm centrifuge at NASA Ames Research Center. In the case of the experimental worms these worms were placed at three different positions on the long arm centrifuge such that the cultures experienced 5x unit gravity, 10x unit gravity, or 15x unit gravity. In each experiment set there are 3 replicates for each G level vs. non centrifuged worms.

tag: culture

value: mixed stage worms

value: spun at 15 X G, 4d on 20G centrifuge

source_name: mixed stage worms 1 X G control

value: 1 X G control


title: 5xG vs 1xG rep3

description:
Simple annotation: C. elegans, Increased gravity
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33747.gif
Physical Characteristics: 5g

source_name: mixed stage worms spun at 5 X G, 4d on 20G centrifuge

value: spun at 5 X G, 4d on 20G centrifuge


title: chlorophenol treatment - rep3

status: Public on Jun 21 2013

city: Lausanne

first: Silvia

middle: K.

last: Moreno-Forero

state: Vaud

address: Batiment Biophore, Unil Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description:
Gene expression after 2 days at 97% relative air humidity on agar surface with 1 mM 4-chlorophenol
Sample name: Agar+4chl3

hyb_protocol: The volume of different samples was adjusted for the hybridization in order to have at least 2 pmol of labelled Cy3 per array on the slide. Sixty ng of labeled cDNA were loaded onto each microarray, hybridized for 17 hours at 65°C, and washed and scanned as described for labeled cRNA in the One-Color Microarray-Based Gene Expression Analysis Manual (Agilent). The fragmentation step (heating to 60°C for 30 minutes) was omitted.

scan_protocol: Microarray slides were scanned using an Agilent High-Resolution Microarray Scanner (G2505), immediately after hybridization using the One-Color microarray -based gene expression analysis protocol provided by Agilent (scan area 61x21.6mm XDRHi:100% XDRLo:10%).

data_processing: Data were normalized by quantile and scaled with the baseline to the median of all samples. All genes were filtered by expression and were retained when the signal intensity was above the 20th percentile in at least one of the samples.

organism: Pseudarthrobacter chlorophenolicus A6

source_name: Arthrobacter chlorophenolicus A6, agar surface + 1mM 4-chlorophenol

label_protocol: An amount of 2-5 µg of RNA was mixed with 1.25 µl random primers (500 µg/ml; Promega) in a total volume of 12 µl and incubated at 70 °C for 10 min followed by 4 °C for 5 min. Each tube received 13 µl of mastermix containing 0.625 µl Cyanine 3-dCTP (1 mM; Perkin-Elmer), 0.625 µl Superase-In (20 U/µl; Ambion), 1 µl Superscript II (200 U/µl; Invitrogen), 5 µl 5x 1st strand buffer, 2.5 µl DTT (100 mM), 0.25 µl dATP-dGTP-dTTP mixture (10 mM each), 0.125 µl dCTP (5 mM) and 2.875 µl nuclease-free water. Labeled cDNA was produced by incubation at 42 °C for 120 min, followed by 70 °C for 10 min and 4 °C for 5 min. RNA was hydrolyzed under alkaline conditions as follows. After the addition of 2.5 µl 1 M NaOH, samples were heated at 65 °C for 20 min, allowed to cool to room temperature for 10 min and neutralized by the addition of 2.5 µl 3 M Na-acetate (pH 5.2) and 2.5 µl 1 M HCl. The labeled cDNA was then purified using the MinElute PCR Purification Kit (Qiagen) according to the manufacturer’s instructions. The product was eluted in 20 µl EB buffer and quantity and incorporation efficiency were determined using the MICROARRAY function on a NanoDrop spectrophotometer (ThermoFisher Scientific, Waltham, MA).

growth_protocol: Arthrobacter chlorophenolicus strain A6 was grown at 28 °C and 250 rpm in Lysogeny broth (LB). At mid-exponential phase, the bacterial culture was centrifuged for 10 min at 3838 ×g. The pellet was resuspended in sterile demineralized water to obtain a bacterial suspension with an optical density at 600 nm (OD600) of 0.15.

extract_protocol: Bacterial pellets were thawed at room temperature and then resuspended in 200 µl TE buffer (30 mM Tris-Cl, 1 mM EDTA, pH 8.0) containing 15 mg of lysozyme and 2 mg of proteinase K per ml. The suspension was incubated at room temperature for 30 min with regular vortexing. Then 700 µl lysis solution of the Biorad Aurum Total RNA Mini Kit (Bio-Rad Laboratories; Veenendaal, The Netherlands) was added and the total volume was transferred to a 2 ml screw cap tube containing 100 mg of 0.1:0.5 mm beads (1:1) (Merlin Bioproducts; Breda, The Netherlands). Tubes were shaken in a Mini-Beadbeater (Biospec Products, Breukelen, The Netherlands) twice for 1 min at 5000 rpm with a 1 min interval on ice. Tubes were centrifuged for 10 sec and the solution without beads was transferred to a fresh tube. After the addition of 500 µl 70% isopropanol, samples were further treated according to the Biorad Aurum Total RNA Mini Kit protocol. Columns were eluted with 80 µl elution buffer. An additional 30 min DNase treatment was performed with Ambion TURBO DNA-free (Applied Biosystems; Nieuwerkerk a/d ijssel, The Netherlands). After the DNase treatment, the RNA was precipitated with 1/10 volume of 7.5 M ammonium acetate (Sigma-Aldrich; Zwijndrecht, The Netherlands), 1/50 volume glycogen (5 mg/ml) (Fermentas; St. Leon-Rot, Germany) and 2.5 volumes of ethanol. RNA pellets were washed with 80% ethanol and resuspended in 12 µl nuclease-free water. RNA quality was verified with Experion RNA StdSens (Bio-Rad Laboratories).

treatment_protocol: Two-week old bean plants (Phaseolus vulgaris, green snap bean, variety Blue Lake Bush 274) with the first two leaves fully expanded were dipped into the bacterial suspension. Five plants were incubated at 97% air humidity for two days in a growth chamber; this was the high humidity phyllosphere treatment. Five other plants were incubated for 1 day at 97% air humidity, followed by a second day at 50% air humidity; this was the low humidity phyllosphere treatment. In addition, 500 µl of bacterial suspension was spread on 1/10 strength Tryptone Soy Agar (TSA; Oxoid, Cambridge, UK) with 15 g agar per liter; this was the agar surface treatment. Another 500 µl was spread on 1/10 strength TSA supplemented with 1 mM 4-chlorophenol; this was the chlorophenol treatment. Both agar treatments were incubated at 97% humidity for two days. The growth chamber maintained a day-night cycle of 16 h and 8 h at 21 °C and 16 °C, respectively. For each treatment, four replications were prepared independently. Bacteria were collected from leaves by sequentially putting five leaves from five different plants in 20 ml RNA protection solution [two parts RNAprotect bacteria reagent (Qiagen; Venlo, The Netherlands) and one part phosphate-buffered saline (PBS)] with 5 sec vortexing, 7 min sonication and 5 sec vortexing for each leaf. The solution was centrifuged for 20 min at 3838 × g and bacterial pellets were frozen at -80 °C until RNA extraction. Bacteria from agar plates were washed from the surface with 1 ml RNAprotect solution according to the manufacturer’s instructions (Qiagen) and frozen at -80 °C until RNA extraction.

tag: growth medium

value: agar surface + 1 mM 4-chlorophenol

tag: humidity


title: chlorophenol treatment - rep4

description:
Gene expression after 2 days at 97% relative air humidity on agar surface with 1 mM 4-chlorophenol
Sample name: Agar+4chl4


title: 5XG vs 1xG rep2

description:
Simple annotation: C. elegans, Increased gravity
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28572.gif
Physical Characteristics: 5g

tag: treatment


title: chlorophenol treatment - rep2

description:
Gene expression after 2 days at 97% relative air humidity on agar surface with 1 mM 4-chlorophenol
Sample name: Agar+4chl2


title: 10xG vs 1xG rep3

description:
Simple annotation: C. elegans, Increased gravity
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26102.gif
Physical Characteristics: 10g

source_name: mixed stage worms spun at 10 X G, 4d on 20G centrifuge

value: spun at 10 X G, 4d on 20G centrifuge


title: agar surface treatment - rep4

description:
Gene expression after 2 days at 97% relative air humidity on agar surface
Sample name: Agar4

source_name: Arthrobacter chlorophenolicus A6, agar surface

value: agar surface


title: chlorophenol treatment - rep1

description:
Gene expression after 2 days at 97% relative air humidity on agar surface with 1 mM 4-chlorophenol
Sample name: Agar+4chl1


title: 5xG vs 1xG rep1

description:
Simple annotation: C. elegans, Increased gravity
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26098.gif
Physical Characteristics: 5g


title: 10xG,vs 1xG rep1

description:
Simple annotation: C. elegans, Increased gravity
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31434.gif
Physical Characteristics: 10g


title: agar surface treatment - rep2

description:
Gene expression after 2 days at 97% relative air humidity on agar surface
Sample name: Agar2


title: agar surface treatment - rep1

description:
Gene expression after 2 days at 97% relative air humidity on agar surface
Sample name: Agar1


title: low humidity phyllosphere treatment - rep2

description:
Gene expression after 1 day at 97% and 1 day at 50% relative air humidity in bean phyllosphere
Sample name: Low-Phy2

source_name: Arthrobacter chlorophenolicus A6, low humidity phyllosphere

value: bean phyllosphere


title: low humidity phyllosphere treatment - rep1

description:
Gene expression after 1 day at 97% and 1 day at 50% relative air humidity in bean phyllosphere
Sample name: Low-Phy1


title: low humidity phyllosphere treatment - rep4

description:
Gene expression after 1 day at 97% and 1 day at 50% relative air humidity in bean phyllosphere
Sample name: Low-Phy4


title: low humidity phyllosphere treatment - rep3

description:
Gene expression after 1 day at 97% and 1 day at 50% relative air humidity in bean phyllosphere
Sample name: Low-Phy3


title: 15xG vs 1xG rep1

description:
Simple annotation: C. elegans, Increased gravity
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26100.gif
Physical Characteristics: 15g


title: high humidity phyllosphere treatment - rep4

description:
Gene expression after 2 days at 97% relative air humidity in bean phyllosphere
Sample name: High-Phy4

source_name: Arthrobacter chlorophenolicus A6, high humidity phyllosphere