title: GES-1 cells_noninfected_24h_rep3

city: Zhen Jiang

first: Hong

last: ZHU

state: Jiang Su

address: No.301,Xue Fu Road, Jing Kou District

institute: Jiangsu University

description: Coding and non-coding gene expression data of GES-1 cells from control group 3.

hyb_protocol: After fragmentation, samples were hybridized in GeneChip® Hybridization Oven 645 according to the user manual of GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: After the wash protocols completing, the probe arrays were scanned by using the GeneChip® Scanner 3000 7G according to instructions for scanning probe arrays.

data_processing: The data were analyzed with Affymetrix Expression Console™ Software (version 1.3).

source_name: Human gastric epithelial cell

label_protocol: Biotinylated samples were prepared according to the user manual of GeneChip® WT Terminal Labeling Kit.

growth_protocol: GES-1 cells were maintained in humidified air with 5% CO2 at 37°C before use.

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

treatment_protocol: GES-1 cells were seeded in six-well cell culture plates before treated. The following day, 80% confluent monolayer cells were washed in PBS, and the medium was replaced with fresh medium. Then, H.pylori was added to cells for 24 hours at a multiplicity of infection (MOI) of 100 as experimental groups. Cells without H.pylori infection were maintained for indicated time periods as control groups. After 24hr-infection, cells were washed in PBS to wash away the non-adherent H.pylori, then harvested in Trizol reagent and preserved at -80°C until RNA isolation.

value: Human gastric epithelial cell, GES-1 cell line


title: stimulated subject 120_control

status: Public on Nov 03 2015

type: RNA

city: Munich

first: Janine

last: Arloth

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description:
subject 120
Sample 189

hyb_protocol: Biotin-labeled, amplified material was hybridized to Illumina Human-HT-12 v3 and v4 BeadChips, according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA; 11322355 Rev. A, 11286331 Rev. A).

scan_protocol: Microarrays were scanned on the Illumina Bead Array Reader (Illumina, Inc., San Diego, CA) with default outlier detection according to the manufacturer's instructions and summarized raw probe intensities were exported using Illumina’s GenomeStudio.

data_processing:
Microarray expression analysis was performed in R (http://www.r-project.org/). All 29,075 probes present on both microarrays (excluding X and Y chromosomes as well as cross-hybridizing probes) were first filtered by an Illumina detection P value of 0.05 in at least 50% of the samples, leaving 11,994 expressed probes for further analysis. Subsequently, each transcript was transformed and normalized through variance stabilization and normalization (VSN). Filtered data was controlled for confounding by batch effects or unknown factors using Surrogate Variable Analysis with the sva package in Bioconductor.
Raw and processed data are available on the series record. Processed data contains the VSN normalized and transformed signal.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Sample labeling was performed using the Illumina TotalPrep RNA Amplification Kit (Ambion, TX, USA) according to the manufacturer's instructions.

extract_protocol: RNA was extracted from whole blood collected in PAXgene Blood RNA tubes using the PAXgene Blood RNA Kit (PreAnalytiX GmbH, Hombrechtikon, Switzerland).

tag: tissue

value: whole blood

tag: gender

value: male

tag: stimulus

value: stimulated

tag: sample type

value: control


title: GES-1 cells_hp26695_24h_rep1

country: China

description: Coding and non-coding gene expression data of GES-1 cells from H.pylori-infected group 1.

tag: cell type


title: GES-1 cells_noninfected_24h_rep2

description: Coding and non-coding gene expression data of GES-1 cells from control group 2.


title: Baseline subject 34

type: genomic

description:
Sample name: Sample 66
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

hyb_protocol: Standard Illumina protocol, HumanMethylation450.

scan_protocol: Standard Illumina protocol, BeadStudio.

data_processing: Microarray methylation analysis was performed in R (http://www.r-project.org/). Quality control of methylation data, including intensity read outs, filtering (detection p-value > 0.01 in at least 75% of the samples), cellular composition estimation, as well as beta and M-value calculation were done using the minfi Bioconductor R package version 1.10.2. Filtered beta values were reduced by eliminating any CpG sites on sex chromosomes, as well as probes found to have SNPs at the CpG site itself or in the single-base extension site with a MAF ≥ 1% in the 1,000 Genomes Project European population and/or non-specific binding probes according to 4. Additionally, we performed a re-alignment of the array probe sequences using Bismark. This yielded a total of 425,883 CpG sites for further analysis. The data were then normalized with functional normalization. Technical batch effects were identified by inspecting the association of the first principal components of the methylation levels with processing (experiment) date as technical batch. The data were then adjusted using ComBat.

molecule: genomic DNA

source_name: whole blood, control, baseline

extract_protocol: Invitrogen Puregene Genomic DNA kit.

tag: subject

tag: disease state

value: female

tag: age

tag: dna methylation-predicted age

tag: treatment

value: baseline

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes

tag: granulocytes


title: Stimulated subject 23

description:
Sample name: Sample 45
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

source_name: whole blood, control, stimulated

label_protocol: Standard Illumina protocol, HumanMethylation450.

value: dexamethasone stimulated


title: stimulated subject 133_control

description:
subject 133
Sample 188


title: Stimulated subject 63

description:
Sample name: Sample 123
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

source_name: whole blood, case, stimulated

value: major depressive disorder


title: parental PANC-1_biological  p23_1

city: Muenster

first: Sameer

last: Dhayat

address: Albert-Schweitzer-Campus 1 ( W1)

institute: Comprehensive Cancer Center Muenster

hyb_protocol: The original manufacturer´s (Affymetrix/Genisphere) protocol (FlashTag  Biotin HSR RNA) was used.

scan_protocol: The Affymetrix GeneChip System Scanner 3000 7G and the recommended scanning procedure für the performed arrays were used.

data_processing:
Partek´s Genomics Suite, miRNA workflow
Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish

source_name: PANC-1 without gemcitabine treatment

growth_protocol: PANC-1 cells were cultured in phenol red free Dulbecco's Modified Eagle Medium (DMEM; Lonza, Walkersville, USA) supplemented with 10% heat inactivated fetal calf serum (Gibco, Carlsbad, USA), 2mM L-glutamine (Gibco), and 1mM sodium pyruvate (Sigma, St. Louis, USA) in a humidified incubator containing 95% air and 5% CO2 at 37°C.

extract_protocol: Total RNA was isolated from parental and chemoresistant PDAC cell lines using Trizol reagent (Qiagen, Hilden, Germany) and miRNeasy Mini Kits (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Gemcitabine-resistant PANC-1 (PANC-1-GR) cell clones were produced by exposing the parental cells to repeated pulsatile gemcitabine treatment over 3 days with constant sublethal concentrations followed by recovery-periods with agent-free medium until the cells recovered exponentially. Parental PANC-1 cells were treated with 0.4µM gemcitabine cycles for approximately 9 months.

tag: cell line background

value: mutant p53 human pancreatic adenocarcinoma cell line

tag: cell clone

tag: cell subtype

value: Gemcitabine-resistant variants of PANC-1

tag: treated with

tag: morphology

value: spindle-shaped cells


title: Stimulated subject 73

description:
Sample name: Sample 142
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: tissue

tag: gender


title: baseline subject 133_control

description:
subject 133
Sample 187

tag: stimulus

tag: sample type


title: parental PANC-1_biological  p23_3

label_protocol: The original manufacturer´s (Affymetrix/Genisphere) protocol (FlashTag  Biotin HSR RNA) was used.

tag: cell type


title: GES-1 cells_noninfected_24h_rep1

description: Coding and non-coding gene expression data of GES-1 cells from control group 1.


title: GES-1 cells_hp26695_24h_rep3

description: Coding and non-coding gene expression data of GES-1 cells from H.pylori-infected group 3.


title: GES-1 cells_hp26695_24h_rep2

description: Coding and non-coding gene expression data of GES-1 cells from H.pylori-infected group 2.


title: stimulated subject 128_control

description:
subject 128
Sample 186


title: baseline subject 210_control

description:
subject 210
Sample 191


title: Baseline subject 23

description:
Sample name: Sample 44
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: subject

tag: disease state

tag: age

tag: dna methylation-predicted age

tag: treatment


title: stimulated subject 213_control

description:
subject 213
Sample 180


title: Stimulated subject 47

description:
Sample name: Sample 92
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer cells

tag: b cells

tag: monocytes


title: baseline subject 128_control

description:
subject 128
Sample 185


title: Baseline subject 80

description:
Sample name: Sample 157
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.

source_name: whole blood, case, baseline

tag: granulocytes


title: baseline subject 213_control

description:
subject 213
Sample 179


title: Baseline subject 47

description:
Sample name: Sample 93
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 11_control

description:
subject 11
Sample 182


title: stimulated subject 205_control

description:
subject 205
Sample 178


title: baseline subject 11_control

description:
subject 11
Sample 181


title: Stimulated subject 80

description:
Sample name: Sample 156
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 205_control

description:
subject 205
Sample 177


title: Baseline subject 52

description:
Sample name: Sample 100
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 110_control

description:
subject 110
Sample 176


title: Stimulated subject 52

description:
Sample name: Sample 101
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 24

description:
Sample name: Sample 47
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 110_control

description:
subject 110
Sample 175


title: Baseline subject 24

description:
Sample name: Sample 46
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 79_control

description:
subject 79
Sample 173


title: Baseline subject 76

description:
Sample name: Sample 149
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 79_control

description:
subject 79
Sample 174


title: stimulated subject 200_control

description:
subject 200
Sample 172


title: Stimulated subject 76

description:
Sample name: Sample 148
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 105_control

description:
subject 105
Sample 170


title: baseline subject 200_control

description:
subject 200
Sample 171


title: Stimulated subject 32

description:
Sample name: Sample 63
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 6

description:
Sample name: Sample 11
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 6

description:
Sample name: Sample 12
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 104_control

description:
subject 104
Sample 167


title: Baseline subject 32

description:
Sample name: Sample 62
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 105_control

description:
subject 105
Sample 169


title: Stimulated subject 22

description:
Sample name: Sample 43
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 9_control

description:
subject 9
Sample 165


title: Stimulated subject 55

description:
Sample name: Sample 106
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 104_control

description:
subject 104
Sample 168


title: Baseline subject 55

description:
Sample name: Sample 107
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 211_control

description:
subject 211
Sample 164


title: Stimulated subject 29

description:
Sample name: Sample 57
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 9_control

description:
subject 9
Sample 166


title: baseline subject 211_control

description:
subject 211
Sample 163


title: stimulated subject 135_control

description:
subject 135
Sample 162


title: baseline subject 135_control

description:
subject 135
Sample 161


title: Baseline subject 41

description:
Sample name: Sample 81
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 41

description:
Sample name: Sample 80
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 2

description:
Sample name: Sample 4
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 29

description:
Sample name: Sample 56
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 2

description:
Sample name: Sample 3
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 122_control

description:
subject 122
Sample 159


title: stimulated subject 122_control

description:
subject 122
Sample 160


title: Baseline subject 50

description:
Sample name: Sample 98
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Stimulated subject 50

description:
Sample name: Sample 97
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 22

description:
Sample name: Sample 42
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 30_control

description:
subject 30
Sample 155


title: Stimulated subject 3

description:
Sample name: Sample 6
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: Baseline subject 3

description:
Sample name: Sample 5
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 95_control

description:
subject 95
Sample 153


title: stimulated subject 95_control

description:
subject 95
Sample 154


title: stimulated subject 10_control

description:
subject 10
Sample 152


title: Baseline subject 43

description:
Sample name: Sample 85
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: baseline subject 10_control

description:
subject 10
Sample 151


title: Stimulated subject 43

description:
Sample name: Sample 84
Blood cell counts in the characteristics field are the predicted blood cell count compositions based on the Houseman prediction algorithm.


title: stimulated subject 103_control

description:
subject 103
Sample 150


title: baseline subject 103_control

description:
subject 103
Sample 149


title: baseline subject 57_control

description:
subject 57
Sample 147


title: stimulated subject 30_control

description:
subject 30
Sample 156


title: stimulated subject 57_control

description:
subject 57
Sample 148


title: stimulated subject 130_control

description:
subject 130
Sample 146


title: baseline subject 130_control

description:
subject 130
Sample 145


title: PB_300ppm_PB_38A

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

country: USA

institute: US EPA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

organism: Mus musculus

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

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

tag: strain

tag: exposed to

value: 300ppm phenobarbital (PB)

value: liver


title: PB_600ppm_PB_23A

tag: gender

value: 600ppm phenobarbital (PB)

tag: tissue


title: PB_300ppm_PB_15A


title: PB_600ppm_PB_23B


title: stimulated subject 84_control

description:
subject 84
Sample 144

tag: stimulus

tag: sample type


title: baseline subject 84_control

description:
subject 84
Sample 143


title: stimulated subject 102_control

description:
subject 102
Sample 142


title: PB_300ppm_PB_15B


title: PB_150ppm_PB_89B

value: 150ppm phenobarbital (PB)


title: PB_600ppm_PB_98C


title: PB_300ppm_PB_38C


title: PB_600ppm_PB_98B


title: baseline subject 102_control

description:
subject 102
Sample 141


title: PB_150ppm_PB_89C


title: stimulated subject 99_control

description:
subject 99
Sample 140


title: baseline subject 99_control

description:
subject 99
Sample 139


title: PB_150ppm_PB_2C


title: stimulated subject 63_control

description:
subject 63
Sample 136


title: stimulated subject 141_control

description:
subject 141
Sample 126


title: baseline subject 63_control

description:
subject 63
Sample 135


title: PB_75ppm_PB_20B

value: 75ppm phenobarbital (PB)


title: PB_75ppm_PB_20C


title: stimulated subject 23_control

description:
subject 23
Sample 124


title: evt_rep5

city: Melbourne

first: Daniel

middle: Glyn

last: Hurley

address: Level 4, Bldg 193, EEE

department: Systems Biology Laboratory

country: Australia

institute: The University of Melbourne

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

scan_protocol: GeneChips were scanned using the Affymetrix Command Console software v3.2

data_processing: Data was RMA-normalised following background correction and log-transformation.  The ‘limma’ package in the statistical language R was used to assess the evidence for differential abundance of RNA transcripts between each of the three cell types (EVT, CTP and SP).   A blocked analysis was performed to correct for within-patient variance.  Benjamini-Hochberg false-discovery rate control (FDR) was used to adjust p-values for differential expression.

label_protocol: Purified cDNA was biotin-labelled and hybridised to Affymetrix PrimeView microarrays (Affymetrix, California) according to the manufacturer's instructions

extract_protocol: RNA was extracted using the Invitrogen PureLink mini-kit (Life Technologies, California) according to the manufacturer's instructions.  RNA quality was assessed using Experion RNA HighSens chips (Biorad, Auckland) according to the manufacturer’s instructions. RNA was converted to cDNA and amplified using a NuGEN Ovation Pico WTA system V2 kit according to the manufacturer’s instructions.

value: placenta

tag: cell type

value: extravillous trophoblast

value: e

tag: placental_gestation (weeks)


title: baseline subject 23_control

description:
subject 23
Sample 123

value: whole blood

value: male


title: PB_75ppm_PB_13B


title: baseline subject 141_control

description:
subject 141
Sample 125

value: control


title: DEHP_6K_DEHP2_8C

value: 6K di(2-ethylhexyl) phthalate (DEHP)


title: DEHP_6K_DEHP3_44A


title: PB_150ppm_PB_2B


title: PB_75ppm_PB_13C


title: DEHP_3K_DEHP3_71A

value: 3K di(2-ethylhexyl) phthalate (DEHP)


title: evt_rep4

value: d


title: stimulated subject 19_control

description:
subject 19
Sample 122

value: stimulated


title: DEHP_6K_DEHP4_64C


title: evt_rep3

value: c


title: DEHP_3K_DEHP4_35A


title: evt_rep2

value: b


title: baseline subject 19_control

description:
subject 19
Sample 121

value: baseline


title: DEHP_3K_DEHP2_67C

value: liver


title: stimulated subject 29_control

description:
subject 29
Sample 120


title: baseline subject 29_control

description:
subject 29
Sample 119


title: HDM sensitized atopic subject # AN31 HDM stimulated

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

institute: Telethon Kids Institute

hyb_protocol: The samples were hybridized to Human Gene ST1.0 microarrays according to standard Affymetrix protocols. This was performed by at the Ramaciotti Centre for Genomics, The University of New South Wales.

scan_protocol: The samples were scanned on an Affymetrix scanner according to standard Affymetrix protocols at the Ramaciotti Centre for Genomics, The University of New South Wales.

data_processing: The microarray data was preprocessed in R employing the RMA algorithm and a custom chip description file (hugene10st_Hs_ENTREZG, v19). ComBat was used to adjust the data for batch effects.

label: Biotin

source_name: CD4 T cells isolated from PBMC

label_protocol: The samples were labelled using standardized kits from Affymetrix at the Ramaciotti Centre for Genomics, The University of New South Wales.

growth_protocol: PBMC were cultured in AIM-V medium.

extract_protocol: Total RNA was extracted employing TRIzol followed by RNeasy.

treatment_protocol:
PBMC were cultured in medium alone or in the presence of HDM extract (10 ug/ml).
At the termination of the cultures, CD4 T cells were isolated using immunomagnetic separation.

tag: cell population

value: CD4 T cell

tag: igg


title: stimulated subject 31_control

description:
subject 31
Sample 118


title: DEHP_1.5K_3A

value: 1.5K di(2-ethylhexyl) phthalate (DEHP)


title: HDM sensitized atopic subject # AN32 medium control


title: evt_rep1

value: a


title: baseline subject 31_control

description:
subject 31
Sample 117


title: DEHP_1.5K_40A


title: HDM sensitized atopic subject # AN32 HDM stimulated


title: stimulated subject 26_control

description:
subject 26
Sample 114


title: baseline subject 26_control

description:
subject 26
Sample 113


title: DEHP_1.5K_72B


title: DEHP_0.75K_5A

value: 0.75K di(2-ethylhexyl) phthalate (DEHP)


title: DEHP_6K_DEHP1_29B


title: DEHP_1.5K_60A


title: DEHP_3K_DEHP1_9A


title: stimulated subject 15_control

description:
subject 15
Sample 110


title: DEHP_0.75K_16C


title: HDM sensitized atopic subject # AN30 medium control


title: HDM sensitized atopic subject # AN29 HDM stimulated


title: DEHP_0.75K_30A


title: HDM sensitized atopic subject # AN28 HDM stimulated


title: stimulated subject 129_control

description:
subject 129
Sample 108


title: HDM sensitized atopic subject # AN29 medium control


title: HDM sensitized atopic subject # AN30 HDM stimulated


title: baseline subject 129_control

description:
subject 129
Sample 107


title: DNOP_10K_DNOP4_27A

value: 10K_di-n-octyl phthalate (DNOP)


title: HDM sensitized atopic subject # AN31 medium control


title: DEHP_0.75K_61A


title: stimulated subject 94_control

description:
subject 94
Sample 106


title: HDM sensitized atopic subject # AN28 medium control


title: baseline subject 94_control

description:
subject 94
Sample 105


title: baseline subject 15_control

description:
subject 15
Sample 109


title: DNOP_10K_DNOP1_92A


title: stimulated subject 28_control

description:
subject 28
Sample 104


title: DNOP_5K_DNOP4_90D

value: 5K_di-n-octyl phthalate (DNOP)


title: HDM sensitized atopic subject # AN27 HDM stimulated


title: baseline subject 28_control

description:
subject 28
Sample 103

value: whole blood


title: DNOP_5K_DNOP3_24B

value: male


title: HDM sensitized atopic subject # AN27 medium control


title: stimulated subject 132_control

description:
subject 132
Sample 100

value: control


title: DNOP_10K_DNOP2_14B


title: HDM sensitized atopic subject # AN26 medium control


title: HDM sensitized atopic subject # AN25 HDM stimulated


title: baseline subject 132_control

description:
subject 132
Sample 99


title: DNOP_2.5K_48A

value: 2.5K_di-n-octyl phthalate (DNOP)


title: HDM sensitized atopic subject # AN25 medium control


title: baseline subject 83_control

description:
subject 83
Sample 97

value: female


title: baseline subject 125_control

description:
subject 125
Sample 95


title: HDM sensitized atopic subject # AN26 HDM stimulated


title: HDM sensitized atopic subject # AN23 HDM stimulated


title: HDM sensitized atopic subject # AN24 medium control


title: HDM sensitized atopic subject # AN24 HDM stimulated


title: DNOP_5K_DNOP2_58B


title: stimulated subject 24_control

description:
subject 24
Sample 94


title: DNOP_5K_DNOP1_39A


title: HDM sensitized atopic subject # AN21 HDM stimulated


title: baseline subject 24_control

description:
subject 24
Sample 93


title: DNOP_1.25K_91A

value: 1.25K_di-n-octyl phthalate (DNOP)


title: DNOP_1.25K_31B


title: DNOP_2.5K_51A


title: HDM sensitized atopic subject # AN23 medium control


title: HDM sensitized atopic subject # AN21 medium control


title: HDM sensitized atopic subject # AN20 medium control


title: stimulated subject 106_control

description:
subject 106
Sample 92

value: stimulated


title: HDM sensitized atopic subject # AN20 HDM stimulated


title: DNOP_2.5K_42A


title: HDM sensitized atopic subject # AN19 HDM stimulated


title: DNOP_2.5K_85B

description: 2.5K _DNOP2_REP2_85B

value: 2.5KK_di-n-octyl phthalate (DNOP)


title: DNOP_1.25K_55A


title: DNOP_1.25K_76B


title: BBP_12K_87A

value: 12K BBPn-butyl benzyl phthalate (BBP)


title: HDM sensitized atopic subject # AN19 medium control


title: BBP_12K_56D


title: baseline subject 106_control

description:
subject 106
Sample 91

value: baseline


title: stimulated subject 127_control

description:
subject 127
Sample 90


title: baseline subject 127_control

description:
subject 127
Sample 89


title: HDM sensitized atopic subject # AN17 HDM stimulated


title: stimulated subject 72_control

description:
subject 72
Sample 86


title: baseline subject 72_control

description:
subject 72
Sample 85


title: baseline subject 81_control

description:
subject 81
Sample 79


title: stimulated subject 140_control

description:
subject 140
Sample 78


title: BBP_6K_34C

value: 6K BBPn-butyl benzyl phthalate (BBP)

value: liver


title: HDM sensitized atopic subject # AN16 HDM stimulated

value: CD4 T cell


title: BBP_6K_86D


title: HDM sensitized atopic subject # AN15 HDM stimulated


title: HDM sensitized atopic subject # AN15 medium control


title: BBP_12K_22A


title: HDM sensitized atopic subject # AN16 medium control


title: baseline subject 140_control

description:
subject 140
Sample 77


title: HDM sensitized atopic subject # AN17 medium control


title: BBP_6K_81B


title: stimulated subject 81_control

description:
subject 81
Sample 80


title: HDM sensitized atopic subject # AN14 HDM stimulated


title: HDM sensitized atopic subject # AN11 HDM stimulated


title: HDM sensitized atopic subject # AN14 medium control


title: BBP_6K_57B


title: BBP_3K_94C

value: 3K BBPn-butyl benzyl phthalate (BBP)


title: HDM sensitized atopic subject # AN07 HDM stimulated


title: BBP_12K_25C


title: BBP_1.5K_69A

value: 1.5K ppm n-butyl benzyl phthalate (BBP)


title: HDM sensitized atopic subject # AN07 medium control


title: baseline subject 25_control

description:
subject 25
Sample 75


title: BBP_1.5K_17A


title: stimulated subject 138_control

description:
subject 138
Sample 72


title: stimulated subject 25_control

description:
subject 25
Sample 76


title: baseline subject 138_control

description:
subject 138
Sample 71


title: BBP_3K_78C

description: 3K_BBP2 _REP2_78C


title: stimulated subject 77_control

description:
subject 77
Sample 70


title: baseline subject 77_control

description:
subject 77
Sample 69


title: HDM sensitized atopic subject # AN06 HDM stimulated


title: cont_12D_PB

value: phenobarbital control (PB)


title: baseline subject 126_control

description:
subject 126
Sample 67


title: BBP_1.5K_47A

description: 1.5K_BBP1 _REP1_47A


title: HDM sensitized atopic subject # AN06 medium control


title: HDM sensitized atopic subject # AN05 HDM stimulated


title: baseline subject 75_control

description:
subject 75
Sample 65


title: HDM sensitized atopic subject # AN05 medium control


title: cont_82B_PB


title: stimulated subject 126_control

description:
subject 126
Sample 68


title: Leucocytes_MS patient in remission_rep23

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

hyb_protocol: GeneChip Hybridization, Wash and Stain kit was used for hybridization in a GeneChip Hybridization oven 640 and in a GeneChip Fluidics Station 450 using the protocol FS450-0003, as explained in the protocol provided by Affymetrix.

scan_protocol: Arrays were scanned in a GeneChip 7G scanner and analysed in Affymetrix GeneChip Command Console Scan Control v4.0.0.1567.

data_processing: Quality control, summarization and normalization of the data were performed with miRNA QC Tool v.1.0.33.0 following the following workflow: Background detection, RMA Global Background correction, Quantile normalization and summarization with median polish.

source_name: MS remission

label_protocol: Total RNA was labeled using FlashTag Biotin HSR RNA labeling kit (Genisphere)

extract_protocol: LeucoLOCK Total RNA isolation system with the alternative protocol to recover small RNA fraction (ThermoFisher)

value: leucocytes

tag: disease state

value: MS remission

tag: age


title: HDM sensitized atopic subject # AN04 medium control


title: HDM sensitized atopic subject # AN04 HDM stimulated


title: HDM sensitized atopic subject # AN02 HDM stimulated


title: BBP_1.5K_10B

value: male


title: cont_41A_PB


title: cont_12C_PB


title: stimulated subject 142_control

description:
subject 142
Sample 64

value: whole blood

value: control


title: Leucocytes_MS patient in remission_rep22


title: cont_75A_Phth

value: phthate control (CPTH)


title: stimulated subject 125_control

description:
subject 125
Sample 96


title: HDM sensitized atopic subject # AN02 medium control


title: Leucocytes_MS patient in remission_rep24


title: stimulated subject 75_control

description:
subject 75
Sample 66


title: cont_75C_Phth

description: 0ppm_CPTH4 _REP4_75C


title: HDM sensitized atopic subject # AN01 HDM stimulated


title: Leucocytes_MS patient in remission_rep20

value: female


title: Leucocytes_MS patient in remission_rep21


title: cont_75D_Phth


title: baseline subject 65_control

description:
subject 65
Sample 61


title: stimulated subject 65_control

description:
subject 65
Sample 62

value: stimulated


title: cont_63A_Phth


title: cont_63B_Phth


title: HDM sensitized atopic subject # AA31 HDM stimulated


title: stimulated subject 60_control

description:
subject 60
Sample 56


title: cont_45C_Phth

description: 0ppm_CPTH2 _REP2_45C


title: baseline subject 60_control

description:
subject 60
Sample 55


title: stimulated subject 6_control

description:
subject 6
Sample 54


title: baseline subject 142_control

description:
subject 142
Sample 63


title: HDM sensitized atopic subject # AN01 medium control


title: HDM sensitized atopic subject # AA31 medium control


title: baseline subject 6_control

description:
subject 6
Sample 53


title: Leucocytes_MS patient in remission_rep17


title: cont_45D_Phth

description: 0ppm_CPTH2 _REP2_45D


title: stimulated subject 209_control

description:
subject 209
Sample 52


title: Leucocytes_MS patient in remission_rep18


title: Leucocytes_MS patient in remission_rep14


title: Leucocytes_MS patient in remission_rep13


title: BBP_3K_96B


title: HDM sensitized atopic subject # AA29 HDM stimulated


title: cont_32C_Phth

description: 0ppm_CPTH1 _REP1_32C


title: HDM sensitized atopic subject # AA30 HDM stimulated


title: stimulated subject 83_control

description:
subject 83
Sample 98


title: Leucocytes_MS patient in remission_rep15


title: baseline subject 209_control

description:
subject 209
Sample 51


title: cont_32B_Phth

description: 0ppm_CPTH1 _REP1_32B


title: Leucocytes_MS patient in remission_rep19


title: Leucocytes_MS patient in remission_rep16


title: BBP_3K_66C


title: HDM sensitized atopic subject # AA29 medium control


title: cont_32A_Phth


title: HDM sensitized atopic subject # AA30 medium control


title: parental PANC-1_biological  p29_3

description: MicroRNA data expression from parental PANC-1 cells

growth_protocol: PANC-1 and MIA-PaCa-2 cells were cultured in phenol red free Dulbecco's Modified Eagle Medium (DMEM; Lonza, Walkersville, USA) supplemented with 10% heat inactivated fetal calf serum (Gibco, Carlsbad, USA), 2mM L-glutamine (Gibco), and 1mM sodium pyruvate (Sigma, St. Louis, USA) in a humidified incubator containing 95% air and 5% CO2 at 37°C. The medium for MIA-PaCa-2 cells was also supplemented by 2% heat inactivated horse serum (Gibco).

treatment_protocol: Gemcitabine-resistant PANC-1 (PANC-1-GR) and MIA-PaCa-2 (MIA-PaCa-2-GR) cell clones were produced by exposing the parental cells to repeated pulsatile gemcitabine treatment over 3 days with constant sublethal concentrations followed by recovery-periods with agent-free medium until the cells recovered exponentially. Parental PANC-1 cells were treated with 0.4µM gemcitabine cycles for approximately 9 months. Parental MIA-PaCa-2 cells were exposed to 0.06µM gemcitabine cycles for approximately 12 months.

tag: cell line background

value: mutant p53 human pancreatic adenocarcinoma cell line

tag: cell clone

tag: cell subtype

value: Gemcitabine-resistant variants of PANC-2

tag: morphology

value: spindle-shaped cells

tag: treated with

value: PANC-1 without gemcitabine treatment


title: parental PANC-1_biological  p29_2


title: baseline subject 85_control

description:
subject 85
Sample 49

value: baseline


title: parental PANC-1_biological  p29_1


title: HDM sensitized atopic subject # AA27 HDM stimulated

value: CD4 T cell


title: stimulated subject 82_control

description:
subject 82
Sample 48


title: baseline subject 82_control

description:
subject 82
Sample 47


title: Leucocytes_MS patient in remission_rep11


title: Leucocytes_MS patient in remission_rep12


title: Leucocytes_MS patient in remission_rep10


title: Leucocytes_MS patient in remission_rep7


title: HDM sensitized atopic subject # AA26 medium control


title: HDM sensitized atopic subject # AA27 medium control


title: HDM sensitized atopic subject # AA25 HDM stimulated


title: stimulated subject 86_control

description:
subject 86
Sample 46


title: stimulated subject 85_control

description:
subject 85
Sample 50


title: baseline subject 86_control

description:
subject 86
Sample 45


title: Leucocytes_MS patient in remission_rep8


title: Gemcitabine-resistant PANC-1_biological  p29_3

description: MicroRNA data expression from gemcitabine-resistant PANC-1 cell clones

source_name: PANC-1 with 29 cycles gemcitabine treatment

value: plump rounded morphology and enhanced formation of pseudopodia

value: 29 cycles gemcitabine treatment


title: Gemcitabine-resistant PANC-1_biological  p29_1


title: stimulated subject 59_control

description:
subject 59
Sample 44


title: Leucocytes_MS patient in remission_rep9


title: HDM sensitized atopic subject # AA26 HDM stimulated


title: Mia-PaCa-2_biological  p29_2

description: MicroRNA data expression from parental MIA-PaCa-2 cells

source_name: Mia-PaCa-2 without gemcitabine treatment

value: Gemcitabine-resistant variants of PANC-1


title: HDM sensitized atopic subject # AA25 medium control


title: Leucocytes_MS patient in remission_rep6

value: leucocytes


title: Gemcitabine-resistant PANC-1_biological  p29_2


title: baseline subject 59_control

description:
subject 59
Sample 43


title: HDM sensitized atopic subject # AA24 medium control


title: Mia-PaCa-2_biological  p29_3

value: Mia-PaCa-2 without gemcitabine treatment


title: baseline subject 80_control

description:
subject 80
Sample 42


title: Leucocytes_MS patient in remission_rep5

value: MS remission


title: HDM sensitized atopic subject # AA24 HDM stimulated


title: HDM sensitized atopic subject # AA23 HDM stimulated


title: HDM sensitized atopic subject # AN11 medium control


title: Gemcitabine-resistant Mia-PaCa-2_biological  p29_3

description: MicroRNA data expression from gemcitabine-resistant MIA-PaCa-2 cell clones

source_name: Mia-PaCa-2 with 29 cycles gemcitabine treatment


title: Mia-PaCa-2_biological  p29_1


title: stimulated subject 56_control

description:
subject 56
Sample 40

value: whole blood

value: male


title: stimulated subject 80_control

description:
subject 80
Sample 41

value: control


title: Gemcitabine-resistant Mia-PaCa-2_biological  p29_2


title: baseline subject 56_control

description:
subject 56
Sample 39


title: baseline subject 208_control

description:
subject 208
Sample 37


title: stimulated subject 208_control

description:
subject 208
Sample 38


title: Leucocytes_MS patient in remission_rep3

value: female


title: HDM sensitized atopic subject # AA23 medium control


title: Leucocytes_MS patient in remission_rep2


title: Leucocytes_MS patient in remission_rep4


title: Leucocytes_MS patient in remission_rep1


title: HDM sensitized atopic subject # AA22 HDM stimulated


title: Leucocytes_MS patient in relapse_rep22

source_name: MS relapse

value: MS relapse


title: Leucocytes_MS patient in relapse_rep24


title: HDM sensitized atopic subject # AA22 medium control


title: stimulated subject 7_control

description:
subject 7
Sample 36

value: stimulated


title: HDM sensitized atopic subject # AA21 medium control


title: Leucocytes_MS patient in relapse_rep23


title: Leucocytes_MS patient in relapse_rep21


title: baseline subject 73_control

description:
subject 73
Sample 33


title: HDM sensitized atopic subject # AA19 HDM stimulated


title: HDM sensitized atopic subject # AA20 HDM stimulated


title: Gemcitabine-resistant Mia-PaCa-2_biological  p29_1

value: mutant p53 human pancreatic adenocarcinoma cell line


title: HDM sensitized atopic subject # AA21 HDM stimulated


title: HDM sensitized atopic subject # AA19 medium control


title: Leucocytes_MS patient in relapse_rep20


title: HDM sensitized atopic subject # AA18 HDM stimulated


title: HDM sensitized atopic subject # AA18 medium control


title: baseline subject 7_control

description:
subject 7
Sample 35


title: stimulated subject 66_control

description:
subject 66
Sample 32


title: Leucocytes_MS patient in relapse_rep18


title: Leucocytes_MS patient in relapse_rep17


title: Leucocytes_MS patient in relapse_rep19


title: baseline subject 66_control

description:
subject 66
Sample 31


title: HDM sensitized atopic subject # AA16 HDM stimulated


title: HDM sensitized atopic subject # AA20 medium control


title: Leucocytes_MS patient in relapse_rep16


title: stimulated subject 69_control

description:
subject 69
Sample 30


title: HDM sensitized atopic subject # AA16 medium control


title: baseline subject 69_control

description:
subject 69
Sample 29


title: stimulated subject 73_control

description:
subject 73
Sample 34


title: HDM sensitized atopic subject # AA15 HDM stimulated


title: Leucocytes_MS patient in relapse_rep15


title: stimulated subject 12_control

description:
subject 12
Sample 28


title: HDM sensitized atopic subject # AA15 medium control


title: Leucocytes_MS patient in relapse_rep13


title: Leucocytes_MS patient in relapse_rep14


title: baseline subject 12_control

description:
subject 12
Sample 27


title: stimulated subject 58_control

description:
subject 58
Sample 26


title: Leucocytes_MS patient in relapse_rep12


title: baseline subject 58_control

description:
subject 58
Sample 25


title: stimulated subject 204_control

description:
subject 204
Sample 24


title: baseline subject 204_control

description:
subject 204
Sample 23


title: stimulated subject 21_control

description:
subject 21
Sample 22


title: baseline subject 21_control

description:
subject 21
Sample 21


title: Leucocytes_MS patient in relapse_rep8


title: HDM sensitized atopic subject # AA12 medium control


title: stimulated subject 78_control

description:
subject 78
Sample 20


title: HDM sensitized atopic subject # AA12 HDM stimulated


title: baseline subject 78_control

description:
subject 78
Sample 19


title: Leucocytes_MS patient in relapse_rep3


title: Leucocytes_MS patient in relapse_rep9


title: Leucocytes_MS patient in relapse_rep7


title: Leucocytes_MS patient in relapse_rep11


title: Leucocytes_MS patient in relapse_rep2


title: baseline subject 68_control

description:
subject 68
Sample 17


title: HDM sensitized atopic subject # AA09 HDM stimulated


title: IkL/L LSK cells rep 3

city: Illkirch

first: Attila

last: Oravecz

address: 1 rue Laurent Fries

country: France

institute: IGBMC

hyb_protocol: 10 μg of cRNAs were hybridized for 16 hours at 45°C on GeneChip® Mouse 430 2.0 arrays (Affymetrix)

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm.

data_processing: CEL files were processed using Robust Multi-array Average (RMA) algorithms from Bioconductor (R v.2.8) with default settings to calculate probe set signal intensities

source_name: sorted LSK cells from IkL/L mouse bone marrow

label_protocol: Biotinylated cRNA targets were prepared according to Affymetrix recommendations in  GeneChip Expression Analysis Technical Manual  (P/N 702232 Rev.2) starting from 100 ng of total RNA  in a two cycle target labeling assay

extract_protocol: 1 WT mouse was used fo each RNA sample. Cells from 2 mice were pooled for sorting from IkL/L mutants for each RNA sample.Total RNA was extracted with the Qiagen RNAeasy micro  kit

tag: strain

tag: genotype/variation

value: IkL/L mutant

value: bone marrow

value: sorted lin- Sca1+ c-Kit+ (LSK) cells


title: HDM sensitized atopic subject # AA08 medium control

value: CD4 T cell


title: HDM sensitized atopic subject # AA03 HDM stimulated


title: HDM sensitized atopic subject # AA11 HDM stimulated


title: Leucocytes_MS patient in relapse_rep5

tag: gender


title: HDM sensitized atopic subject # AA09 medium control


title: HDM sensitized atopic subject # AA11 medium control


title: Leucocytes_MS patient in relapse_rep10

tag: tissue


title: HDM sensitized atopic subject # AA03 medium control


title: HDM sensitized atopic subject # AA01 medium control


title: WT LSK cells rep 3

source_name: sorted LSK cells from WT mouse bone marrow

value: wild type


title: Leucocytes_MS patient in relapse_rep6


title: Leucocytes_MS patient in relapse_rep4


title: stimulated subject 68_control

description:
subject 68
Sample 18

tag: stimulus


title: WT LSK cells rep 1


title: stimulated subject 233_control

description:
subject 233
Sample 16

tag: sample type


title: baseline subject 233_control

description:
subject 233
Sample 15

value: baseline


title: Leucocytes_MS patient in relapse_rep1


title: cultured PBMC from healthy control stimulated with PHA

hyb_protocol: GeneChip Hybridization, Wash and Stain kit was used for hybridization in a GeneChip Hybridization oven 640 and in a GeneChip Fluidics Station 450 using the protocol FS450-0002, as explained in the protocol provided by Affymetrix.

data_processing: Quality control, normalization and summarization of the data were performed in Expression Console software build 1.4.0.38 (Affymetrix). Only human probes.

source_name: cultured healthy control PBMC with PHA

growth_protocol: PBMCs were isolated from whole blood and cryopreserved in liquid nitrogen until used. After thawing, PBMCs were cultured in a P48 plate (200.000cells/well) for 72h.

extract_protocol: miRNeasy mini kit (Qiagen)

treatment_protocol: To induce PBMC activation,  Phytohemagglutinin (PHA) (ThermoFisher) (0.5%) was used.

value: PBMC

value: healthy control


title: WT LSK cells rep 2

tag: cell type


title: stimulated subject 76_control

description:
subject 76
Sample 14


title: HDM sensitized atopic subject # AA01 HDM stimulated


title: IkL/L LSK cells rep 1


title: IkL/L LSK cells rep 2


title: HDM sensitized atopic subject # AA08 HDM stimulated


title: cultured PBMC from healthy control, no stimulated

source_name: cultured healthy control PBMC


title: Leucocytes_healthy control_rep24

source_name: Healthy control

value: leucocytes

value: Healthy control


title: cultured PBMC from MS patient stimulated with PHA

source_name: cultured MS PBMC with PHA

value: MS patient


title: baseline subject 76_control

description:
subject 76
Sample 13

source_name: whole blood

value: whole blood


title: Leucocytes_healthy control_rep22


title: stimulated subject 64_control

description:
subject 64
Sample 12

value: control


title: cultured PBMC from MS patient, no stimulated

source_name: cultured MS PBMC

value: female


title: baseline subject 64_control

description:
subject 64
Sample 11


title: stimulated subject 71_control

description:
subject 71
Sample 8


title: baseline subject 71_control

description:
subject 71
Sample 7


title: baseline subject 74_control

description:
subject 74
Sample 5


title: stimulated subject 74_control

description:
subject 74
Sample 6


title: Leucocytes_healthy control_rep18


title: Leucocytes_healthy control_rep19


title: Leucocytes_healthy control_rep21


title: Leucocytes_healthy control_rep17

value: male


title: Leucocytes_healthy control_rep20


title: Leucocytes_healthy control_rep23


title: GFS749 (VAESBJ PCI-2)

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: HDAC inhibitor treatment, VAESBJ cell line

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: Gene expression values derived from Illumina GenomeStudio software were subject to quantile normalization.

source_name: VAESBJ cell line

label_protocol: According to Illumina protocol.

growth_protocol: Human ES cell lines used for this study were VAESBJ, HS-ES, Epi-544. VAESBJ was obtained from the American Type Culture Collection; HS-ES was obtained from Hiroshi Sonobe (Kochi Medical School, Nankoku, Japan); Epi-544 was established in our laboratory (All three are P53 wild-type as sequenced in our lab). ES cells were cultured in DMEM 1X supplemented with 10% FBS (Life Technologies).

extract_protocol: According to Illumina protocol.

treatment_protocol: Pan-HDAC inhibitor PCI2 was obtained from Pharmacyclics; suberoylanilide hydroxamic acid (SAHA) and MS-275 were acquired from Dr. David McConkey, MD Anderson (initially obtained from Syndax Pharmaceuticals, Inc.) and dissolved in DMSO to create stock solutions. All additional dilutions were completed using the respective cell culture medium for each cell line.

tag: cell line

value: VAESBJ

tag: treatment

value: HDAC inhibitor treatment


title: GFS683 (HS ctrl)

description: Control/DMS, HS-ES cell line

source_name: HS-ES cell line

value: HS-ES

value: Control/DMS


title: GFS748 (VAESBJ DMSO2)

description: Control/DMS, VAESBJ cell line


title: Leucocytes_healthy control_rep16


title: GFS746 (VAESBJ DMSO1)

description: Control/DMS, VAESBJ cell line


title: Leucocytes_healthy control_rep12


title: GFS747 (VAESBJ PCI-1)


title: Leucocytes_healthy control_rep13


title: GFS673 (544PC12)

description: HDAC inhibitor treatment, Epi-544 cell line

source_name: Epi-544 cell line


title: GFS684 (HS PC12)

description: HDAC inhibitor treatment, HS-ES cell line


title: Leucocytes_healthy control_rep11


title: GFS680 (HEES PC12)


title: Leucocytes_healthy control_rep9


title: GFS679 (HEES ctrl)

description: Control/DMS, HS-ES cell line


title: GFS674 (544 ctrl)

description: Control/DMS, Epi-544 cell line


title: Leucocytes_healthy control_rep10


title: Leucocytes_healthy control_rep15


title: Desm39b 30d G10 1

description: 33 days GSI treatment, Desm39b model

source_name: Desm39b desmoid tumor cells

growth_protocol: All DT cell strains were isolated in our laboratory. All DT cells were maintained in DMEM-12 medium media  and serum concentration. Cells were incubated at 37°C in a humidified atmosphere with 5% CO2 and maintained using  standard cell culture techniques.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: We utilized three cells strains (Desm14, Desm27 and Desm39b) with  no treatment (control, called G-0) or treated with 10μM of PF-03084014 (called G-10). The regimen for each treatment was 8 days and 30 days. We included duplicates for all samples. Sample related data can be found in table S2.

value: desmoid tumor

value: treated (G-10)


title: Leucocytes_healthy control_rep7


title: Leucocytes_healthy control_rep14


title: GFS681 (Epi Ctrl)

description: Control/DMS, Epi-544 cell line


title: Leucocytes_healthy control_rep8


title: Desm39b 33d G0 2

description: 33 days control treatment, Desm39b model

value: control (G-0)


title: GFS682 (Epi PC12)


title: Desm39b 33d G0 1


title: Leucocytes_healthy control_rep6


title: Leucocytes_healthy control_rep4


title: Leucocytes_healthy control_rep2


title: Desm39b 33d G10 2

description: 33 days GSI treatment, Desm39b model


title: Desm39b 7d G0 2

description: 7 days control treatment, Desm39b model


title: Leucocytes_healthy control_rep3


title: Desm39b 7d G10 2

description: 7 days GSI treatment, Desm39b model


title: Leucocytes_healthy control_rep1


title: Desm27 33d G0 2

description: 33 days control treatment, Desm27 model

source_name: Desm27  desmoid tumor cells


title: Desm39b 7d G0 1

description: 7 days control treatment, Desm39b model


title: Leucocytes_healthy control_rep5


title: Desm39b 7d G10 1

description: 7 days GSI treatment, Desm39b model


title: Desm27 33d G10 1

description: 33 days GSI treatment, Desm27 model


title: IkER 4OHT rep2

hyb_protocol: 1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix)

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: CEL files were processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: ILC87-Ik1-ER cells treated with 4OHT for 24h, sample 2

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations

growth_protocol: The ILC87 cell line is derived from a thymic tumor of an Ikarosf/f Lck-cre+ mouse. ILC87 cells were transduced with the MigR1:Ik1-ER retrovirus encoding the full length Ikaros-1 isoform fused to the ligand binding domain of the estrogen receptor (ER), followed by an IRES and the GFP reporter. Sorted GFP positive cells stably expressing Ik1-ER were grown in RPMI medium w/25mM HEPES and 10% heat-inactivated FCS in standard humidified incubator at 5% CO2

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy micro kit.

treatment_protocol: ILC87 cells were treated with 100 nM 4-hydroxytamoxifen (4OHT, Sigma) or vehicle (EtOH) for 24 hours


title: Desm27 33d G10 2

description: 33 days GSI treatment, Desm27 model


title: IkER EtOH rep2

source_name: ILC87-Ik1-ER cells treated with EtOH for 24h, sample 2


title: Desm27 32d G0 1

description: 33 days control treatment, Desm27 model


title: IkER 4OHT rep1

source_name: ILC87-Ik1-ER cells treated with 4OHT for 24h, sample 1


title: IkER EtOH rep1

source_name: ILC87-Ik1-ER cells treated with EtOH for 24h, sample 1


title: Desm14 31d G10 1

description: 31 days GSI treatment, Desm14 model

source_name: Desm14 desmoid tumor cells


title: Desm14 31d G0 1

description: 31 days control treatment, Desm14 model


title: Desm27 7d G0 2

description: 7 days control treatment, Desm27 model


title: Desm27 7d G10 1

description: 7 days GSI treatment, Desm27 model


title: Desm27 7d G10 2

description: 7 days GSI treatment, Desm27 model


title: trickling filter effluent, biological replicate 2

city: Evanston

first: George

middle: F

last: Wells

state: Illinois

address: 2145 Sheridan Road, Tech A236

department: Civil & Environmental Engineering

institute: Northwestern University

description: Affymetrix G2 PhyloChip

hyb_protocol: The labeled DNA was denatured (99°C for 5 min) and hybridized to PhyloChip arrays at 48°C overnight (> 16 h) at 60 rpm in a rotisserie oven with prewarmed hybridization cocktail (biotin-labeled target, hybridization solution, and control oligonucleotides.)  Microarray washing and staining occurred on a GeneChip Fluidics Station 400 (Affymetrix, Santa Clara, CA) following standard manufacturer’s protocols.

scan_protocol: Arrays were scanned using a GeneArray Scanner (Affymetrix, Santa Clara, CA) with a 488-nm argon-ion laser with emission detection at 520 nm.

data_processing:
The scan was captured as a pixel image using standard Affymetrix software (GeneChip Microarray Analysis Suite, version 5.1) that reduced the data to an individual signal value for each probe.
Probes producing hybridization intensities in the lowest 2% of all measured intensities were considered background, and the average background intensity was subtracted from the fluorescence intensity of all remaining probes. To correct for variation associated with quantification of amplicon target (quantification variation) and downstream variation associated with target fragmentation, labeling, hybridization, washing, staining and scanning (microarray technical variation), a two-step PhyloChip data normalization procedure was performed in the R statistical programming environment (http://www.r-project.org/). First, for each PhyloChip experiment, a scaling factor best explaining the intensities of the spiked control probes under a multiplicative error model was estimated using a maximum-likelihood procedure (Ivanov et al. 2009). The intensities in each experiment were multiplied with its corresponding optimal scaling factor. Second, the intensities for each experiment were corrected for the variation in total array intensity by dividing the intensities with its corresponding total array intensity separately for Bacteria and Archaea.  Scoring of probe pairs as positive or negative followed previously described protocols (DeSantis et al. 2007).  For each set of probe pairs comprising an OTU, the positive fraction (PosFrac, or pf) was defined as the fraction of total probe pairs in a probe set that were scored as positive.  An OTU was considered present when its PosFrac was greater than 0.9.  Hierarchical taxonomic nodes (subfamily, family, order, class, phylum, domain) were considered present if at least one underlying OTU was present.  OTUs that were not detected in at least one sample (pf>0.9) are not included in the matrix table and were not considered in downstream analyses.

organism:
uncultured bacterium
uncultured archaeon

source_name: Palo Alto Regional Water Quality Control Plant Trickling Filter Effluent

label_protocol: Bacterial and archaeal 16S rRNA genes (~1450-bp) were separately PCR amplified for application to the PhyloChip platform using universal primers 27F.1 (5’-AGRGTTTGATCMTGGCTCAG-3’) and 1492R (5’-GGTTACCTTGTTACGACTT-3’) for the Bacterial domain and primer pair 4Fa (5’-TCCGGTTGATCCTGCCRG-3’) and 1492R for Archaeal domain.  Each PCR reaction mix contained 1X buffer with 0.8 mM dNTP mixture (Takara Bio Inc., Japan), 1.25U Ex Taq polymerase (Takara Bio Inc., Japan), 1 μg/μl BSA (Roche Applied Science, Indianapolis, IN), 300 nM of each primer, and 10 ng DNA.  PCR conditions were set to 1 cycle of 3 min at 95°C, followed by 30 cycles of 95°C (30 s), annealing (30 s), 72°C (60 s), and a final extension at 72°C for 7 min.  With the exception of the duplicate influent samples, DNA extracts were amplified using a range of eight different annealing temperatures between 48°C and 58°C.  Due to low DNA concentrations, two DNA extracts from raw influent samples were amplified in duplicate at three different annealing temperatures (48oC, 54.2oC, and 58oC).  All amplicons from different annealing temperatures associated with a single sample were combined, and pooled amplicons were purified with the NovaGen SpinPrep PCR Clean-up Kit (EMD4Biosciences, Gibbstown, NJ).  Presence or absence of the expected amplicon was verified via agarose gel electrophoresis.  Amplicons were further purified in selected samples via agarose gel electrophoresis with the Qiagen QIAquick Gel Extraction Kit (Qiagen Inc., Valencia, CA).  Pooled purified amplicons were quantified via agarose gel electrophoresis using the GelDoc XR System and Quantity One software (Biorad, Hercules, CA) with an E-Gel Low Range Quantitative DNA Ladder (Invitrogen, Carlsbad, CA).  500 ng of bacterial 16S rRNA gene amplicons and 100 ng of archaeal 16S rRNA gene amplicons were pooled for each sample for use in downstream microarray processing steps. Pooled bacterial and archaeal 16S rRNA gene amplicons from each sample were spiked with internal standards consisting of known concentrations of amplicons of yeast and bacterial metabolic genes (Brodie et al. 2006), and then fragmented to 50-200 bp using Dnase I (0.02 U/ mg DNA, Invitrogen, Carlsbad, CA) and One-Phor-All buffer (GE Healthcare, Piscataway, NJ), as per the standard Affymetrix protocol.  Terminal 3’ labeling of fragmented amplicons via biotinylation was accomplished using the GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA) with recombinant Terminal Deoxynucleotitidyl Transferase (Promega, Madison, WI), as per the manufacturer’s instructions.

growth_protocol: Environmental Samples

extract_protocol: Activated sludge and trickling filter biofilm samples were washed using 1 ml Tris-EDTA buffer (1 mM, pH=7.0) and genomic DNA (gDNA) was extracted in triplicate using the FastDNA Spin Kit for Soil (MP Biomedicals, Solon, OH) following the manufacturer’s protocol, except for the initial bead-beating step.  A Vortex Adapter (MO BIO laboratories, Inc., Carlsbad, CA) with the Vortex Genie 2T (Scientific Industries, Inc., Bohemia, NY) was used to physically disrupt cells in lysing matrix at maximum speed for 15 min.  gDNA extraction from  raw influent and trickling filter effluent proceeded via incubation of filters in lysis solution (800 μl water, 100 μl 10% SDS (Invitrogen, Carlsbad, CA) and 100μl 10mg/ml Proteinase K (Invitrogen, Carlsbad, CA) at 55oC for 2.5 h.  Filtrate from the lysis incubation was purified with the FastDNA Spin Kit for Soil (MP Biomedicals, Solon, OH) following the manufacturer’s protocol but without the initial bead-beating step.

treatment_protocol: Sampling along a transect within the PARWQCP occurred on 12 November 2008.  Upon temporary shutdown of the rotating distributor arm in one of the trickling filters, a surface PVC media module (0.9 m deep) was removed from the reactor, and 1-3 g biofilm samples were obtained with a sterile spatula, placed in sterile 1.5 ml tubes, weighed, and stored at -20oC.  Concurrently, samples of influent, trickling filter effluent, and activated sludge were obtained.  Activated sludge samples represented a 24-h composite from the combined outlet of all four aeration basins using a Sigma 900 refrigerated automatic sampler (Hach, Loveland, CO). Eight 1.5 ml activated sludge samples were centrifuged onsite for 5 min at 5000 g, decanted, and stored at -20oC.  Raw influent and trickling filter effluent samples were transported on ice to the laboratory, vacuum filtered in 10 ml aliquots onto 0.22 μm Hydrophilic Durapore PVDF filters (25 mm diameter, Millipore, Billerica, MA), and archived at -20oC.

tag: biomaterial source

value: trickling filter effluent


title: trickling filter effluent, biological replicate 1

description: Affymetrix G2 PhyloChip


title: trickling filter effluent, biological replicate 3

description: Affymetrix G2 PhyloChip


title: Desm27 7d G0 1

description: 7 days control treatment, Desm27 model


title: Desm14 32d G10 2

description: 31 days GSI treatment, Desm14 model


title: Desm14 8d G10 2

description: 8 days GSI treatment, Desm14 model


title: Desm14 32d G0 2

description: 31 days control treatment, Desm14 model


title: Desm14 8d G0 1

description: 8 days control treatment, Desm14 model


title: trickling filter biofilm, biological replicate 3

description: Affymetrix G2 PhyloChip

source_name: Palo Alto Regional Water Quality Control Plant Trickling Filter biofilm

value: trickling filter biofilm


title: influent, biological replicate 1

description: Affymetrix G2 PhyloChip

source_name: Palo Alto Regional Water Quality Control Plant Influent

value: raw influent


title: influent, biological replicate 2

description: Affymetrix G2 PhyloChip


title: trickling filter biofilm, biological replicate 2

description: Affymetrix G2 PhyloChip


title: trickling filter biofilm, biological replicate 1

description: Affymetrix G2 PhyloChip


title: activated sludge, biological replicate 3

description: Affymetrix G2 PhyloChip

source_name: Palo Alto Regional Water Quality Control Plant Activated Sludge Aeration Basin

value: activated sludge


title: activated sludge, biological replicate 1

description: Affymetrix G2 PhyloChip


title: activated sludge, biological replicate 2

description: Affymetrix G2 PhyloChip

value: acivated sludge


title: Desm14 8d G10 1

description: 8 days GSI treatment, Desm14 model


title: Desm14 8d G0 2

description: 8 days control treatment, Desm14 model


title: MYB112IOE-5hEST-1

city: Potsdam-Golm

first: Magda

middle: Ewa

last: Lotkowska

address: Karl-Liebknecht-Str.24-25, Haus 20

institute: Potsdam University

description:
Seedling, biological rep 1
Gene expression data from MYB112-IOE-line 1, 5 h after estradiol treatment

hyb_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

data_processing: Raw data (CEL files) obtained from RNA hybridisation experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004) using the GCRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and  gives one value for each probe set instead of keeping probe level information (Wu et al., 2004). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

organism: Arabidopsis thaliana

source_name: Arabidopsis MYB112-IOE-line 1 Seedlings treated with Est

growth_protocol: MYB112-IOE plants were cultured on MS agar plates at 22˚C continous light (100 µmol m-2 s-1).

extract_protocol: Extraction of total RNA was performed using RNeasy Plant Mini Kit (Quiagen) according to the manufacturer's instructions.

treatment_protocol: After two weeks, seedlings were transferred to MS liquid medium while shaking. Sixteen hours later, β-estradiol (Sigma-Aldrich) was added to the medium to a final concentration of 10 μM. Subsequently, shoots were harvested at 3 h or 5 h timepoints after estradiol addition.

value: shoot

tag: cultivar

tag: genotype

value: 2-week-old seedling

tag: treatment group


title: MYB112IOE-3hDMSO

description:
Seedling, biological rep 1
Gene expression data from MYB112-IOE-line 1, 3 h after DMSO treatment

scan_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

source_name: Arabidopsis MYB112-IOE-line 1 Seedlings treated with DMSO

tag: age


title: MYB112IOE-5hDMSO-2

description:
Seedling, biological rep 2
Gene expression data from MYB112-IOE-line 1, 5 h after DMSO treatment

label_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual


title: MYB112IOE-3hEST

description:
Seedling, biological rep 1
Gene expression data from MYB112-IOE-line 1, 3 h after estradiol treatment


title: MYB112IOE-5hEST-2

description:
Seedling, biological rep 2
Gene expression data from MYB112-IOE-line 1, 5 h after estradiol treatment


title: MYB112IOE-5hDMSO-1

description:
Seedling, biological rep 1
Gene expression data from MYB112-IOE-line 1, 5 h after DMSO treatment


title: skin from challenged side at 48hrs dog #4

status: Public on Nov 02 2015

city: Collegeville

first: David

last: Mayhew

state: PA

address: 1250 South Collegeville Road

department: Target Sciences, Computation Biology, R&D

institute: GlaxoSmithKline

description: Gene expression data from skin biopsies at 48 hrs on HDM-challenged side of the dog

hyb_protocol: The biotin labeled samples were then hybridized to a Canine Genome 2.0 Array using a Genechip Hybridization Kit according to the manufacturer's instruction.

scan_protocol: The microarray chips were washed and stained using a Genechip Hybridization Wash and Stain Kit then scanned using a Genechip Scanner. All reagents and readers were used according to the manufacturer’s instruction.

data_processing: The microarray gene expression data were analyzed using ArrayStudio 7.0.  Data were normalized using robust multiarray averaging and scaled to a mean target intensity of 150.  Differentially expressed transcripts were identified with a Student's t-test (FDR < 5% and at least 1.5 fold-change)

organism: Canis lupus familiaris

source_name: skin biopsy (challenge) at 48 hrs

label_protocol: The RNA samples were converted to cDNA with Superscript Vilo cDNA synthesis Master Mix and cDNA samples were labeled with biotion with the FL-Ovation cDNA Biotin Module V2.

growth_protocol: Eight Maltese-beagle atopic dogs (five males, three females; 5.5 to 10.5 years old), epicutaneously sensitized to Dermatophagoides farinae HDM, were selected after demonstration of acute AD skin lesion following epicutaneous DHM challenge.

extract_protocol: After heavy sedation and local anesthesia, skin biopsies were collected at each time point.  Biopsies were mince in a Precellys homogenizer and total mRNA extracted using Qiagen Rneasy kit.

treatment_protocol: HDM patches (or mineral oil controls) were applied onto the lateral thoracic skin of the dogs.

tag: dog

value: skin biopsies

tag: time point

value: 48 hrs

value: HDM-challenged side


title: skin from challenged side at 48hrs dog #1


title: skin from challenged side at 24hrs dog #7

description: Gene expression data from skin biopsies at 24 hrs on HDM-challenged side of the dog

source_name: skin biopsy (challenge) at 24 hrs

value: 24 hrs


title: skin from challenged side at 24hrs dog #4


title: skin from challenged side at 48hrs dog #8


title: skin from challenged side at 24hrs dog #6


title: skin from challenged side at 48hrs dog #3


title: skin from challenged side at 48hrs dog #6


title: skin from challenged side at 24hrs dog #5


title: skin from challenged side at 24hrs dog #8


title: skin from challenged side at 48hrs dog #7


title: skin from challenged side at 6hrs dog #4

description: Gene expression data from skin biopsies at 6 hrs on HDM-challenged side of the dog

source_name: skin biopsy (challenge) at 6 hrs

value: 6 hrs


title: skin from challenged side at 48hrs dog #5


title: skin from challenged side at 24hrs dog #1


title: skin from challenged side at 6hrs dog #7


title: skin from challenged side at 6hrs dog #3


title: skin from challenged side at 48hrs dog #2


title: skin from challenged side at 6hrs dog #5


title: skin from challenged side at 24hrs dog #2


title: skin from challenged side at 24hrs dog #3


title: skin from challenged side at 6hrs dog #2


title: skin from challenged side at 6hrs dog #8


title: skin from control side at 6hrs dog #7

description: Gene expression data from skin biopsies at 6 hrs on control-side of the dog

source_name: skin biopsy (control) at 6 hrs

value: control-side


title: skin from control side at 6hrs dog #8


title: stathmin_KO2 rep 3

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

description:
Biological replicate 3 of 4
745_1_4

hyb_protocol: The Hybridization was performed acording to Ambion protocol

scan_protocol: Slides were analysed by Agilent Microarray Scanner G2565AA

data_processing: Background subtraction method: Marginal log-likelihood of foreground values for normal + exponential model and its derivatives.Whithin Normalization method: loess. Between Normalization method: quantile. Filtered by 20% of the IQR

label_protocol: cDNA synthesis, cDNA purification, in vitro transcription of amino-allyl RNA (aRNA), aRNA dye coupling, and purification of dye-labeled aRNA were performed using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, Austin, TX) following manufacturer's guidelines

growth_protocol: fibroblasts have been collected at high confluence  after 24 hours of serum starvation. Standard growth at 37°C and 5% CO2

extract_protocol: All steps have been performed according to RNeasy Mini Kit instructions.

treatment_protocol: Cells have been lysed directly in the cell culture dish with lysis buffer (RLT buffer, RNeasy Mini Kit)

tag: strain background

value: stathmin knock-out

tag: developmental stage

tag: tissue origin

value: embryos

value: Mouse Embryonic Fibroblasts at passage 3

source_name: reference RNA from pooled MEFs


title: skin from control side at 6hrs dog #5


title: skin from control side at 6hrs dog #6


title: p27_stathmin_DKO rep 3

description:
Biological replicate 3 of 3
889_1_3

tag: genotype/variation

value: p27 and stathmin double knock-out


title: stathmin_KO2 rep 4

description:
Biological replicate 4 of 4
889_1_4


title: skin from control side at 6hrs dog #2

tag: tissue


title: p27_KO1 rep 4

description:
Biological replicate 4 of 4
889_1_2

value: p27 knock-out


title: p27_stathmin_DKO rep 2

description:
Biological replicate 2 of 3
745_1_3


title: skin from control side at 6hrs dog #3


title: stathmin_KO2 rep 2

description:
Biological replicate 2 of 4
744_1_4


title: WT rep 4

description:
Biological replicate 4 of 4
889_1_1

source_name: WT

value: wild type


title: p27_KO1 rep 2

description:
Biological replicate 2 of 4
744_1_2


title: WT rep 3

description:
Biological replicate 3 of 4
745_1_1


title: skin from challenged side at 6hrs dog #6


title: skin from control side at 6hrs dog #1


title: skin from control side at 6hrs dog #4


title: skin from challenged side at 6hrs dog #1


title: WT rep 2

description:
Biological replicate 2 of 4
744_1_1


title: p27_KO1 rep 3

description:
Biological replicate 3 of 4
745_1_2


title: stathmin_KO2 rep 1

description:
Biological replicate 1 of 4
743_1_4


title: p27_stathmin_DKO rep 1

description:
Biological replicate 1 of 3
743_1_3


title: p27_KO1 rep 1

description:
Biological replicate 1 of 4
743_1_2


title: Oryza Sativa Indica IR64 control stress_Leaf_rep1.

city: Beijing

first: Wensheng

last: Wang

address: 12# Zhong-guan-cun south street

institute: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences

hyb_protocol: cRNA was then hybridized to the Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences at 45 °C with rotation for 16h (Affymetrix GeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained on the Affymetrix Fluidics Station 450 followed by scanning on Affymetrix GeneChip Scanner 3000. All above mentioned experiment steps were processed in CapitalBio Corporation in Beijing.

scan_protocol: GeneChip Operating Software (GCOS1.4) was used to analyze the hybridization data. The scanned images were firstly examined by visual inspection then satisfactory images were analyzed to generate raw data saved as CEL files using the default settings of GCOS1.4.

data_processing: dChip software was used to perform normalization of all arrays by an invariant set approach according to the dChip user’s manual. The SAM (Significant Analysis of Microarray) software was applied in two types of unpaired method for the comparison analysis to identify differential expressed genes (DEGs) between cold stress sample and control sample in one genotype and between two genotypes at each time point. As there is not a fixed standard threshold for significant differential gene expression, we identified the DEGs using the empirical criterion of more than 5-fold change and cut-off p < 0.05 in SAM based on three independent biological replicates. The DEGs were performed in average linkage hierarchical clustering analysis using GeneCluster version 3.0 software

organism: Oryza sativa

source_name: IR64, control

label_protocol: Biotin-tagged cRNA was generated from an in vitro transcription reaction using the MessageAmpTM II aRNA Amplification Kit and then fragmented into strands of 35 to 200 bases in length following the Affymetrix’s protocol.

growth_protocol: Seeds were surface-sterilized in 0.1% NaClO (v/v) and rinsed several times before allowed to germinate at 37 oC in an incubator. After 3 days, germinated seeds were transferred to a 20-L tank filled with Yoshida nutrient solution. The seedlings were cultured in Yoshida solution for 11 days after germination. Weak plants were removed from the tank. The seedlings were grown in a phytotron with 29/22°C day/night temperature and minimum relative humidity of 70%. The pH of the nutrient solution was adjusted daily to 5.5 by adding sulfuric acid and was refreshed every week.

extract_protocol: RNA preparation was processed as recommended by the Instruction of Affymetrix (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix). Briefly total RNA was isolated from liquid nitrogen frozen sample using TRIZOL reagent and the following steps were then processed in the CapitalBio Corporation, Beijing.

treatment_protocol: At the 3-leaf stage, Salinity treatment was applied by adding NaCl in 3 steps to reach a final concentration of 140mM. The seedlings were independently subjected to one of three different treatments [Control; NaCl (140mM); NaCl (140mM) +ABA (10uM)]. Leaf and Root samples were collected during salinity stress, salinity+ABA and control treatments. Three biological replicates were prepared for microarray analysis. After collection, samples were snap frozen in liquid nitrogen and kept in a -80 °C freezer for total RNA extraction.

value: control

value: Leaf

value: wildtype

value: 3-leaf seedling stage


title: Oryza Sativa Indica IR64 control stress_Root_rep2.

value: Root


title: Oryza Sativa Indica IR64 control stress_Leaf_rep2.


title: Oryza Sativa Indica IR64 control stress_Root_rep1.


title: Control 120 days sample 1

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from murine astrocytes

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Mouse Genome 430A GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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

source_name: G93A non transgenic littermate 2823

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol:
10 um lumbar spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
From each animal 1500 astrocytes were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)
PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

value: spinal cord

value: astrocyte

tag: gender

value: male

value: 120 days


title: Control 90 days sample 3

source_name: G93A non transgenic littermate 5025

value: 90 days


title: Control 90 days sample 1

source_name: G93A non transgenic littermate 5008


title: Oryza Sativa Indica IR64 salinity+ABA stress_Leaf_rep3.

source_name: IR64, salinity (140mM)+ABA(10uM) stress, 4 days


title: Control 120 days sample 2

source_name: G93A non transgenic littermate 2829


title: Oryza Sativa Indica IR64 control stress_Leaf_rep3.


title: WT rep 1

description:
Biological replicate 1 of 4
743_1_1


title: Control 120 days sample 3

source_name: G93A non transgenic littermate 2836


title: Oryza Sativa Indica IR64 salinity stress_Root_rep2.

source_name: IR64, salinity stress(140mM), 4 days

value: salinity stress(140mM), 4 days


title: G93A 120 days sample 1

source_name: G93A mouse 2534

value: SOD1 G93A


title: Oryza Sativa Indica IR64 salinity stress_Root_rep1.


title: Oryza Sativa Indica IR64 control stress_Root_rep3.


title: Oryza Sativa Indica IR64 salinity+ABA stress_Root_rep1.

value: salinity (140mM)+ABA(10uM) stress, 4 days


title: G93A 90 days sample 3

source_name: G93A mouse 5024


title: G93A 120 days sample 2

source_name: G93A mouse 2832


title: Oryza Sativa Indica IR64 salinity stress_Leaf_rep2.


title: Oryza Sativa Indica IR64 salinity+ABA stress_Leaf_rep1.


title: Oryza Sativa Indica IR64 salinity+ABA stress_Root_rep2.


title: Control 90 days sample 2

source_name: G93A non transgenic littermate 5012


title: Oryza Sativa Indica IR64 salinity stress_Leaf_rep3.


title: G93A 120 days sample 3

source_name: G93A mouse 2835


title: Oryza Sativa Indica IR64 salinity+ABA stress_Leaf_rep2.


title: Oryza Sativa Indica IR64 salinity stress_Root_rep3.


title: Oryza Sativa Indica IR64 salinity+ABA stress_Root_rep3.


title: G93A 90 days sample 2

source_name: G93A mouse 5013


title: innoculation of PBS/BSA and PBS/BSA vehicle in C57BL/6 mice rep4

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: 4651_HFR_1_mouse_22_pbsbsa-pbsbsa-vehicle-104-B11-5835_01_3712

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip mouse 430 2.0 ST arrays according to manufacturer's recommendations

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

data_processing:
The data were analyzed with EC 1.1 using Affymetrix default analysis
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.1.2800.28061

label_protocol: cDNA was generated from 5ng of total RNA using WT-Ovation™ Pico system (version 1) RNA Amplification System followed by double stranded cDNA synthesis using WT-Ovation™ Exon Module.

growth_protocol: Wild-type C57BL/6 mice were obtained from Division of Cancer Research (DCT), Frederick, MD.

extract_protocol: For mRNA analysis, RNA was extracted using RNeasy spin columns (Qiagen) followed by DNAse treatment.

treatment_protocol: Mice were inoculated intranasally under isoflurane anaesthesia with 50 µL of a 1:10,000 dilution (0.2 TCID50 units) of pneumonia virus (Family Paramyxovirdae, genus Pneumovirus ) or Each mouse received 50 µL of Lactobacillus plantarum NCIMB 88Micr26  or 50 µL diluent (phosphate buffered saline (pbs) with 0.1% bsa (pbs/bsa) diluent control per inoculation.

tag: strain

tag: inoculated with

value: PBS/BSA and PBS/BSA vehicle

value: whole lung tissue


title: innoculation of PBS/BSA and PBS/BSA vehicle in C57BL/6 mice rep2

description: 4649_HFR_1_mouse_20_pbsbsa-pbsbsa-vehicle-98-A02-5829_01_3719


title: innoculation of PBS/BSA and pneumonia virus in C57BL/6 mice rep6

description: 4647_HFR_1_mouse_18_pbsbsa-pbsbsa-PVM-130-A11-5861_01_3705

value: PBS/BSA and pneumonia virus


title: Oryza Sativa Indica IR64 salinity stress_Leaf_rep1.


title: innoculation of PBS/BSA and PBS/BSA vehicle in C57BL/6 mice rep5

description: 4652_HFR_1_mouse_23_pbsbsa-pbsbsa-vehicle-105-B07-5836_01_3710

value: wild type


title: Oryza Sativa Indica 177 control stress_Leaf_rep3.

description: 177-103, an F6 line derived from introgression lines in the IR64 genetic background

source_name: 177-103(salinity tolerant introgression line under IR64 genetic background), control

value: control

value: IR64 genetic background


title: innoculation of PBS/BSA and PBS/BSA vehicle in C57BL/6 mice rep1

description: 4648_HFR_1_mouse_19_pbsbsa-pbsbsa-vehicle-97-A03-5828_01_3698


title: innoculation of PBS/BSA and PBS/BSA vehicle in C57BL/6 mice rep3

description: 4650_HFR_1_mouse_21_pbsbsa-pbsbsa-vehicle-103-A05-5834_01_3903


title: Oryza Sativa Indica 177 control stress_Leaf_rep1.

value: Leaf

value: 177-103, an F6 line derived from introgression lines


title: innoculation of L. plantarum and PBS/BSA vehicle control of C57BL/6 mice rep6

description: 4641_HFR_1_mouse_12_LP-LP-vehicle-120-B05-5851_01_3911


title: Oryza Sativa Indica 177 control stress_Root_rep2.

value: Root

value: 3-leaf seedling stage


title: G93A 90 days sample 1

source_name: G93A mouse 5007

value: spinal cord

tag: cell type

value: astrocyte


title: innoculation of PBS/BSA and pneumonia virus in C57BL/6 mice rep3

description: 4644_HFR_1_mouse_15_pbsbsa-pbsbsa-PVM-123-B03-5854_01_3813


title: innoculation of PBS/BSA and pneumonia virus in C57BL/6 mice rep4

description: 4645_HFR_1_mouse_16_pbsbsa-pbsbsa-PVM-124-B06-5855_01_3693


title: Oryza Sativa Indica 177 salinity stress_Root_rep3.

source_name: 177-103(salinity tolerant introgression line under IR64 genetic background), salinity stress(140mM), 4 days

tag: treatment


title: innoculation of PBS/BSA and pneumonia virus in C57BL/6 mice rep2

description: 4643_HFR_1_mouse_14_pbsbsa-pbsbsa-PVM-122-B08-5853_01_3852


title: innoculation of PBS/BSA and pneumonia virus in C57BL/6 mice rep1

description: 4642_HFR_1_mouse_13_pbsbsa-pbsbsa-PVM-121-A12-5852_01_3895


title: innoculation of PBS/BSA and pneumonia virus in C57BL/6 mice rep5

description: 4646_HFR_1_mouse_17_pbsbsa-pbsbsa-PVM-129-A07-5860_01_3704


title: Oryza Sativa Indica 177 salinity+ABA stress_Root_rep3.

source_name: 177-103(salinity tolerant introgression line under IR64 genetic background), salinity (140mM)+ABA(10uM) stress, 4 days


title: Oryza Sativa Indica 177 control stress_Leaf_rep2.


title: innoculation of L. plantarum and PBS/BSA vehicle control of C57BL/6 mice rep5

description: 4640_HFR_1_mouse_11_LP-LP-vehicle-119-B10-5850_01_3842


title: Oryza Sativa Indica 177 control stress_Root_rep1.


title: Oryza Sativa Indica 177 salinity+ABA stress_Leaf_rep3.


title: Oryza Sativa Indica 177 control stress_Root_rep3.


title: Oryza Sativa Indica 177 salinity+ABA stress_Leaf_rep1.


title: innoculation of L. plantarum and PBS/BSA vehicle control of C57BL/6 mice rep3

description: 4638_HFR_1_mouse_09_LP-LP-vehicle-109-A10-5840_01_3825


title: Oryza Sativa Indica 177 salinity+ABA stress_Root_rep2.


title: Oryza Sativa Indica 177 salinity+ABA stress_Root_rep1.


title: Oryza Sativa Indica 177 salinity stress_Root_rep2.


title: Oryza Sativa Indica 177 salinity stress_Leaf_rep2.


title: Oryza Sativa Indica 177 salinity stress_Leaf_rep3.


title: Oryza Sativa Indica 177 salinity+ABA stress_Leaf_rep2.


title: innoculation of L. plantarum and PBS/BSA vehicle control of C57BL/6 mice rep4

description: 4639_HFR_1_mouse_10_LP-LP-vehicle-110-A04-5841_01_3848


title: innoculation of L. plantarum and PBS/BSA vehicle control of C57BL/6 mice rep1

description: 4636_HFR_1_mouse_07_LP-LP-vehicle-107-A08-5838_01_3757


title: innoculation of L. plantarum and pneumonia virus of C57BL/6 mice rep6

description: 4635_HFR_1_mouse_06_LP-LP-PVM-141-B04-5872_01_3833

value: L. plantarum and pneumonia virus


title: innoculation of L. plantarum and PBS/BSA vehicle control of C57BL/6 mice rep2

description: 4637_HFR_1_mouse_08_LP-LP-vehicle-108-A01-5839_01_3758


title: Oryza Sativa Indica 177 salinity stress_Leaf_rep1.


title: innoculation of L. plantarum and pneumonia virus of C57BL/6 mice rep5

description: 4634_HFR_1_mouse_05_LP-LP-PVM-140-B02-5871_01_3836


title: Rostral.LC.60d.3

city: Los Angeles

first: Weihong

last: Ge

state: CA

address: 635 Charles E Young Dr South 355

institute: UCLA

hyb_protocol: Following fragmentation,  tagged cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array containing 30,000 rat transcripts. The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data was extracted from scanned images using Affymetrix GCOS software. The raw data was normalized using a multi-array (RMA) method using the Expression Console software, followed by log2 transformation.

organism: Rattus norvegicus

label_protocol: BiotinylatedcRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Samples for microarray analysis were homogenized in 1 ml Trizol (Invitrogen, Carlsbad, CA), and RNA extracted using RNEasy miniprep columns (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: At 1, 3, 10, 20, 30, 60, 90days post surgery, animals were sacrificed, and 5mm segments of spinal cord at the lesion site, as well as immediately caudal or rostral to the lesion segment were collected labeled with R for rostral, C for caudal, and M for lesion site

tag: location

value: Rostral region 5mm tissue

value: Lesion control(LC)

tag: time (day)


title: Rostral.LC.90d.3


title: innoculation of L. plantarum and pneumonia virus of C57BL/6 mice rep4

description: 4633_HFR_1_mouse_04_LP-LP-PVM-139-B09-5870_01_3827


title: Rostral.LC.30d.2


title: Oryza Sativa Indica 177 salinity stress_Root_rep1.

description: 177-103, an F6 line derived from introgression lines in the IR64 genetic background

value: salinity stress(140mM), 4 days

tag: genotype

tag: cultivar


title: Rostral.LC.90d.1


title: innoculation of L. plantarum and pneumonia virus of C57BL/6 mice rep3

description: 4632_HFR_1_mouse_03_LP-LP-PVM-135-A09-5866_01_3823


title: Rostral.LC.30d.3


title: Rostral.LC.90d.2


title: Rostral.LC.60d.2


title: innoculation of L. plantarum and pneumonia virus of C57BL/6 mice rep1

description: 4630_HFR_1_mouse_01_LP-LP-PVM-133-A06-5864_01_3709


title: normal mammary gland, biological rep3

city: Frederick

last: Salomon

state: MD

address: 1050 Boyles Drive, Bldg. 560 Room 1246

department: NCI

description: normal mammary gland

hyb_protocol: Samples were hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 Array (platform accession number GPL1261) in the Affymetrix GeneChip Hybridization Oven 640 for 16 hours overnight according to the manufacturer's recommendations (Affymetrix).

scan_protocol: All arrays were scanned using Affymetrix GeneChip Scanner 3000 7G and processed using GeneChip® Command Console Software (AGCC).

data_processing: Microarray analysis was done using Partek Genomic Suite 6.6 (PGS, Version 6.6, Partek Inc.) using default parameters. Briefly, microarray CEL files were pre-processed using the RMA (Robust Multi-Array Average) background correction and quantile normalization to correct for array biases. Probe level intensities were log-transformed using base 2 and summarized using the Median Polish. One sample (6518LM) was excluded from further analysis because it failed multiple quality metrics.

source_name: normal mammary gland

label_protocol: cDNA samples were processed using the GeneChip HT 3' IVT Express Kit (Affymetrix, Santa Clara, California) according to the manufacturer's protocol.

growth_protocol: Balb/C nude mice were inoculated subcutaneously with 50,000 JygMC(A) cells into the 4th mammary gland, which resulted in tumor growth and subsequent metastasis to the lungs. Mouse mammary primary tumor were dissected 30 days after the cell injection, while lung nodules were collected 50 days after the injection. Normal tissue samples were harvested from healthy Balb/C nude mice.

extract_protocol: All tissue samples were snap frozen in liquid nitrogen. RNAs were extracted using TRIzol reagent according to the manufacturer's recommendations (Invitrogen, Carlsbad, CA). Total RNA from cells in culture was isolated and purified using the RNeasy Mini Kit and subjected to DNAse treatment (Qiagen, Gaithersburg, MD) in accordance to manufacturer’s instructions. Following, 1ug of total RNA was reverse transcribed using the RETROscript® kit (Ambion, Carlsbad, CA) according to the manufacturer's recommendations.

value: normal mammary gland

tag: date

value: BalbC nude


title: normal mammary gland, biological rep2

description: normal mammary gland


title: Rostral.LC.60d.1


title: Rostral.LC.20d.3


title: Rostral.LC.30d.1


title: normal lung parenchyma, biological rep2

description: normal lung parenchyma

source_name: normal lung parenchyma

value: normal lung parenchyma


title: Rostral.LC.10d.2


title: mammary tumors, biological rep11

description: Primary tumor

source_name: Primary tumor

value: Mammary Primary tumor


title: Rostral.LC.20d.2


title: normal mammary gland, biological rep1

description: normal mammary gland


title: Rostral.LC.10d.3


title: mammary tumors, biological rep10

description: Primary tumor


title: Rostral.LC.20d.1


title: mammary tumors, biological rep8

description: Primary tumor


title: normal lung parenchyma, biological rep1

description: normal lung parenchyma


title: mammary tumors, biological rep7

description: Primary tumor


title: mammary tumors, biological rep5

description: Primary tumor


title: Rostral.LC.03d.1


title: Rostral.LC.03d.2


title: mammary tumors, biological rep4

description: Primary tumor


title: Rostral.LC.03d.3


title: Rostral.LC.10d.1


title: mammary tumors, biological rep9

description: Primary tumor


title: mammary tumors, biological rep2

description: Primary tumor


title: Rostral.LC.01d.3


title: mammary tumors, biological rep3

description: Primary tumor


title: Rostral.LC.01d.2


title: Rostral.ET.90d.2

value: Empty tube(ET)


title: mammary tumors, biological rep6

description: Primary tumor


title: Rostral.LC.01d.1


title: mammary tumor metastases to lung, biological rep8

description: Lung metastasis

source_name: Lung metastasis

value: Lung metastasis


title: Rostral.ET.90d.1


title: Rostral.ET.90d.3


title: mammary tumors, biological rep1

description: Primary tumor


title: mammary tumor metastases to lung, biological rep9

description: Lung metastasis


title: Rostral.ET.60d.1


title: mammary tumor metastases to lung, biological rep4

description: Lung metastasis


title: mammary tumor metastases to lung, biological rep1

description: Lung metastasis


title: Rostral.ET.60d.3


title: mammary tumor metastases to lung, biological rep5

description: Lung metastasis


title: Rostral.ET.20d.3


title: Rostral.ET.30d.2


title: mammary tumor metastases to lung, biological rep6

description: Lung metastasis


title: mammary tumor metastases to lung, biological rep7

description: Lung metastasis


title: Cell line

description: Monolayer Cell Line

source_name: Monolayer cell line

value: Cell line


title: Rostral.ET.30d.3


title: Rostral.ET.20d.2


title: Rostral.ET.60d.2


title: mammary tumor metastases to lung, biological rep2

description: Lung metastasis


title: Rostral.ET.30d.1


title: Rostral.ET.03d.3


title: Rostral.ET.03d.2


title: mammary tumor metastases to lung, biological rep3

description: Lung metastasis


title: Rostral.ET.01d.1


title: Rostral.ET.10d.2


title: Rostral.ET.01d.2


title: Rostral.ET.10d.1


title: Rostral.ET.20d.1


title: Rostral.ET.03d.1


title: Rostral.NT3.90d.2


title: Rostral.ET.01d.3


title: 3D spheres cell line

description: 3D spheres Cell line

source_name: 3D spheres cell line


title: Rostral.NT3.90d.3


title: Rostral.NT3.90d.1


title: Rostral.NT3.60d.3


title: Rostral.NT3.60d.2


title: Rostral.NT3.60d.1


title: Rostral.NT3.20d.3


title: Rostral.NT3.30d.3


title: Rostral.NT3.30d.2


title: Rostral.NT3.20d.2


title: Rostral.NT3.10d.2


title: Rostral.NT3.30d.1


title: Rostral.NT3.20d.1


title: Rostral.NT3.10d.3


title: Rostral.NT3.10d.1


title: normal lung parenchyma, biological rep3

description: normal lung parenchyma


title: Rostral.NT3.03d.2


title: Rostral.NT3.03d.1


title: Rostral.NT3.03d.3


title: Uninjured .x.2

source_name: Uninjured

value: Uninjured 5mm tissue

value: Uninjured

value: x


title: Rostral.NT3.01d.1


title: Uninjured .x.3


title: Middle.LC.90d.3

value: Middle region 5mm tissue