title: WT.MEF.IFNa

city: Nottingham

first: Andreas

last: Begitt

address: Clifton Boulevard

department: School of Life Sciences

institute: University of Nottingham

hyb_protocol: Labeled cDNAs were hybridized to whole mouse genome microarrays (4x44k, Agilent) using Agilent’s Gene Expression Hybridization kit, Microarray Hybridization Chamber kit, and the microarray hybridization oven as per Agilent's protocol.

scan_protocol: Hybridized arrays were scanned with Agilent G2565CA microarray scanner by Dr. Lisa Olohan (University of Liverpool, Liverpool, UK).

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and linear LOWESS normalization.

source_name: primary WT-MEFs untreated

label_protocol: Total RNA (100ng) were reverse transcribed to cDNA using AffinityScript Multiple Temperature cDNA Synthesis kit (Agilent) and labeled using Two-color RNA Spike-In kit (Agilent) according the manufacturer’s protocols.

extract_protocol: Total RNA from 1.1x10e6 cells was isolated using the Absolutely RNA Miniprep Kit (Agilent) according to the manufacturer’s recommendations. The integrity of the isolated RNA was confirmed by electrophoresis using 1.5% (w/v) agarose gels with TBE running buffer. RNA was flash-frozen on dry ice and stored at -80⁰C.

treatment_protocol: Primary embryonic fibroblasts (MEFs) from wild type or KI littermates mice were kept in growth medium (DMEM supplemented with 10% FBS and 1% penicillin/streptomycin) in a humidified incubator with 5% CO2 at 37⁰C. When cultures reached ~80% confluence, MEFs were passaged using trypsin according to standard cell culture protocols. For gene expression determination, ~80% confluent cultures were kept for 15hrs in serum-reduced DMEM (1% FBS) to discern expression profiles in the absence of mitogenic stimuli. This was followed by 6hrs in growth medium without or with either mouse IFN-alpha (1000 U/ml) or mouse IFN-gamma (50 U/ml).. Cells were then washed in phosphate-buffered saline (PBS), trypsinized, and collected by centrifugation (1000 x g for 10min at room temperature). Subsequently total RNA was extracted immediately, or cells were stored at -80⁰C for later RNA extraction.

tag: strain

tag: cell type

value: Primary embryonic fibroblasts (MEFs)

tag: agent

value: untreated

source_name: primary WT-MEFs treated with IFNa for 6hrs

value: IFNa


title: KI.MEF.IFNa

status: Public on Jan 12 2014

type: RNA

country: United Kingdom

molecule: total RNA

organism: Mus musculus

source_name: primary KI-MEFs untreated

tag: genotype/variation

value: KI

source_name: primary KI-MEFs treated with IFNa for 6hrs


title: Patient 6

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

country: France

institute: INSA

description: This sample is of human frozen breast cancer tumors

hyb_protocol: One µg ds-cDNA was Cy3 labeled using One-Color DNA labeling kit (NimbleGen Roche Diagnostics, Meylan, France). Hybridization on our Roche NimbleGen 4x72K custom microarray, washing slides and scan were performed according to the manufacturer’s protocol (NimbleGen Roche Diagnostics, Meylan, France).

scan_protocol: Scanning was performed on NimbleGen MS 200 scanner, following the standard operating protocol. See www.nimblegen.com. DEVA software v1.2 (NimbleGen Roche Diagnostics, Meylan, France) was used to extract the raw intensity values.

data_processing: All data (.pair files) were RMA background corrected (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), log2-transformed, summarized by a robust mean. Then an housekeeping normalization was done on the experimental data.

organism: Homo sapiens

source_name: Human frozen breast cancer tumors

label_protocol: Double-stranded cDNA (ds-cDNA) was synthesized from 2 μg of total RNA using SuperScript One cycle kit (Invitrogen Life Technologies, Saint-Aubin, France) with random primers and Oligo(dT) primers, then cleaned with MinElute PCR Purification Kit (Qiagen, Courtaboeuf, France)

growth_protocol: 151 frozen breast cancer tumors from the tumor bank of the Claudius Regaud Institute (ICR Toulouse, France) were selected

extract_protocol: Total RNA was extracted from 12 µm-thickcryostat sections of with Qiazol and RNeasy Lipid Tissue Kit (Qiagen, Courtaboeuf, France). The concentration of total RNA obtained from each tumor sample was determined using a Nanodrop® spectrophotometer (Labtech, Palaiseau, France) and the integrity of the RNA was assessed using a 2100 Bioanalyzer® (Agilent Technologies, Massy, France). The percentage of tumor cells was evaluated on frozen a section stained with hematoxylin-eosin.

tag: tumor bank

tag: individual

tag: disease state

value: invasive breast carcinoma

tag: tumor stage


title: Patient 9

value: Claudius Regaud Institute (ICR Toulouse, France)


title: Patient 5


title: Patient 2


title: KI.MEF.IFNg

source_name: primary KI-MEFs treated with IFNg for 6hrs

value: IFNg


title: schiz_str_18

status: Public on Jan 11 2014

city: Groton

first: Thomas

middle: A

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

country: USA

institute: Pfizer

hyb_protocol: Five (5) ug of fragmented, biotin-labeled cDNA was hybridized to Affymetrix Human Genome U133_Plus 2 Gene Chips for 18 hours, then washed/stained according to manufacturer's recommendations using the Affymetrix 450 fluidics station.

scan_protocol: Gene chips were scanned using an Affymetrix 3000 array scanner.

data_processing: R/Bioconductor was used to apply the Robust Multi-Array Average (RMA) methodology to generate expression values.  Brain regions were normalized separately.

label: biotin

source_name: Associative striatum, schizophrenia

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

extract_protocol: Trizol extraction of total RNA was performed.

tag: age

tag: gender

value: F

tag: race

value: W

tag: pmi

tag: ph

tag: rin

tag: tissue

value: Associative striatum

value: schizophrenia


title: schiz_str_16

value: B


title: schiz_str_15

value: M


title: WT.MEF.IFNg

value: WT

source_name: primary WT-MEFs treated with IFNg for 6hrs


title: schiz_str_12


title: schiz_str_17


title: schiz_str_9


title: schiz_str_10


title: schiz_str_8


title: schiz_str_14


title: schiz_str_13


title: schiz_str_7


title: schiz_str_11


title: schiz_str_4


title: schiz_str_6


title: schiz_str_1


title: schiz_str_3


title: schiz_str_5


title: schiz_str_2


title: MDD_str_16

source_name: Associative striatum, major depressive disorder

value: major depressive disorder


title: MDD_str_13


title: MDD_str_15


title: MDD_str_9


title: MDD_str_7


title: MDD_str_12


title: MDD_str_11


title: MDD_str_4


title: MDD_str_1


title: MDD_str_6


title: MDD_str_14


title: control_str_18

source_name: Associative striatum, control

value: control


title: MDD_str_5


title: MDD_str_2


title: MDD_str_10


title: MDD_str_17


title: control_str_11


title: MDD_str_8


title: control_str_14


title: control_str_17


title: control_str_16


title: control_str_12


title: control_str_13


title: control_str_5


title: control_str_15


title: control_str_9


title: control_str_6


title: control_str_7


title: control_str_10


title: control_str_8


title: control_str_4


title: control_str_2


title: control_str_1


title: bipolar_str_13

source_name: Associative striatum, bipolar disorder

value: bipolar disorder


title: bipolar_str_16


title: bipolar_str_9


title: bipolar_str_7


title: bipolar_str_17


title: bipolar_str_18


title: bipolar_str_4


title: bipolar_str_12


title: bipolar_str_1


title: schiz_pfc_9

source_name: Pre-frontal cortex (BA46), schizophrenia

value: Pre-frontal cortex (BA46)


title: bipolar_str_6


title: bipolar_str_10


title: bipolar_str_3


title: bipolar_str_5


title: bipolar_str_2


title: control_str_3


title: bipolar_str_14


title: schiz_pfc_4


title: schiz_pfc_7


title: schiz_pfc_6


title: bipolar_str_8


title: bipolar_str_11


title: schiz_pfc_5


title: schiz_pfc_1


title: schiz_pfc_18


title: schiz_pfc_19


title: schiz_pfc_16


title: schiz_pfc_14


title: schiz_pfc_13


title: schiz_pfc_11


title: schiz_pfc_12


title: schiz_pfc_3


title: MDD_pfc_9

source_name: Pre-frontal cortex (BA46), major depressive disorder


title: schiz_pfc_10


title: MDD_pfc_6


title: MDD_pfc_1


title: MDD_pfc_3


title: MDD_pfc_19


title: MDD_pfc_5


title: MDD_pfc_4


title: MDD_pfc_8


title: Sa vs Ref 6h-replicate 4 -green

city: Castanet Tolosan

first: Rachel

last: Rupp

address: chemin de borde rouge

department: animal genetics

institute: INRA

hyb_protocol: GeneTac automated hybridization station

scan_protocol: BlueFuse

data_processing:
filtering according to spot quality (uniformity and saturation) provided by BlueFuse: spots with (flag=E and quality=0) excluded.
Normalisation: log (Intensity) of each dye was reduced and centered within slide using a in-house programme with the SAS software

organism: Bos taurus

source_name: cultured mammary epithelialcells

label_protocol: RNA labeling  was carried out with the  fluorescent cyanine dyes Cy3 or Cy5

extract_protocol: Total RNA  extracted by a double extraction method using first Trizol (InvitroGen) and then RNeasy (Qiagen) column purification

tag: breed

value: Holstein

tag: stimulus

tag: time


title: Sa vs Ref 6h-replicate 4 -red

value: SA


title: MDD_pfc_16


title: Sa vs Ref 3h-replicate 4 -green


title: MDD_pfc_11


title: Sa vs Ref 6h-replicate 3 -green


title: Sa vs Ref 3h-replicate 4 -red


title: MDD_pfc_15


title: MDD_pfc_13


title: MDD_pfc_17


title: MDD_pfc_14


title: Sa vs Ref 6h-replicate 3 -red


title: MDD_pfc_7


title: MDD_pfc_12


title: Sa vs Ref 3h-replicate 3 -green


title: MDD_pfc_10


title: LPS vs Ref 6h-replicate 4 -green


title: Sa vs Ref 3h-replicate 3 -red


title: LPS vs Ref 6h-replicate 4-red

value: LPS


title: control_pfc_9

source_name: Pre-frontal cortex (BA46), control


title: control_pfc_7


title: control_pfc_6


title: LPS vs Ref 3h-replicate 4 -red


title: control_pfc_5


title: LPS vs Ref 6h-replicate 3 -red


title: control_pfc_4


title: LPS vs Ref 6h-replicate 3 -green


title: control_pfc_3


title: LPS vs Ref 3h-replicate 3 -green


title: control_pfc_2


title: LPS vs Ref 3h-replicate 3 -red


title: LPS vs Ref 6h-replicate 2 -green


title: LPS vs Ref 3h-replicate 4 -green


title: LPS vs Ref 3h-replicate 2 -green


title: LPS vs Ref 6h-replicate 2 -red


title: LPS vs Ref 3h-replicate 2 -red


title: control_pfc_18


title: control_pfc_8


title: LPS vs Ref 6h-replicate 1 -green


title: control_pfc_1


title: LPS vs Ref 3h-replicate 1 -green


title: LPS vs Ref 6h-replicate 1 -red


title: control_pfc_15


title: LPS vs Ref 3h-replicate 1 -red


title: SA vs Ref 6h-replicate 2 -green


title: SA vs Ref 6h-replicate 2 -red


title: control_pfc_17


title: control_pfc_12


title: control_pfc_19


title: SA vs Ref 3h-replicate 2 -green


title: control_pfc_10


title: control_pfc_14


title: control_pfc_16


title: bipolar_pfc_9

source_name: Pre-frontal cortex (BA46), bipolar disorder


title: control_pfc_11


title: control_pfc_13


title: SA vs Ref 3h-replicate 2 -red


title: SA vs Ref 6h-replicate 1 -red


title: bipolar_pfc_8


title: bipolar_pfc_7


title: SA vs Ref 3h-replicate 1 -red


title: SA vs Ref 3h-replicate 1 -green


title: SA vs Ref 6h-replicate 1 -green


title: bipolar_pfc_3


title: bipolar_pfc_4


title: bipolar_pfc_6


title: bipolar_pfc_1


title: bipolar_pfc_15


title: bipolar_pfc_16


title: bipolar_pfc_17


title: BM_treated_6H_rep1 (HDT_P211)

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

hyb_protocol: Samples were hybridized on Affymetrix Mouse Gene 1.0 ST

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

data_processing: Raw data were processed with the RMA normalisation (Bioconductor R affy package) to generate log2 normalized intensity signal.

source_name: Bone marrow sample from viral transduction model

label_protocol: The labeling of the extracted RNA was performed according to the manufacturer's instruction (Affymetrix)

growth_protocol: Samples stored at -80 C

extract_protocol: Tumor samples (10 to 50 mg) were extracted using Manual-Rneasy Mini (Qiagen)

value: bone marrow

tag: fusion protein

value: PML/RARA

tag: model

value: viral transduction

tag: background

tag: treatment

value: retinoic acid

tag: batch


title: bipolar_pfc_5

value: W

tag: disease state


title: bipolar_pfc_14


title: BM_treated_6H_rep1 (HDT_P210)


title: BM_untreated_12H_rep1 (HDT_P195)


title: bipolar_pfc_13

value: F


title: bipolar_pfc_2


title: bipolar_pfc_10


title: bipolar_pfc_11


title: BM_treated_6H_rep1 (HDT_P190)

value: pml-/-


title: BM_untreated_6H_rep1 (HDT_P189)


title: BM_untreated_6H_rep1 (HDT_P209)


title: BM_treated_12H_rep1 (HDT_P181)


title: BM_treated_12H_rep1 (HDT_P184)


title: BM_untreated_12H_rep1 (HDT_P182)


title: BM_treated_12H_rep1 (HDT_P188)


title: bipolar_pfc_12


title: schiz_hip_9

source_name: hippocampus, schizophrenia

value: B

value: hippocampus

value: schizophrenia


title: BM_treated_12H_rep1 (HDT_P180)

value: WT


title: schiz_hip_6

value: M


title: schiz_hip_7


title: BM_treated_12H_rep1 (HDT_P178)


title: schiz_hip_8


title: BM_treated_12H_rep1 (HDT_P179)


title: BM_untreated_12H_rep1 (HDT_P176)


title: BM_treated_6H_rep1 (HDT_P170)


title: schiz_hip_4


title: schiz_hip_2


title: BM_treated_12H_rep1 (HDT_P173)


title: BM_treated_12H_rep1 (HDT_P175)


title: BM_untreated_12H_rep1 (HDT_P172)


title: schiz_hip_5


title: BM_treated_6H_rep1 (HDT_P168)


title: BM_treated_6H_rep1 (HDT_P171)


title: schiz_hip_1


title: schiz_hip_19


title: schiz_hip_3


title: schiz_hip_18


title: schiz_hip_12


title: schiz_hip_14


title: BM_treated_6H_rep1 (HDT_P162)


title: schiz_hip_11


title: BM_untreated_6H_rep1 (HDT_P167)


title: BM_untreated_6H_rep1 (HDT_P161)


title: schiz_hip_10


title: BM_treated_6H_rep1 (HDT_251)


title: BM_treated_6H_rep1 (HDT_P165)


title: MDD_hip_9

source_name: hippocampus, major depressive disorder

value: major depressive disorder


title: BM_treated_6H_rep1 (HDT_250)


title: MDD_hip_8


title: BM_untreated_6H_rep1 (HDT_249)


title: BM_untreated_6H_rep1 (HDT_245)


title: BM_treated_6H_rep1 (HDT_247)


title: MDD_hip_3


title: BM_treated_6H_rep1 (HDT_244)


title: MDD_hip_7


title: BM_treated_6H_rep1 (HDT_242)


title: MDD_hip_6


title: BM_treated_6H_rep1 (HDT_246)


title: MDD_hip_2


title: BM_treated_6H_rep1 (HDT_239)


title: MDD_hip_1


title: MDD_hip_19


title: MDD_hip_4


title: BM_treated_12H_rep1 (HDT_099)

source_name: Bone marrow sample from transgenic model

value: transgenics


title: MDD_hip_16


title: BM_treated_6H_rep1 (HDT_238)


title: BM_untreated_6H_rep1 (HDT_237)


title: MDD_hip_17


title: MDD_hip_15


title: BM_untreated_6H_rep1 (HDT_241)


title: MDD_hip_13


title: BM_treated_6H_rep1 (HDT_095)


title: BM_treated_6H_rep1 (HDT_094)


title: BM_untreated_12H_rep1 (HDT_096)


title: MDD_hip_12


title: MDD_hip_11


title: MDD_hip_10


title: BM_treated_12H_rep1 (HDT_100)


title: MDD_hip_14


title: control_hip_6

source_name: hippocampus, control

value: control


title: BM_treated_6H_rep1 (HDT_093)


title: control_hip_8


title: BM_treated_6H_rep1 (HDT_090)


title: BM_untreated_12H_rep1 (HDT_098)


title: control_hip_7


title: control_hip_3


title: control_hip_4


title: control_hip_2


title: BM_treated_6H_rep1 (HDT_091)


title: BM_untreated_6H_rep1 (HDT_089)


title: BM_treated_12H_rep1 (HDT_087)


title: BM_treated_12H_rep1 (HDT_086)


title: BM_treated_12H_rep1 (HDT_083)


title: BM_treated_12H_rep1 (HDT_085)


title: BM_treated_6H_rep1 (HDT_092)


title: BM_untreated_6H_rep1 (HDT_088)


title: BM_treated_12H_rep1 (HDT_084)


title: BM_treated_6H_rep1 (HDT_050)

value: PLZF/RARA


title: control_hip_18


title: control_hip_17


title: BM_untreated_12H_rep1 (HDT_081)


title: control_hip_15


title: control_hip_16


title: control_hip_1


title: BM_untreated_12H_rep1 (HDT_080)


title: control_hip_19


title: HFD-UNX_4

city: Zurich

first: Zhibo

last: Gai

state: Schweiz

address: Wagistrasse 14

department: Department of Clinical Pharmacology and Toxicology

country: Switzerland

institute: University Hospital Zurich

description: Gene expression in remnant kidney after 20 weeks of high fat diet

hyb_protocol: 1.6 μg of the obtained Cy3-labeled cRNA was hybridized to Mouse GE 4x44K v2 Microarrays (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol. Briefly, cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Genome Microarray 4x44K v2 (Agilent-026655) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Microarray Scanner System (Agilent, Santa Clara, CA).

data_processing: Raw intensity data were obtained using Agilent's Feature Extraction Software version 10.7 for array image analysis and the calculation of spot intensity measurements.  Data analysis was carried out with R/Bioconductor.  The processed intensities and normalized across samples were loaded by using quantile normalization.

source_name: UNX kidney, HFD 20 weeks, mouse 4

label_protocol: 100 ng of total RNA was reverse-transcribed into double-stranded cDNA, which was linearly amplified and labelled with Cy3 dye. Quantification was done by using a Nanodrop spectrophotometer (Witec, Luzern, Switzerland) and quality assessment  was done with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

extract_protocol: RNA was extracted from frozen kidney using RNeasy Microarray Tissue mini kit (73304, Qiagen, Germany), followed by on column DNase digestion to remove any contaminating genomic DNA.

treatment_protocol: Male C57/BJ mice aged 6 weeks were randomly assigned to uninephrectomy (UNX) or sham procedures and fed with a high fat diet or control chow diet. Mice were divided into 4 groups of 6: Sham-chow, UNX-chow, Sham-HFD and UNX-HFD.  For uninephrectomy, the left kidney was surgically removed via a left paramedian incision on the back under anesthesia.  The adrenal gland was carefully freed from the upper pole of the renal capsule before the renal pedicle was ligated and the kidney removed.  For sham surgery, the kidney was manipulated without ablation.  All mice were sacrificed under anesthesia 20 weeks after surgery and kidneys were harvested.

tag: strain

value: uninephrectomy

tag: diet

value: high fat

value: kidney

value: male


title: control_hip_5

tag: age

tag: gender


title: BM_treated_12H_rep1 (HDT_082)

value: bone marrow

value: PML/RARA

value: retinoic acid


title: BM_treated_6H_rep1 (HDT_048)


title: HFD-sham_3

description: Gene expression in sham kidney after 20 weeks of high fat diet

source_name: sham kidney, HFD 20 weeks, mouse 3

value: sham


title: BM_treated_12H_rep1 (HDT_043)


title: BM_untreated_12H_rep1 (HDT_041)


title: BM_untreated_6H_rep1 (HDT_045)


title: BM_treated_12H_rep1 (HDT_044)


title: HFD-UNX_3

source_name: UNX kidney, HFD 20 weeks, mouse 3


title: BM_treated_6H_rep1 (HDT_047)


title: HFD-sham_2

source_name: sham kidney, HFD 20 weeks, mouse 2


title: control_hip_14

tag: race

value: W

tag: pmi


title: BM_treated_6H_rep1 (HDT_049)


title: BM_untreated_6H_rep1 (HDT_046)


title: bipolar_hip_9

source_name: hippocampus, bipolar disorder

tag: ph

tag: rin

value: hippocampus

value: bipolar disorder


title: control_hip_13

value: F

tag: tissue


title: HFD-UNX_2

source_name: UNX kidney, HFD 20 weeks, mouse 2


title: HFD-UNX_1

source_name: UNX kidney, HFD 20 weeks, mouse 1


title: control_hip_12


title: BM_treated_6H_rep1 (HDT_026)

value: WT


title: BM_treated_12H_rep1 (HDT_020)


title: control_hip_11


title: BM_untreated_12H_rep1 (HDT_017)


title: BM_untreated_6H_rep1 (HDT_023)


title: LFD-UNX_4

description: Gene expression in remnant kidney after 20 weeks of chow diet

source_name: UNX kidney, LFD 20 weeks, mouse 4

value: low fat


title: bipolar_hip_7


title: BM_treated_6H_rep1 (HDT_025)

value: transgenics


title: control_hip_10

value: M

value: control


title: BM_treated_12H_rep1 (HDT_019)

value: PLZF/RARA


title: BM_untreated_6H_rep1 (HDT_024)


title: bipolar_hip_8


title: bipolar_hip_6


title: LFD-UNX_2

source_name: UNX kidney, LFD 20 weeks, mouse 2

value: uninephrectomy


title: bipolar_hip_5


title: Foxd1-/-_Day8, biological rep2

city: Barcelona

first: Miki

last: Ebisuya

address: PRBB Building, C/ Dr. Aiguader, 88

department: EMBL Barcelona

country: Spain

institute: EMBL

description: Gene expression data from Foxd1-/- MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4), day 8.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol with Affymetrix Scanner 3000 7G

data_processing: The probeset signals were calculated using Agilent GeneSpring software.

label_protocol: Biotinylated cRNAs were prepared from 300 ng total RNAs according to the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay manual.

growth_protocol: MEFs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% foetal bovine serum (FBS).

extract_protocol: Total RNAs were extracted using Qiagen RNeasy kit according to the manufacturer’s protocol. On-column DNase digestion was performed.

treatment_protocol: MEFs were infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4) at day 0.

tag: day

tag: genotype/variation


title: bipolar_hip_2


title: Foxd1+/-_Day8, biological rep1

description: Gene expression data from Foxd1+/- MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4), day 8.


title: HFD-sham_1

source_name: sham kidney, HFD 20 weeks, mouse 1

value: high fat

value: kidney


title: LFD-sham_4

description: Gene expression in sham kidney after 20 weeks of chow diet

source_name: sham kidney, LFD 20 weeks, mouse 4

value: male


title: bipolar_hip_4


title: LFD-UNX_3

source_name: UNX kidney, LFD 20 weeks, mouse 3


title: LFD-sham_3

source_name: sham kidney, LFD 20 weeks, mouse 3


title: Foxd1+/+_Day8, biological rep1

description: Gene expression data from Foxd1+/+ MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4), day 8.


title: LFD-UNX_1

source_name: UNX kidney, LFD 20 weeks, mouse 1


title: LFD-sham_2

source_name: sham kidney, LFD 20 weeks, mouse 2


title: Foxd1+/+_Day8, biological rep2

source_name: Foxd1+/+ MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4)


title: bipolar_hip_1


title: Foxd1+/-_Day8, biological rep2

source_name: Foxd1+/- MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4)


title: Foxd1-/-_Day8, biological rep1

source_name: Foxd1-/- MEFs infected with retroviruses encoding the three transcription factors (Oct4, Sox2 and Klf4)


title: LFD-sham_1

source_name: sham kidney, LFD 20 weeks, mouse 1


title: bipolar_hip_15


title: bipolar_hip_14


title: bipolar_hip_13


title: bipolar_hip_19


title: bipolar_hip_18


title: bipolar_hip_10


title: bipolar_hip_12


title: bipolar_hip_11


title: bipolar_hip_16


title: patient 28 normal tissue no smoking no obese Par042U133Plus2.0.CEL

status: Public on Jan 10 2014

city: Jacksonville

first: Daniel

last: Serie

state: Florida

address: 4500 San Pablo Rd

institute: Mayo Clinic

hyb_protocol: The products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA. The IVT products were then column-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips® at 45º C for 16 h. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin

scan_protocol: Arrays were scanned in an Affymetrix GeneChip® Scanner 3000

data_processing: Base-2 logarithm transformed intensity data from the two batches of samples were normalized within each batch using frozen robust multi-array analysis (frozen RMA).

source_name: kidney tissue

label_protocol: Microarray analysis was conducted according to manufacturer’s instructions for the Affymetrix One Cycle Target Labeling and Control Reagents kit

extract_protocol: The Mayo Biospecimen Accessioning and Processing Core performed RNA extractions using kits and protocols from the Qiagen miRNEasy kit and Qiagen Qiacube instrument.

tag: patient

value: normal

tag: smoking

value: no

tag: obese

tag: duplicate

value: yes


title: patient 28 tumor tissue no smoking no obese Par041U133Plus2.0.CEL

value: tumor

tag: batch


title: patient 160 tumor tissue no smoking no obese Par007U133Plus2.0.CEL


title: patient 160 normal tissue no smoking no obese Par008U133Plus2.0.CEL


title: patient 523 tumor tissue no smoking no obese Par053HG-U133_Plus_2.cel


title: patient 785 tumor tissue no smoking no obese Par045HG-U133_Plus_2.cel


title: patient 41 normal tissue no smoking yes obese Par044U133Plus2.0.CEL


title: patient 521 normal tissue no smoking yes obese Par052HG-U133_Plus_2.cel


title: patient 559 tumor tissue no smoking no obese Par055HG-U133_Plus_2.cel


title: patient 785 normal tissue no smoking no obese Par046HG-U133_Plus_2.cel


title: patient 806 tumor tissue no smoking no obese Par049HG-U133_Plus_2.cel


title: patient 41 tumor tissue no smoking yes obese Par043U133Plus2.0.CEL


title: patient 806 normal tissue no smoking no obese Par050HG-U133_Plus_2.cel


title: patient 20 normal tissue no smoking yes obese Par038U133Plus2.0.CEL


title: patient 684 tumor tissue no smoking no obese Par057HG-U133_Plus_2.cel


title: patient 799 tumor tissue no smoking no obese Par047HG-U133_Plus_2.cel


title: patient 407 tumor tissue no smoking yes obese Par033U133Plus2.0.CEL


title: patient 20 tumor tissue no smoking yes obese Par037U133Plus2.0.CEL


title: patient 452 tumor tissue no smoking no obese Par035U133Plus2.0.CEL


title: patient 264 normal tissue no smoking yes obese Par024U133Plus2.0.CEL


title: patient 275 tumor tissue no smoking no obese Par027U133Plus2.0.CEL


title: patient 252 normal tissue no smoking yes obese Par022U133Plus2.0.CEL


title: patient 452 normal tissue no smoking no obese Par036U133Plus2.0.CEL


title: patient 521 tumor tissue no smoking yes obese Par051HG-U133_Plus_2.cel


title: patient 264 tumor tissue no smoking yes obese Par023U133Plus2.0.CEL


title: patient 275 normal tissue no smoking no obese Par028U133Plus2.0.CEL


title: patient 407 normal tissue no smoking yes obese Par034U133Plus2.0.CEL


title: patient 363 normal tissue no smoking yes obese Par032U133Plus2.0.CEL


title: patient 363 tumor tissue no smoking yes obese Par031U133Plus2.0.CEL


title: patient 202 normal tissue no smoking no obese Par018U133Plus2.0.CEL


title: patient 202 tumor tissue no smoking no obese Par017U133Plus2.0.CEL


title: patient 181 tumor tissue no smoking yes obese Par013U133Plus2.0.CEL


title: patient 69 normal tissue no smoking yes obese Par006U133Plus2.0.CEL


title: patient 196 normal tissue no smoking no obese Par016U133Plus2.0.CEL


title: patient 18 tumor tissue no smoking no obese Par001U133Plus2.0.CEL


title: patient 177 normal tissue no smoking yes obese Par012U133Plus2.0.CEL


title: patient 163 tumor tissue no smoking yes obese Par009U133Plus2.0.CEL


title: patient 60 normal tissue no smoking yes obese Par004U133Plus2.0.CEL


title: patient 196 tumor tissue no smoking no obese Par015U133Plus2.0.CEL


title: patient 60 tumor tissue no smoking yes obese Par003U133Plus2.0.CEL


title: patient 181 normal tissue no smoking yes obese Par014U133Plus2.0.CEL


title: patient 163 normal tissue no smoking yes obese Par010U133Plus2.0.CEL


title: Nam7-gim-2

type: mixed

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

institute: Institut Pasteur

description: Comparison of RNA to DNA using molecular barcodes (the ratios reflect relative abundance of the DamP RNA molecules)

hyb_protocol: Hybridization was done in Roche RapidHyb buffer

scan_protocol: Genepix 4200AL and GenePix Pro v7

data_processing: The scans were processed using GenePix Pro, v7. The values from the obtained gpr files were filtered to keep only values for spots with an SNR > 10. Next, we selected the signal corresponding to the expected DAMP mRNA barcodes (noted XXX-U in the Spot_ID column) and performed a median based normalization of the signal.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae DamP pool with NAM7 deletion

label_protocol: Cy3 and Cy5 5' tagged oligonucleotides were used to amplify the barcode region with universal primers. PCR products were then mixed, precipitated in the presence of linear poly-acrylamide and prepared for hybridization

growth_protocol: The pool of DamP strains was combined with the three different mutant strains using the GIM protocol (Decourty et al., PNAS 2008). After selection of double mutant haploid cells, the pool of haploid strains was growth for 18 generations under double antibiotic selection (G418 and nurseothricin).

extract_protocol: RNA was extracted using a hot phenol/chloroform procedure. Genomic DNA was extracted from a different aliquot of the same sample through mechanical lysis (vortexing with glass beads). RNA was DNAse treated and reverse transcribed with an oligonucleotide specific for the DAMP extension. PCR amplification of the barcode region was followed by a second PCR amplification with Cy3 5' tagged oligonucleotide.

treatment_protocol: Cells in exponential growth were recovered by purification, washed once in cold water and stored at -80C until RNA or DNA extraction

tag: deletion

value: DamP pool with NAM7

value: Mix of haploid strains derived from BY4742/BY4741

molecule: genomic DNA


title: patient 888 normal tissue yes smoking no obese Par142HG-U133_Plus_2.cel


title: patient 69 tumor tissue no smoking yes obese Par005U133Plus2.0.CEL


title: patient 1018 tumor tissue yes smoking no obese Par133HG-U133_Plus_2.cel


title: patient 18 normal tissue no smoking no obese Par002U133Plus2.0.CEL


title: patient 263 tumor tissue yes smoking no obese Par137HG-U133_Plus_2.cel


title: patient 878 tumor tissue yes smoking no obese Par139HG-U133_Plus_2.cel


title: Nmd2-gim-2

source_name: S. cerevisiae DamP pool with NMD2 deletion

value: DamP pool with NMD2

tag: strain


title: Nmd2-gim-1


title: patient 1048 normal tissue no smoking no obese Par136HG-U133_Plus_2.cel


title: patient 878 normal tissue yes smoking no obese Par140HG-U133_Plus_2.cel


title: patient 263 normal tissue yes smoking no obese Par138HG-U133_Plus_2.cel


title: patient 177 tumor tissue no smoking yes obese Par011U133Plus2.0.CEL


title: patient 1048 tumor tissue no smoking no obese Par135HG-U133_Plus_2.cel


title: patient 888 tumor tissue yes smoking no obese Par141HG-U133_Plus_2.cel


title: patient 1018 normal tissue yes smoking no obese Par134HG-U133_Plus_2.cel


title: Nam7-gim-1


title: bipolar_hip_3

source_name: hippocampus, bipolar disorder

value: F

value: W

value: hippocampus

tag: disease state

value: bipolar disorder


title: Yel068c-gim-2

source_name: S. cerevisiae DamP pool with YEL068C deletion

value: DamP pool with YEL068C


title: patient 871 tumor tissue yes smoking no obese Par131HG-U133_Plus_2.cel


title: patient 829 normal tissue yes smoking no obese Par126HG-U133_Plus_2.cel


title: patient 853 normal tissue yes smoking no obese Par128HG-U133_Plus_2.cel


title: patient 871 normal tissue yes smoking no obese Par132HG-U133_Plus_2.cel


title: patient 853 tumor tissue yes smoking no obese Par127HG-U133_Plus_2.cel


title: patient 746 tumor tissue yes smoking no obese Par123HG-U133_Plus_2.cel


title: patient 746 normal tissue yes smoking no obese Par124HG-U133_Plus_2.cel


title: patient 865 tumor tissue yes smoking yes obese Par129HG-U133_Plus_2.cel


title: patient 740 tumor tissue yes smoking yes obese Par121HG-U133_Plus_2.cel


title: patient 723 tumor tissue no smoking no obese Par115HG-U133_Plus_2.cel


title: patient 740 normal tissue yes smoking yes obese Par122HG-U133_Plus_2.cel


title: patient 726 normal tissue no smoking no obese Par118HG-U133_Plus_2.cel


title: patient 829 tumor tissue yes smoking no obese Par125HG-U133_Plus_2.cel


title: patient 739 normal tissue no smoking no obese Par120HG-U133_Plus_2.cel


title: patient 723 normal tissue no smoking no obese Par116HG-U133_Plus_2.cel


title: patient 865 normal tissue yes smoking yes obese Par130HG-U133_Plus_2.cel


title: patient 712 tumor tissue no smoking no obese Par113HG-U133_Plus_2.cel


title: patient 739 tumor tissue no smoking no obese Par119HG-U133_Plus_2.cel


title: patient 712 normal tissue no smoking no obese Par114HG-U133_Plus_2.cel


title: patient 726 tumor tissue no smoking no obese Par117HG-U133_Plus_2.cel


title: patient 705 normal tissue yes smoking yes obese Par112HG-U133_Plus_2.cel


title: patient 705 tumor tissue yes smoking yes obese Par111HG-U133_Plus_2.cel


title: patient 670 normal tissue yes smoking no obese Par110HG-U133_Plus_2.cel


title: Sample 3_Agilent 244K

type: genomic

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

description: Case 6_S01_CGH-v4_95_Feb07

hyb_protocol: The protocol Oligonucleotide Array-Based CGH for Genomic DNA Analysis (ULS labeling for Blood, Cells, Tissues or FFPE) was used.

scan_protocol: Scanned on an Agilent G2565B scanner.

data_processing: Raw data were generated from scanned images using Agilent Feature Extraction Software (10.10.1.1). Log2ratios of background corrected values for tumour over normal DNA were calculated. Normalization was carried out on Agilent's CGH Analytics, integrated on the Agilent Genomic Workbench Standard Edition 6.5.0.58, using data from the internal set of control probes included in the microarray. Detection of Copy Number Alterations (CNAs) was performed using the ADM-2 algorithm, also implemented within the Agilent's genomics suite Genomic Workbench v5.0, with a threshold of 6.5 and a minimum of 5 consecutive probes and default settings of Nexus 6.0 Discovery Edition (Biodiscovery, El segundo, CA).  All alterations were analyzed by visual inspection of two different observers.

source_name: TUMOR, MYC-NEG LYMPHOMA CASE 6

label_protocol: As per manufacturer (Agilent)

extract_protocol: Genomic DNA was extracted from 8 B-cell lymphoma samples using the phenol-chloroform extraction method according to previously published protocols with minor modification. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis. All extracted DNAs had at least a PCR control gene band of 200 bp.

value: MYC-negative B-cell lymphoma

source_name: Normal genomic DNA

value: sex-matched control DNA


title: Sample 7_Agilent 244K

description: Case 11_CGH_1010_Sep10

source_name: TUMOR, MYC-NEG LYMPHOMA CASE 11


title: Sample 8_Agilent 244K

description: Case 12_S01_CGH_1010_Sep10

source_name: TUMOR, MYC-NEG LYMPHOMA CASE 12


title: HO1_no_rep2

city: Hsin Chu City

first: Hui-Teng

last: Cheng

address: No. 25, Lane 422, Section 1, Jingguo Road

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital Hsin-Chu Branch

hyb_protocol: Fluorescent targets were hybridized to the Rat Whole Genome OneArrayR (ROA v1) with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times), and the slides were dried by centrifugation.

scan_protocol: Scanned by an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).   The technical repeat data was tested by Pearson correlation coefficient calculation to check the reproducibility (R value > 0.975). The signal intensity of each spot was loaded into Rosetta Resolver SystemR (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver SystemR could remove both systematic and random errors. In brief, spots which ﬂag is less than 0 in all arrays were filtered out. Spots that passed the criteria were normalized by median scaling normalization method.
Normalized spot intensities were further transformed to gene expression log2 ratios between the control and treatment groups under Rosetta Resolver error model adjustment. The spots with log2 ratio ≥ 1 or log2 ratio ≤ -1 and P-value < 0.05 are tested for further analysis.

organism: Rattus norvegicus

label_protocol: Fluorescent aRNA targets were prepared from 2.5 μg total RNA samples using OneArrayR Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: Primary rat mesangial cell line was created from isolated rat glomeruli. Rat kidney cortex was grounded and passed through graded sieving (250 μm, 150 μm and 75 μm) to obtain single glomeruli. They were plated in culture dish supplemented with RPMI with 10% FBS (Hyclone Defined Fetal Bovine Serum). Mesangial cells outgrew other cell types in around 3 weeks and were verified by the presence of alpha-smooth muscle actin and the absence of pan-cytokeratin (from Santa Cruz; epithelial cell marker).

extract_protocol: Total RNA is extracted by Trizol method (done by the Phalanx)

treatment_protocol: Hydrogen peroxide at final concentration of 100 micromolar for 2 hours

tag: cell type

value: Primary rat mesangial cells

value: heme oxygenase-1 knocked down

tag: treated with


title: Sample 6_Agilent 244K

description: Case 10_CGH-v4_95_Feb07

source_name: TUMOR, MYC-NEG LYMPHOMA CASE 10

tag: gender

value: female


title: Sample 2_Agilent 244K

description: Case 5_S01_CGH-v4_95_Feb07

source_name: TUMOR, MYC-NEG LYMPHOMA CASE 5

value: male


title: HO1_H2O2_2hr_rep2

value: 100uM H2O2 for 2hrs


title: Sample 4_Agilent 244K

description: Case 7_S01_CGH-v4_95_Feb07

source_name: TUMOR, MYC-NEG LYMPHOMA CASE 7


title: patient 252 tumor tissue no smoking yes obese Par021U133Plus2.0.CEL

value: no

value: yes


title: patient 670 tumor tissue yes smoking no obese Par109HG-U133_Plus_2.cel

value: tumor


title: patient 652 normal tissue no smoking no obese Par108HG-U133_Plus_2.cel

value: normal


title: Powdery mildew-colonized leaves, water-vapor treated, rep 3

city: Springfield

first: Laszlo

middle: G

last: Kovacs

state: Missouri

address: 901 S  National Avenue

department: Biology

institute: Missouri State University

description:
Vitis_PH-3
Gene expression data from powdery mildew-infected grape leaves treated with water vapor 24 hours prior to sampling.

hyb_protocol: Hybridization of GeneChips were performed following guidelines of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA, 2000). cRNA was cleaned using the Affymetrix One-Cycle Target Labeling kit, and 15 µg of cRNA was heated at 94ºC for 35 min to break RNA molecules to 35- to 200-nucleotide fragments. The RNA was supplemented with hybridization buffer, and the resulting cocktail was heat-denatured for 5 min, incubated at 45ºC for 5 min, and centrifuged prior to loading on the GeneChip. Hybridization took place in an Affy hybridization oven model 640, at 45ºC for 16h. Washing and staining was performed on an Affymterix Fluidic Station 450. Fluorescence was amplified with streptavidin-phycoerythrin (SAPE) staining, followed by the addition of a biotinylated antibody (anti-streptavidin) solution, and by a final SAPE staining. Washing was performed using the he fluidics protocol Midi_Euk2v3.

scan_protocol: Images of hybridized GeneChip were captured in an Affymetrix GCS 3000 laser scanner and visualized using Affymetrix GeneChip Command Console (AGCC) following standard protocols.

data_processing: To calculate signal intensity values and detection calls in the Matrix Table, raw intensity data were processed using the Affymetrix Expression Console software version 1.1. Normalization was done using the robust multiarray averaging (RMA) method.

organism: Vitis vinifera

source_name: PM-infected (11 dpi) young grape leaf, treated with water vapor

label_protocol: Labeling of RNA samples was performed using Affymetrix kits following guidelines of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA, 2000). Briefly, total RNA (5 µg) was reverse transcribed using the One Cycle cDNA Synthesis kit, the resulting cDNA was cleaned using the GeneChip Sample Cleanup Module and in vitro transcribed using the GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Growth conditions of 85% relative humidity, 500 µmol m-2 light intensity (produced by fluorescent light bulbs) with 14/10 h day/night cycle and 26°C temperature were provided by PGR15 plant growth chamber (Conviron).

extract_protocol: Total RNA was extracted as follows: Leaf tissues were ground in liquid nitrogen and homogenized in extraction buffer (2% Hexadecyltrimethyl Ammonium Bromide 1% sodium dodecyl sulfate, 2.5M NaCl, 0.5M Tris, 50mM EDTA, 5% beta-mercaptoethanol, and 3% polyvinyl poly-pyrrolidone). The samples were stored at -80°C until processing, at which time they were thawed at 45ºC and centrifuged (13,000g, 20 min, 4ºC). The supernatant was supplemented with 1/2 volume of chloroform, vortexed, and centrifuged (13,000g, 15 min, 4ºC). The supernatant was supplemented with 1/5 volume of 12 M LiCl and incubated for 2 h at 4ºC, then centrifuged (13,000g, 30 min, 4ºC) and the supernatant was discarded. The pellet was washed with 80% ethanol twice and dissolved in water. Ten micrograms of total RNA were treated with Turbo DNase I (Ambion) and purified using an RNeasy column (Qiagen) following the manufacturers’ guidelines.

treatment_protocol: These experiments utilized one year-old greenhouse-cultivated potted vines with a single actively growing herbaceous shoot. Two unfolded, but still expanding (with shiny cuticle at nodes 3 and 4 from the growing tip of the shoot), leaves on each vine were mock-inoculated or inoculated with powdery mildew (PM, Erysiphe necator) conidia in the greenhouse. Inoculation was done by touching the upper surface of the leaf with a detached grape leaf supporting PM colonies that were actively producing conidia. Mock-inoculation of reference vines was done by touching leaves with a detached PM-free healthy grape leaves. Three days post-inoculation (dpi), PM- or mock-inoculated vines were transferred to a growth chamber with conditions of 85% RH, 14/10 h diurnal cycle, 26°C. Following 7 days of cultivation in the growth chamber (10 dpi), the plants were treated with 15 µM of methyl salicylate (MeSA) or water evaporated in the atmosphere of the growth chamber under airflow generated by a computer fan. Following 24 h of treatment (11 dpi) with MeSA or water, mildew-infected or reference leaves were harvested and flash frozen in liquid nitrogen. Plants actively growing during these treatments, and therefore by the time leaves were collected, they were fully expanded and located between node positions 4 and 7.

tag: genotype/variety

value: Cabernet Sauvignon

tag: inoculated with

value: water vapor

value: leaf blade


title: patient 562 normal tissue no smoking no obese Par106HG-U133_Plus_2.cel


title: patient 652 tumor tissue no smoking no obese Par107HG-U133_Plus_2.cel


title: HO1_no_rep1


title: Methyl-salicylate-treated leaves, healthy, rep 1

description:
Vitis_C15-1
Gene expression data from healthy grape leaves treated with methyl salicylate vapor (15 µM) 24 hours prior to sampling.

source_name: Healthy (mock-inoculated) young grape leaf, treated with MeSA vapor (15 µM)

value: none (mock-inoculated)

value: 15 µM of methyl salicylate (MeSA)


title: Powdery mildew-colonized leaves, water-vapor treated, rep 2

description:
Vitis_PH-2
Gene expression data from powdery mildew-infected grape leaves treated with water vapor 24 hours prior to sampling.

value: powdery mildew (PM, Erysiphe necator) conidia


title: Sample 1_Agilent 244K

description: Case 4_S01_CGH-v4_95_Feb07

source_name: TUMOR, MYC-NEG LYMPHOMA CASE 4

value: MYC-negative B-cell lymphoma


title: Methyl-salicylate-treated leaves, healthy, rep 2

description:
Vitis_C15-2
Gene expression data from healthy grape leaves treated with methyl salicylate vapor (15 µM) 24 hours prior to sampling.


title: HO1_H2O2_2hr_rep1


title: patient 562 tumor tissue no smoking no obese Par105HG-U133_Plus_2.cel


title: GFP_H2O2_2hr_rep1

value: control (transfected with GFP-vector)


title: Powdery mildew-colonized leaves, water-vapor treated, rep 1

description:
Vitis_PH-1
Gene expression data from powdery mildew-infected grape leaves treated with water vapor 24 hours prior to sampling.


title: patient 498 normal tissue no smoking no obese Par104HG-U133_Plus_2.cel


title: Reference leaves, healthy, water-vapor treated, rep 3

description:
Vitis_CH-3
Gene expression data from healthy grape leaves treated with water vapor 24 hours prior to sampling.

source_name: Healthy (mock-inoculated) young grape leaf, treated with water vapor


title: patient 498 tumor tissue no smoking no obese Par103HG-U133_Plus_2.cel


title: MEFs_IFNb_sample2

city: Brussels

first: Michiels

last: Thomas

address: avenue Hippocrate, 74 (B1.74.07)

department: de Duve

country: Belgium

institute: Université Catholique de Louvain

hyb_protocol: The Affymetrix GeneChip 3'IVT Express Labeling Assay Protocol was followed for thybridation and array washing

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix)

data_processing: The data were analyzed with Genechip expression console using the MAS5.0 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: murine embryonic fibroblast_IFN-b 5U/mL_24 hrs

label_protocol: The Affymetrix GeneChip 3'IVT Express Labeling Assay Protocol was followed for the biotin-labeled aRNA preparation

growth_protocol: Mixed cortical/hippocampal neurons and MEFs were derived from embryonic day 14.5 (E14.5) mouse embryos. Neurons were seeded onto poly-D-ornithine/laminin-coated glass coverslip and cultured in serum-free Neurobasal/B27 medium(Invitrogen). The purity of neuron cultures (>95%) was determined after staining with anti-MAP-2 (Synaptic System) and anti-glial fibrillary acid protein (Dako). MEfs were seeded onto culture dish and routinely divided every 3 days. L929 cells were growned in DMEM complemented with penicillin/streptomycin and fetal serum bovine (10%).

extract_protocol: Total RNA was isolated according to the manufacturer's protocol with an RNAeasy kit (Qiagen)

treatment_protocol: Mock Treatment or IFN-b treatment was performed on neurons cultured for 4 to 5 days and MEFs and L929 seeded the day before. The cultures were incubated for 24 hours at 37°C in a humidified incubator with 5% CO2.

tag: tissue origin

value: murine primary fibroblasts (MEFs)

value: IFN-beta 5U/mL for 24hrs


title: Reference leaves, healthy, water vapor-treated, rep 1

description:
Vitis_CH-1
Gene expression data from healthy grape leaves treated with water vapor 24 hours prior to sampling.

tag: tissue


title: Reference leaves, healthy, water-vapor treated, rep 2

description:
Vitis_CH-2
Gene expression data from healthy grape leaves treated with water vapor 24 hours prior to sampling.


title: GFP_H2O2_2hr_rep2

value: Primary rat mesangial cells


title: MEFs_IFNb_sample1

value: embryonic day 14.5 (E14.5) mouse embryos


title: MEFs_mock_sample2

source_name: murine embryonic fibroblast_mock

value: mock


title: Yel068c-gim-1

value: DamP pool with YEL068C

value: Mix of haploid strains derived from BY4742/BY4741


title: MEFs_mock_sample1


title: GFP_no_rep1


title: patient 427 normal tissue yes smoking no obese Par102HG-U133_Plus_2.cel

source_name: kidney tissue

value: yes

value: no


title: patient 427 tumor tissue yes smoking no obese Par101HG-U133_Plus_2.cel

value: tumor


title: L929_IFNb

source_name: L929 fibroblast_IFN-b 5U/mL_24 hrs

tag: cell line

value: fibroblast


title: PthA4 biological rep2

city: Campinas

first: Celso

middle: Eduardo

last: Benedetti

state: SP

address: R. Giuseppe Maximo Scolfaro 10000

country: Brazil

institute: Laboratorio Nacional de Biociencias

description: Gene expression data in response to PthA4 expression

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

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner .

data_processing:
The data were analyzed with the Affymetrix GCOS software using the RMA algorithm, using Affymetrix default analysis settings and global scaling as normalization method.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

organism: Citrus sinensis

source_name: epicotyls_PthA4 expression

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.6 ug mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Sweet orange seeds were germinated and grown in the dark for 40 days

extract_protocol: RNA from transfected epicotyls were extracted 72 h after bacterial incubation and used for microarray analysis

treatment_protocol: Etiolated epicotyls were sectioned and incubated for 15 minutes in a fresh suspension of Agrobacterium tumefaciens carrying the pBI121 vector, or pBI121 with the effector genes pthA2, pthA4 or pthC1 cloned downstream of the 35S promoter

tag: cultivar

value: Sweet orange cultivar 'Hamlin'

tag: age

value: 40 days-old seedlings

value: Etiolated epicotyls

tag: transfected with

value: A. tumefaciens carrying pBI121 vector containing pthA4 gene

tag: time point

value: 72h after bacterial-plant incubation


title: PthC1 biological rep2

description: Gene expression data in response to PthC1 expression

source_name: epicotyls_PthC1 expression

value: A. tumefaciens carrying pBI121 vector containing pthC1 gene


title: PthC1 biological rep1


title: L929_mock

source_name: L929 fibroblast_mock


title: patient 205 tumor tissue no smoking no obese Par098HG-U133_Plus_2.cel

tag: patient

tag: smoking

tag: obese

tag: duplicate


title: patient 205 normal tissue no smoking no obese Par097HG-U133_Plus_2.cel

value: normal

tag: batch


title: Methyl-salicylate-treated leaves, healthy, rep 3

description:
Vitis_C15-3
Gene expression data from healthy grape leaves treated with methyl salicylate vapor (15 µM) 24 hours prior to sampling.

value: Cabernet Sauvignon

value: none (mock-inoculated)

value: 15 µM of methyl salicylate (MeSA)

value: leaf blade


title: patient 160 tumor tissue no smoking no obese Par099HG-U133_Plus_2.cel


title: patient 194 tumor tissue no smoking no obese Par096HG-U133_Plus_2.cel


title: GFP_no_rep2

tag: cell type

value: Primary rat mesangial cells

tag: genotype/variation

value: control (transfected with GFP-vector)


title: patient 160 normal tissue no smoking no obese Par100HG-U133_Plus_2.cel


title: PthA4 biological rep1


title: neurons_IFNb_sample2

source_name: mixed cortical/hippocampal neuron_IFN-b 5U/mL_24 hrs

tag: strain

value: embryonic day 14.5 (E14.5) mouse embryos

value: mixed cortical/hippocampal neuron

tag: treated with

value: IFN-beta 5U/mL for 24hrs


title: PthA2 biological rep4

description: Gene expression data in response to PthA2 expression

source_name: epicotyls_PthA2 expression

value: A. tumefaciens carrying pBI121 vector containing pthA2 gene


title: neurons_mock_sample2

source_name: mixed cortical/hippocampal neuron_mock

value: mock


title: neurons_IFNb_sample1


title: PthA2 biological rep2

value: Sweet orange cultivar 'Hamlin'

value: 40 days-old seedlings


title: patient 192 normal tissue no smoking no obese Par093HG-U133_Plus_2.cel

value: no


title: patient 194 normal tissue no smoking no obese Par095HG-U133_Plus_2.cel


title: PthA2 biological rep3

value: Etiolated epicotyls

value: 72h after bacterial-plant incubation


title: PthA2 biological rep1


title: Xid2

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

country: Sweden

institute: SciLifeLab. Stockholm University

hyb_protocol: As recommended by Affymetrix.  The cRNA synthesis and hybridisations

scan_protocol: As recommended by Affymetrix.

data_processing: MAS5 normalised

label: Biotin

source_name: Splenic T1 cells

label_protocol: As recommended by Affymetrix. Biotin labeled material

extract_protocol: Splenic B-cells were collected from 1-week-old CBA (used as controls), Xid/CBA (obtained from Charles River Laboratories, Sweden), and BtkKO/CBA mice (created by back-crossing BtkKO/SW129 mice on CBA background strain for nine generations). In the spleens of 1-week-old mice, all B-cells are of T1 origin [26]. CD19+ (PE-conjugated rat anti-mouse-CD19 antibodies) B-cells were sorted in a FACS Vantage Diva Cell sorter, Beckton–Dickinson. The purity of the cells was >92%. Total RNA from T1 B-cells was extracted with RNeasy Mini kit (Qiagen, Valencia, CA, USA). The Affymetrix small sample protocol consisting of two rounds of amplification was used to obtain a larger amount of cRNA. Hundred ng cRNA was hybridised to MOE430 2.0 GeneChips®. The cRNA synthesis and hybridisations were performed in the BEA core facility at Department of Biosciences, Karolinska Institutet, Novum, Huddinge, Sweden.

tag: genotype

value: Xid

value: CBA

value: Splenic B-cells

tag: developmental stage

value: Transitional Type 1


title: GUS biological rep1

description: Gene expression data in response to GUS (uid) expression

source_name: epicotyls_GUS (uid) expression

tag: tissue

value: A. tumefaciens carrying pBI121 vector


title: patient 144 tumor tissue yes smoking yes obese Par092HG-U133_Plus_2.cel

value: tumor

value: yes


title: CBA1

value: wild type


title: CBA2


title: Xid1


title: patient 129 tumor tissue no smoking no obese Par090HG-U133_Plus_2.cel


title: GUS biological rep3


title: neurons_mock_sample1

tag: tissue origin

value: embryonic day 14.5 (E14.5) mouse embryos

value: mixed cortical/hippocampal neuron


title: GUS biological rep4

tag: cultivar


title: patient 121 tumor tissue yes smoking yes obese Par088HG-U133_Plus_2.cel


title: GUS biological rep2

tag: age


title: patient 144 normal tissue yes smoking yes obese Par091HG-U133_Plus_2.cel

value: normal


title: patient 129 normal tissue no smoking no obese Par089HG-U133_Plus_2.cel


title: patient 121 normal tissue yes smoking yes obese Par087HG-U133_Plus_2.cel


title: Btk KO2

value: Btk KO


title: Xc and Ch 8hpi biological rep2

description: Gene expression data in response to Xc and Ch infiltration

source_name: leaves_Xc and Ch infiltration

growth_protocol: Six-month old sweet orange plants were grown in green house

extract_protocol: mRNA from treated leaves was extracted and used for the labeling and chip hydrization

treatment_protocol: Fully expanded leaves of sweet orange were infiltrated with a suspension of Xc in the presence or absence of 50 uM Ch. Leaves infiltrated with Ch or water were used as controls

value: Sweet orange cultivar 'Pera'

value: six-month old  plants

value: fully expanded leaves

tag: infiltrated with

value: suspension of  Xanthomonas citri (Xc) in the presence of cycloheximide (Ch)

value: 8h post inoculation (8hpi)


title: Btk KO1


title: patient 110 tumor tissue yes smoking no obese Par086HG-U133_Plus_2.cel

value: no


title: Xc 8hpi biological rep1

description: Gene expression data in response to Xc infiltration

source_name: leaves_Xc infiltration

value: suspension of  Xanthomonas citri (Xc) in the absence of cycloheximide (Ch)

tag: time point


title: patient 110 normal tissue yes smoking no obese Par085HG-U133_Plus_2.cel

tag: patient


title: Xc 8hpi biological rep2


title: Xc and Ch 8hpi biological rep1


title: Polymicrobial bone 39B

city: Gainesville

first: Kesavalu

middle: Naidu

last: Lakshmyya

state: FL

address: 1600 SW Archer road, D11-24

department: Periodontology

institute: University of Florida, College of Dentistry

description: Gene expression data from polymicrobial pathogens infected bone.

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized  using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles.

source_name: Polymicrobial infected bone 4

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

growth_protocol: Polymicrobial pathogens growth protocol: P. gingivalis FDC 381 was cultured ion blood agar plates, T. denticola ATCC 35404 was cultured in GM-1 growth medium, and T. forsythia ATCC 43037 was cultured in trypticase soy agar II basal media supplemented with yeast extract, phytone peptone, sheep blood (5%), and N-acetylmuramic acid (NAM) under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per milliliter.

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

treatment_protocol: Infection/treatment protocol: P. gingivalis/T. denticola/T. forsythia were injected at 5 x 108 each mixed together as polybacteria 1.5X109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N = 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection.  The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.

value: BALB/c

value: calvarial bone

tag: infection

value: polymicrobial pathogens (P. gingivalis/T. denticola/T. forsythia)

value: 9 weeks


title: Ch 8hpi biological rep2

description: Gene expression data in response to Ch infiltration

source_name: leaves_Ch infiltration

value: cycloheximide (Ch alone control)


title: Polymicrobial bone 38B

source_name: Polymicrobial infected bone 3


title: H2O 8hpi biological rep2

description: Gene expression data in response to water infiltration

source_name: leaves_water infiltration

value: water (control)


title: patient 103 normal tissue yes smoking no obese Par083HG-U133_Plus_2.cel

tag: smoking

value: yes

tag: obese


title: Polymicrobial bone 40B

source_name: Polymicrobial infected bone 5


title: patient 192 tumor tissue no smoking no obese Par094HG-U133_Plus_2.cel

source_name: kidney tissue

value: tumor

tag: batch

tag: duplicate


title: patient 103 tumor tissue yes smoking no obese Par084HG-U133_Plus_2.cel


title: Ch 8hpi biological rep1


title: H2O 8hpi biological rep1


title: patient 96 tumor tissue no smoking no obese Par080HG-U133_Plus_2.cel


title: Polymicrobial tissue 39T

description: Gene expression data from polymicrobial pathogens infected tissue.

source_name: Polymicrobial infected tissue 4

value: calvarial tissue


title: patient 98 normal tissue yes smoking yes obese Par081HG-U133_Plus_2.cel

value: normal


title: Polymicrobial tissue 41T

source_name: Polymicrobial infected tissue 5


title: Polymicrobial tissue 38T

source_name: Polymicrobial infected tissue 3


title: patient 98 tumor tissue yes smoking yes obese Par082HG-U133_Plus_2.cel


title: Polymicrobial bone 37B

source_name: Polymicrobial infected bone 2


title: patient 96 normal tissue no smoking no obese Par079HG-U133_Plus_2.cel


title: Polymicrobial tissue 37T

source_name: Polymicrobial infected tissue 2


title: Polymicrobial bone 36B

source_name: Polymicrobial infected bone 1


title: patient 92 tumor tissue no smoking no obese Par078HG-U133_Plus_2.cel


title: Polymicrobial tissue 36T

source_name: Polymicrobial infected tissue 1


title: LPA+IFNt, rep 3

city: Olsztyn

first: Dorota

last: Boruszewska

address: Tuwima 10

department: Department of Reproductive Immunology and Pathology

country: Poland

institute: PAS

description: Gene expression data from co-cultured stromal and epithelial cells from bovine endometrium stimulated with LPA plus IFNt.

hyb_protocol: Following fragmentation, 12 µg of biotin-labeled aRNA were hybridized to GeneChip Bovine Genome Array for 16 hours at 45oC in a rotating Affymetrix GeneChip Hybridization Oven 640. GeneChips were then washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The signal intensity for each probe on each chip was calculated from scanned images using Affymetrix GeneChip® Command Console® (AGCC) software. The Pearson's analysis were applied to estimate the correlation between linear variables, therefore, examine the homogeneity of the samples. Signal intensities were analyzed using Partek Genomic Suite v 6.6 software (Partek Incorporated, St. Louis, USA). Probe intensities were background corrected, normalized, and summarized using the GC Robust Multichip Average method. Background correction was applied based on the global distribution of the PM (Perfect Match) probe intensities and affinity for each probe was calculated based on their sequence data. Quantile normalization and median-polish summarization to each probe set was applied. Qualitative analysis was performed for example Principal Component Analysis to identify outliers and artifacts on the microarray. After quality check the one-way Analysis of Variance (ANOVA) was performed on the data, which allowed to create lists of significantly and differentially expressed genes between the experimental variants (control (PBS), LPA and LPA plus IFNt). Probe sets (control vs. LPA and control vs. LPA+IFNt) were considered differentially expressed when the signed Fold Change was ≥ 2, the p-value was < 0.05 and the FDR (False Discovery Rate) was < 0. 05. To compare LPA vs. LPA+IFNt group signed Fold Change ≥ 2 and only p-value cut-off < 0. 05 were used. The selected lists were subjected to cluster analysis to find genes and samples with similar profiles with the use of Hierarchical Clustering Algorithm.

source_name: bovine co-cultured endometrial stromal and epithelial cells exposed to LPA plus IFNt

label_protocol: Three replicates of total RNA (100 ng) from each three experimental conditions were used for aRNA synthesis. aRNA amplification, labeling and fragmentation were conducted according to the Affymetrix GeneChip 3’ IVT Express kit protocol (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Bovine uteri were obtained at a local slaughterhouse within 20 min of exsanguinations and were transported on ice to the laboratory within 40 min. The animals were slaughtered on Days 2–5 of the estrous cycle (n=9). Estimation of the stages of the estrous cycle was additionally confirmed by macroscopic observation of the ovaries and uterus. The epithelial and stromal cells from bovine endometrium were enzymatically separated using solution I and II, respectively (solution I: sterile HBBS containing 2.4 U/mL dispase-Gibco, Grand Island, NY, USA; 0.005% DNase IV-Sigma Aldrich, Madison, USA; 0.05% collagenase I-Sigma Aldrich; solution II: HBBS with 0.005% DNase IV and 0.05% collagenase I). The final pellets of both the stromal and epithelial cells were suspended in a culture medium, Dulbecco-modified Eagle’s medium (DMEM, Sigma Aldrich) containing 10% fetal calf serum (Sigma Aldrich) and 10 000 U/mL penicillin G, 10 mg/mL streptomycin and 25 μg/mL amphotericin B (antibiotic antimycotic solution, Sigma Aldrich). The cells were collectively seeded to co-culture at a density of 1 x 106 viable cells/mL on 3 to 1 (stromal to epithelial cells) ratio in 6-well plates (Costar®,Corning® CellBIND® Surface, Corning B.V. Life Sciences, Amsterdam, The Netherlands) and cultured at 38.5oC in a humidified atmosphere of 5%CO2, 95%air.

extract_protocol: Total RNA extraction from the endometrial cells was carried out using TRIzol Reagent (Sigma Aldrich) followed by the Total RNA Mini Kit (A&A Biotechnology, Poland) according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo Scientific, Wilmington, USA) and quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Since the epithelial and stromal cells attached 24–48 h after plating, the medium in the culture was replaced with fresh DMEM supplemented with 0.1% BSA (Sigma Aldrich) and antibiotic antimycotic solution (Sigma Aldrich). The cells were then exposed to LPA agonist (1-Oleoyl-sn-glycerol 3-phosphate sodium salt, LPA; 10-6M, Sigma Aldrich), interferont (IFNt; 103AVU;donated by Dr FW Bazer of Texas A&M University, College Station, TX, USA;) and LPA plus IFNt for 6h.

tag: breed

value: Holstein/Polish Black and White

tag: cell type

value: bovine endometrial stromal and epithelial cells

tag: treatment

value: LPA+IFNt


title: OECRY1_Bj_rep2

city: New Delhi

first: Pooja

last: Sharma

state: New Delhi

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: 5-day-old, white light grown (100 µmol m–2s–1)

hyb_protocol: The labeled cRNA samples were hybridized on to a Gene Expression B.napus (Brassica) Oligo Microarray 4x44K (AMADID: 22520) 600ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software v 10.5.1.1 of Agilent and The normalization was done using GeneSpring GX Software.

organism: Brassica juncea

source_name: 5-day-old, OECRY1, white light grown (100 µmol m–2s–1)

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Total RNA from whole seedlings was extracted and cleaned up with the Qiagen RNeasy Plant Mini Prep Kit as per the manufacturer’s instructions (Qiagen). Total RNA purity was assessed by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop technologies, Rockland, USA) and the RNA integrity was checked using RNA 6000 Nano Lab Chip on the 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) following the manufacturer’s protocol

tag: genotype/variation

value: whole seedling

tag: growth condition

value: white light grown (100 µmol m–2s–1)


title: OECRY1_Bj_rep1

tag: tissue


title: LPA+IFNt, rep 2


title: patient 92 normal tissue no smoking no obese Par077HG-U133_Plus_2.cel

value: no


title: WT_Bj_rep2

source_name: 5-day-old, wild type seedling, white light grown (100 µmol m–2s–1)

value: wild type


title: patient 55 normal tissue yes smoking yes obese Par073HG-U133_Plus_2.cel


title: patient 55 tumor tissue yes smoking yes obese Par074HG-U133_Plus_2.cel


title: patient 53 tumor tissue yes smoking no obese Par072HG-U133_Plus_2.cel


title: patient 53 normal tissue yes smoking no obese Par071HG-U133_Plus_2.cel


title: LPA, rep 2

description: Gene expression data from co-cultured stromal and epithelial cells from bovine endometrium stimulated with LPA.

source_name: bovine co-cultured endometrial stromal and epithelial cells exposed to LPA

value: LPA


title: J411

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

country: Canada

institute: University of Alberta

description: Array 40

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed  with oligonucleotides by Agilent for all EmbryoGENE related projects.

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

data_processing: FlexArray software was used for data normalization following first with simple background subtraction, LOWESS normalization within and between arrays.

organism: Sus scrofa

source_name: Risk

label_protocol:
Antisense RNA was generated and  labeled using Ampilfication and Labeling Kit (KREATECH).
Ampilfication and Labeling Kit (KREATECH)

extract_protocol: Total RNA was isolated by Trizol reagent and cleaned up by RNeasy Mini Kit (QIAGEN).

tag: animal age

value: 30 days embryo

tag: number per pool

source_name: Reference (all the 80 samples pooled from ch1)


title: WT_Bj_rep1


title: LPA,  rep 3


title: Control, rep 3

description: Gene expression data from co-cultured stromal and epithelial cells from bovine endometrium stimulated with PBS.

source_name: bovine co-cultured endometrial stromal and epithelial cells, control

value: PBS


title: patient 74 normal tissue yes smoking no obese Par075HG-U133_Plus_2.cel


title: LPA+IFNt, rep 1


title: LPA, rep 1


title: patient 74 tumor tissue yes smoking no obese Par076HG-U133_Plus_2.cel


title: Control, rep 2


title: J311

description: Array 39


title: Control, rep 1


title: patient 28 normal tissue no smoking no obese Par065HG-U133_Plus_2.cel


title: patient 43 tumor tissue no smoking no obese Par070HG-U133_Plus_2.cel


title: patient 28 tumor tissue no smoking no obese Par066HG-U133_Plus_2.cel


title: J111

description: Array 37


title: patient 43 normal tissue no smoking no obese Par069HG-U133_Plus_2.cel


title: M29_1

city: Perth

first: Tea

last: Shavlakadze

state: WA

address: Anatomy Building, Hackett entrance number 2

department: School of Anatomy, Physiology and Human Biology

country: Australia

institute: the University of Western Australia

description: Gene expression in ageing gastrocnemius muscle

hyb_protocol: Whole Mouse Genome Oligo Microarray kit (Agilent, G4112A).

scan_protocol: The microarray slides were washed and scanned using Agilent microarray scanner (G2505B).

data_processing: Signal intensities were extracted by Agilent feature extraction software.

source_name: C57Bl/6J Female

label_protocol: The target labeling was performed using Cy3 and the kit plus (Agilent, #5184-3523) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from gastronemius muscles, using Trizol reagent (Invitrogen). The RNA was quantified spectrophotometrically and its integrity validated by the OD260/OD280 absorption ratio (>1.8) and by visualization on an agarose gel.  The quality of RNA was assessed by Agilent 2100 Bioanalyzer, RNA 6000 Nano LabChip kit and Agilent 2100 Expert Software (Agilent Technologies, Inc., Santa Clara, CA, USA). All samples with RIN scores >7.5 were selected for the array experiment.

treatment_protocol: No treatment. Muscle were obtained from un-treated female C57Bl/6J mice.

tag: strain

tag: age

value: 29 months old

tag: gender

value: Female

value: gastrocnemius muscle


title: patient 42 normal tissue yes smoking no obese Par067HG-U133_Plus_2.cel

tag: patient

value: yes


title: I311

description: Array 35


title: J211

description: Array 38


title: M29_2


title: patient 42 tumor tissue yes smoking no obese Par068HG-U133_Plus_2.cel

value: tumor


title: I111

description: Array 33


title: H411

description: Array 32


title: patient 16 normal tissue no smoking no obese Par063HG-U133_Plus_2.cel


title: M24_4

value: 24 months old


title: patient 16 tumor tissue no smoking no obese Par064HG-U133_Plus_2.cel


title: patient 14 tumor tissue yes smoking no obese Par062HG-U133_Plus_2.cel


title: M29_4


title: M24_3


title: I211

description: Array 34


title: M29_3


title: I411

description: Array 36


title: M24_2


title: patient 14 normal tissue yes smoking no obese Par061HG-U133_Plus_2.cel

value: normal


title: H111

description: Array 29


title: H211

description: Array 30


title: M15_2

value: 15 months old


title: M15_4


title: patient 1 tumor tissue no smoking no obese Par060HG-U133_Plus_2.cel


title: H311

description: Array 31


title: M15_3


title: G311

description: Array 27

source_name: Non-Risk


title: G411

description: Array 28


title: F411

description: Array 24


title: M24_1


title: M3_2

value: 3 months old


title: patient 1 normal tissue no smoking no obese Par059HG-U133_Plus_2.cel

source_name: kidney tissue


title: M15_1


title: M3_3


title: F311

description: Array 23


title: M3_4


title: G211

description: Array 26


title: G111

description: Array 25


title: M3_1


title: liver of control mice (IJ-17)

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

institute: CRCHUL

hyb_protocol: The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 17±1h of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol (http://media.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G to produce the intensity files and the image data were analyzed by using the Expression Console Software for quality control (www.affymetrix.com).

data_processing: Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (RMA) described by Irizarry et al. (Irizarry et al, 2003). Microarray analyses were performed by the CHU de Québec Research Center (CHUL) Gene Expression Platform, Quebec, Canada.

source_name: liver of control mice

label_protocol: Chips were processed with total RNA (200 ng per sample) according to the WT Expression kit for Affymetrix Whole Transcrit Expression Arrays protocol (Ambion, Austin, TX ), labeled using the WT Terminal Labeling and hybridized to the arrays as described by the manufacturer (Affymetrix, Santa Clara, CA).

extract_protocol: Liver, intra-abdominal adipose and biceps femoris muscle tissues were collected from cachectic Pdx1-cre;LSL-KrasG12D;INK4a/arffl/fl or LSL-KrasG12D;INK4a/arffl/fl control mice (10 weeks-old) and immediately drawn in cold guanidinium thiocyanate (4 M) solution, followed by protein denaturation and RNAs extraction according to Chirgwin’s protocol (Chirgwin et al, 1979). Total RNA was purified on RNeasy mini kit column (Qiagen, Mississauga, ON, Canada) before labeling protocol.

treatment_protocol: Cachectic transgenic mice were defined as Pdx1-cre;LSL-KrasG12D;INK4a/arffl/fl mice, developing systematically spontaneous pancreatic adenocarcinoma and died between 8 and 12 weeks-old. Animals were obtained by crossbreeding the following strains: Pdx1-Cre (Gu et al, 2002) (kindly given by D. Melton), LSL-KrasG12D (Aguirre et al, 2003) and INK4a/arffl/fl (Aguirre et al, 2003; Bardeesy et al, 2006) (kindly given by R. Depinho, Dana-Faber Cancer Institute, MA). Mice were kept within the Experimental Animal House of the Centre de Cancérologie de Marseille (CRCM) pole Luminy, following institutional guidelines.

tag: disease state

value: control

value: liver

value: 10 weeks-old


title: liver of pancreatic cancer-induced cachectic mice (IJ-16)

value: pancreatic cancer-induced cachexia syndrome


title: liver of pancreatic cancer-induced cachectic mice (IJ-18)


title: F211

description: Array 22


title: F111

description: Array 21


title: liver of control mice (IJ-15)


title: E411

description: Array 20


title: E311

description: Array 19


title: liver of control mice (IJ-14)


title: SUDHL5_Affy SNP6

description: Hybridized to SNP 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations 450, and scanned using the Gene Chip Scanner 3000.

data_processing:
Image data were analysed with Genotyping Console 4.0 to obtain the CEL data files, which were also exported to the Nexus Biodiscovery Edition for data analysis and visualization. Quality controls assessed by Genotyping Console included Contrast Quality Control (CQC>0.4) produced by Birdseed and Median of the Absolute values of all Pairwise Differences (MAPD<0.35). Samples were analysed individually with the Nexus Biodiscovery Edition using the SNP-FASST2 segmentation algorithm and using segment reporting tool filters: minimum of 100 Kb minimum genomic size of a segment, as well as by visual inspection.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Cell line

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood and cell lines using the Qiagen Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.


title: muscle of pancreatic cancer-induced cachectic mice (IJ-10)

value: biceps femoris muscle


title: E211

description: Array 18


title: muscle of pancreatic cancer-induced cachectic mice (IJ-12)


title: Sample 5_Agilent 108K

description: Case 9_S01_CGH_107_Sep09_1_4

source_name: TUMOR, MYC-NEG LYMPHOMA CASE 8

value: MYC-negative B-cell lymphoma

value: male

source_name: Normal genomic DNA

value: sex-matched control DNA


title: D411

description: Array 16

value: 30 days embryo


title: 8 mg/kg bw furan_rep1

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (300ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505B) according to manufacturer's recommendations.  Data was extracted from the scanned images using Feature Extraction Version 10.7.3.1.

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

source_name: Liver

label_protocol: Sample RNA (200 ng) was used together with a mouse universal reference RNA to synthesize, amplify and label cRNA using the Low Input Quick Amp Labeling Kit (Agilent Cat #: 5190-0444). Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP. Labeled cRNA was purified using the RNease Mini Kit (Qiagen). Amplification and labeling efficiency of cRNA were quantified using a NanoDrop spectrophotometer.

growth_protocol: 5-6 week old female specific pathogen free B6C3F1 mice were purchased from Charles River Breeding Laboratories (Portage, ME) and were allowed to acclimatize for at least 7 days prior to the start of the study. Feed (NIH-07; Zeigler Brothers, Inc., Gardners, PA) and tap water were available ad libitum. Mice were housed five per cage in polycarbonate cages in a specific pathogen free (SPF) and Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) accredited facility. All procedures were conducted in compliance with the Animal Welfare Act Regulations (9CFR1–4). Mice were handled and treated according to the guidelines provided in the National Institute of Health (NIH) Guide for the Care and Use of Laboratory Animals (ILAR, 1996; http://dels.nas.edu/ilar/).

extract_protocol: Mice were anaesthetized under carbon dioxide inhalation followed by exsanguination. Livers were removed, placed in cryovials and immediately snap frozen in liquid nitrogen.  Tissues were stored at -80oC until RNA extraction was performed.  Total RNA was extracted from ~100mg frozen tissue using the RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios > 1.83 and RINs > 8.9.

treatment_protocol: Mice were dosed via oral gavage for 21 days. Four different doses of furan dissolved in corn oil were used: 1, 2, 4 and 8 mg/kg bw.  Control animals were gavaged with cornoil oil only.   Tissues were collected 4 hours following the final dose.

value: 8 mg/kg bw furan

value: female

source_name: Universal Mouse Reference RNA

tag: sample type

value: universal reference


title: 8 mg/kg bw furan_rep3


title: liver of pancreatic cancer-induced cachectic mice (IJ-13)


title: muscle of control mice (IJ-9)

source_name: muscle of control mice


title: 8 mg/kg bw furan_rep4


title: 8 mg/kg bw furan_rep5


title: 8 mg/kg bw furan_rep2


title: 4 mg/kg bw furan_rep4

value: 4 mg/kg bw furan


title: D311

description: Array 15


title: E111

description: Array 17


title: muscle of control mice (IJ-8)


title: muscle of control mice (IJ-11)


title: Case2_Affy SNP6

description: Hybridized to SNP 6.0

source_name: Peripheral Blood

value: Male


title: Case3_Affy SNP6

description: Hybridized to SNP 6.0

value: Female


title: Case8_Affy SNP6

description: Hybridized to SNP 6.0


title: 4 mg/kg bw furan_rep3


title: HT_Affy SNP6

description: Hybridized to SNP 6.0


title: muscle of pancreatic cancer-induced cachectic mice (IJ-7)


title: 4 mg/kg bw furan_rep2


title: Case1_Affy SNP6

description: Hybridized to SNP 6.0


title: C211

description: Array 10


title: D211

description: Array 14


title: D111

description: Array 13


title: C411

description: Array 12


title: adipose tissue of control mice (IJ-5)

source_name: adipose tissue of control mice

value: intra-abdominal adipose


title: C311

description: Array 11


title: 2 mg/kg bw furan_rep5

value: 2 mg/kg bw furan


title: B411

description: Array 8


title: adipose tissue of control mice (IJ-2)

value: control


title: 2 mg/kg bw furan_rep2

value: liver


title: adipose tissue of pancreatic cancer-induced cachectic mice (IJ-4)

value: 10 weeks-old


title: 2 mg/kg bw furan_rep4


title: adipose tissue of control mice (IJ-3)


title: C111

description: Array 9


title: 2 mg/kg bw furan_rep3


title: 4 mg/kg bw furan_rep1


title: 2 mg/kg bw furan_rep1


title: MNIVF, patient D

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

description: Cumulus cells (CC) gene expression of mature, metaphase II (MII) oocytes that developed to the stage of morulae on day 5 of a modified natural IVF procedure from patient D.

hyb_protocol: GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Santa Clara, USA) were hybridized for 16 hours and washed using GeneChip Fluidics Station 450 according to manufacturer’s recommendations.

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

data_processing:
Data were normalized using RMA algorithm from R/Bioconductor/XPS package.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.na30.1.hg19.probeset.csv

source_name: CC of MII-morulae oocyte, MNIVF procedure, patient D

label_protocol: 200 ng of RNA was amplified and converted to cDNA using the WT Expression Kit (Ambion, Austin, USA). The resulting cDNA was fragmented and labeled using the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, USA).

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted using TRI reagent (Sigma– Aldrich, St. Louis, USA) according to manufacturer’s instruction with small modification due to the small sample volume. Glycogen (Ambion, Woodward, USA) was used as a carrier to increase RNA yield. Briefly, CC from individual follicle were homogenized in 500 μL TRI reagent supplemented with 125 μg of glycogen. After incubation at room temperature, 100 μL chloroform was added and the sample was vortexed vigorously. After 15 min centrifugation at 12,000 x g and 4°C, RNA was transferred from aqueous phase and precipitated with 250 μL of isopropanol. After 25 min centrifugation at 12,000 x g and 4°C, RNA pellet was washed 3 times with 75% ethanol. Total RNA was resuspended in 15 μL of RNase-free water and stored at -80°C.  The integrity of RNA was assessed on Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) to assure high quality of total RNA. Total RNA quantity and purity was measured with a Nanodrop ND-1000 spectrophotometer (Nanodrop Techonologies Inc., Wilmington, DE, USA).

treatment_protocol: The MNIVF group of patients underwent transvaginal ultrasonographic examination on day 9 of the cycle. Measurement of serum oestradiol and testing of urine for LH surge presence was performed at the same time. For serum oestradiol measurement, a commercially available kit (Oestradiol-2; Sorin Biomedica, Saluggia, Italy) was used. The detection of LH surge was also made with a commercially available kit (RapiTest LH; Morwell Diagnostics GmbH, Egg, Switzerland). As soon as the dominant follicle reached ≥ 16 mm in diameter, serum oestradiol exceeded 0,39 nmol/l and there was no LH surge detected in urine sample, 5000 IU of human chorionic gonadotrophin (HCG) (Pregnyl; N.V. Organon, Oss, The Netherlands) was injected subcutaneously. Ultrasound-guided transvaginal oocyte aspiration was performed 31-32 h after HCG administration.  The GnRH agonists group of patients buserelin acetate (Suprefact; Hoechst AG, Frankfurt/Main, Germany) was administered subcutaneously from day 22, with a daily dose of 0.6ml (600pg). When criteria for ovarian desensitization were fulfilled (serum oestradiol <0.05nmol/l, follicles <5mm in diameter), patients were subcutaneously administered 225 IU of gonadotrophin folitropin alpha (Gonal F; Industria Farmaceutica Serono S.p.A., Bari, Italy). When at least three follicles were ≥17mm in diameter and serum oestradiol exceeded 0.40nmol/l per follicle, 10.000 IU of HCG (Pregnyl; N.V. Organon) was administered. Ultrasound guided transvaginal oocyte aspiration was performed 34-36h after HCG administration.  In the GnRH antagonist group 225 IU of gonadotrophin folitropin alpha (Gonal F; Industria Farmaceutica Serono S.p.A., Bari, Italy) was administered subcutaneously on day 2 of the cycle. The GnRH antagonist cetrorelix acetate (Cetrotide; Asta Medica AG, Frankfurt, Germany) was administered subcutaneously at a dose of 0,25mg when the dominant follicle measured 13mm in diameter. When at least three follicles were ≥17mm in diameter and serum oestradiol exceeded 0.40nmol/l per follicle, 10.000 IU of HCG (Pregnyl; N.V. Organon) was administered. Ultrasound guided transvaginal oocyte aspiration was performed 34-36h after HCG administration.  Immediately after cumulus-oocyte complex (COC) retrieval, a part of cumulus cells (CC) surrounding a single oocyte was removed by using a sharp needle. Individual CC samples were washed in PBS, snap-frozen in liquid nitrogen and stored in vials at -80°C until RNA isolation.   The oocytes were cultured individually in Universal IVF medium (MediCult a/s, Jyllinge, Denmark) and fertilization was carried out 2 h after oocyte retrieval. After 24 h, fertilization status was assessed. Embryos were later cultured in a sequential media (BlastAssistSystem; MediCult, Denmark) for five days and one or two embryos at the stage of morulae or blastocyst were transferred on day 5; supernumerary good quality blastocysts were cryopreserved.  Implantation was assessed 14 days after embryo transfer using serum β- HCG measurement. To confirm intrauterine pregnancy and the number of gestational sacs with heartbeat activity, transvaginal ultrasound was performed 4 weeks after embryo transfer.

value: D

tag: ivf procedure

value: MNIVF (modified natural IVF)

tag: stimulus

tag: oocyte maturity

value: MII-morulae

tag: cell id

value: s


title: B211

description: Array 6


title: MNIVF, patient AU

description: Cumulus cells (CC) gene expression of mature, metaphase II (MII) oocytes that developed to the stage of blastocyst on day 5 of a modified natural IVF procedure from patient AU.

source_name: CC of MII-blastocyst oocyte, MNIVF procedure, patient AU

value: AU

value: MII-blastocyst


title: adipose tissue of pancreatic cancer-induced cachectic mice (IJ-1)

value: pancreatic cancer-induced cachexia syndrome


title: B311

description: Array 7

value: 30 days embryo


title: adipose tissue of pancreatic cancer-induced cachectic mice (IJ-6)


title: 1 mg/kg bw furan_rep1

value: 1 mg/kg bw furan

value: female

value: universal reference


title: B111

description: Array 5


title: A411

description: Array 4


title: COH, patient L

description: Cumulus cells (CC) gene expression of mature, metaphase II (MII) oocytes that developed to the stage of blastocyst on day 5 of IVF procedure from GnRH Agonist treated patient L.

source_name: CC of MII-blastocyst oocyte, COH IVF procedure, GnRH Agonist treated patient L

value: L

value: COH (controlled ovarian hyperstimulation) IVF

value: GnRH Agonist


title: A311

description: Array 3

source_name: Reference (all the 80 samples pooled from ch1)


title: 1 mg/kg bw furan_rep4


title: COH, patient J

description: Cumulus cells (CC) gene expression of mature, metaphase II (MII) oocytes that developed to the stage of blastocyst on day 5 of IVF procedure from GnRH Antagonist treated patient J.

source_name: CC of MII-blastocyst oocyte, COH IVF procedure, GnRH Antagonist treated patient J

value: J

value: GnRH Antagonist


title: A211

description: Array 2


title: 1 mg/kg bw furan_rep2

value: liver


title: Control_rep5

value: Control


title: 1 mg/kg bw furan_rep3


title: MNIVF, patient AH

description: Cumulus cells (CC) gene expression of mature, metaphase II (MII) oocytes that developed to the stage of morulae on day 5 of a modified natural IVF procedure from patient AH.

source_name: CC of MII-morulae oocyte, MNIVF procedure, patient AH

value: AH

value: MNIVF (modified natural IVF)


title: A111

description: Array 1

source_name: Non-Risk


title: COH, patient AH

description: Cumulus cells (CC) gene expression of mature, metaphase II (MII) oocytes that developed to the stage of blastocyst on day 5 of IVF procedure from GnRH Agonist treated patient AH.

source_name: CC of MII-blastocyst oocyte, COH IVF procedure, GnRH Agonist treated patient AH


title: COH, patient D

description: Cumulus cells (CC) gene expression of mature, metaphase II (MII) oocytes that developed to the stage of blastocyst on day 5 of IVF procedure from GnRH Antagonist treated patient D.

source_name: CC of MII-blastocyst oocyte, COH IVF procedure, GnRH Antagonist treated patient D

value: D


title: COH, patient AU

description: Cumulus cells (CC) gene expression of mature, metaphase II (MII) oocytes that developed to the stage of blastocyst on day 5 of IVF procedure from GnRH Agonist treated patient AU.

source_name: CC of MII-blastocyst oocyte, COH IVF procedure, GnRH Agonist treated patient AU

value: AU


title: Control_rep3


title: HK-2 Control 3

status: Public on Jan 09 2014

city: Cardiff

first: Robert

middle: Hywel

last: Jenkins

state: Cardiff

address: Heath Park

department: Institute of Molecular and Experimental Medicine

institute: Cardiff University

hyb_protocol: Labelled miRNAs were hybridized onto 3D-GeneTM miRNA oligo chips, v16 (Toray Industries Inc, Tokyo, Japan) according to manufacturer’s instructions

scan_protocol: The chips were stringently washed, and fluorescent signals were scanned with a 3D-GeneTM Scanner 3000 (Toray Industries Inc, Tokyo, Japan) according to manufacturer’s instructions

data_processing: Hybridized probe spots with signal intensity greater than the mean intensity plus 2 standard deviations of the background signal were considered to be valid.  The background average was subtracted from the signal intensity and multiplied by the normalisation factor (25 divided by the medium signal intensity of all the subtracted background data) to generate the global normalised data.

source_name: Proximal tubular epithelial cells_control

label_protocol: 500 ng of total RNA was labelled with mercury LNA microRNA Array Power Labelling kit (Exiqon, Vedbaek, Denmark) according to manufacturer’s instructions

growth_protocol: HK-2 cells were cultured in DMEM/Ham’s F12 supplemented with 10 % FCS, 2 µM L-glutamine, 20 mM HEPES, 5 µg/ml insulin, 5 µg/ml transferrin, 40 ng/ml hydrocortisone and 5 ng/ml sodium selenite.  Cells were grown at 37°C in 5 % CO2 and 95 % air

extract_protocol: Total RNA was extracted from cells with TRI-Reagent solution (Ambion, Austin, TX, USA) according to manufacturer’s instructions

treatment_protocol: HK-2 cells were treated with 0.2 % FCS with/without 5 µg/ml Aristolochic Acid for 48 hrs

tag: cell line

tag: tissue origin

value: kidney

tag: cell type

value: proximal tubular epithelial cells

tag: treated with

value: none (control)


title: HK-2 AA 2

source_name: Proximal tubular epithelial cells_aristolochic acid

value: 5ug/ml aristolochic acid (AA)


title: Control_rep1

source_name: Liver

tag: treatment

tag: tissue

value: female


title: HK-2 Control 2


title: HK-2 AA 3


title: Control_rep2

source_name: Universal Mouse Reference RNA

value: universal reference


title: HK-2 AA 1


title: HK-2 Control 1