title: 20006-V1

description:
6116733076_H
Donor 06 day 0 after vericella zoster vaccination

source_name: Donor 06 day 0


title: 20046-V1

status: Public on Sep 12 2016

type: RNA

city: Palo Alto

first: Jorg

last: Goronzy

state: CA

address: Rm E4201, Bldg100, 3801 Miranda Ave

department: Medicine

country: USA

institute: Stanford University

description:
This is twin sibling of Donor 37
Donor 46 day 0 after vericella zoster vaccination

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with Genespring software

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Donor 46 day 0

label_protocol: Standard Illumina label protocol

extract_protocol: total RNA extraction

tag: age

tag: gender

value: F

tag: tissue

value: whole blood


title: 20039-V1

description: Donor 39 day 0 after vericella zoster vaccination

source_name: Donor 39 day 0


title: 20008-V2

description:
6116733076_F
Donor 08 day 3 after vericella zoster vaccination

source_name: Donor 08 day 3


title: 20007-V1

description:
6116733076_D
Donor 07 day 0 after vericella zoster vaccination

source_name: Donor 07 day 0

value: M


title: Guthrie T-82

type: genomic

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: infant blood from archival Guthrie cards

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

scan_protocol: Standard Illumina Protocol

data_processing: Raw IDAT files were processed with Illumina’s GenomeStudio software V2011.1 and background normalized using negative control probes to generate methylation β-values which were used for all downstream analyses.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Guthrie card blood

label_protocol: Standard Illumina Protocol

growth_protocol: LNCaP prostate cancer cells were cultured as described in PMID 11850822. Normal prostate epithelial cells (PrEC) were cultured according to the manufacturer’s instructions in prostate epithelial growth medium (PrEGM, catalogue no. CC-3166; Cambrex Bio Science) as described in PMID 20173741. Patient-matched cancer associated fibroblasts (CAFs) and non-malignant tissue associated fibroblasts (NAFs) (n=3 pairs) were isolated and validated as described in PMID 23558784

extract_protocol: Genomic DNA for LNCaP and PrEC cell lines was extracted using QIAamp DNA Mini and Blood Mini kit following the manufacturer’s protocol for cultured cells (Qiagen). Genomic DNA was extracted from the CAF and NAF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Genomic DNA was extracted from the Guthrie cards using GenSolve technology (IntegenX) followed by purification using the QIAamp DNA micro kit (Qiagen) and an additional ethanol precipitation step.

value: infant blood


title: 20003-V1

description:
6116733076_G
Donor 03 day 0 after vericella zoster vaccination

source_name: Donor 03 day 0


title: 20008-V1

description:
6116733076_C
Donor 08 day 0 after vericella zoster vaccination

source_name: Donor 08 day 0


title: 20003-V2

description:
6116733076_E
Donor 03 day 3 after vericella zoster vaccination

source_name: Donor 03 day 3


title: Guthrie T-76


title: 20010-V2

description:
6116733075_L
Donor 10 day 3 after vericella zoster vaccination

source_name: Donor 10 day 3


title: NAF A

source_name: NAF

value: non-malignant tissue associated fibroblasts (NAF)


title: 20007-V2

description:
6116733076_A
Donor 07 day 3 after vericella zoster vaccination

source_name: Donor 07 day 3


title: NAF B

description: non-malignant tissue associated fibroblast


title: 20010-V1

description:
6116733075_K
Donor 10 day 0 after vericella zoster vaccination

source_name: Donor 10 day 0


title: 20004-V1

description:
6116733075_H
Donor 04 day 0 after vericella zoster vaccination

source_name: Donor 04 day 0


title: CAF A

description: cancer associated fibroblast

source_name: CAF

value: cancer associated fibroblasts (CAF)


title: Guthrie T-75


title: Guthrie T-73


title: 20001-V1

description:
6116733075_I
Donor 01 day 0 after vericella zoster vaccination

source_name: Donor 01 day 0


title: 20009-V1

description:
6116733075_D
Donor 09 day 0 after vericella zoster vaccination

source_name: Donor 09 day 0


title: NAF C


title: PrEC Rep2

description: primary cell culture of prostate epithelial cells

source_name: PrEC cells

value: primary prostate epithelial cells (PrEC)


title: Guthrie T-80


title: 20005-V2

description:
6116733075_J
Donor 05 day 3 after vericella zoster vaccination

source_name: Donor 05 day 3


title: PrEC Rep1


title: 20006-V2

description:
6116733075_G
Donor 06 day 3 after vericella zoster vaccination

source_name: Donor 06 day 3


title: LNCaP Rep2

description: transformed prostate cancer cell line

source_name: LNCaP cells

value: prostate cancer cell line (LNCaP)


title: CAF B

description: cancer associated fibroblast


title: LNCaP Rep1

description: transformed prostate cancer cell line


title: 20002-V1

description:
6116733076_B
Donor 02 day 0 after vericella zoster vaccination

source_name: Donor 02 day 0


title: CAF C

description: cancer associated fibroblast


title: 20001-V2

description:
6116733075_A
Donor 01 day 3 after vericella zoster vaccination

source_name: Donor 01 day 3


title: 20009-V2

description:
6116733075_C
Donor 09 day 3 after vericella zoster vaccination

source_name: Donor 09 day 3


title: 4 wk Saline_6

status: Public on Sep 11 2016

city: Melbourne

first: John

last: Bateman

address: Flemington Road

department: Skeletal Biology

institute: Murdoch Childrens Research Institute

description: Serum and knee joints from the same mice were collected and analysed for this study

hyb_protocol: miRNA expression profiling was performed using SurePrint mouse miRNA microarray technology, release 19 (G4872A, Agilent Technologies) at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia). Briefly, 10 ng of miRNA was labelled and hybridized using the miRNA microarray system with miRNA complete labelling and Hyb kit version 3.0 (Agilent Technologies) by following manufacturer’s instructions.

scan_protocol: The arrays were scanned on a G2565CA microarray scanner and the features were extracted using Agilent Feature Extraction 12.0.07 software

data_processing: The raw data was processed in statistical language R, using a limma package (limma_3.20.9). Samples were background corrected with Normexp (offset = 50) and normalized with cyclic loess. Only probes that were deemed expressed (10 % greater signal than the negative controls) in at least 5 samples were maintained for differential expression analysis. Array weights were applied to data to down-weight lesser-quality arrays, improving the precision and power of the overall differential expression analysis. Probes were summarised at the miRNA level. Data was adjusted for multiple testing using Benjamini and Hochberg method to control for false discovery rate.

organism: Mus musculus

source_name: Serum

growth_protocol: All mice were housed 2-5 animals/30×20×18cm individually-ventilated-cage with filter lids, provided with sterilised bedding and environmental enrichment, maintained at 21-22°C with a 12-hour light/dark cycle, and received water and complete pelleted food ad libitum. Mice received no post-arthritis-induction medication, were maintained in their pre-operative groups and were allowed unrestricted cage exercise. Mice with sham and DMM surgery were co-housed as were saline and AIA animals.

extract_protocol: At the designated times post arthritis induction mice were deeply anesthetised with 4% isoflurane prior to blood collection. A midline incision was made to enter the abdominal cavity and allow visualization of the heart through the diaphragm. Maximal blood volume (0.5-1ml) was then collected via cardiac puncture (3ml syringe 18 gauge needle), transferred into a sterile tube, and allowed to sit at room temperature for 30 minutes. The tubes were then centrifuged (6000 rpm for 20 min) and the serum harvested and transferred into polypropylene tubes in 0.25ml aliquots and stored at -80°C until all time points were harvested for further processing. Serum was thawed on ice, gently mixed and then microRNA was isolated from 100µl of serum of each mouse using a miRNeasy serum/plasma kit (Qiagen) according to the manufacturers instructions. RNA integrity and miRNA quantity was assessed by capillary electrophoresis with a Bioanalyzer 2100 (Agilent) using a small RNA kit according to the manufacturer’s specifications.

treatment_protocol: Post-traumatic OA was surgically induced in eighteen 11 week old male wild type C57BL6 mice by unilateral destabilization of the medial meniscus (DMM). Briefly, under isoflourane anaesthesia the medial meniscotibial ligament was exposed (by medial parapatellar arthrotomy and intrapatellar fat pad elevation, without tissue resection) and transected with curved dissecting forceps by one surgeon (CBL). Joints were flushed with sterile saline to remove any blood prior to separate closure of the joint capsule (simple continuous 8/0 Vicryl), subcutaneous tissue (mattress suture 8/0 Vicryl) and skin (cyanoacrylate). Unilateral sham-operations were also performed in 18 mice, where all procedures were identical except the medial menisco-tibial ligament was visualised but not transected. Antigen induced arthritis (AIA) was induced in eighteen 8 week old male wild type C57BL6 mice. Briefly, mice were immunized on day 0 and day 14 with 200 µg methylated bovine serum albumin (mBSA; Sigma) prepared as an emulsion in combination with Freund’s complete adjuvant (CFA containing 2mg/ml mTB). The mBSA emulsion was administered as two 50l intradermal injections into the dorsal skin in the region of the tail base. Arthritis was induced on day 21 by intra-articular injection of 10µl mBSA (20mg/ml dissolved in sterile saline) into the right knee joint. Control mice (n = 18) were immunised as described above but received an intra-articular injection of 10l saline into the right knee joint.

tag: strain

value: Male


title: 1 wk DMM_6

label_protocol: miRNA expression profiling was performed using SurePrint mouse miRNA microarray technology, release 19 (G4872A, Agilent Technologies) at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia). Briefly, 10 ng of miRNA was labelled and hybridized using the miRNA microarray system with miRNA complete labelling and Hyb kit version 3.0 (Agilent Technologies) by following manufacturer’s instructions.


title: 1 wk AIA_6


title: 4 wk AIA_6


title: 16 wk Saline_6


title: 1 wk Sham_6


title: healthy control group, biological rep1

city: beijing

first: ai

middle: aa

last: gao

address: NO10, Xi tou tiao, Youanmen,Fengtai District

country: China

institute: School of Public Health, Capital Medical University

description:
DNA Methylation profiles from healthy control 1
SentrixBarcode: 7973201015
SentrixPosition: R06C01
Sample_ID: C1
Well: A06

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

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

data_processing: GenomeStudio V2011.1; methylation module 1.9.0

source_name: healthy control 1

growth_protocol: Peripheral blood samples were obtained during physical exam of workers.

extract_protocol: Genomic DNA was prepared using DNA extraction kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: All blood samples from each subject were centrifuged and subjected to DNA extraction.

tag: stress

value: control

tag: cell type

value: peripheral blood mononuclear cells


title: 16 wk AIA_6


title: 20004-V2

description:
6116733075_E
Donor 04 day 3 after vericella zoster vaccination

source_name: Donor 04 day 3


title: 1 wk Saline_6


title: healthy control group, biological rep2

description:
DNA Methylation profiles from healthy control 2
SentrixBarcode: 7973201015
SentrixPosition: R01C02
Sample_ID: C2
Well: A07

source_name: healthy control 2


title: 4 wk DMM_6


title: healthy control group, biological rep4

description:
DNA Methylation profiles from healthy control 4
SentrixBarcode: 7973201015
SentrixPosition: R03C02
Sample_ID: C4
Well: A09

source_name: healthy control 3


title: benzene-exposed group, biological rep4

description:
DNA Methylation profiles from benzene-exposed worker 4
SentrixBarcode: 7973201015
SentrixPosition: R05C01
Sample_ID: B4
Well: A05

source_name: benzene-exposed worker 4

value: benzene-exposure


title: 20005-V1

description:
6116733075_B
Donor 05 day 0 after vericella zoster vaccination

source_name: Donor 05 day 0


title: 16 wk Sham_6


title: 20002-V2

description:
6116733075_F
Donor 02 day 3 after vericella zoster vaccination

source_name: Donor 02 day 3


title: 16 wk DMM_5


title: benzene-exposed group, biological rep2

description:
DNA Methylation profiles from benzene-exposed worker 2
SentrixBarcode: 7973201015
SentrixPosition: R03C01
Sample_ID: B2
Well: A03

source_name: benzene-exposed worker 2


title: healthy control group, biological rep3

description:
DNA Methylation profiles from healthy control 3
SentrixBarcode: 7973201015
SentrixPosition: R02C02
Sample_ID: C3
Well: A08


title: benzene-exposed group, biological rep3

description:
DNA Methylation profiles from benzene-exposed worker 3
SentrixBarcode: 7973201015
SentrixPosition: R04C01
Sample_ID: B3
Well: A04

source_name: benzene-exposed worker 3


title: 16 wk Sham_5


title: 1 wk Saline_5


title: 4 wk Sham_6


title: 4 wk Sham_5


title: 16 wk Saline_5


title: 1 wk Sham_5


title: 16 wk Sham_4


title: 4 wk AIA_5


title: 1 wk DMM_5


title: Adipose_T4_Post-LPS [Scorr (2852) 419-4]

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

description:
Gene expression data from human adipose
Scorr (2852) 419-4

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Human Genome U133Plus 2.0 arrays. Microarrays were washed and then stained with amplified fluorescence markers

scan_protocol: Signals were collected on a confocal scanner at 3 μm resolution (excitation at 570 nm)

data_processing: Microarray Suite version 5.0 (MAS 5.0) was used to quantitate expression levels of average signal from two sequential scans. Array signal intensities passed a two-stage QC process including affyQCReport package. All arrays had similar background values and distributions of intensity.

source_name: Human Adipose 24hours post-LPS

label_protocol: cDNA and cRNA was prepared from 100ng RNA using standard protocols

extract_protocol: RNA was extracted from adipose using the Qiagen Rneasy Lipid tissue Mini kit

treatment_protocol: We administered endotoxin (LPS, 3ng/kg IV) to healthy human volunteers to evoke endotoxemia, and obtained subcutaneous adipose biopsies at 0, 4, 12 and 24 hours post-LPS

value: Adipose


title: 16 wk AIA_5


title: 1 wk AIA_5


title: Adipose_T2_Post-LPS [Scorr (2850) 419-2]

description:
Gene expression data from human adipose
Scorr (2850) 419-2

source_name: Human Adipose 4hours post-LPS


title: Adipose_T1_Pre-LPS [Scorr (2849) 419-1]

description:
Gene expression data from human adipose
Scorr (2849) 419-1

source_name: Human Adipose Pre-LPS


title: 4 wk Saline_5


title: Adipose_T3_Post-LPS [Scorr (2643) 357-3]

description:
Gene expression data from human adipose
Scorr (2643) 357-3

source_name: Human Adipose 12hours post-LPS


title: Adipose_T3_Post-LPS [Scorr (2647) 396-3]

description:
Gene expression data from human adipose
Scorr (2647) 396-3


title: 16 wk AIA_4


title: Adipose_T2_Post-LPS [Scorr (2646) 396-2]

description:
Gene expression data from human adipose
Scorr (2646) 396-2


title: Adipose_T3_Post-LPS [Scorr (2851) 419-3]

description:
Gene expression data from human adipose
Scorr (2851) 419-3


title: Adipose_T4_Post-LPS [Scorr (2644) 357-4]

description:
Gene expression data from human adipose
Scorr (2644) 357-4


title: Adipose_T2_Post-LPS [Scorr (2642) 357-2]

description:
Gene expression data from human adipose
Scorr (2642) 357-2


title: Adipose_T1_Pre-LPS [Scorr (2645) 396-1]

description:
Gene expression data from human adipose
Scorr (2645) 396-1


title: benzene-exposed group, biological rep1

description:
DNA Methylation profiles from benzene-exposed worker 1
SentrixBarcode: 7973201015
SentrixPosition: R02C01
Sample_ID: B1
Well: A02

source_name: benzene-exposed worker 1


title: benzene poisoning group, biological rep4

description:
DNA Methylation profiles from benzene poisoning patient 4
SentrixBarcode: 7973201015
SentrixPosition: R01C01
Sample_ID: A4
Well: A01

source_name: benzene poisoning patient 4

value: benzene poisoning


title: 1 wk DMM_4

description: Serum and knee joints from the same mice were collected and analysed for this study


title: 1 wk Saline_4


title: 1 wk Sham_4


title: Adipose_T1_Pre-LPS [Scorr (2641) 357-1]

description:
Gene expression data from human adipose
Scorr (2641) 357-1


title: Adipose_T1_Pre-LPS [Scorr (2637) 332-1b]

description:
Gene expression data from human adipose
Scorr (2637) 332-1b


title: Adipose_T2_Post-LPS [Scorr (2638) 332-2b]

description:
Gene expression data from human adipose
Scorr (2638) 332-2b


title: Adipose_T4_Post-LPS [Scorr (2640) 332-4b]

description:
Gene expression data from human adipose
Scorr (2640) 332-4b


title: benzene poisoning group, biological rep1

description:
DNA Methylation profiles from benzene poisoning patient 1
SentrixBarcode: 7973201015
SentrixPosition: R04C02
Sample_ID: A1
Well: A10

source_name: benzene poisoning patient 1


title: benzene poisoning group, biological rep3

description:
DNA Methylation profiles from benzene poisoning patient 3
SentrixBarcode: 7973201015
SentrixPosition: R06C02
Sample_ID: A3
Well: A12

source_name: benzene poisoning patient 3


title: 4 wk AIA_4

source_name: Serum


title: 4 wk Saline_4


title: 1 wk AIA_4


title: 16 wk Sham_3


title: 4 wk Sham_4


title: 4 wk DMM_5


title: 16 wk DMM_4


title: 4 wk DMM_4


title: Adipose_T2_Post-LPS [Scorr (2634) 260-2]

description:
Gene expression data from human adipose
Scorr (2634) 260-2


title: Adipose_T3_Post-LPS [Scorr (2639) 332-3b]

description:
Gene expression data from human adipose
Scorr (2639) 332-3b


title: 16 wk DMM_3


title: Adipose_T4_Post-LPS [Scorr (2632) 251-4]

description:
Gene expression data from human adipose
Scorr (2632) 251-4


title: Adipose_T3_Post-LPS [Scorr (2635) 260-3]

description:
Gene expression data from human adipose
Scorr (2635) 260-3


title: Adipose_T1_Pre-LPS [Scorr (2633) 260-1]

description:
Gene expression data from human adipose
Scorr (2633) 260-1


title: Adipose_T4_Post-LPS [Scorr (2636) 260-4]

description:
Gene expression data from human adipose
Scorr (2636) 260-4


title: 4 wk Sham_3


title: 4 wk DMM_3


title: benzene poisoning group, biological rep2

description:
DNA Methylation profiles from benzene poisoning patient 2
SentrixBarcode: 7973201015
SentrixPosition: R05C02
Sample_ID: A2
Well: A11

source_name: benzene poisoning patient 2


title: Adipose_T3_Post-LPS [Scorr (2631) 251-3]

description:
Gene expression data from human adipose
Scorr (2631) 251-3


title: Adipose_T2_Post-LPS [Scorr (2630) 251-2]

description:
Gene expression data from human adipose
Scorr (2630) 251-2


title: Adipose_T4_Post-LPS [Scorr (2628) 211-4]

description:
Gene expression data from human adipose
Scorr (2628) 211-4


title: Adipose_T3_Post-LPS [Scorr (2627) 211-3]

description:
Gene expression data from human adipose
Scorr (2627) 211-3


title: Adipose_T1_Pre-LPS [Scorr (2629) 251-1]

description:
Gene expression data from human adipose
Scorr (2629) 251-1


title: Adipose_T1_Pre-LPS [Scorr (2625) 211-1]

description:
Gene expression data from human adipose
Scorr (2625) 211-1


title: 1 wk AIA_3

description: Serum and knee joints from the same mice were collected and analysed for this study


title: Adipose_T4_Post-LPS [Scorr (2624) 203-4]

description:
Gene expression data from human adipose
Scorr (2624) 203-4


title: 1 wk DMM_3


title: 4 wk AIA_3


title: Adipose_T3_Post-LPS [Scorr (2623) 203-3]

description:
Gene expression data from human adipose
Scorr (2623) 203-3


title: Adipose_T2_Post-LPS [Scorr (2626) 211-2]

description:
Gene expression data from human adipose
Scorr (2626) 211-2


title: Adipose_T2_Post-LPS [Scorr (2622) 203-2]

description:
Gene expression data from human adipose
Scorr (2622) 203-2


title: 1 wk Saline_3


title: 16 wk Saline_3


title: 1 wk Sham_3


title: 16 wk AIA_3


title: 4 wk Saline_3


title: 4 wk DMM_2


title: Adipose_T1_Pre-LPS [Scorr (2621) 203-1]

description:
Gene expression data from human adipose
Scorr (2621) 203-1


title: Posterior_column_gene_level_analysis_1

city: Nagoya

first: Kinji

last: Ohno

address: 65 Tsurumai, Showa-ku

department: Graduate School of Medicine

country: Japan

institute: Nagoya University

description: Raw data file: sensory neuron 1.CEL

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix).

scan_protocol: Array scanning was performed using the Afftmetrix GeneChip Scanner 7G according to the manufacturer's instruction.

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis were performed with Expression Console 1.3.1.187.
gene_level_analysis:
affymetrix-algorithm-name = iterplier-gene-full
affymetrix-algorithm-version = 2.0
program-name = Expression Console
exon_level_analysis:
affymetrix-algorithm-name = rma-exon-full : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console

source_name: Posterior column

label_protocol: Fluorescent cDNA probes for microarray analysis were synthesized using FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies) and WT-Ovation Exon Module (NuGEN Technologies).

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using Rneasy Micro kit (Qiagen), and was linearly amplified by Ovation Pico WTA System (NuGEN Technologies).

treatment_protocol: not applicable

value: Spinal cord

tag: cells

value: Posterior column


title: Adipose_T1_Pre-LPS [Scorr (2617) 183-1]

description:
Gene expression data from human adipose
Scorr (2617) 183-1


title: Adipose_T3_Post-LPS [Scorr (2619) 183-3]

description:
Gene expression data from human adipose
Scorr (2619) 183-3


title: Anterior_horn_cells_gene_level_analysis_3

description: Raw data file: motor neuron 3.CEL

source_name: Anterior horn cells

value: Anterior horn cells


title: Adipose_T2_Post-LPS [Scorr (2618) 183-2]

description:
Gene expression data from human adipose
Scorr (2618) 183-2


title: Adipose_T4_Post-LPS [Scorr (2620) 183-4]

description:
Gene expression data from human adipose
Scorr (2620) 183-4


title: AVS023 (30 µg/mL)+IL-1β (1ng/mL)_rep2

city: Bangkok

first: Onusa

last: Thamsermsang

address: Prannok Road.

department: Pharmacology

country: Thailand

institute: Faculty of Medicine Siriraj Hospital, Mahidol University

description:
SAMPLE 22
replicate 2

hyb_protocol: the whole genome expression direct hybridization assay protocol (Illumina, USA)

scan_protocol: HiScan array scanner protocol (Illumina, USA)

data_processing: The data were prepocessed and analyzed by Microsoft Excel version 2013.The normalization of the data set were performed using normalization factor constant calculated from 12 housekeeping genes based on sample 1. The list of housekeeping genes were refered from Qiagen website (http://www.sabiosciences.com/rt_pcr_product/HTML/PAHS-000A.html). To calculate a normalized constant of each treatment, the signal intensities of housekeeping genes were averaged and calculated relative ratio that following below equation  Relative ratio = [Mean of housekeeping gene intensities (treatment)/ Mean of housekeeping gene intensities (control)]. For adjusting the unequal intensity distribution that affect from experiment procedure and other factors in experimental design. The normalized factor of each group was applied to get corrected or nearly truthful value of individual signal intensity following the equation. Corrected intensity =  [1xsignal intensity /normalized factor] ; normalized factor of each treatment was calculated from previous relative ratio equation

source_name: AVS023 (30 µg/mL)+IL-1β (1ng/mL), dermal fibroblasts

label_protocol: RNA (cRNA) and amplification and biotin labelling were carried out according to the Illumina TotalPrep™ RNA Amplification kit (Life Technologies, USA)

growth_protocol: fibroblasts 2x105 cells (per well) were seeded into 6-wells plate and incubated until confluency 80%

extract_protocol: Total RNA were isolated by Illutra RNA spin Mini RNA isolation Kit (GE Healthcare, UK) following instruction

treatment_protocol: AVS023, gallic acid and piperine (various concentrations) were pre-treated for 30 min after that IL-1β (1ng/mL) were added and incubated for 4 h

tag: race

value: Caucacian

tag: Sex

value: Female

value: dermal fibroblasts

tag: pre-treatment

tag: pre-treatment dose

value: 30 µg/mL

tag: stimulation

tag: passage number


title: AVS023 (10 µg/mL)+IL-1β (1ng/mL)_rep2

description:
SAMPLE 21
replicate 2

source_name: AVS023 (10 µg/mL)+IL-1β (1ng/mL), dermal fibroblasts

value: 10 µg/mL


title: Anterior_horn_cells_gene_level_analysis_2

description: Raw data file: motor neuron 2.CEL


title: Posterior_column_gene_level_analysis_3

description: Raw data file: sensory neuron 3.CEL


title: Posterior_column_gene_level_analysis_2

description: Raw data file: sensory neuron 2.CEL


title: Adipose_T4_Post-LPS [Scorr (2616) 171-4]

description:
Gene expression data from human adipose
Scorr (2616) 171-4


title: AVS023 (3 µg/mL)+IL-1β (1ng/mL)_rep2

description:
SAMPLE 20
replicate 2

source_name: AVS023 (3 µg/mL)+IL-1β (1ng/mL), dermal fibroblasts

value: 3 µg/mL


title: 16 wk Sham_2


title: Piperine (30 µg/mL)+IL-1β (1ng/mL)_rep2

description:
SAMPLE 19
replicate 2

source_name: Piperine (30 µg/mL)+IL-1β (1ng/mL), dermal fibroblasts

value: Piperine


title: Anterior_horn_cells_gene_level_analysis_1

description: Raw data file: motor neuron 1.CEL


title: 16 wk Sham_1


title: Adipose_T4_Post-LPS [Scorr (2648) 396-4]

description:
Gene expression data from human adipose
Scorr (2648) 396-4


title: 16 wk DMM_2


title: 4 wk Sham_2


title: 16 wk Saline_4


title: Adipose_T3_Post-LPS [Scorr (2615) 171-3]

description:
Gene expression data from human adipose
Scorr (2615) 171-3


title: 16 wk DMM_1


title: 4 wk DMM_1


title: Gallic acid (3 µg/mL)+IL-1β (1ng/mL)_rep2

description:
SAMPLE 17
replicate 2

source_name: Gallic acid (3 µg/mL)+IL-1β (1ng/mL), dermal fibroblasts

value: Gallic acid


title: Piperine (1 µg/mL)+IL-1β (1ng/mL)_rep2

description:
SAMPLE 18
replicate 2

source_name: Piperine (1 µg/mL)+IL-1β (1ng/mL), dermal fibroblasts

value: 1 µg/mL


title: Adipose_T2_Post-LPS [Scorr (2614) 171-2]

description:
Gene expression data from human adipose
Scorr (2614) 171-2

source_name: Human Adipose 4hours post-LPS


title: Gallic acid (0.3 µg/mL)+IL-1β (1ng/mL)_rep2

description:
SAMPLE 15
replicate 2

source_name: Gallic acid (0.3 µg/mL)+IL-1β (1ng/mL), dermal fibroblasts

value: 0.3 µg/mL


title: Adipose_T3_Post-LPS [Scorr (2612) 169-3]

description:
Gene expression data from human adipose
Scorr (2612) 169-3

source_name: Human Adipose 12hours post-LPS


title: Adipose_T1_Pre-LPS [Scorr (2613) 171-1]

description:
Gene expression data from human adipose
Scorr (2613) 171-1

source_name: Human Adipose Pre-LPS


title: 4 wk Sham_1

value: Male


title: IL-1β (1ng/mL)_rep2

description:
SAMPLE 13
replicate 2

source_name: IL-1β (1ng/mL), dermal fibroblasts


title: Gallic acid (1 µg/mL)+IL-1β (1ng/mL)_rep2

description:
SAMPLE 16
replicate 2

source_name: Gallic acid (1 µg/mL)+IL-1β (1ng/mL), dermal fibroblasts


title: Adipose_T2_Post-LPS [Scorr (2611) 169-2]

description:
Gene expression data from human adipose
Scorr (2611) 169-2


title: Indomethacin (50 µM)+IL-1β (1ng/mL)_rep2

description:
SAMPLE 14
replicate 2

source_name: Indomethacin (50 µM)+IL-1β (1ng/mL), dermal fibroblasts

value: Indomethacin

value: 50 µM


title: Adipose_T1_Pre-LPS [Scorr (2610) 169-1]

description:
Gene expression data from human adipose
Scorr (2610) 169-1

value: Adipose


title: 1 wk Sham_2

description: Serum and knee joints from the same mice were collected and analysed for this study

source_name: Serum


title: Adipose_T2_Post-LPS [Scorr (2608) 88-2]

description:
Gene expression data from human adipose
Scorr (2608) 88-2


title: Control_rep2

description:
SAMPLE 12
replicate 2

source_name: Control, dermal fibroblasts

value: Control


title: AVS023 (10 µg/mL)+IL-1β (1ng/mL)_rep1

description:
SAMPLE 10
replicate 1


title: Adipose_T3_Post-LPS [Scorr (2609) 88-3]

description:
Gene expression data from human adipose
Scorr (2609) 88-3


title: AVS023 (30 µg/mL)+IL-1β (1ng/mL)_rep1

description:
SAMPLE 11
replicate 1


title: 1 wk Saline_2


title: Adipose_T1_Pre-LPS [Scorr (2607_Rehyb) 88-1]

description:
Gene expression data from human adipose
Scorr (2607_Rehyb) 88-1


title: 16 wk AIA_2


title: 1 wk DMM_2


title: Adipose_T4_Post-LPS [Scorr (2606) 63-4]

description:
Gene expression data from human adipose
Scorr (2606) 63-4

source_name: Human Adipose 24hours post-LPS


title: 4 wk AIA_2


title: Piperine (30 µg/mL)+IL-1β (1ng/mL)_rep1

description:
SAMPLE 8
replicate 1


title: Adipose_T3_Post-LPS [Scorr (2605) 63-3]

description:
Gene expression data from human adipose
Scorr (2605) 63-3


title: AVS023 (3 µg/mL)+IL-1β (1ng/mL)_rep1

description:
SAMPLE 9
replicate 1


title: Gallic acid (3 µg/mL)+IL-1β (1ng/mL)_rep1

description:
SAMPLE 6
replicate 1


title: Piperine (1 µg/mL)+IL-1β (1ng/mL)_rep1

description:
SAMPLE 7
replicate 1


title: Adipose_T2_Post-LPS [Scorr (2604) 63-2]

description:
Gene expression data from human adipose
Scorr (2604) 63-2


title: 1 wk AIA_2


title: 4 wk Saline_2


title: Adipose_T1_Pre-LPS [Scorr (2603) 63-1]

description:
Gene expression data from human adipose
Scorr (2603) 63-1


title: Gallic acid (0.3 µg/mL)+IL-1β (1ng/mL)_rep1

description:
SAMPLE 4
replicate 1


title: Adipose_T4_Post-LPS [Scorr (2602) 30-4]

description:
Gene expression data from human adipose
Scorr (2602) 30-4


title: Adipose_T3_Post-LPS [Scorr (2601) 30-3]

description:
Gene expression data from human adipose
Scorr (2601) 30-3


title: 16 wk Saline_2


title: Gallic acid (1 µg/mL)+IL-1β (1ng/mL)_rep1

description:
SAMPLE 5
replicate 1


title: 4 wk Saline_1


title: EPN_821_1

city: Aurora

first: Ichiro

last: Nakachi

state: CO

address: 12700 East 19th Avenue, RC2 9th floor

department: Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine

institute: University of Colorado Denver

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 25

scan_protocol: standard Illumina protocols for HumanOmni2.5-Quad chips using iScan

data_processing: Genotyped data, Log R ratio (LRR) and B allele frequency (BAF) were generated using GenomeStudio (Illumina). All samples (primary and first recurrent ependymoma) examined were analyzed as pairs with matched reference blood samples or unpairs.

label: C-Bio and A-DNP

source_name: primary ependymoma

extract_protocol: Biopsies and blood were snap frozen at the time of surgery and DNA was subsequently isolated from each sample using the Quiagen RNA/DNA All Prep kit per manufacturer's instructions.  Extracted DNA was quantified, verified to be of high molecular weight.

tag: individual

value: patient 821

value: brain tumor (ependymoma)

tag: ependymoma sub-group

value: primary ependymoma

value: male


title: Adipose_T2_Post-LPS [Scorr (2600) 30-2]

description:
Gene expression data from human adipose
Scorr (2600) 30-2


title: 4 wk AIA_1


title: IL-1β (1ng/mL)_rep1

description:
SAMPLE 2
replicate 1

value: Caucacian

value: Female

value: dermal fibroblasts


title: Control_rep1

description:
SAMPLE 1
replicate 1


title: Indomethacin (50 µM)+IL-1β (1ng/mL)_rep1

description:
SAMPLE 3
replicate 1


title: EPN_930_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 29

hyb_protocol: standard Illumina protocols for HumanOmni2.5-Quad chips

source_name: recurrent ependymoma

value: patient 930

value: recurrent ependymoma


title: 16 wk Saline_1


title: EPN_821_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 26

label_protocol: standard Illumina protocols for HumanOmni2.5-Quad chips


title: EPN_816_G

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 24

source_name: blood

value: patient 816

value: blood (reference)


title: EPN_930_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 28


title: 1 wk Saline_1


title: EPN_816_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 23


title: Adipose_T1_Pre-LPS [Scorr (2599) 30-1]

description:
Gene expression data from human adipose
Scorr (2599) 30-1


title: 1 wk Sham_1

description: Serum and knee joints from the same mice were collected and analysed for this study


title: EPN_821_G

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 27


title: EPN_816_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 22


title: 1 wk AIA_1


title: EPN_691_G

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 18

value: patient 691


title: EPN_811_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 20

value: patient 811


title: 1 wk DMM_1

value: Male


title: 16 wk AIA_1


title: EPN_811_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 19


title: bp er inflorescences; biological rep3

status: Public on Sep 10 2016

city: Toronto

first: Dan

last: Riggs

state: ON

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: University of Toronto

hyb_protocol: All steps as described by Affymetrix, including hybridization controls, 16 hours at 45°C with 60rpm rotation; Washing and detection as described by Affymetrix.

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: Raw data subjected to GCOS/MAS normalization and a linear scaling factor  was applied to set the TGT value to 500

organism: Arabidopsis thaliana

source_name: bp er inflorescences

label_protocol: Two cycle cDNA synthesis and biotin labeling of cRNA as described by Affymetrix, employing the GeneChip IVT Labeling Kit

growth_protocol: Plants were grown in 4 pots in Premier Promix PGX in a Conviron ATC60 growth chamber at 22°C under fluorescent lighting (125μE/m2) with a 16hr day:8hr night photoperiod

extract_protocol: inflorescences of the appropriate stage were collected into liquid nitrogen, powered using a mortar and pestle, and the RNA extracted by employing a Qiagen Plant RNA extraction kit.  On-column DNAse digestion was conducted and aliquots were used to generate cDNA.  PCR was employed with control primers of the ACT7 gene that spanned two introns to test for the presence of genomic DNA; all samples gave rise to PCR products indicative of high quality cDNA with no gDNA contamination and were then used for preparing cDNA probes for microarray hybridization

tag: genotype/variation

value: bp er parent line

tag: tissue/development stage

value: inflorescences including floral stages 1-13


title: bp er fil inflorescences; biological rep 3

source_name: bp er fil inflorescences

value: bp er fil suppressor line


title: bp er fil inflorescences; biological rep 2


title: bp er fil inflorescences; biological rep 1


title: EPN_483_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 13

value: patient 483


title: bp er inflorescences; biological rep2


title: EPN_507_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 14

value: patient 507

value: brain tumor (ependymoma)


title: EPN_811_G

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 21

value: male


title: bp er inflorescences; biological rep1


title: HEND247 [IgM]

type: protein

city: Irvine

first: Carolina

last: Lessa Aquino

address: 302 MedSurge II

institute: University of California Irvine

hyb_protocol: Slides were washed 3 times with TTBS after each incubation

scan_protocol: Slides were scanned in a Perkin Elmer ScanArray confocal laser and intensities were quantified using QuantArray package

data_processing: Array signal intensity was quantified using QuantArray software. Spots intensity raw data were obtained as the mean pixel signal intensity with automatic correction forspot-specific background. Data was normalized by dividing the raw signal for each IVTT protein spot by the median of the sample-specific IVTT control spots (fold-overcontrol [FOC]) and then taking the base-2 logarithm of the ratio (log2 FOC).

molecule: protein

source_name: control serum sample (endemic)

label_protocol: Biotinylated anti-human IgG, diluted 1/2000 in Blocking Buffer or anti-human IgM, diluted 1/400 in Blocking Buffer, was added to the arrays for one-hour incubation at room temperature. Bound antibodies were detected by one-hour incubation with streptavidin-conjugated SureLight P3.

extract_protocol: Human sera samples were diluted 1/100 in Protein Array Blocking Buffer containing E. coli lysate 10 mg/mL (McLab) at a final concentration of 10% v/v and incubated for 30 min at room temperature under constant mixing to remove background reactivity to E. coli proteins in the IVTT reactions. E. coli protein-antibody complexes were removed from the sample dilution mix via centrifugation prior to addition to the microarray

tag: age

tag: platelet count

tag: hematocrit

tag: acute mat titer

tag: convalescent mat titer

tag: elisa

tag: pcr

tag: lab confirmation

tag: mat result

tag: number of days of symptoms

tag: respiratory failure

tag: icu admission

tag: oliguric renal failure


title: HEND244 [IgM]

tag: gender


title: EPN_459_G

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 11

tag: individual

value: patient 459

tag: tissue

value: female


title: HEND245 [IgM]


title: EPN_691_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 16

tag: ependymoma sub-group

value: primary ependymoma


title: HEND243 [IgM]

tag: age


title: HEND242 [IgM]

tag: platelet count


title: HEND241 [IgM]

tag: hematocrit


title: HEND246 [IgM]

tag: acute mat titer


title: HEND240 [IgM]

tag: convalescent mat titer


title: HEND239 [IgM]

tag: elisa


title: HEND237 [IgM]

tag: pcr


title: HEND238 [IgM]

tag: lab confirmation


title: HEND236 [IgM]

tag: mat result


title: EPN_483_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 12


title: HEND234 [IgM]

tag: number of days of symptoms


title: HEND233 [IgM]

tag: respiratory failure


title: HEND235 [IgM]

tag: icu admission


title: HEND232 [IgM]

tag: oliguric renal failure


title: HEND231 [IgM]

tag: gender


title: EPN_507_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 15

tag: individual


title: HEND228 [IgM]


title: EPN_459_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 10

tag: tissue


title: HEND227 [IgM]


title: HEND229 [IgM]


title: EPN_459_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 9

tag: ependymoma sub-group


title: HEND225 [IgM]

tag: age


title: HEND221 [IgM]

tag: platelet count


title: HEND220 [IgM]

tag: hematocrit


title: HEND223 [IgM]

tag: acute mat titer


title: HEND218 [IgM]

tag: convalescent mat titer


title: HEND217 [IgM]

tag: elisa


title: EPN_691_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 17


title: HEND226 [IgM]

tag: pcr


title: HEND215 [IgM]

tag: lab confirmation


title: HEND214 [IgM]

tag: mat result


title: HEND216 [IgM]

tag: number of days of symptoms


title: HEND213 [IgM]

tag: respiratory failure


title: EPN_321_G

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 6

value: patient 321


title: Posterior_column_exon_level_analysis_3

description: Raw data file: sensory neuron 3.CEL

source_name: Posterior column

tag: strain

value: Spinal cord

tag: cells

value: Posterior column


title: EPN_195_G

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 3

value: patient 195

value: blood (reference)

tag: gender


title: EPN_364_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 7

tag: individual

value: patient 364


title: HEND211 [IgM]

tag: icu admission

tag: oliguric renal failure


title: EPN_364_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 8

tag: tissue

tag: ependymoma sub-group

value: recurrent ependymoma


title: GCRC6 [IgM]

source_name: control serum sample (not endemic)

tag: age

tag: platelet count

tag: hematocrit


title: EPN_321_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 5


title: GCRC5 [IgM]

tag: acute mat titer

tag: convalescent mat titer

tag: elisa


title: GCRC50 [IgM]

tag: pcr

tag: lab confirmation

tag: mat result


title: GCRC48 [IgM]

tag: number of days of symptoms

tag: respiratory failure


title: HEND212 [IgM]

tag: gender


title: GCRC49 [IgM]


title: Posterior_column_exon_level_analysis_1

description: Raw data file: sensory neuron 1.CEL

tag: strain

tag: cells


title: GCRC44 [IgM]

tag: icu admission

tag: oliguric renal failure


title: GCRC43 [IgM]


title: Anterior_horn_cells_exon_level_analysis_2

description: Raw data file: motor neuron 2.CEL

source_name: Anterior horn cells

tag: tissue

value: Anterior horn cells


title: Anterior_horn_cells_exon_level_analysis_3

description: Raw data file: motor neuron 3.CEL


title: GCRC36 [IgM]

tag: age


title: GCRC38 [IgM]

tag: platelet count


title: GCRC39 [IgM]

tag: hematocrit


title: GCRC37 [IgM]

tag: acute mat titer


title: Anterior_horn_cells_exon_level_analysis_1

description: Raw data file: motor neuron 1.CEL


title: GCRC35 [IgM]

tag: convalescent mat titer


title: GCRC7 [IgM]

tag: elisa


title: GCRC34 [IgM]

tag: pcr


title: GCRC33 [IgM]

tag: lab confirmation


title: GCRC32 [IgM]

tag: mat result


title: GCRC46 [IgM]

tag: number of days of symptoms


title: EPN_321_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 4

tag: individual

tag: ependymoma sub-group


title: GCRC45 [IgM]

tag: gender

tag: respiratory failure


title: GCRC47 [IgM]

tag: icu admission


title: GCRC40 [IgM]

tag: oliguric renal failure


title: GCRC2 [IgM]


title: GCRC30 [IgM]


title: GCRC31 [IgM]


title: GCRC3 [IgM]


title: GCRC9 [IgM]


title: GCRC17 [IgM]


title: GCRC16 [IgM]


title: GCRC15 [IgM]


title: GCRC14 [IgM]


title: Posterior_column_exon_level_analysis_2

description: Raw data file: sensory neuron 2.CEL

tag: strain

tag: tissue

tag: cells


title: GCRC1 [IgM]

tag: age

tag: platelet count

tag: hematocrit


title: EPN_195_2

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 2


title: HEND222 [IgM]

tag: acute mat titer

tag: convalescent mat titer

tag: elisa


title: SEV2883.3 [IgM]

source_name: convalescent serum sample

tag: pcr

tag: lab confirmation

value: positive

tag: mat result


title: GCRC12 [IgM]

tag: number of days of symptoms


title: SEV2871.3 [IgM]

tag: gender


title: GCRC13 [IgM]

tag: respiratory failure


title: SEV2872.3 [IgM]

tag: icu admission


title: GCRC4 [IgM]

tag: oliguric renal failure


title: EPN_195_1

description:
Genomic DNA was genotyped using HumanOmni2.5-Quad chip (Illumina).
SAMPLE 1

tag: individual

tag: ependymoma sub-group


title: GCRC11 [IgM]


title: SEV2833.3 [IgM]


title: HEND219 [IgM]


title: SEV2805.3 [IgM]


title: GCRC10 [IgM]


title: SEV2781.3 [IgM]


title: GCRC41 [IgM]


title: SEV2807.3 [IgM]


title: SEV2811.3 [IgM]


title: SEV2799.3 [IgM]


title: SEV2854.3 [IgM]


title: SEV2780.3 [IgM]


title: SEV2778.3 [IgM]


title: SEV2818.3 [IgM]


title: SEV2797.3 [IgM]


title: SEV2774.3 [IgM]


title: GCRC42 [IgM]


title: SEV2767.3 [IgM]


title: SEV2772.3 [IgM]


title: SEV2765.3 [IgM]


title: SEV2760.3 [IgM]


title: SEV2754.3 [IgM]


title: HEND230 [IgM]


title: SEV2750.3 [IgM]


title: SEV2714.3 [IgM]


title: SEV2705.3 [IgM]

value: negative


title: SEV2743.3 [IgM]


title: SEV2699.3 [IgM]


title: SEV2732.3 [IgM]


title: SEV2729.3 [IgM]


title: SEV2721.3 [IgM]


title: SEV2695.3 [IgM]


title: SEV2666.3 [IgM]


title: SEV2883.1 [IgM]

source_name: acute serum sample

value: no

value: yes


title: SEV2659.3 [IgM]


title: SEV2811.1 [IgM]


title: SEV2872.1 [IgM]


title: SEV2871.1 [IgM]


title: SEV2780.1 [IgM]


title: SEV2854.1 [IgM]


title: SEV2774.1 [IgM]


title: SEV2807.1 [IgM]


title: SEV2781.1 [IgM]


title: SEV2797.1 [IgM]


title: SEV2818.1 [IgM]


title: SEV2805.1 [IgM]


title: SEV2833.1 [IgM]


title: SEV2799.1 [IgM]


title: SEV2765.1 [IgM]


title: SEV2772.1 [IgM]


title: SEV2767.1 [IgM]


title: SEV2760.1 [IgM]


title: SEV2754.1 [IgM]


title: SEV2729.1 [IgM]


title: SEV2750.1 [IgM]


title: SEV2732.1 [IgM]


title: SEV2778.1 [IgM]


title: SEV2699.1 [IgM]


title: SEV2705.1 [IgM]


title: SEV2714.1 [IgM]


title: SEV2666.1 [IgM]


title: SEV2695.1 [IgM]


title: SEV2659.1 [IgM]


title: MILD3915.3 [IgM]


title: MILD3880.3 [IgM]


title: MILD3934.3 [IgM]

value: Probable


title: MILD3925.3 [IgM]


title: MILD3863.3 [IgM]


title: SEV2743.1 [IgM]

value: male


title: MILD2512.3 [IgM]


title: MILD2510.3 [IgM]


title: MILD3949.3 [IgM]


title: MILD2451.3 [IgM]


title: MILD3559.3 [IgM]


title: MILD2235.3 [IgM]


title: SEV2721.1 [IgM]


title: MILD2146.3 [IgM]


title: MILD1396.3 [IgM]


title: MILD1858.3 [IgM]


title: MILD2025.3 [IgM]


title: MILD1955.3 [IgM]


title: MILD2000.3 [IgM]


title: MILD3844.3 [IgM]


title: MILD3529.3 [IgM]


title: MILD1302.3 [IgM]


title: MILD3386.3 [IgM]


title: MILD1371.3 [IgM]


title: MILD896.3 [IgM]


title: MILD2173.3 [IgM]


title: MILD339.3 [IgM]


title: MILD297.3 [IgM]


title: MILD499.3 [IgM]


title: MILD831.3 [IgM]


title: MILD3925.1 [IgM]


title: MILD3949.1 [IgM]


title: MILD3915.1 [IgM]


title: MILD3529.1 [IgM]


title: MILD3559.1 [IgM]


title: MILD3863.1 [IgM]


title: MILD3386.1 [IgM]


title: MILD2512.1 [IgM]


title: MILD394.3 [IgM]

value: Indeterminado (FC)


title: MILD2451.1 [IgM]


title: MILD2235.1 [IgM]


title: MILD2146.1 [IgM]


title: MILD2025.1 [IgM]


title: MILD2510.1 [IgM]


title: MILD3934.1 [IgM]

value: female

value: Provavel


title: MILD2173.1 [IgM]


title: MILD123.3 [IgM]


title: MILD2000.1 [IgM]


title: MILD1955.1 [IgM]


title: MILD3880.1 [IgM]


title: MILD499.1 [IgM]


title: MILD896.1 [IgM]


title: MILD1858.1 [IgM]


title: MILD1371.1 [IgM]


title: MILD1302.1 [IgM]


title: MILD831.1 [IgM]


title: MILD394.1 [IgM]


title: MILD3844.1 [IgM]


title: MILD1396.1 [IgM]


title: MILD297.1 [IgM]


title: MILD339.1 [IgM]


title: MILD123.1 [IgM]


title: HEND247 [IgG]


title: HEND244 [IgG]


title: HEND246 [IgG]


title: HEND245 [IgG]


title: HEND242 [IgG]


title: HEND241 [IgG]


title: HEND243 [IgG]


title: HEND236 [IgG]


title: HEND240 [IgG]


title: HEND239 [IgG]


title: HEND237 [IgG]


title: HEND238 [IgG]


title: HEND234 [IgG]


title: HEND233 [IgG]


title: HEND229 [IgG]


title: HEND235 [IgG]


title: HEND232 [IgG]


title: HEND231 [IgG]


title: HEND230 [IgG]


title: HEND221 [IgG]


title: HEND220 [IgG]


title: HEND225 [IgG]


title: HEND222 [IgG]


title: HEND223 [IgG]


title: HEND227 [IgG]


title: HEND228 [IgG]


title: HEND226 [IgG]


title: HEND218 [IgG]


title: HEND219 [IgG]


title: HEND216 [IgG]


title: HEND217 [IgG]


title: HEND214 [IgG]


title: HEND212 [IgG]


title: HEND213 [IgG]


title: GCRC9 [IgG]


title: HEND211 [IgG]


title: GCRC7 [IgG]


title: GCRC50 [IgG]


title: GCRC6 [IgG]


title: GCRC49 [IgG]


title: GCRC48 [IgG]


title: GCRC46 [IgG]


title: HEND215 [IgG]


title: GCRC44 [IgG]


title: GCRC47 [IgG]


title: GCRC43 [IgG]


title: GCRC41 [IgG]


title: GCRC40 [IgG]


title: GCRC35 [IgG]


title: GCRC36 [IgG]


title: GCRC45 [IgG]


title: GCRC38 [IgG]


title: GCRC34 [IgG]


title: GCRC33 [IgG]


title: GCRC42 [IgG]


title: GCRC39 [IgG]


title: GCRC32 [IgG]


title: GCRC31 [IgG]


title: GCRC5 [IgG]


title: GCRC37 [IgG]


title: GCRC16 [IgG]


title: GCRC17 [IgG]


title: GCRC2 [IgG]


title: GCRC30 [IgG]


title: GCRC3 [IgG]


title: GCRC14 [IgG]


title: GCRC4 [IgG]


title: GCRC12 [IgG]


title: SEV2883.3 [IgG]


title: SEV2818.3 [IgG]


title: SEV2854.3 [IgG]


title: SEV2811.3 [IgG]


title: SEV2872.3 [IgG]


title: GCRC1 [IgG]


title: SEV2871.3 [IgG]


title: SEV2807.3 [IgG]


title: GCRC15 [IgG]


title: SEV2780.3 [IgG]


title: GCRC11 [IgG]


title: SEV2767.3 [IgG]


title: SEV2799.3 [IgG]


title: GCRC13 [IgG]


title: SEV2833.3 [IgG]


title: SEV2797.3 [IgG]


title: SEV2778.3 [IgG]


title: SEV2774.3 [IgG]


title: SEV2772.3 [IgG]


title: SEV2781.3 [IgG]


title: SEV2743.3 [IgG]


title: SEV2754.3 [IgG]


title: SEV2732.3 [IgG]


title: GCRC10 [IgG]


title: SEV2760.3 [IgG]


title: SEV2765.3 [IgG]


title: SEV2805.3 [IgG]


title: SEV2729.3 [IgG]


title: SEV2705.3 [IgG]


title: SEV2666.3 [IgG]


title: SEV2699.3 [IgG]


title: SEV2750.3 [IgG]


title: SEV2714.3 [IgG]


title: SEV2721.3 [IgG]


title: SEV2883.1 [IgG]


title: SEV2871.1 [IgG]


title: SEV2854.1 [IgG]


title: SEV2872.1 [IgG]


title: SEV2659.3 [IgG]


title: SEV2695.3 [IgG]


title: SEV2818.1 [IgG]


title: SEV2833.1 [IgG]


title: SEV2799.1 [IgG]


title: SEV2807.1 [IgG]


title: SEV2805.1 [IgG]


title: SEV2797.1 [IgG]


title: SEV2781.1 [IgG]


title: SEV2780.1 [IgG]


title: SEV2811.1 [IgG]


title: SEV2778.1 [IgG]


title: SEV2774.1 [IgG]


title: SEV2765.1 [IgG]


title: ces-D, 21°C, rep 4

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description: Gene expression data from ces-D A. thaliana mutant control plants (21°C, 3 d, continous light at 80 µmol.s-1.m-2)

hyb_protocol: Standard NASC hybridization protocol

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: The raw CEL files were normalized using the RMA background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes (DEG) were identified by a two-way ANOVA, and p-values were adjusted using the FDR (false-discovery rate) method to correct for multiple comparisons.

source_name: A. thaliana ces-D, 21 d old, control (3 d, 21°C)

label_protocol: Total RNA according to the standard Affymetrix protocol (WT Expression Kit User Manual, 2010, Affymetrix).

growth_protocol: Seeds were soil grown under log day conditions (16 h light at 80 µmol.s-1.m-2 / 8 h dark) at 21°C for 21 d.

extract_protocol: Total RNA was extracted with a Omega Bio-Tek plant RNA extraction kit (cat. No. R6827-02) according to the manufacturer's instructions.

treatment_protocol: Plants were treated with 4°C for 3 d under continuous light (80 µmol.s-1.m-2).

tag: tissue

value: aerial parts

tag: genetic background

tag: genotype/variation

value: ces-D

tag: treatment


title: bri1-301, 21°C, rep 3

description: Gene expression data from bri1-301 A. thaliana mutant control plants (21°C, 3 d, continous light at 80 µmol.s-1.m-2)

source_name: A. thaliana bri1-301, 21 d old, control (3 d, 21°C)

tag: age


title: qM, 21°C, rep 4

description: Gene expression data from qM A. thaliana mutant control plants (21°C, 3 d, continous light at 80 µmol.s-1.m-2)

source_name: A. thaliana qM, 21 d old, control (3 d, 21°C)

value: qM


title: SEV2767.1 [IgG]

tag: platelet count

tag: hematocrit

tag: acute mat titer

tag: convalescent mat titer


title: qM, 21°C, rep 2

value: control plants (21°C, 3 d, continous light at 80 µmol.s-1.m-2)


title: qM, 21°C, rep 3


title: ces-D, 21°C, rep 2


title: ces-D, 21°C, rep 3


title: bri1-301, 21°C, rep 4


title: bri1-301, 21°C, rep 1


title: Col-0, 21°C, rep 1

description: Gene expression data from wild type A. thaliana control plants (21°C, 3 d, continous light at 80 µmol.s-1.m-2)

source_name: A. thaliana Col-0, 21 d old, control (3 d, 21°C)

value: wild type


title: Col-0, 21°C, rep 4


title: bri1-301, 21°C, rep 2


title: ces-D, 21°C, rep 1


title: Col-0, 21°C, rep 3


title: Col-0, 21°C, rep 2


title: qM, 21°C, rep 1


title: SEV2750.1 [IgG]

tag: elisa

tag: pcr

tag: lab confirmation

tag: mat result


title: SEV2743.1 [IgG]

tag: gender

tag: number of days of symptoms

tag: respiratory failure

tag: icu admission


title: SEV2772.1 [IgG]

tag: oliguric renal failure


title: SEV2754.1 [IgG]


title: ces-D, 4°C, rep 3

description: Gene expression data from ces-D A. thaliana mutant treated with 4°C for 3 d under continous light (80 µmol.s-1.m-2)

source_name: A. thaliana ces-D, 21 d old, 3 d treatment with 4°C

tag: tissue

tag: genetic background


title: LS180_siControl_2 (siMYU)

city: Tokyo

first: Testu

last: Akiyama

address: 1-1-1, Yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

institute: Tokyo University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data sets were imported into Gene Spring for normalization and statistical analysis.

source_name: LS180, Control siRNA

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was prepared using TRIsure (BIO LINE)

tag: cell line

tag: treatment

value: control


title: SEV2760.1 [IgG]

tag: age

tag: platelet count


title: SEV2732.1 [IgG]

tag: hematocrit

tag: acute mat titer


title: SEV2729.1 [IgG]

tag: convalescent mat titer

tag: elisa


title: ces-D, 4°C, rep 4

tag: genotype/variation

value: 4°C for 3 d under continous light (80 µmol.s-1.m-2)


title: LS180_siMYU

source_name: LS180, MYU siRNA

value: siRNA targeting MYU


title: SEV2721.1 [IgG]

tag: pcr

tag: lab confirmation

value: positive

tag: mat result


title: SEV2714.1 [IgG]

tag: gender

tag: number of days of symptoms

tag: respiratory failure


title: ces-D, 4°C, rep 2

tag: tissue


title: LS180_siMYC

source_name: LS180, MYC siRNA

value: siRNA targeting MYC


title: SEV2705.1 [IgG]

value: negative

value: no

tag: icu admission

tag: oliguric renal failure


title: SEV2699.1 [IgG]

value: yes


title: LS180_siControl_1 (siCTNNB1)

tag: cell line

tag: treatment


title: yDucts, biological replica D

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description:
yDucts_D
Gene expression data from yDucts.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software.

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization.

label: Biotin

source_name: Murine pancreatic ductal organoids obtained from R26-rtTA; tetO-YAP S127A acini after doxycycline-inducible expression of YAP (yDucts)

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's instructions.

growth_protocol: Ducts and yDucts were maitained as organoids embedded in 100% Matrigel overlaid by Advanced DMEM/F12 supplemented with B27, N-Acetylcysteine, gastrin, murine EGF, human Noggin, human FGF10, Nicotinamide, R-Spondin1 and antibiotics.

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

tag: cell type

value: pancreatic ductal organoids from R26-rtTA; tetO-YAP S127A acini after inducible expression of YAP

tag: growth

value: pancreatic organoid medium


title: LS180_siControl_1 (siMYC)


title: LS180_siCTNNB1

source_name: LS180, CTNNB1 siRNA

value: siRNA targeting CTNNB2


title: bri1-301, 4°C, rep 4

description: Gene expression data from bri1-301 A. thaliana mutant treated with 4°C for 3 d under continous light (80 µmol.s-1.m-2)

source_name: A. thaliana bri1-301, 21 d old, 3 d treatment with 4°C

tag: genetic background

tag: age


title: ces-D, 4°C, rep 1


title: yDucts, biological replica C

description:
yDucts_C
Gene expression data from yDucts.


title: SEV2695.1 [IgG]

value: male

tag: platelet count

tag: hematocrit

tag: acute mat titer

tag: convalescent mat titer

tag: elisa


title: bri1-301, 4°C, rep 3

value: aerial parts

tag: genotype/variation


title: yDucts, biological replica B

description:
yDucts_B
Gene expression data from yDucts.


title: yDucts, biological replica A

description:
yDucts_A
Gene expression data from yDucts.


title: Ducts, biological replica C

description:
Ducts_C
Gene expression data from Ducts.

source_name: Murine pancreatic ductal organoids (Ducts)

value: pancreatic ductal organoids


title: Ducts, biological replica B

description:
Ducts_B
Gene expression data from Ducts.


title: Ducts, biological replica A

description:
Ducts_A
Gene expression data from Ducts.


title: bri1-301, 4°C, rep 2


title: Acini, biological replica D

description:
Acini_D
Gene expression data from acini.

source_name: Murine pancreatic exocrine acini

value: pancreatic exocrine acini

value: freshly isolated


title: SEV2666.1 [IgG]

tag: gender

tag: pcr

tag: lab confirmation

tag: mat result

tag: number of days of symptoms


title: Ducts, biological replica D

description:
Ducts_D
Gene expression data from Ducts.


title: Acini, biological replica B

description:
Acini_B
Gene expression data from acini.


title: Acini, biological replica C

description:
Acini_C
Gene expression data from acini.


title: SEV2659.1 [IgG]

tag: respiratory failure

tag: icu admission

tag: oliguric renal failure


title: bri1-301, 4°C, rep 1

tag: tissue

tag: treatment


title: MILD3934.3 [IgG]

tag: age

value: female

value: Probable


title: MILD3915.3 [IgG]

tag: platelet count


title: MILD3949.3 [IgG]

tag: hematocrit


title: yNSCs, biological replica A

description:
yNSC_A
Gene expression data from yNSCs.

source_name: Murine neural stem cells obtained from cortical neurons after doxycycline-inducible expression of YAP wild type (yNSCs)

growth_protocol: Neurons were cultured in Neurobasal, B27, Glutamine, antibiotics, AraC. NSCs and yNSCs were cultured in DMEM/F12 (Gibco, Life Technologies) with N2, murine EGF, murine bFGF, heparin, glutamine and antibiotics.

tag: cell type

value: neural stem cells from cortical neurons after inducible expression of YAP

tag: growth

value: NSC medium


title: qM, 4°C, rep 1

description: Gene expression data from qM A. thaliana mutant treated with 4°C for 3 d under continous light (80 µmol.s-1.m-2)

source_name: A. thaliana qM, 21 d old, 3 d treatment with 4°C

tag: genetic background

value: qM


title: qM, 4°C, rep 4

tag: genotype/variation

value: 4°C for 3 d under continous light (80 µmol.s-1.m-2)


title: yNSCs, biological replica C

description:
yNSC_C
Gene expression data from yNSCs.


title: MILD3925.3 [IgG]

source_name: convalescent serum sample

tag: gender

tag: acute mat titer

tag: convalescent mat titer

tag: elisa

value: positive

value: negative


title: MILD3880.3 [IgG]

tag: pcr

tag: lab confirmation

tag: mat result

tag: number of days of symptoms


title: qM, 4°C, rep 3

tag: tissue


title: NSCs, biological replica C

description:
NSC_C
Gene expression data from NSCs.

source_name: Murine neural stem cells (NSCs)

value: neural stem cells


title: Acini, biological replica A

description:
Acini_A
Gene expression data from acini.


title: NSCs, biological replica A

description:
NSC_A
Gene expression data from NSCs.


title: Col-0, 4°C, rep 4

description: Gene expression data from wild type A. thaliana treated with 4°C for 3 d under continous light (80 µmol.s-1.m-2)

source_name: A. thaliana Col-0, 21 d old, 3 d treatment with 4°C

value: wild type

tag: treatment


title: Col-0, 4°C, rep 3

tag: age


title: NSCs, biological replica B

description:
NSC_B
Gene expression data from NSCs.


title: Col-0, 4°C, rep 1


title: qM, 4°C, rep 2


title: yNSCs, biological replica B

description:
yNSC_B
Gene expression data from yNSCs.


title: MILD3863.3 [IgG]

tag: platelet count

tag: respiratory failure

tag: icu admission

tag: oliguric renal failure


title: MILD3844.3 [IgG]

tag: hematocrit


title: MILD3559.3 [IgG]


title: Col-0, 4°C, rep 2

tag: genetic background

tag: genotype/variation


title: MILD2512.3 [IgG]

tag: gender

tag: acute mat titer


title: MILD2510.3 [IgG]

tag: convalescent mat titer

tag: elisa


title: Org, biological replica B

description:
Org_B
Gene expression from Org.

source_name: Murine mammary organoids derived from FACS-purified mammary stem cells (Org)

growth_protocol: Org and yOrg were maintained as organoids embedded in 100% Matrigel overlaid by Advanced DMEM/F12 supplemented with Hepes, GlutaMax, antibiotics, EGF, bFGF, heparin, noggin and R-Spondin1.

tag: cell type

value: organoids from native mammary stem cells

tag: growth

value: mammary organoid medium


title: MILD3529.3 [IgG]

tag: pcr

tag: lab confirmation

tag: mat result

tag: number of days of symptoms


title: MILD3386.3 [IgG]

tag: age

tag: platelet count


title: MILD2451.3 [IgG]

value: male

tag: respiratory failure

tag: icu admission


title: Org, biological replica A

description:
Org_A
Gene expression from Org.


title: yOrg, biological replica C

description:
yOrg_C
Gene expression from yOrg.

source_name: Murine mammary organoids obtained from FACS-purified luminal differentiated cells after doxycycline-inducible expression of YAP (yOrg)

value: organoids from luminal differentiated mammary cells after inducible expression of YAP


title: Neurons, biological replica A

description:
Neuron_A
Gene expression data from cortical neurons.

source_name: Murine cortical neurons

value: cortical neurons

value: neuron medium


title: Org, biological replica C

description:
Org_C
Gene expression from Org.


title: Neurons, biological replica B

description:
Neuron_B
Gene expression data from cortical neurons.


title: Neurons, biological replica C

description:
Neuron_C
Gene expression data from cortical neurons.


title: yOrg, biological replica B

description:
yOrg_B
Gene expression from yOrg.


title: Lum, biological replica C

description:
Lum_C
Gene expression from mammary luminal differentiated cells.

source_name: Murine luminal differentiated mammary cells (FACS-purified) (Lum)

value: luminal differentiated mammary cells

value: freshly purified


title: 0.5 Gy 750 Rep3

first: Sally

last: Amundson

department: Center for Radiological Research

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Immediately after washing, slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Qucik Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: EPI-200 was purchased from MatTek (Ashland, MA). At arrival, tissue plates were allowed to equilibrate to room temperature for 1h and then tissues were transferred to 6-well tissue culture dishes filled with NMM-100 medium (0.9ml/well) and cultured according to the manufacturer's instructions as previously described (Curren et al., 2006. PMID: 16781186).

extract_protocol: Total RNA was isolated using the Illustra RNAspin Mini Isolation Kit (GE Healthcare, Piscataway, NJ) according to the manufacturer's instructions and stored at -80°C. Briefly, the procedure included homogenization in a Potter homogenizer, binding to a spin column and on-column treatment with DNase I. The impurities were washed out and RNA was eluted in RNase-free water. RNA yield and quality were assessed with the NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA) and the Bioanalyzer 2100 (Agilent Technologies, Foster City, CA).

treatment_protocol: For irradiation, samples were installed on a carousel and exposed to 0 or 0.5 Gy 9 MeV He-4 ions as simulated alpha particles using the track segment irradiation facility of the 5.5-MV Singletron accelerator at the Radiological Research Accelerator Facility (RARAF) of Columbia University.  After irradiation, samples were returned to  plates filled with fresh culture medium and cultured for 16h.

tag: tissue

value: EPI-200 3D epithelial cell model

tag: radiation dose

tag: time after irradiation

value: 16 hours

tag: distance from irradiated plane


title: Lum, biological replica B

description:
Lum_B
Gene expression from mammary luminal differentiated cells.


title: yOrg, biological replica A

description:
yOrg_A
Gene expression from yOrg.


title: Control 500 Rep3

value: 0 Gy

value: 500-750 microns


title: 0.5Gy Center Rep3

value: 0-250 microns


title: Control 750 Rep3


title: Control 250 Rep3

value: 250-500 microns


title: 0.5Gy 250 Rep3


title: 0.5 Gy 500 Rep3


title: Lum, biological replica A

description:
Lum_A
Gene expression from mammary luminal differentiated cells.


title: Control Center Rep3


title: 0.5 Gy 750 Rep2


title: MILD2235.3 [IgG]

tag: gender

tag: hematocrit

tag: acute mat titer

value: positive

value: negative

tag: oliguric renal failure


title: MILD2173.3 [IgG]

value: female

tag: convalescent mat titer

tag: elisa


title: MILD2146.3 [IgG]

tag: pcr

tag: lab confirmation


title: MILD2025.3 [IgG]

tag: mat result

tag: number of days of symptoms


title: pig-control-rep2

city: wuhan

first: Lin

last: xian

state: Hubei

address: shizishan street,number 1

department: College of Veterinary Medicine

institute: Huazhong Agricutural University

description: Gene expression after 6 days in lung from pig inoculated with PBS

hyb_protocol: 0.875 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions.On completion of the fragmentation reaction, 55μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent 4x44K Porcine Oligo Microarrays） 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 DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.

data_processing: Agilent Feature Extraction was applied to read the data, Scan resolution 5μm, PMT 100%, 10% and LOWESS normalization

organism: Sus scrofa

source_name: Lung, Control, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). NanoDrop ND-1000 Spectrophotometer(Shanghaibio, China) was used to check the dye incorporation and cRNA yield.

growth_protocol: A total of 12 piglets of high-heathy status were purchased from a commercial herd and raised in isolated facilities. All pigs were determined to be negative for the antibodies against influenza virus and  SS2 by Hemagglutination Inhibition test (HI) and and Enzyme-linked immunosorbent assay (ELISA) respectively on all pigs' sera prior to challenge.

extract_protocol: RNA extraction from pig lungs from the same part were performed using TRIzol following standard instructions (Invitrogen, Carlsbad, CA) and a clean-up was carried out using RNeasy columns (Qiagen, Beijing, China). Agilent 2100 Bioanalyzer was applied to evaluated the RNA integrity and concentration under the manufacturer's instruction (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Pigs from each group were sacrificed to collect lung tissues, which were immediately preserved in liquid nitrogen and subsequently stored in a -80℃ freezer.

value: lung

tag: disease state


title: MILD1858.3 [IgG]

tag: age

tag: platelet count

tag: respiratory failure


title: MILD1396.3 [IgG]

tag: icu admission


title: MILD1371.3 [IgG]


title: MILD1955.3 [IgG]


title: MILD2000.3 [IgG]


title: 0.5Gy Center Rep2

tag: tissue

tag: radiation dose

tag: time after irradiation


title: 0.5 Gy 500 Rep2

tag: distance from irradiated plane


title: pig-control-rep1

source_name: Lung, Control, replicate1


title: MILD1302.3 [IgG]

tag: gender

tag: hematocrit

tag: acute mat titer


title: 0.5Gy 250 Rep2


title: pig-H1N1-SS2-rep3

description: Gene expression  in lung from pig  infected with H1N1-SS2 (H1N1 inoculation for 3 days and then challenged with SS2 )

source_name: Lung, H1N1-SS2, replicate3

value: H1N1 and SS2 co-infected


title: Control 500 Rep2


title: pig-H1N1-SS2-rep1

description: Gene expression in lung from pig  infected with H1N1-SS2 (H1N1 inoculation for 3 days and then challenged with SS2 )

source_name: Lung, H1N1-SS2, replicate1


title: pig-SS2-rep2

description: Gene expression after 3 days in lung from pig infected with SS2 (PBS inoculation for 3 days and then challenged with SS2 for 3 days)

source_name: Lung, SS2, replicate2

value: SS2 infected


title: Control 250 Rep2


title: 0.5 Gy 750 Rep1


title: pig-control-rep3

source_name: Lung, Control, replicate3


title: 0.5 Gy 500 Rep1


title: pig-H1N1-rep3

description: Gene expression after 6 days in lung from pig infected with H1N1 virus

source_name: Lung, H1N1, replicate3

value: H1N1 infected


title: pig-H1N1-rep2

source_name: Lung, H1N1, replicate2


title: Control 750 Rep2


title: MILD896.3 [IgG]

value: male

tag: convalescent mat titer

tag: elisa

tag: oliguric renal failure


title: 0.5Gy 250 Rep1


title: pig-H1N1-SS2-rep2

description: Gene expression after 3 day in lung from pig  infected with H1N1-SS2 (H1N1 inoculation for 3 days and then challenged with SS2 )

source_name: Lung, H1N1-SS2, replicate2


title: pig-SS2-rep3

source_name: Lung, SS2, replicate3


title: MILD499.3 [IgG]

source_name: convalescent serum sample

tag: pcr

tag: lab confirmation

tag: mat result


title: Control Center Rep2


title: MILD339.3 [IgG]

tag: age

tag: number of days of symptoms


title: dpy-20 ISOLATED GONADS 3

city: Basel

first: Rafal

last: Ciosk

state: Schweiz

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

description:
RNA was purified from isolated gonads
gonadal RNA extract

hyb_protocol: labeled material was loaded onto Affymetrix GeneChip C. elegans Tiling 1.0R Arrays and hybridized at 65ºC for 16 h. The arrays were washed in an Affymetrix Fluidics station with the protocol FS450_0001.

scan_protocol: Affymetrix GeneChip Scanner 3000 with autoloader using Affymetrix GCC Scan Control v. 3.0.0.1214 software.

data_processing:
All tiling arrays were processed in R using bioconductor and the packages tilingArray and preprocessCore. The arrays were RMA background corrected and log2 transformed on the oligo level using the following command: expr <- log2(rma.background.correct(exprs(readCel2eSet(filenames,rotated=TRUE)))). We mapped the oligos from the tiling array (bpmap file from www.affymetrix.com) to the c.elegans genome assembly ce6 (www.genome.ucsc.edu) using bowtie allowing no error and unique mappig position. Expressions for individual transcripts were calculated by intersecting the genomic positions of the oligos with transcript annotation (WormBase WS190) and averaging the intensity of the respective oligos.
probeId_to_tr_min10probes, expr_RMA_TR_Notch, expr_RMA_TR_meses, Table_S1
probeId_to_tr_min10probes contains the microarray positions, expr_RMA_TR_Notch, expr_RMA_TR_meses are our annotation files with the expression data, Table_S1 contains the fold changes

organism: Caenorhabditis elegans

source_name: dpy-20 ISOLATED GONADS

label_protocol: Affymetrix GeneChip WT Amplified Double Stranded cDNA Synthesis Kit according to the manufacturer’s instructions. The Affymetrix GeneChip WT Double-Stranded cDNA Terminal Labeling Kit was used for the fragmentation and labeling of 7.5 microg cDNA

growth_protocol: Standard procedures were used to maintain animals. Worms were grown at 25°C.

extract_protocol: PicoPure RNA Isolation Kit (Applied Biosystems) according to the manufacturer’s recommendations.

treatment_protocol: RNA was extracted from isolated gonads of hermaphrodite worms. The age of the worms was 1,5 days after reaching adulthood.

value: gonad

tag: genotype

tag: strain used - lab list codes or cgc strain names


title: MILD297.3 [IgG]

tag: platelet count

tag: respiratory failure

tag: icu admission


title: pig-H1N1-rep1

source_name: Lung, H1N1, replicate1

tag: tissue

tag: disease state


title: pig-SS2-rep1

source_name: Lung, SS2, replicate1


title: MILD831.3 [IgG]

tag: gender

tag: hematocrit


title: MILD394.3 [IgG]

tag: acute mat titer

tag: convalescent mat titer

value: Indeterminado (FC)


title: 0.5Gy Center Rep1

tag: radiation dose

tag: time after irradiation

tag: distance from irradiated plane


title: embryo_KO_d3

city: Baltimore

first: Caitlin

middle: D

last: Hanlon

state: MARYLAND

address: 725 N Wolfe St, Hunterian G10

department: Cell Biology

institute: JHMI

description: KO = foxL1 knockout embryo

hyb_protocol: Following fragmentation cRNAs were hybridized 16hes at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix' GeneChip Scanner 3000 7G and default parameters described by the manufacturer.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform. RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

organism: Drosophila melanogaster

source_name: foxL1 null

label_protocol: Biotinylated cRNAs were prepared with the GeneChip HT 3' IVT Express Kit per manufacturer's instructions.

growth_protocol: Embryos were collected from OregonR (OR) or foxL1 null (foxL1del/foxL1cr) flies for eight hours at room temperature and then aged for 11 additional hours at room temperature.

extract_protocol: 300ul of Trizol was added to embryos on ice. Samples were homogenized with pestles by hand for 30-60seconds. 200ul of Trizol was then added and sampes were centrifuged at 13000rpm for 10minutes at 4C. The supernatent was tranferred to a new tube and 150ul of chloroform was added. Tubes were vortexed for 15seconds and then incubated at room temperature for 2-3 minutes. Samples were then centrifuged at 13000rpm for 15min at 4C. The upper phase was placed in a new tube and 0.7 volues of isopropanol was added. Samples were incubated at room temperature for 5 minutes and then centrifuged at 13000rpm for 15min at 4C. The pellet was then washed with 70% EtOH/DEPC H2O and centrifuged at 13000rpm for 10min at 4C. The pellet was then dried on a heat block and resuspended in 100ul RNAsefree H2O. An RNeasy kit was then used to further purify the RNA.  RNA concentrations were around 2ug/ul. Approximately 200ng was used per experiment.

treatment_protocol: Embryos were dechorionated in 50% bleach for three minutes and then thoroughly washed with ddH2O.

value: embryo

tag: embryonic stage


title: MILD3949.1 [IgG]

source_name: acute serum sample

tag: age

tag: elisa

tag: pcr

tag: lab confirmation

tag: mat result

tag: oliguric renal failure


title: WP3-HHP shock 120 min-rep6

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

institute: Shanghai Jiao Tong University

description:
raw data file: HHP120min-cy3+HHP0min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy3 and WP3 cDNA-HHP shock 120 min was labled with Cy3

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing:
For every microarray slide, there are 16416 spots, which were divided into 48 blocks. For every block, there are 18 columns and 19 rows. 16416=48*18*19.  There are 3 spots for a single gene on a single microarray slide, thus we get 3 ratios of the expression level of this gene in 2 samples (rep1, rep2 and rep3).  As dye-swaps were performed (label cDNA with different fluorecent dye), we can get another 3 ratios of the expression level of this gene in 2 samples (rep4, rep5 and rep6).
The replicate spots on the array were printed in the same row in adjacent columns.  Replicate number was assigned to the spots in ascending column order. For example, WP00027 is printed  in block 1, row 2, columns 13, 14 and 15. Replicate 1/4 is column 13, 2/5 is column 14 and replicate 3/6 is column 15.
S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model.  Microarray spots with P values <0.01 in the T-test and log2 ratio>1 or <-1 were regarded as differentially expressed genes.

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were incubated at 50 MPa for 120 min.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: culture protocol

value: WP3 cells were cultured at 20°C in 2216E medium

source_name: WP3 cells at mid-exponential phase and were treated with 12% (w/v) NaCl for 30 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 50 MPa for 120 min


title: MILD3934.1 [IgG]

tag: platelet count

value: Provavel

tag: number of days of symptoms

tag: respiratory failure

tag: icu admission


title: Control 500 Rep1

tag: tissue

value: EPI-200 3D epithelial cell model

value: 0 Gy

value: 16 hours

value: 500-750 microns


title: embryo_KO_d2

description: KO = foxL1 knockout embryo

tag: genotype


title: embryo_WT_d3

description: WT = wildtype embryo (OregonR = OR)

source_name: OR

value: Oregon R wild-type


title: Control 750 Rep1

tag: radiation dose


title: dpy-20 ISOLATED GONADS 2

tag: strain used - lab list codes or cgc strain names


title: WP3-HHP shock 120 min-rep4


title: embryo_WT_d1

description: WT = wildtype embryo (OregonR = OR)


title: embryo_KO_d1

description: KO = foxL1 knockout embryo


title: embryo_WT_d2

description: WT = wildtype embryo (OregonR = OR)


title: dpy-20 ISOLATED GONADS 1


title: Control 250 Rep1

tag: time after irradiation

tag: distance from irradiated plane

value: 250-500 microns


title: Control Center Rep1

value: 0-250 microns


title: MILD123.3 [IgG]

tag: age

tag: gender

tag: hematocrit

tag: acute mat titer

tag: convalescent mat titer

value: positive

value: negative


title: WP3-HHP shock 120 min-rep5


title: mes-6 dpy-20 ISOLATED GONADS 3

source_name: mes-6 dpy-20 ISOLATED GONADS


title: Choroidal_melanocytes_M3_3% oxygen_passage2_rep1

city: Quebec City

first: Solange

last: Landreville

state: Quebec

address: 1050 chemin Sainte-Foy, Room H2-02

department: Ophthalmology

institute: Université Laval

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Primary choroidal melanocyte cells M3, cultured at 3% oxygen, passage 2, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification  (QIAGEN, Toronto, ON).  Dye incorporation and cRNA yield were checked with the Nanophotometer pearl(Montréal Biotech).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Toronto, ON)  from Primary choroidal melanocyte cells isolated from normal eyes supplied by the National Eyes Bank from the CHU de Québec (QC, Canada).

value: Primary human Melanocyte cells

value: 83 years


title: Choroidal_melanocytes_M1_3% oxygen_passage2_rep1

source_name: Primary choroidal melanocyte cells M1, cultured at 3% oxygen, passage 2, replicate 1

value: male

value: 82 years


title: Choroidal_melanocytes_M2_3% oxygen_passage2_rep1

source_name: Primary choroidal melanocyte cells M2, cultured at 3% oxygen, passage 2, replicate 1

value: female

value: 51 years


title: WP3-HHP shock 120 min-rep3

description:
raw data file: HHP0min-cy3+HHP120min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy3 and WP3 cDNA-HHP shock 120 min was labled with Cy5

value: WP3 cells were cultured at 20°C in 2216E medium

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 50 MPa for 120 min


title: MILD3915.1 [IgG]

tag: elisa

tag: pcr

tag: lab confirmation

tag: mat result

tag: oliguric renal failure


title: unc-4 ISOLATED GONADS 3

source_name: unc-4 ISOLATED GONADS

value: gonad


title: unc-4 ISOLATED GONADS 2


title: WP3-HHP shock 120 min-rep2

tag: culture protocol


title: mes-2 unc-4 ISOLATED GONADS 3

source_name: mes-2 unc-4 ISOLATED GONADS

tag: tissue


title: MILD3880.1 [IgG]

tag: platelet count

tag: number of days of symptoms

tag: respiratory failure

tag: icu admission


title: WP3-HHP shock 120 min-rep1


title: mes-2 unc-4 ISOLATED GONADS 2

tag: genotype

tag: strain used - lab list codes or cgc strain names


title: MILD3863.1 [IgG]

tag: age

tag: gender


title: WP3-HHP shock 30 min-rep6

description:
raw data file: HHP30min-cy3+HHP0min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy3 and WP3 cDNA-HHP shock 30 min was labled with Cy3

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were incubated at 50 MPa for 30 min.

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 50 MPa for 30 min


title: MILD3559.1 [IgG]

tag: hematocrit

tag: acute mat titer


title: MILD3925.1 [IgG]

tag: convalescent mat titer

tag: elisa


title: MILD3386.1 [IgG]

tag: pcr

tag: lab confirmation


title: MILD3844.1 [IgG]

tag: mat result

tag: oliguric renal failure


title: mes-6 dpy-20 ISOLATED GONADS 2

tag: tissue


title: MILD2512.1 [IgG]

tag: platelet count


title: WP3-HHP shock 30 min-rep5

tag: culture protocol


title: mes-6 dpy-20 ISOLATED GONADS 1


title: MILD2510.1 [IgG]

tag: number of days of symptoms

tag: respiratory failure


title: mes-2 unc-4 ISOLATED GONADS 1

tag: genotype


title: WP3-HHP shock 30 min-rep3

description:
raw data file: HHP0min-cy3+HHP30min-Cy5.gpr
WP3 cDNA-untreated was labled with Cy3 and WP3 cDNA-HHP shock 30 min was labled with Cy5


title: unc-4 ISOLATED GONADS 1

tag: strain used - lab list codes or cgc strain names


title: Choroidal_melanocytes_M1_21% oxygen_passage2_rep1

source_name: Primary choroidal melanocyte cells M1, cultured at 21% oxygen, passage 2, replicate 1

tag: age


title: WP3-HHP shock 30 min-rep2


title: Choroidal_melanocytes_M3_21% oxygen_passage2_rep1

source_name: Primary choroidal melanocyte cells M3, cultured at 21% oxygen, passage 2, replicate 1

tag: gender


title: gld-1 gld-2 glp-1(gf) ISOLATED GONADS, REPEAT 2-3


title: MILD2451.1 [IgG]

tag: hematocrit

tag: icu admission


title: Choroidal_melanocytes_M2_21% oxygen_passage2_rep1

source_name: Primary choroidal melanocyte cells M2, cultured at 21% oxygen, passage 2, replicate 1


title: WP3-HHP shock 30 min-rep1


title: gld-1 gld-2 glp-1(gf) ISOLATED GONADS, REPEAT 2-2


title: WP3-HHP shock 30 min-rep4


title: WP3-cold shock 90 min-rep6

description:
raw data file: Cold90min-cy3+Cold0min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy5 and WP3 cDNA-cold shock 90 min was labeled with Cy3

scan_protocol: All microarrays were scanned with a LuxScan 10K scanner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were incubated at 0°C for 90 min.

source_name: WP3 cells at mid-exponential phase and were incubated at 0°C for 90 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 0℃ for 90 min


title: gld-1 gld-2 glp-1(gf) ISOLATED GONADS, REPEAT 2-1


title: WP3-cold shock 90 min-rep5


title: MILD2235.1 [IgG]

tag: acute mat titer

tag: convalescent mat titer


title: gld-1 gld-2 glp-1(lf) ISOLATED GONADS, REPEAT 2-3


title: MILD2173.1 [IgG]

tag: elisa

tag: pcr


title: gld-1 gld-2 glp-1(lf) ISOLATED GONADS, REPEAT 2-1


title: WP3-cold shock 90 min-rep4


title: MILD2146.1 [IgG]

tag: lab confirmation

tag: mat result


title: MILD2025.1 [IgG]

tag: oliguric renal failure


title: MILD2000.1 [IgG]

tag: platelet count


title: WP3-cold shock 90 min-rep2

description:
raw data file: Cold0min-cy3+Cold90min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy3 and WP3 cDNA-cold shock 90 min was labeled with Cy5

tag: culture protocol


title: gld-1 gld-2 glp-1(gf) ISOLATED GONADS, REPEAT 1-2

tag: tissue


title: gld-1 gld-2 glp-1(gf) ISOLATED GONADS, REPEAT 1-3


title: gld-1 gld-2 glp-1(lf) ISOLATED GONADS, REPEAT 1-3


title: gld-1 gld-2 glp-1(gf) ISOLATED GONADS, REPEAT 1-1


title: WP3-cold shock 90 min-rep1


title: MILD1858.1 [IgG]

tag: number of days of symptoms

tag: respiratory failure


title: WP3-cold shock 60 min-rep6

description:
raw data file: Cold60min-cy3+Cold0min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy5 and WP3 cDNA-cold shock 60 min was labeled with Cy3

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were incubated at 0°C for 60 min.

source_name: WP3 cells at mid-exponential phase and were incubated at 0°C for 60 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 0℃ for 60 min


title: WP3-cold shock 60 min-rep5


title: gld-1 gld-2 glp-1(lf) ISOLATED GONADS, REPEAT 1-2

tag: genotype

tag: strain used - lab list codes or cgc strain names


title: MILD1955.1 [IgG]

tag: age

tag: gender


title: MILD1396.1 [IgG]

tag: hematocrit

tag: icu admission


title: gld-1 gld-2 glp-1(lf) ISOLATED GONADS, REPEAT 2-2


title: MILD1371.1 [IgG]

tag: acute mat titer

tag: convalescent mat titer


title: WP3-cold shock 60 min-rep4


title: WP3-cold shock 60 min-rep3

description:
raw data file: Cold0min-cy3+Cold60min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy3 and WP3 cDNA-cold shock 60 min was labeled with Cy5


title: WP3-cold shock 90 min-rep3


title: WP3-cold shock 60 min-rep2


title: MILD896.1 [IgG]

tag: elisa

tag: pcr


title: MILD1302.1 [IgG]

tag: lab confirmation

tag: mat result


title: MILD499.1 [IgG]

tag: platelet count

tag: oliguric renal failure


title: WP3-cold shock 30 min-rep6

description:
raw data file: Cold30min-cy3+Cold0min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy5 and WP3 cDNA-cold shock 30 min was labeled with Cy3

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were incubated at 0°C for 30 min.

tag: culture protocol

source_name: WP3 cells at mid-exponential phase and were incubated at 0°C for 30 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 0℃ for 30 min


title: WP3-cold shock 60 min-rep1


title: gld-1 gld-2 glp-1(lf) ISOLATED GONADS, REPEAT 1-1

tag: tissue


title: progeroid - restricted - animal 366

status: Public on Sep 09 2016

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th Gen [miRBase 19.0] (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing:
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
The processed data file (Normalized_signal.txt) contains Log2-ratio for each sample to common reference. Column headers are: Probe ID, MicroRNA annotation, Number of Present calls followed by sample ID found in 'description' field.

source_name: liver

label_protocol: MicroRNA experiments were conducted at Exiqon Services, Denmark. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 750 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Ercc1Δ/- mice were obtained by crossing Ercc1Δ/+ (in a pure C57BL6J or FVB background) with Ercc1+/- mice (in a pure FVB or C57BL6J background respectively) to yield Ercc1Δ/- with an F1 C57BL6J/FVB hybrid background. Wild-type F1 littermates were used as controls.All animals used in the studies described in this paper were of the same F1 C57BL6J/FVB hybrid background. Typical unfavorable characteristics, like blindness in an FVB background or deafness in a C57BL6J background, do not occur in this hybrid background. Mice were weighed, visually inspected weekly, and scored for gross morphological and motor abnormalities. Experiments were performed in accordance with the Principles of Laboratory Animal Care and with the guidelines approved by the Dutch Ethical Committee in full accordance with European legislation.

extract_protocol: Total RNA was extracted from liver of 11 week old wild type and Ercc1Δ/- mice on AL and DR feeding regimen (n=5). Total RNA was extracted using QIAzol lysis Reagent and miRNAeasy Mini Kits (QIAGEN, Hilden, Germany), following Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNeasy program and stored at -80°C. The concentration of RNA was measured by Nanodrop (Thermo Fisher Scientific) and quality assessment of the RNA using the 2100 Bio-Analyzer (Agilent Technologies, Amstelveen, the Netherlands) following manufacturer’s instructions.

treatment_protocol: All animals were bred and maintained on AIN93G synthetic pellets (Research Diet Services B.V., Wijk bij Duurstede, The Netherlands). The amount of DR was determined in a prior pilot study but as control food intake of the AL-fed mice was continuously monitored. DR was initiated at 7 weeks of age with 10% (2.1 g/day), when animals almost reached the maximum bodyweight preventing disruption of development of young mice. DR was gradually increased weekly with 10%, until 30% DR (1.6 g/day) was reached at 9 weeks of age. Wild type mice ate on average 3.0 g food per day, resulting in 2.1 g/day for 30% DR. Food was given to the animals just before the start of the dark (active) period to avoid alterations in the biological clock.

value: progeroid  Ercc1 delta/-

tag: diet

value: restricted

value: liver

tag: background strain

value: F1 C57BL6J/FVB

tag: sample type

value: common reference


title: WP3-cold shock 30 min-rep4


title: progeroid - restricted - animal 368

tag: genotype


title: MILD394.1 [IgG]

source_name: acute serum sample

tag: age

tag: gender

value: Indeterminado (FC)

value: negative

value: positive

tag: number of days of symptoms

tag: respiratory failure


title: progeroid - restricted - animal 365


title: MILD339.1 [IgG]

value: male

tag: hematocrit

tag: acute mat titer

tag: convalescent mat titer

tag: icu admission


title: progeroid - control - animal 327

value: control


title: progeroid - restricted - animal 362