title: 00S290


title: No.5-fr1-n1

status: Public on Aug 01 2016

type: RNA

city: Koto

first: Kiyotaka

last: Shiba

state: Tokyo

address: Ariake 3-8-31

country: Japan

institute: Japanese Foundation for Cancer Research

description:
SAMPLE 97
test

data_processing: Fluidigm Real-Time PCR Analysis version 4.1.3 was used for data processing. Quality threshold of 0.65, baseline correction method of linear and Ct threshold method of auto were employed.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: Salivary EVs

label_protocol:
RNAs contained in each fraction were reverse-transcribed into cDNA in 7.5 μl of reaction mixture that contained 2.5 μl of total RNA, 0.075 μl of 100 nM dNTP, 0.095 μl of RNase inhibitor (20 U/μl), 0.5 μl of RT enzyme (50 U/μl), 1.5 μl of ×10 Megaplex RT Primers (Human Pool A v2.1), 0.75 μl of ×10 RT buffer and 2.08 μl of nuclease-free water, at 16 ˚C for 30 minutes; this was followed by 42 ˚C for 30 minutes and 85 ˚C for 5 minutes. The resultant cDNAs were further amplified (pre-PCR amplification reaction) by PCR before quantification. For this purpose, 1.25 μl of cDNAs were mixed with 2.5 μl of ×2 TaqMan PreAmp Master Mix, 1.25 μl of ×0.2 Megaplex PreAmp Primer, and PCR amplification reaction was carried out at 95 ˚C for 10 min, followed by 18 cycles at 95 ˚C for 15 seconds and at 60 ˚C for four minutes. The amounts of cDNA amplified were quantified by the TaqMan method using a BioMark HD system (Fluidigm Corporation, South San Francisco, CA, USA) equipped with 96.96 dynamic array (Fluidigm). The TaqMan primer and probe set used are listed in Supplementary Table 1. A 5-μl sample mixture was prepared for each sample, containing TaqMan Universal Master Mix (No AmpErase UNG, ×2), GE Sample Loading Reagent (Fluidigm, PN 85000746, ×20), and each of the diluted preamplified cDNA samples. Five μl assay mixes were prepared with each of the TaqMan Gene Expression Assay (×20) and the Assay Loading Reagent (Fluidigm, PN 85000736, ×2). After loading, the chip was placed in the BioMark HD and the conditions of at 70 ˚C for 30 minute, 25 ˚C for 10 minute, 95 ˚C for 1 minute, 35 cycles at 96 ˚C for 5 seconds and then 60 ˚C for 20 seconds were used in this research. Obtained data were analyzed with real-time PCR analysis software equipped in a BioMark HD system (Fluidigm). All reagents used were purchased from Applied Biosystems Inc. (Foster City, CA, USA) unless otherwise specified.
FAM(TaqMan system)

growth_protocol: Whole saliva (5ml) from eight healthy volunteers was collected in a consistent manner into 50-ml tubes by spitting and were kept on ice. Immediately after saliva collection, samples were pretreated by sonication.

extract_protocol: RNA was extracted from each fraction using the acid guanidinium thiocyanate-phenol-chloroform extraction method (Trizol, Life technologies).

treatment_protocol: Samples were centrifuged at 2,600 g for 30 minutes at 4 ˚C. The supernatants were collected in 4.7 ml tubes and were centrifuged at 160,000 g for 20 minutes at 4 ˚C. The pellets were washed once with 4.7 ml of PBS followed by centrifugation at 160,000 g for 20 minutes at 4 ˚C. The obtained crude EVs were resuspended in 640 μl of 47% iodixanol (OptiPrep) solution and inserted between 47% and 37% step gradients composed of 47%, 37%, 28%, and 18% iodixanol (OptiPrep) in 3.2 ml tube. Tubes were centrifuged at 160,000 g for 4 hours at 4 ˚C. After centrifugation, firstly, 320 μl of the top fraction was collected as Fraction 1, and then four 640 μl fractions flanking the interphase separating two neighboring were collected. Finally, 320 μl of bottom fraction was collected as Fraction 6.

tag: individual

value: Healthy volunteer 5

tag: ev source

value: whole saliva

tag: ev fraction

tag: technical replicate


title: No.4-fr6-n4

description:
SAMPLE 96
test

value: Healthy volunteer 4


title: 00S168

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol with the exception that 7ul of bisulfite treated material was input into the whole genome amplicifaction reaction instead of 4ul.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: case blood

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: Genomic DNA was extracted from frozen whole blood samples using a standard cell lysis, proteinase K digestion, phenol/chloroform, ethanol precipitation method.

tag: Sex

value: F

tag: age

tag: disease status

tag: tissue

value: whole blood


title: 00S043

value: M


title: 00S172


title: No.4-fr6-n2

description:
SAMPLE 94
test


title: No.4-fr6-n3

description:
SAMPLE 95
test


title: C2367

source_name: control blood


title: No.5-fr2-n3

description:
SAMPLE 103
test


title: No.5-fr2-n1

description:
SAMPLE 101
test


title: No.5-fr2-n2

description:
SAMPLE 102
test


title: No.4-fr5-n4

description:
SAMPLE 92
test


title: C0117


title: C0218


title: C0194


title: No.5-fr1-n4

description:
SAMPLE 100
test


title: No.4-fr6-n1

description:
SAMPLE 93
test


title: No.4-fr5-n3

description:
SAMPLE 91
test


title: C2412


title: F389-01


title: No.4-fr4-n4

description:
SAMPLE 88
test


title: No.4-fr4-n3

description:
SAMPLE 87
test


title: C2352


title: No.4-fr5-n1

description:
SAMPLE 89
test


title: No.4-fr5-n2

description:
SAMPLE 90
test


title: 0S2188


title: C2548


title: C0282


title: No.4-fr4-n2

description:
SAMPLE 86
test


title: C0055


title: No.4-fr4-n1

description:
SAMPLE 85
test


title: C2322


title: C0056


title: No.4-fr3-n4

description:
SAMPLE 84
test


title: C0051


title: No.4-fr3-n3

description:
SAMPLE 83
test


title: No.4-fr3-n2

description:
SAMPLE 82
test


title: C0183


title: No.4-fr3-n1

description:
SAMPLE 81
test


title: C2317


title: C2345


title: C0085


title: C0170


title: No.4-fr2-n3

description:
SAMPLE 79
test


title: No.4-fr2-n4

description:
SAMPLE 80
test


title: No.4-fr2-n1

description:
SAMPLE 77
test


title: C2440


title: No.4-fr2-n2

description:
SAMPLE 78
test


title: No.4-fr1-n3

description:
SAMPLE 75
test


title: C0326


title: No.4-fr1-n4

description:
SAMPLE 76
test


title: C0026


title: No.4-fr1-n2

description:
SAMPLE 74
test


title: No.4-fr1-n1

description:
SAMPLE 73
test


title: No.3-fr6-n4

description:
SAMPLE 72
test

value: Healthy volunteer 3


title: C0164


title: C2325


title: C2332


title: No.3-fr6-n3

description:
SAMPLE 71
test


title: C0193


title: C0201


title: C0140


title: C0237


title: C0016


title: C2337


title: C2494


title: C2382


title: No.3-fr4-n4

description:
SAMPLE 64
test


title: No.3-fr6-n2

description:
SAMPLE 70
test


title: No.3-fr5-n1

description:
SAMPLE 65
test


title: No.3-fr5-n4

description:
SAMPLE 68
test


title: No.3-fr5-n3

description:
SAMPLE 67
test


title: No.3-fr6-n1

description:
SAMPLE 69
test


title: No.3-fr4-n3

description:
SAMPLE 63
test


title: C0236


title: C2393


title: C0352


title: No.3-fr3-n3

description:
SAMPLE 59
test


title: C0119


title: No.3-fr4-n1

description:
SAMPLE 61
test


title: No.3-fr4-n2

description:
SAMPLE 62
test


title: No.3-fr3-n4

description:
SAMPLE 60
test


title: C0255


title: C2377


title: No.3-fr3-n2

description:
SAMPLE 58
test


title: No.3-fr3-n1

description:
SAMPLE 57
test


title: C2379


title: No.3-fr5-n2

description:
SAMPLE 66
test


title: C0089


title: No.3-fr2-n2

description:
SAMPLE 54
test


title: C0048


title: No.3-fr2-n1

description:
SAMPLE 53
test


title: C0272


title: C0143


title: C0322


title: C0333


title: No.3-fr1-n4

description:
SAMPLE 52
test


title: C2296


title: C0112


title: C0157


title: C0131


title: No.2-fr6-n4

description:
SAMPLE 48
test

value: Healthy volunteer 2


title: No.3-fr1-n2

description:
SAMPLE 50
test


title: No.3-fr1-n3

description:
SAMPLE 51
test


title: C0241


title: No.3-fr2-n4

description:
SAMPLE 56
test


title: C2350


title: No.2-fr6-n3

description:
SAMPLE 47
test


title: No.2-fr6-n2

description:
SAMPLE 46
test


title: No.2-fr5-n4

description:
SAMPLE 44
test


title: No.2-fr5-n3

description:
SAMPLE 43
test


title: No.3-fr2-n3

description:
SAMPLE 55
test


title: C2366


title: No.2-fr6-n1

description:
SAMPLE 45
test


title: C0121


title: No.3-fr1-n1

description:
SAMPLE 49
test


title: C0012


title: No.2-fr4-n4

description:
SAMPLE 40
test


title: No.2-fr5-n1

description:
SAMPLE 41
test


title: C0197


title: No.2-fr4-n3

description:
SAMPLE 39
test


title: C0284


title: C0247


title: C0009


title: No.2-fr4-n2

description:
SAMPLE 38
test


title: No.2-fr4-n1

description:
SAMPLE 37
test


title: C0286


title: C0064


title: C0300


title: C0315


title: No.2-fr3-n4

description:
SAMPLE 36
test


title: C2492


title: C0261


title: No.2-fr3-n3

description:
SAMPLE 35
test


title: No.2-fr3-n2

description:
SAMPLE 34
test


title: C2385


title: No.2-fr2-n3

description:
SAMPLE 31
test


title: C2292


title: No.2-fr5-n2

description:
SAMPLE 42
test


title: C2515


title: No.2-fr1-n3

description:
SAMPLE 27
test


title: No.2-fr2-n1

description:
SAMPLE 29
test


title: No.2-fr1-n4

description:
SAMPLE 28
test


title: C0205


title: No.2-fr1-n2

description:
SAMPLE 26
test


title: No.2-fr1-n1

description:
SAMPLE 25
test


title: C2435


title: C2300


title: C2323


title: No.2-fr3-n1

description:
SAMPLE 33
test


title: No.2-fr2-n4

description:
SAMPLE 32
test


title: C2438


title: No.1-fr6-n3

description:
SAMPLE 23
test

value: Healthy volunteer 1


title: C0053


title: No.2-fr2-n2

description:
SAMPLE 30
test


title: C0239


title: No.1-fr6-n2

description:
SAMPLE 22
test


title: C2347


title: No.1-fr6-n4

description:
SAMPLE 24
test


title: No.1-fr6-n1

description:
SAMPLE 21
test


title: C2399


title: No.1-fr5-n4

description:
SAMPLE 20
test


title: C2480


title: No.1-fr5-n3

description:
SAMPLE 19
test


title: C0307


title: C0204


title: No.1-fr5-n1

description:
SAMPLE 17
test


title: C0076


title: No.1-fr5-n2

description:
SAMPLE 18
test


title: No.1-fr4-n3

description:
SAMPLE 15
test


title: No.1-fr4-n4

description:
SAMPLE 16
test


title: No.1-fr4-n2

description:
SAMPLE 14
test


title: C2335


title: C2567


title: No.1-fr3-n3

description:
SAMPLE 11
test


title: C2473


title: C0045


title: No.1-fr3-n2

description:
SAMPLE 10
test


title: C2387


title: C0189


title: No.1-fr4-n1

description:
SAMPLE 13
test


title: No.1-fr3-n4

description:
SAMPLE 12
test


title: No.1-fr2-n4

description:
SAMPLE 8
test


title: C0232


title: No.1-fr3-n1

description:
SAMPLE 9
test


title: C0343


title: C0092


title: No.1-fr2-n3

description:
SAMPLE 7
test


title: C0310


title: C0153


title: C0061


title: No.1-fr1-n1

description:
SAMPLE 1
test


title: C2368


title: C0065


title: C2315


title: C0235


title: C2482


title: C2555


title: C0149


title: C0221


title: C2578


title: C2304


title: C0328


title: C0246


title: C0273


title: C0046


title: No.1-fr1-n2

description:
SAMPLE 2
test


title: No.1-fr2-n1

description:
SAMPLE 5
test


title: No.1-fr1-n4

description:
SAMPLE 4
test


title: No.1-fr2-n2

description:
SAMPLE 6
test


title: C2572


title: C0264


title: C2351


title: C0136


title: No.1-fr1-n3

description:
SAMPLE 3
test


title: C0031


title: C0289


title: C0038


title: C0327


title: C0049


title: C2355


title: C0345


title: C0073


title: C0278


title: C0209


title: C0142


title: C2389


title: Individual V1.CD35.1

city: Kongens Lyngby

first: Henrik

middle: Bjørn

last: Nielsen

address: Kemitorvet, b. 208

department: Systems Biology

country: Denmark

institute: Technical University of Denmark

description: gut microbiome from Homo sapiens

hyb_protocol: The hybridization sample mix was incubated 5 min at 95°C and 5 min at 42°C protected from light; 41 ul of the hybridization sample mix was loaded unto a NimbleGen HD2 array as described in NimbleGen One Color Labeling Protocol for Expression Analysis v 3.0.; The array was incubated O/N at 42°C on a NimbleGen hybridazation oven

scan_protocol: The array was scanned according to NimbleGen One Color Labeling Protocol for Expression Analysis v 3.0

data_processing: Robust multi-array (RMA) normalization including background correction, quantile normalization and expression index calculation

organism: human gut metagenome

source_name: stool

label_protocol: The DNA was labelled and purified according to NimbleGen One Color Labeling Protocol for Expression Analysis v 3.0 with Cy3 Random nonamers

extract_protocol: High Pure Isolation kit (Roche) according the manufacturer's recommendations

tag: sample type

value: stool


title: Individual V1.CD7.4

description: gut microbiome from Homo sapiens


title: Individual V1.UC49.1

description: gut microbiome from Homo sapiens


title: Individual V1.UC55.4

description: gut microbiome from Homo sapiens


title: Individual V1.UC52.1

description: gut microbiome from Homo sapiens


title: Individual V1.UC35.4

description: gut microbiome from Homo sapiens


title: Individual V1.UC7.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC25.1

description: gut microbiome from Homo sapiens


title: Individual V1.UC12.4

description: gut microbiome from Homo sapiens


title: Individual V1.UC21.4

description: gut microbiome from Homo sapiens


title: Individual V1.UC2.4

description: gut microbiome from Homo sapiens


title: C2376


title: C0027


title: C2391


title: C2530


title: C0080


title: Individual V1.UC15.3

description: gut microbiome from Homo sapiens


title: Individual V1.UC17.2

description: gut microbiome from Homo sapiens


title: Individual V1.UC14.1

description: gut microbiome from Homo sapiens


title: Individual V1.UC53.4

description: gut microbiome from Homo sapiens


title: C0144


title: Individual V1.UC51.4

description: gut microbiome from Homo sapiens


title: Individual V1.UC11.5

description: gut microbiome from Homo sapiens


title: Individual V1.UC23.1

description: gut microbiome from Homo sapiens


title: C0146


title: C0165


title: C0244


title: C0133


title: C0135


title: C0276


title: C0188


title: C2328


title: Individual V1.UC31.4

description: gut microbiome from Homo sapiens


title: C0068


title: Individual V1.CD17.4

description: gut microbiome from Homo sapiens


title: Individual V1.CD15.3

description: gut microbiome from Homo sapiens


title: C0102


title: Individual V1.UC5.3

description: gut microbiome from Homo sapiens


title: Individual V1.UC8.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD42.0

description: gut microbiome from Homo sapiens


title: C0132


title: Individual V1.UC10.2

description: gut microbiome from Homo sapiens


title: Individual V1.CD21.4

description: gut microbiome from Homo sapiens


title: Individual V1.UC61.0

description: gut microbiome from Homo sapiens


title: C0021


title: C2340


title: C0243


title: C2316


title: C0178


title: C2357


title: Individual V1.CD41.0

description: gut microbiome from Homo sapiens


title: C0203


title: C2360


title: Individual V1.UC26.4

description: gut microbiome from Homo sapiens


title: C0002


title: Individual V1.UC57.0

description: gut microbiome from Homo sapiens


title: C0160


title: C0324


title: C0168


title: C2326


title: Individual V1.UC4.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC49.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC48.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC39.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC46.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC40.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC42.0

description: gut microbiome from Homo sapiens


title: C0184


title: C0268


title: Individual V1.UC53.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC34.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC37.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC29.0

description: gut microbiome from Homo sapiens


title: C0072


title: Individual V1.UC35.0

description: gut microbiome from Homo sapiens


title: C0058


title: C2447


title: Individual V1.UC28.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC44.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC51.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC30.0

description: gut microbiome from Homo sapiens


title: C0234


title: C2569


title: C0078


title: Individual V1.UC36.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC23.0

description: gut microbiome from Homo sapiens


title: C0191


title: Individual V1.UC21.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC45.0

description: gut microbiome from Homo sapiens


title: C0187


title: C0213


title: Individual V1.UC38.0

description: gut microbiome from Homo sapiens


title: C0047


title: Individual V1.UC31.0

description: gut microbiome from Homo sapiens


title: C0169


title: C2472


title: Individual V1.UC25.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC54.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC55.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC19.0

description: gut microbiome from Homo sapiens


title: C0025


title: C0084


title: Individual V1.UC52.0

description: gut microbiome from Homo sapiens


title: C0288


title: C2442


title: C0162


title: C0229


title: C0069


title: C0217


title: C0152


title: C2302


title: Individual V1.UC17.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC27.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC32.0

description: gut microbiome from Homo sapiens


title: C0337


title: Individual V1.UC14.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC12.0

description: gut microbiome from Homo sapiens


title: C0174


title: Individual V1.UC18.0

description: gut microbiome from Homo sapiens


title: Individual V1.UC15.0

description: gut microbiome from Homo sapiens


title: C0029


title: Individual V1.CD9.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD6.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD35.0

description: gut microbiome from Homo sapiens


title: C0320


title: Individual V1.CD7.0

description: gut microbiome from Homo sapiens


title: C2341


title: C0180


title: Individual V1.CD4.0

description: gut microbiome from Homo sapiens


title: C2309


title: Individual V1.CD22.0

description: gut microbiome from Homo sapiens


title: C2327


title: C0348


title: Individual V1.CD36.0

description: gut microbiome from Homo sapiens


title: C2388


title: C0298


title: C2299


title: Individual V1.CD34.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD29.0

description: gut microbiome from Homo sapiens


title: C2418


title: Individual V1.CD21.0

description: gut microbiome from Homo sapiens


title: C0207


title: C2570


title: C0125


title: C0037


title: Individual V1.CD25.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD2.0

description: gut microbiome from Homo sapiens


title: C2402


title: C0262


title: Individual V1.CD13.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD16.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD24.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD11.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD18.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD19.0

description: gut microbiome from Homo sapiens


title: Individual V1.CD3.0

description: gut microbiome from Homo sapiens


title: C0225


title: Individual V1.CD1.0

description: gut microbiome from Homo sapiens


title: C0019


title: C0340


title: C2346


title: C2396


title: Individual V1.CD12.0

description: gut microbiome from Homo sapiens


title: C0159


title: Individual MH0185

description: gut microbiome from Homo sapiens


title: C2307


title: Individual V1.CD14.0

description: gut microbiome from Homo sapiens


title: Individual MH0183

description: gut microbiome from Homo sapiens


title: Individual MH0184

description: gut microbiome from Homo sapiens


title: C0331


title: C0120


title: Individual MH0186

description: gut microbiome from Homo sapiens


title: C0226


title: Individual MH0181

description: gut microbiome from Homo sapiens


title: Individual MH0177

description: gut microbiome from Homo sapiens


title: C0279


title: Individual MH0180

description: gut microbiome from Homo sapiens


title: Individual MH0174

description: gut microbiome from Homo sapiens


title: Individual MH0175

description: gut microbiome from Homo sapiens


title: Individual MH0173

description: gut microbiome from Homo sapiens


title: Individual MH0178

description: gut microbiome from Homo sapiens


title: C0211


title: C2398


title: C2409


title: C0266


title: Individual MH0168

description: gut microbiome from Homo sapiens


title: C2410


title: Individual MH0170

description: gut microbiome from Homo sapiens


title: Individual MH0172

description: gut microbiome from Homo sapiens


title: C0145


title: Individual MH0182

description: gut microbiome from Homo sapiens


title: Individual MH0169

description: gut microbiome from Homo sapiens


title: C2334


title: C2294


title: C0185


title: C2331


title: C0137


title: C0355


title: C2313


title: Individual MH0166

description: gut microbiome from Homo sapiens


title: C0015


title: C2403


title: Individual MH0162

description: gut microbiome from Homo sapiens


title: C2303


title: C0062


title: Individual MH0157

description: gut microbiome from Homo sapiens


title: Individual MH0160

description: gut microbiome from Homo sapiens


title: Individual MH0167

description: gut microbiome from Homo sapiens


title: Individual MH0164

description: gut microbiome from Homo sapiens


title: C0134


title: Individual MH0158

description: gut microbiome from Homo sapiens


title: Individual MH0155

description: gut microbiome from Homo sapiens


title: Individual MH0163

description: gut microbiome from Homo sapiens


title: Individual MH0159

description: gut microbiome from Homo sapiens


title: C0275


title: C2471


title: C0287


title: Individual MH0179

description: gut microbiome from Homo sapiens


title: C2378


title: Individual MH0152

description: gut microbiome from Homo sapiens


title: C0148


title: Individual MH0156

description: gut microbiome from Homo sapiens


title: Individual MH0153

description: gut microbiome from Homo sapiens


title: Individual MH0154

description: gut microbiome from Homo sapiens


title: C2446


title: C0008


title: Individual MH0151

description: gut microbiome from Homo sapiens


title: C2306


title: C0095


title: Individual MH0147

description: gut microbiome from Homo sapiens


title: Individual MH0145

description: gut microbiome from Homo sapiens


title: C0006


title: C0086


title: Individual MH0146

description: gut microbiome from Homo sapiens


title: C0253


title: C2566


title: Individual MH0138

description: gut microbiome from Homo sapiens


title: C0182


title: Individual MH0136

description: gut microbiome from Homo sapiens


title: Individual MH0148

description: gut microbiome from Homo sapiens


title: C2373


title: C2312


title: C0295


title: Individual MH0139

description: gut microbiome from Homo sapiens


title: Individual MH0134

description: gut microbiome from Homo sapiens


title: Individual MH0137

description: gut microbiome from Homo sapiens


title: Individual MH0133

description: gut microbiome from Homo sapiens


title: C0088


title: Individual MH0132

description: gut microbiome from Homo sapiens


title: C0071


title: Individual MH0130

description: gut microbiome from Homo sapiens


title: C0181


title: A8+LPS_12

city: UNSW, SYDNEY

first: Kenneth

middle: K

last: Hsu

state: NSW

address: Rm422, 4E, Wallace Wurth Bld,

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

description:
SAMPLE 51
Test

data_processing:
Gene expression was calculated with the web-based software package or excel based Quagen_ PCRArrayDataanalysis_V4 (SABiosciences).
For the normalization it uses the geometric mean of three housekeeping genes: HPRT, b-actin, GAPDH.
The cut off value for all Cts was set to 37.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Non-normalized file reports raw Ct values for target gene. Value with no amplifiction in Roche LC480 system was reported as 0, for calculation, 0 was replaced by 45
Normalized file reports normalized signal (against housekeeping genes).
Fold-change file reports test(LPS or LPS+S100s)/control(HBSS) (i.e. S100A8/9 complex treated vs HBSS saline treated) ratios.

label: SYBR Green

organism: Mus musculus

source_name: Lung

label_protocol: PCR assays were performed using varified in-house qPCR array (49 genes) in 384-well plates. Reactions were performed using the LightCycler® 480 system (Roche) under standard cycle conditions. Reactions containing 2´SYBR Green master mixture, 4 ml diluted cDNA template or non-amplified controls and 250 nM of each primer in a final volume of 10 ml.

extract_protocol: Total RNA was extracted from the lung by standard procedures using TRIzol® Reagent (Invitrogen), genomic DNA removed with DNase (Turbo DNase, Ambion) before reverse transcription (1.5 mg) using Super Script® VILO™ Master Mix (Invitrogen).

tag: strain

value: BALB/C

value: part of lung tissue

tag: activation agent

value: S100A8 + LPS

tag: time


title: C2365


title: Individual MH0128

description: gut microbiome from Homo sapiens


title: A8+LPS_11

description:
SAMPLE 50
Test


title: Individual MH0141

description: gut microbiome from Homo sapiens


title: C0040


title: C2384


title: A8+LPS_10

description:
SAMPLE 49
Test


title: Individual MH0126

description: gut microbiome from Homo sapiens


title: C2455


title: Individual MH0124

description: gut microbiome from Homo sapiens


title: A8+LPS_9

description:
SAMPLE 48
Test


title: Individual MH0127

description: gut microbiome from Homo sapiens


title: C0030


title: Individual MH0121

description: gut microbiome from Homo sapiens


title: A8+LPS_8

description:
SAMPLE 47
Test


title: Individual MH0122

description: gut microbiome from Homo sapiens


title: Individual MH0116

description: gut microbiome from Homo sapiens


title: Individual MH0125

description: gut microbiome from Homo sapiens


title: Individual MH0123

description: gut microbiome from Homo sapiens


title: C2371


title: A8+LPS_7

description:
SAMPLE 46
Test


title: Individual MH0109

description: gut microbiome from Homo sapiens


title: Individual MH0115

description: gut microbiome from Homo sapiens


title: C2441


title: A8+LPS_6

description:
SAMPLE 45
Test


title: C0238


title: Individual MH0120

description: gut microbiome from Homo sapiens


title: Individual MH0113

description: gut microbiome from Homo sapiens


title: A8+LPS_5

description:
SAMPLE 44
Test


title: C2579


title: A8+LPS_4

description:
SAMPLE 43
Test


title: Individual MH0110

description: gut microbiome from Homo sapiens


title: Individual MH0111

description: gut microbiome from Homo sapiens


title: C0353


title: Individual MH0107

description: gut microbiome from Homo sapiens


title: A8+LPS_3

description:
SAMPLE 42
Test


title: C2348


title: Individual MH0104

description: gut microbiome from Homo sapiens


title: C0083


title: A8+LPS_2

description:
SAMPLE 41
Test


title: A8+LPS_1

description:
SAMPLE 40
Test


title: Individual MH0114

description: gut microbiome from Homo sapiens


title: Individual MH0105

description: gut microbiome from Homo sapiens


title: Individual MH0103

description: gut microbiome from Homo sapiens


title: Individual MH0096

description: gut microbiome from Homo sapiens


title: C2580


title: C0150


title: Individual MH0093

description: gut microbiome from Homo sapiens


title: Individual MH0098

description: gut microbiome from Homo sapiens


title: Individual MH0094

description: gut microbiome from Homo sapiens


title: Individual MH0099

description: gut microbiome from Homo sapiens


title: Individual MH0097

description: gut microbiome from Homo sapiens


title: C0043


title: Individual MH0090

description: gut microbiome from Homo sapiens


title: A9+LPS_5

description:
SAMPLE 33
Test

value: S100A9 + LPS


title: Individual MH0091

description: gut microbiome from Homo sapiens


title: A9+LPS_4

description:
SAMPLE 32
Test


title: C0313


title: Individual MH0095

description: gut microbiome from Homo sapiens


title: Individual MH0102

description: gut microbiome from Homo sapiens


title: Individual MH0106

description: gut microbiome from Homo sapiens


title: Individual MH0089

description: gut microbiome from Homo sapiens


title: A9+LPS_3

description:
SAMPLE 31
Test


title: C2448


title: Individual MH0084

description: gut microbiome from Homo sapiens


title: A9+LPS_1

description:
SAMPLE 29
Test


title: Individual MH0092

description: gut microbiome from Homo sapiens


title: Individual MH0086

description: gut microbiome from Homo sapiens


title: HBSS+LPS_11

description:
SAMPLE 23
Test

value: LPS


title: Individual MH0083

description: gut microbiome from Homo sapiens


title: A9+LPS_2

description:
SAMPLE 30
Test


title: C0290


title: HBSS+LPS_10

description:
SAMPLE 22
Test


title: C2329


title: Individual MH0100

description: gut microbiome from Homo sapiens


title: C0141


title: HBSS+LPS_8

description:
SAMPLE 20
Test


title: Individual MH0077

description: gut microbiome from Homo sapiens


title: Individual MH0080

description: gut microbiome from Homo sapiens


title: Individual MH0075

description: gut microbiome from Homo sapiens


title: Individual MH0073

description: gut microbiome from Homo sapiens


title: Individual MH0081

description: gut microbiome from Homo sapiens


title: Individual MH0078

description: gut microbiome from Homo sapiens


title: Individual MH0082

description: gut microbiome from Homo sapiens


title: C0356


title: HBSS+LPS_7

description:
SAMPLE 19
Test


title: C2298


title: HBSS+LPS_6

description:
SAMPLE 18
Test


title: C2571


title: Individual MH0085

description: gut microbiome from Homo sapiens


title: Individual MH0088

description: gut microbiome from Homo sapiens


title: C0171


title: Individual MH0070

description: gut microbiome from Homo sapiens


title: C0329


title: HBSS+LPS_5

description:
SAMPLE 17
Test


title: Individual MH0071

description: gut microbiome from Homo sapiens


title: HBSS+LPS_9

description:
SAMPLE 21
Test


title: HBSS+LPS_4

description:
SAMPLE 16
Test


title: C0087


title: C0215


title: Individual MH0079

description: gut microbiome from Homo sapiens


title: Individual MH0072

description: gut microbiome from Homo sapiens


title: HBSS+LPS_2

description:
SAMPLE 14
Test


title: Individual MH0068

description: gut microbiome from Homo sapiens


title: HBSS+LPS_3

description:
SAMPLE 15
Test


title: Individual MH0065

description: gut microbiome from Homo sapiens


title: C2422


title: C2451


title: Individual MH0067

description: gut microbiome from Homo sapiens


title: Individual MH0066

description: gut microbiome from Homo sapiens


title: Individual MH0063

description: gut microbiome from Homo sapiens


title: Individual MH0074

description: gut microbiome from Homo sapiens


title: HBSS+PBS_12

description:
SAMPLE 12
Control

value: HBSS


title: Individual MH0062

description: gut microbiome from Homo sapiens


title: C0245


title: Individual MH0058

description: gut microbiome from Homo sapiens


title: HBSS+LPS_1

description:
SAMPLE 13
Test


title: HBSS+PBS_11

description:
SAMPLE 11
Control


title: Individual MH0060

description: gut microbiome from Homo sapiens


title: Individual MH0057

description: gut microbiome from Homo sapiens


title: Individual MH0064

description: gut microbiome from Homo sapiens


title: HBSS+PBS_10

description:
SAMPLE 10
Control


title: C0098


title: Individual MH0061

description: gut microbiome from Homo sapiens


title: HBSS+PBS_9

description:
SAMPLE 9
Control


title: C0199


title: C2428


title: HBSS+PBS_8

description:
SAMPLE 8
Control


title: Individual MH0056

description: gut microbiome from Homo sapiens


title: Individual MH0055

description: gut microbiome from Homo sapiens


title: C2405


title: HBSS+PBS_7

description:
SAMPLE 7
Control


title: Individual MH0051

description: gut microbiome from Homo sapiens


title: Individual MH0059

description: gut microbiome from Homo sapiens


title: Individual MH0069

description: gut microbiome from Homo sapiens


title: C0248


title: Individual MH0054

description: gut microbiome from Homo sapiens


title: HBSS+PBS_6

description:
SAMPLE 6
Control


title: C2557


title: Individual MH0050

description: gut microbiome from Homo sapiens


title: Individual MH0053

description: gut microbiome from Homo sapiens


title: HBSS+PBS_4

description:
SAMPLE 4
Control


title: Individual MH0052

description: gut microbiome from Homo sapiens


title: Patient-AIH post-2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: AIH

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted using miRNesy mini kit (Qiagen).

treatment_protocol: Steroid treatment

tag: disease state

value: type-1 autoimmune hepatitis

tag: treatment

value: steroid

tag: rna source

value: serum


title: C0220


title: HBSS+PBS_3

description:
SAMPLE 3
Control


title: Patient-AIH pre-2

value: untreated


title: C0267

value: F


title: C0139

value: whole blood


title: Control-AIH-1

source_name: Control

value: control


title: C0336

value: M


title: HBSS+PBS_1

description:
SAMPLE 1
Control


title: HBSS+PBS_5

description:
SAMPLE 5
Control


title: Individual MH0046

description: gut microbiome from Homo sapiens


title: C0081


title: HC4

city: Boston

first: Romy

middle: B

last: Christmann

state: MASSACHUSETTS

address: 715 Albany Street E5

country: USA

institute: Boston University School of Medicine

hyb_protocol: Not provided

scan_protocol: The signals of the samples were amplified and microarrays were immediately scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix Santa Clara, CA).

data_processing: The resulting CEL files were summarized using Affymetrix Expression Console (current version 1.1). The MAS5 algorithm with global scaling normalization was used to generate gene-level expression data.

label: biotin

source_name: healthy lung

label_protocol: Biotin-labeled amplified total RNA was purified, fragmented, and hybridized to Affymetrix U133A 2.0 microarrays.

extract_protocol: total RNA was isolated using microRNeasy Mini Kits Qiagen protocol

tag: patient reference

value: lung

tag: diagnosis

value: healthy (control)


title: Individual MH0049

description: gut microbiome from Homo sapiens

value: stool


title: HC5


title: Individual MH0044

description: gut microbiome from Homo sapiens


title: Individual MH0037

description: gut microbiome from Homo sapiens


title: HBSS+PBS_2

description:
SAMPLE 2
Control

value: BALB/C


title: Individual MH0047

description: gut microbiome from Homo sapiens


title: Individual MH0048

description: gut microbiome from Homo sapiens


title: Individual MH0040

description: gut microbiome from Homo sapiens


title: Individual MH0038

description: gut microbiome from Homo sapiens


title: Individual MH0041

description: gut microbiome from Homo sapiens


title: C2419


title: Individual MH0028

description: gut microbiome from Homo sapiens


title: HC3


title: HC2


title: C0196


title: HC1


title: Individual MH0045

description: gut microbiome from Homo sapiens


title: Individual MH0031

description: gut microbiome from Homo sapiens


title: Individual MH0033

description: gut microbiome from Homo sapiens


title: C0050


title: C2311


title: Individual MH0042

description: gut microbiome from Homo sapiens


title: C0263


title: Individual MH0034

description: gut microbiome from Homo sapiens


title: C0281


title: Individual MH0027

description: gut microbiome from Homo sapiens


title: Individual MH0039

description: gut microbiome from Homo sapiens


title: Individual MH0026

description: gut microbiome from Homo sapiens


title: SD17

source_name: SD17 lower lobe

value: SSc-J

value: Systemic Sclerosis with interstitial lung disease (SSc-ILD)


title: C2457


title: SD11

source_name: SD11 middle lobe

value: SSc-H


title: SD16

source_name: SD16 middle lobe

value: SSc-I


title: Individual MH0043

description: gut microbiome from Homo sapiens


title: Individual MH0035

description: gut microbiome from Homo sapiens


title: SD03

source_name: SD03 lower lobe

value: SSc-G


title: SD26

source_name: SD26 lower lobe

value: SSc-K


title: Individual MH0036

description: gut microbiome from Homo sapiens


title: ODC_TR1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression in ODC-knockdown line under normal growth conditions

hyb_protocol: 1650ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Genotypic designed Tobacco_GXP_4x44K (AMADID: 021113). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327) and scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX: 75th percentile shift method/gene based analysis

organism: Nicotiana tabacum

source_name: leaf_ODC-downregulated tobacco RNAi line

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Tobacco wild-type and transgenic lines were grown under the culture room conditions of 16 h light at 25°C

extract_protocol: RNA isolation was performed using Qiagen RNeasy Mini Kit as per the manufacturer’s instructions

tag: venotype/variation

value: var. xanthi

tag: variety

value: ODC-knockdown

value: leaf

tag: leaf order

value: 3rd leaf from the top


title: C0186

value: whole blood


title: C2392

value: F


title: Individual MH0032

description: gut microbiome from Homo sapiens


title: C2383

value: M


title: A9-12h-4

description:
SAMPLE 32
Test

data_processing:
Gene expression was calculated with the web-based software package or excel based Quagen_ PCRArrayDataanalysis_V4 (SABiosciences).
For the normalization it uses the geometric mean of three housekeeping genes: HPRT, b-actin, GAPDH.
The cut off value for all Cts was set to 37.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
4 hour and 6 hour test samples were grouped as the 4-6 hour group
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Non-normalized file reports raw Ct values for target gene. Value with no amplifiction in Roche LC480 system was reported as 0, for calculation, 0 was replaced by 45
Normalized file reports normalized signal (against housekeeping genes).
Fold-change file reports test/control (i.e. S100A9 treated vs HBSS saline treated) ratios.

value: part of lung tissue


title: A9-12h-3

description:
SAMPLE 31
Test


title: C0099


title: WT_TR2

description: Gene expression in wild-type under normal growth conditions

value: wild type


title: C0195


title: A9-12h-2

description:
SAMPLE 30
Test


title: SD02

source_name: SD02 lower lobe

value: SSc-F

value: lung


title: C2420


title: A9-12h-1

description:
SAMPLE 29
Test

value: BALB/C


title: SD22

source_name: SD22 middle lobe

value: SSc-E

value: Systemic Sclerosis with interstitial lung disease (SSc-ILD)


title: SD08

source_name: SD08 middle lobe

value: SSc-D


title: SD13

source_name: SD13 lower lobe


title: WT_TR1


title: Individual MH0022

description: gut microbiome from Homo sapiens

value: stool


title: A9-6h-4

description:
SAMPLE 28
Test

value: 6 h


title: Individual MH0021

description: gut microbiome from Homo sapiens


title: C2364


title: C0094


title: A9-6h-2

description:
SAMPLE 26
Test


title: A9-6h-3

description:
SAMPLE 27
Test


title: SD28

source_name: SD28 middle lobe

value: SSc-C


title: A9-6h-1

description:
SAMPLE 25
Test


title: A9-4h-4

description:
SAMPLE 24
Test

value: 4 h


title: C0198

source_name: control blood


title: C0052


title: C0129


title: C0271


title: A9-4h-2

description:
SAMPLE 22
Test


title: A9-4h-1

description:
SAMPLE 21
Test


title: Individual MH0023

description: gut microbiome from Homo sapiens

source_name: stool


title: C0022


title: A9-4h-3

description:
SAMPLE 23
Test

source_name: Lung


title: C0318


title: A9-1h-4

description:
SAMPLE 20
Test

value: 1 h


title: SD07

source_name: SD07 lower lobe


title: A9-1h-3

description:
SAMPLE 19
Test


title: ODC_TR2

value: var. xanthi

value: ODC-knockdown

value: leaf

value: 3rd leaf from the top


title: A9-1h-2

description:
SAMPLE 18
Test

value: part of lung tissue


title: C0224

value: M

value: whole blood


title: SD14

source_name: SD14 lower lobe

value: SSc-B

value: lung


title: SD23

source_name: SD23 middle lobe

value: SSc-A


title: Individual MH0020

description: gut microbiome from Homo sapiens


title: Individual MH0024

description: gut microbiome from Homo sapiens


title: A9-1h-1

description:
SAMPLE 17
Test

value: BALB/C


title: C2452


title: C2394

value: F


title: C0147


title: SD05

source_name: SD05 middle lobe

value: Systemic Sclerosis with interstitial lung disease (SSc-ILD)


title: HBSS-12h-4

description:
SAMPLE 16
Control

value: HBSS


title: C0292


title: HBSS-12h-3

description:
SAMPLE 15
Control


title: C0036


title: HBSS-12h-2

description:
SAMPLE 14
Control


title: HBSS-12h-1

description:
SAMPLE 13
Control


title: C2338


title: C2423


title: HBSS-6h-2

description:
SAMPLE 10
Control

value: 6 h


title: C0216


title: C0258


title: C0114


title: HBSS-6h-1

description:
SAMPLE 9
Control


title: Individual MH0009

description: gut microbiome from Homo sapiens

value: stool


title: HBSS-6h-4

description:
SAMPLE 12
Control


title: HBSS-4h-3

description:
SAMPLE 7
Control

value: 4 h


title: HBSS-4h-4

description:
SAMPLE 8
Control


title: C2407


title: HBSS-6h-3

description:
SAMPLE 11
Control


title: Individual MH0014

description: gut microbiome from Homo sapiens


title: Individual MH0011

description: gut microbiome from Homo sapiens


title: HBSS-4h-1

description:
SAMPLE 5
Control


title: HBSS-4h-2

description:
SAMPLE 6
Control


title: C2342


title: C0256


title: HBSS-1h-4

description:
SAMPLE 4
Control

value: 1 h


title: C0041


title: C2288


title: C0301


title: Individual MH0016

description: gut microbiome from Homo sapiens


title: HBSS-1h-2

description:
SAMPLE 2
Control


title: TW03

city: Guangzhou

first: ping

last: lan

address: 651 Dongfend East Road

country: China

institute: Sun Yat-sen University Cancer Center

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner (part number G2505C).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing:
Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).
Normalized signal intensity. The corrected value is the signal of the probe after background correction = Foreground-Background Intensity. If the corrected value is a negative number, then the final normalized value is defined as null.

source_name: nasopharyngeal carcinoma cell line TW03

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: cell line

value: nasopharyngeal carcinoma cell line TW03


title: HBSS-1h-1

description:
SAMPLE 1
Control


title: A8-12h_3

description:
SAMPLE 21
Test

data_processing:
Gene expression was calculated with the web-based software package or excel based Quagen_ PCRArrayDataanalysis_V4 (SABiosciences).
For the normalization it uses the geometric mean of three housekeeping genes: HPRT, b-actin, GAPDH.
The cut off value for all Cts was set to 37.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
4 hour and 6 hour test samples were grouped as the 4-6 hour group
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Non-normalized file reports raw Ct values for target gene. Value with no amplifiction in Roche LC480 system was reported as 0, for calculation, 0 was replaced by 45
Normalized file reports normalized signal (against housekeeping genes).
Fold-change file reports test/control (i.e. S100A8 treated vs HBSS saline treated) ratios.


title: A8-12h_1

description:
SAMPLE 19
Test


title: SD31

source_name: SD31 lower lobe

value: SSc-D


title: A8-12h_4

description:
SAMPLE 22
Test


title: A8-12h_2

description:
SAMPLE 20
Test


title: A8-6h_5

description:
SAMPLE 18
Test


title: A8-6h_3

description:
SAMPLE 16
Test


title: A8-6h_4

description:
SAMPLE 17
Test


title: A8-6h_2

description:
SAMPLE 15
Test


title: NP69

source_name: nasopharyngeal epithelial cell line NP69


title: A8-6h_1

description:
SAMPLE 14
Test


title: A8-4h_4

description:
SAMPLE 13
Test


title: HBSS-1h-3

description:
SAMPLE 3
Control


title: A8-4h_3

description:
SAMPLE 12
Test


title: A8-4h_2

description:
SAMPLE 11
Test


title: A8-4h_1

description:
SAMPLE 10
Test


title: A8-1h_4

description:
SAMPLE 9
Test


title: EK06-8.HPV59.p15.vs.EK09-10.(purelink)

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
raw data file ch1: US22502676_251901512401_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: US22502676_251901512400_S01_CGH_107_Sep09_1_1.txt

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Dewaving: The data have been de-waved as described in Van de Wiel et al. (2009) using the R package NoWaves. This is available from www.few.vu.nl/~mavdwiel/nowaves.html. Agilent 105K normals were used as calibration. Normalization: mode normalization.

source_name: DNA from hrHPV transformed keratinocytes

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol

tag: hpv type

source_name: DNA from keratinocytes

tag: reference

value: DNA from untransformed keratinocytes


title: EK09-10.HPV16.p100.vs.EK09-10

description:
raw data file ch1: US22502676_251901512401_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: MACF_251901512381_S01_CGH_107_Sep09_1_1.txt


title: A8-1h_3

description:
SAMPLE 8
Test

value: part of lung tissue


title: A8-1h_2

description:
SAMPLE 7
Test


title: sc_6443

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen 7

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

description: Female adipose tissue.

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K BeadChip using standard Illumina protocol.

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

data_processing:
Quantile normalization was applied, followed by BMIQ normalization. Batch effects were checked and removed from the dataset.
Data was normalized and analyzed using GenomeStudio software, R packages and Qlucore software.

label: Biotin

source_name: obese female, subcutaneous adipose tissue, insulin resistant

label_protocol: Standard Illumina protocol for Human Methylation 450K DNA Analysis BeadChip.

extract_protocol: Genomic DNA was prepared from adipose tissue using the QIAamp DNA Mini kit (cat no. 51304, Qiagen, Hilden, Germany).

value: subcutaneous adipose tissue

tag: gender

value: female

tag: phenotype

value: obese

value: systemic insulin resistance

tag: insulin resistance

value: resistant

tag: individual identifier


title: EK06-8.HPV45.p19.vs.EK06-8

description:
raw data file ch1: US22502676_251901512401_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: MACF_251901512380_S01_CGH_107_Sep09_1_2.txt


title: A8-1h_1

description:
SAMPLE 6
Test

tag: strain

value: BALB/C

tag: tissue

tag: activation agent


title: HBSS_5

description:
SAMPLE 5
Control

tag: time


title: EK06-8.HPV59.p45.x.EK09-10.(purelink)

description:
raw data file ch1: US22502676_251901512399_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: US22502676_251901512399_S01_CGH_107_Sep09_1_2.txt


title: sc_6436

description: Female adipose tissue.

source_name: obese female, subcutaneous adipose tissue, insulin sensitive

tag: disease state

value: no systemic insulin resistance

value: sensitive


title: EK09-10.HPV59.p17.x.EK09-10.(purelink)

description:
raw data file ch1: US22502676_251901512399_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: US22502676_251901512399_S01_CGH_107_Sep09_1_2.txt


title: sc_6466

description: Female adipose tissue.


title: EK09-10.HPV51C.p46.x.EK09-10.(purelink)


title: EK09-11.HPV51.p15.vs.EK09-10.(purelink)

description:
raw data file ch1: US22502676_251901512400_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: US22502676_251901512400_S01_CGH_107_Sep09_1_1.txt


title: HBSS_4

description:
SAMPLE 4
Control

value: HBSS


title: sc_6408

description: Female adipose tissue.


title: EK09-11.HPV59.p15.vs.EK09-10.(purelink)


title: sc_6401

description: Female adipose tissue.


title: sc_6304

description: Female adipose tissue.


title: HBSS_2

description:
SAMPLE 2
Control


title: HBSS_3

description:
SAMPLE 3
Control


title: sc_6427

description: Female adipose tissue.


title: sc_6295

description: Female adipose tissue.


title: EK06-8.HPV35.p45.x.EK09-10.(purelink)

description:
raw data file ch1: US22502676_251901512397_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: US22502676_251901512399_S01_CGH_107_Sep09_1_2.txt


title: sc_6426

description: Female adipose tissue.


title: sc_6302

description: Female adipose tissue.


title: sc_6453

description: Female adipose tissue.


title: sc_6290

description: Female adipose tissue.


title: HBSS_1

description:
SAMPLE 1
Control


title: sc_6455

description: Female adipose tissue.


title: sc_6446

description: Female adipose tissue.


title: sc_6424

description: Female adipose tissue.


title: sc_6409

description: Female adipose tissue.


title: EK09-11.HPV35.p45.x.EK09-10.(purelink)

description:
raw data file ch1: US22502676_251901512397_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: US22502676_251901512399_S01_CGH_107_Sep09_1_2.txt


title: sc_6444

description: Female adipose tissue.


title: EK09-11.HPV59.p45.x.EK09-10.(purelink).


title: Normal Patient - C_3

city: Aurora

first: Csaba

last: Galambos

state: CO

address: 12700 East 19th Ave

institute: The University of Colorado Denver

description:
Control
Control Group_prenatal-1665

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPLP0, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based SABiosciences data analysis software automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
The averaged_data.txt contains normalized, averaged data 'Control patient Group' and 'Group1 - DS patients' (against housekeeping genes).
The fold_change.txt  reports test/control (i.e., Control/DS) ratios.

label_protocol: Samples were either reverse-transcribed with RT2 First Strand Kit (Qiagen 330401), and Quantitative RT-PCR was performed on a LightCycler LC480 System (Roche).

growth_protocol: Human lung tissue obtained from the University of Maryland, Baltimore through its NICHD Brain and Tissue Bank for Developmental Disorders (NICH Contract #HHSN275200900011C, Ref. No. N01-HD-9-0011).

extract_protocol: RNAqueous Total RNA Isolation Kit (Life Technologies AM1912), DNase I treated with the Ambion TURBO DNA-free kit (Invitrogen AM1907) and tested for quality with an Agilent 2100 Bioanalyzer.

tag: subject status

value: Normal Patient - C

value: Lung


title: sc_6285

description: Female adipose tissue.


title: EK09-10.HPV51.p15.x.EK09-10.(purelink).

description:
raw data file ch1: US22502676_251901512398_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: US22502676_251901512399_S01_CGH_107_Sep09_1_2.txt


title: Normal Patient - C_2

description:
Control
Control Group_prenatal-1370


title: EK09-10.HPV35.p15.x.EK09-10.(purelink).

description:
raw data file ch1: US22502676_251901512398_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: US22502676_251901512399_S01_CGH_107_Sep09_1_2.txt


title: Down Syndrome Patient - DS_5

description:
Diseased
Group 1_DS_prenatal-277

value: Down Syndrome Patient - DS


title: EK06-8.HPV51.p15.vs.EK09-10.(purelink)

description:
raw data file ch1: US22502676_251901512400_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: US22502676_251901512400_S01_CGH_107_Sep09_1_1.txt


title: Down Syndrome Patient - DS_4

description:
Diseased
Group 1_DS_prenatal-1883


title: S2013.MUC1-WT vs S2013.Neo

city: Omaha

first: Ryan

last: Hanson

state: Nebraska

address: 42nd and Emile

department: Eppley

institute: University of Nebraska Medical Center

description: Ratio of MUC1-WT/Neo

hyb_protocol: Oligos are hybridized overnight at 42 degrees celsius

scan_protocol: Axon 4000B scanner

data_processing: The gene expression data was processed and analyzed by UNMC bioinformatics core using the Bioconductor LIMMA Package.  All data is presented as the ratio for one sample over the other.  Several filters and normalization were applied prior to analysis and median background was subtracted. Intensity filter was applied if either the red and green channels are below 100 intensities, or poor quality spots. The Log2 transformation was applied to all ratios. Two-step normalization was then done to “center” each array using lowess smoother within array and Aquartile normalization between arrays. Genes were excluded if the percent of spots missing or filtered out exceeded 50%. Empty spots and control spots have been excluded.

label_protocol: Amino Allyl MessageAmpII aRNA Amplification and Hybridization for Phalanx OneArray Slides protocol

growth_protocol: cells were grown in DMEM containing 10% FBS until 80-90% confluent before RNA extraction

extract_protocol: Total RNA was isolated from S2013 cells expressing indicated MUC1 forms or Neo control vector using mirVANA kit. Total RNA quality was analyzed using a bio-analyzer.

value: S2013 cells overexpressing wildtype MUC1

value: S2013 cells transfected with Neo control vector


title: S2013.MUC1-Ser vs S2013.Neo

description: Ratio of MUC1-Ser/Neo

value: S2013 cells expressing a serine mutant of MUC1


title: Down Syndrome Patient - DS_3

description:
Diseased
Group 1_DS_prenatal-m4025m


title: S2013.MUC1-WT vs S2013.MUC1-Ser

description: Ratio MUC1-WT/MUC1-Ser


title: sc_6268

description: Female adipose tissue.


title: sc_6247

description: Female adipose tissue.


title: EK06-8.HPV70.p14.x.EK09-11.p5

description:
raw data file ch1: MACF_251901512383_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: MACF_251901512383_S01_CGH_107_Sep09_1_1.txt

value: DNA from untransformed keratinocytes


title: Normal Patient - C_4

description:
Control
Control Group_prenatal-4931


title: Down Syndrome Patient - DS_2

description:
Diseased
Group 1_DS_prenatal-1881


title: sc_6232

description: Female adipose tissue.


title: sc_6230

description: Female adipose tissue.


title: sc_6221

description: Female adipose tissue.


title: G3 C3 Vs G1 C3

city: Saskatoon

first: Fernanda

last: Dias

address: 52 Campus Dr

country: Canada

institute: University of Saskatchewan

description: Array 6

hyb_protocol: Hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Tecan scanning protocol.

data_processing: data was normalized with loess

organism: Bos taurus

label_protocol: Labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Samples were dissected and snap frozen in liquid nitrogen

extract_protocol: SOP_Embryogene for trizol extraction.

treatment_protocol: Experimental protocol used to test the effect of the duration of FSH superstimulation on gene expression of granulosa cells in cattle. Transvaginal ultrasound-guided follicle ablation was performed 5 to 8 days after ovulation to synchronize wave emergence (Day 0). Beginning on Day 0, FSH was given at 12-hour intervals for 4 days (conventional FSH group) or 7 days (long FSH group; n=6 cows per group). Cows were given PGF2α twice on Day 3 in the conventional FSH group or Day 6 in the long FSH group. Cows were ovariectomized 24 hours after LH treatment.

tag: breed (cattle)

value: beef

tag: reproductive status (cattle)

value: Multiparity

tag: exogenous hormone ovarian stimulation

value: gonadotropin FSH

value: 7 days

tag: cell type

value: granulosa cells

value: 4 days


title: Down Syndrome Patient - DS_1

description:
Diseased
Group 1_DS_prenatal-315


title: sc_6217

description: Female adipose tissue.

value: subcutaneous adipose tissue

value: female

value: obese


title: EK09-11.HPV45.p20.x.EK09-11.p5

description:
raw data file ch1: MACF_251901512383_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: MACF_251901512383_S01_CGH_107_Sep09_1_1.txt


title: G3 C2 Vs G1 C2

description: Array 5


title: EK09-10.HPV33A.p17.x.EK09-10.p5

description:
raw data file ch1: MACF_251901512382_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: MACF_251901512381_S01_CGH_107_Sep09_1_1.txt


title: EK09-11.HPV66.p13.x.EK09-11.p5


title: EK09-10.HPV31.p16.x.EK09-10.p5

description:
raw data file ch1: MACF_251901512382_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: MACF_251901512381_S01_CGH_107_Sep09_1_1.txt


title: G1 C3 Vs G3 C3

description: Array 3


title: G3 C1 Vs G1 C1

description: Array 4


title: sc_6212

description: Female adipose tissue.

value: no systemic insulin resistance

value: sensitive


title: sc_6220

description: Female adipose tissue.

value: systemic insulin resistance

value: resistant


title: EK09-10.HPV18A.p17.x.EK09-10.p5


title: Normal Patient - C_1

description:
Control
Control Group_prenatal-1855

value: Normal Patient - C

value: Lung


title: EK09-10.HPV16.p15.x.EK09-10.p5


title: G1 C1 Vs G3 C1

description: Array 1


title: sc_6207

description: Female adipose tissue.


title: EK09-11.HPV70.p15.x.EK09-10.p5

description:
raw data file ch1: MACF_251901512381_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: MACF_251901512381_S01_CGH_107_Sep09_1_1.txt


title: EK09-10.HPV35.p40.x.EK09-10.(purelink)


title: EK09-10.HPV70.p15.x.EK09-10.p5

description:
raw data file ch1: MACF_251901512381_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: MACF_251901512381_S01_CGH_107_Sep09_1_1.txt


title: EK09-10.HPV66.p12.x.EK09-10.p5


title: sc_6200

description: Female adipose tissue.


title: W4 Neurons at Day 16 As 1 [miRNA]

city: Baltimore

first: Lena

last: Smirnova PhD

state: MD

address: 615 North Wolfe St

department: School of Public Health

institute: The Johns Hopkins University

description:
W4 ND16 As 1
miRNA expression data from neurally differentiated W4 mES cells after exposure to As

hyb_protocol: The samples were hybridized on Affymetrix GeneChip® miRNA 2.0 arrays for 16 hours. Following hybridization, arrays were washed and stained using an automated GeneChip® Fluidics Station 450

scan_protocol: Samples were scanned with a GeneChip® Scanner 3000

data_processing: The data files (.CEL) were imported to Partek 6.5 software. The RMA method was used to perform background adjustment, quantile normalization and summarization of the log-expression values for each gene on each array. We performed a differential expression analysis using t statistics methods implemented in the Partek software.

source_name: neurally differentiated mES cells line W4, As

label_protocol: One µg of RNA, isolated on day 16 of neural differentiation form solvent control treated, VPA- and arsenite-treated cells, was labeled with FlashTag™ Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA) for Affymetrix GeneChip® miRNA 2.0 arrays (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's recommendations. A simple colorimetric Enzyme Linked Oligosorbent Assay (ELOSA) was used to confirm successful biotin labeling.

growth_protocol: mES cells line W4 were cultivated upto 16 days in F12-DMEM/Neurobasal medium supplemented with B27, N2, bFGF, Laminin, BSA, insulin and β-mercaptoethanol on PLO-coated 6-well paltes in order to induce neural differentiation.

extract_protocol: After 16 days of treatment and differentiation RNA was extracted using Trizol reagent according to manufacturer's protocol.

treatment_protocol: mES cells were treated with sub-toxic concentrations of developmental neurotoxicants, VPA (300uM) or As (0.75uM) during 16 days of neural differentiation. As a control cells were incubated to solvents (PBS for VPA and H20 for As). Medium was exchanged every second day.

tag: cell line

value: mouse embryonic stem cell line W4

tag: toxicant treatment


title: sc_6156

description: Female adipose tissue.


title: W4 Neurons at Day 16 As 3 [miRNA]

description:
W4 ND16 As 3
miRNA expression data from neurally differentiated W4 mES cells after exposure to As


title: EK09-11.HPV18.p45.x.EK09-11.p5

description:
raw data file ch1: MACF_251901512378_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: MACF_251901512378_S01_CGH_107_Sep09_1_1.txt

tag: hpv type

tag: reference

value: DNA from untransformed keratinocytes


title: W4 Neurons at Day 16 As 2 [miRNA]

description:
W4 ND16 As 2
miRNA expression data from neurally differentiated W4 mES cells after exposure to As


title: W4 Neurons at Day 16 H2O 3 [miRNA]

description:
W4 ND16 H20 3
miRNA expression data from neurally differentiated W4 mES cells

source_name: neurally differentiated mES cells line W4, H2O (solvent control)

value: control (H2O)


title: sc_6199

description: Female adipose tissue.

tag: gender

tag: phenotype


title: sc_6155

description: Female adipose tissue.

tag: insulin resistance

tag: individual identifier


title: EK09-10.HPV45.p25.x.EK09-11.p5

description:
raw data file ch1: MACF_251901512378_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: MACF_251901512378_S01_CGH_107_Sep09_1_1.txt


title: sc_6160

description: Female adipose tissue.

tag: tissue


title: EK09-10.HPV33.p46.x.EK09-11.p5


title: W4 Neurons at Day 16 H2O 1 [miRNA]

description:
W4 ND16 H20 1
miRNA expression data from neurally differentiated W4 mES cells


title: sc_6144

description: Female adipose tissue.


title: W4 Neurons at  Day 16 VPA 3 [miRNA]

description:
W4 ND16 VPA 3
miRNA expression data from neurally differentiated W4 mES cells after exposure to VPA

source_name: neurally differentiated mES cells line W4, VPA

value: VPA (300uM)


title: G1 C2 Vs G3 C2

description: Array 2

value: beef

value: Multiparity

value: gonadotropin FSH


title: EK09-10.HPV66.p45.x.EK06-8.p2

description:
raw data file ch1: MACF_251901512380_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: MACF_251901512380_S01_CGH_107_Sep09_1_2.txt


title: sc_6123

description: Female adipose tissue.


title: sc_6145

description: Female adipose tissue.


title: W4 Neurons at Day 16 VPA 1 [miRNA]

description:
W4 ND16 VPA 1
miRNA expression data from neurally differentiated W4 mES cells after exposure to VPA


title: sc_6113

description: Female adipose tissue.


title: W4 Neurons at Day 16 VPA 2 [miRNA]

description:
W4 ND16 VPA 2
miRNA expression data from neurally differentiated W4 mES cells after exposure to VPA


title: W4 Neurons at Day 16 H2O 2 [miRNA]

description:
W4 ND16 H20 2
miRNA expression data from neurally differentiated W4 mES cells


title: EK09-11.HPV66.p45.x.EK09-11.p5

description:
raw data file ch1: MACF_251901512379_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: MACF_251901512379_S01_CGH_107_Sep09_1_2.txt


title: W4 Neurons at Day 16 PBS 1 [miRNA]

description:
W4 ND16 PBS 1
miRNA expression data from neurally differentiated W4 mES cells

source_name: neurally differentiated mES cells line W4, PBS (solvent control)

value: control (PBS)


title: sc_6125

description: Female adipose tissue.

value: subcutaneous adipose tissue


title: sc_6102

description: Female adipose tissue.

value: female


title: W4 Neurons at Day 16 PBS 2 [miRNA]

description:
W4 ND16 PBS 2
miRNA expression data from neurally differentiated W4 mES cells


title: sc_6149

description: Female adipose tissue.

value: obese


title: sc_6107

description: Female adipose tissue.

value: no systemic insulin resistance


title: W4 Neurons at Day 16 PBS 3 [miRNA]

description:
W4 ND16 PBS 3
miRNA expression data from neurally differentiated W4 mES cells


title: EK09-11.HPV70.p45.x.EK09-11.p5

description:
raw data file ch1: MACF_251901512379_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: MACF_251901512379_S01_CGH_107_Sep09_1_2.txt


title: EK09-11.HPV16.p45.x.EK09-11.p5


title: sc_6094

description: Female adipose tissue.

value: sensitive


title: EK09-10.HPV45.p45.x.EK09-10.p5.

description:
raw data file ch1: 251901512377_251901512377_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: 251901512377_251901512377_S01_CGH_107_Sep09_1_1.txt


title: EK06-8.HPV33.p45.x.EK06-8.p2

description:
raw data file ch1: MACF_251901512380_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: MACF_251901512380_S01_CGH_107_Sep09_1_2.txt


title: EK06-8.HPV70.p45.x.EK06-8.p2


title: EK09-10.HPV18.p45.x.EK09-10.p5

description:
raw data file ch1: 251901512377_251901512377_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: 251901512377_251901512377_S01_CGH_107_Sep09_1_1.txt


title: EK09-11.HPV31.p40.x.EK09-11.p5

description:
raw data file ch1: 251901512374_251901512374_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: MACF_251901512379_S01_CGH_107_Sep09_1_2.txt


title: sc_6093

description: Female adipose tissue.


title: sc_6091

description: Female adipose tissue.


title: sc_6084

description: Female adipose tissue.

value: systemic insulin resistance


title: inflammatory monocytes/macrophages_20 Gy radiation treatment_mouse4

city: Philadelphia

first: Anusha

last: Kalbasi

state: Pennsylvania

address: 3400 Civic Center Blvd.

department: Radiation Oncology

institute: University of Pennsylvania

description: Gene Expression data from flow sorted, inflammatory monocytes/macrophages with 20 Gy radiation treatment at day +1

hyb_protocol: Following fragmentation, 5.5 ug of the biotin labeled cDNA was hybridzied for  16 hours at 45C on Mouse Gene 2.0 ST GeneChips (Affymetrix) using the GeneChip Hybridization oven 645. Following hybridization, the GeneChips were washed at low (6x SSPE) and high (100 mM MES, 0.1M NaCl_ stringency and stained with streptaviden-phycoerythrin

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

data_processing: Affymetrix CEL files (containing probe intensities) were exported from Command Console software and imported into the Partek Genomics suite, where RMA was applied, yielding normalized, log2-transformed signal intensities. SAM (Significance Analysis for Microarrays, Stanford University) was applied using a two-class (GSI vs. DMSO) paired (by experiment) design. Fold change and Q-value (representing false discovery rate) were calculated for each gene.

source_name: inflammatory monocytes/macrophages, radiated, day +1

label_protocol: Briefly, 25ng  of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated an RNA priming region.  Second-strand cDNA synthesis was followed by ribo-SPIA linear amplification of each transcript using an isothermal reaction with RNase, RNA primer and DNA polymerase, and the resulting ssDNA was assessed by Bioanalyzer, fragmented and biotinylated by terminal transferase end labeling.

growth_protocol: PDAC cell line 152 was cultured in DMEM supplemented with 10% FCS, 83 ug/mL gentamicin, and 1% L-glutamine. Upon reaching sufficient numbers, PDAC cell lines were detached and implanted subcutaneously at 4.0-5.0x105 cells in 200 uL of PBs into the right flank of mice as indicated. Tumors were allowed to develop over 14 days to approximately 5 mm in diameter.

extract_protocol: RNA was extracted using the Qiagen RNEasy Micro Kit as described by manufacturer’s protocol. Samples were stored at -80 C.

treatment_protocol: Established tumors were irradiated with 20 Gy using the Small Animal Radiation Research Platform (SARRP) or were given sham treatment. One day later, mice were euthanized prior to tumor harvesting. Inflammatory monocytes/macrophages were isolated via flow cytometry as described and stored in trizol.

tag: age

value: 8 week old

value: Female

tag: strain

tag: tumor type

value: Subcutaneously implanted pancreatic cancer tumor cell line

tag: tumor cell line 152 origin

value: Derived from spontaneously arising tumors in KrasLSL-G12D/+, Trp53LSL-R172H/+, Pdx1-Cre (KPC) mice

tag: flow sorting parameters of tumor associted macrophages

value: CD45+ CD11b+ Ly6Chi


title: sc_6086

description: Female adipose tissue.

tag: disease state

value: resistant


title: EK09-10.HPV70.p46.x.EK09-10.p5.

value: DNA from untransformed keratinocytes


title: inflammatory monocytes/macrophages_no radiation treatment (sham)_mouse4

description: Gene Expression data from flow sorted, inflammatory monocytes/macrophages with no radiation treatment (sham) at day +1

source_name: inflammatory monocytes/macrophages, sham, day +1


title: sc_6085

description: Female adipose tissue.


title: inflammatory monocytes/macrophages_no radiation treatment (sham)_mouse2


title: EK09-10.HPV31.p45.x.EK09-10.p5

description:
raw data file ch1: 2251901512358_251901512358_S01_CGH_107_Sep09_1_2.txt
raw data file ch2: 2251901512358_251901512358_S01_CGH_107_Sep09_1_2.txt


title: Tbet- Memory B cells, biological rep1

city: San Diego

first: Burton

middle: Earle

last: Barnett

state: California

address: 3210 Merryfield Row

institute: Poseida Therapeutics

description: Gene expression data from Tbet- and Tbet- B cells

hyb_protocol: cDNA was amplied with NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays at the University of Pennsylvania’s Microarray facility.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Power Tools were used to process and quantile normalize fluorescent hybridization signals using Robust Multichip Averaging. Transcript values were log2 normalized.

source_name: Tbet GFP reporter mice after infection

label_protocol: Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

growth_protocol: Mice were aged to 6-8 weeks before infection

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

treatment_protocol: Mice were infected I.V. with LCMV clone 13 and sacrificed at day 10 post-infection. Splenocytes were stained according to M&M and FACS purified

value: Splenocytes

tag: infection

value: LCMV clone 13 I.V. day 10


title: inflammatory monocytes/macrophages_no radiation treatment (sham)_mouse3


title: inflammatory monocytes/macrophages_no radiation treatment (sham)_mouse1


title: sc_6083

description: Female adipose tissue.


title: Tbet- Memory B cells, biological rep3


title: Tbet- Memory B cells, biological rep2


title: sc_6080

description: Female adipose tissue.


title: Tbet+ Memory B cells, biological rep3

description: Gene expression data from Tbet+ and Tbet- B cells


title: inflammatory monocytes/macrophages_20 Gy radiation treatment_mouse3


title: inflammatory monocytes/macrophages_20 Gy radiation treatment_mouse1


title: inflammatory monocytes/macrophages_20 Gy radiation treatment_mouse2


title: sc_6073

description: Female adipose tissue.


title: Tbet+ Memory B cells, biological rep1


title: Tbet+ Memory B cells, biological rep2


title: EK09-10.HPV16.p40.x.EK09-10.p5

description:
raw data file ch1: 251901512358_251901512358_S01_CGH_107_Sep09_1_1.txt
raw data file ch2: 2251901512358_251901512358_S01_CGH_107_Sep09_1_2.txt


title: sc_6072

description: Female adipose tissue.


title: III-13 polyp1

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

institute: QIMR Berghofer MEdical Research Institute

hyb_protocol: As per manufacturer’s instructions (Illumina, San Diego CA)

scan_protocol: Arrays were scanned  on iScan

data_processing: Data was extracted using Genotyping module (v1.8.4) in Genomestudio v2010.3 (Illumina, San Diego CA) to calculate B-allele frequencies (BAF) and logR values.

source_name: Patient III-13 - Polyp number 1

label_protocol: DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA) (HumanOmni2.5-8 BeadChips).

extract_protocol: DNAwas extracted using the QIAamp DNA Micro kit (Qiagen)

tag: tissue type

value: fundic gland polyps


title: Naïve B cells, biological rep1

description: Gene expression data from Naive B cells


title: Naïve B cells, biological rep3

description: Gene expression data from Naive B cells


title: III-13 polyp3

source_name: Patient III-13 - Polyp number 3


title: Hnf4aΔH male

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

source_name: Hnf4aΔH male

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: RNA samples were extracted from livers of 45-day old  Hnf4aΔH and Hnf4af/f male mice using miRNesy mini kit (Quiagen).

tag: Sex

value: Male

value: Liver


title: sc_6051

description: Female adipose tissue.

value: subcutaneous adipose tissue

value: female


title: sc_6039

description: Female adipose tissue.

value: obese

value: no systemic insulin resistance


title: sc_6037

description: Female adipose tissue.

value: systemic insulin resistance


title: III-29 polyp2

source_name: Patient III-29 - Polyp number 2


title: Naïve B cells, biological rep2

description: Gene expression data from Naive B cells


title: sc_6032

description: Female adipose tissue.


title: sc_6055

description: Female adipose tissue.


title: III-29 polyp1

source_name: Patient III-29 - Polyp number 1


title: sc_6070

description: Female adipose tissue.


title: Hnf4af/f male

source_name: Hnf4af/f male


title: IL-1B 52544

first: John

middle: P.

last: Lynch

state: PA

address: 421 Curie Blvd

department: Medicine

description: SCJ intestinal metaplasia nodule

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

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

source_name: SCJ intestinal metaplasia nodule

label_protocol: Affymetrix WT Expression Kit (Ambion)

growth_protocol: squamocolumnar nodular metaplsai was dissected from Cdx2/IL-1beta and Il-1beta transgenic mice after 12 months of treatment with deoxycholic acid

extract_protocol: QIAGEN Rneasy

tag: genotype


title: sc_6047

description: Female adipose tissue.

value: sensitive


title: IL-1B 52545

description: SCJ intestinal metaplasia nodule


title: Cdx2/IL-1B 52542

description: SCJ intestinal metaplasia nodule


title: sc_5999

description: Female adipose tissue.


title: IV-4 polyp3

source_name: Patient IV-4 - Polyp number 3


title: III-13 polyp2

source_name: Patient III-13 - Polyp number 2


title: sc_6025

description: Female adipose tissue.

source_name: obese female, subcutaneous adipose tissue, insulin sensitive


title: IV-4 polyp2

source_name: Patient IV-4 - Polyp number 2


title: P.7.Pre

city: Montreal

first: Koren

last: Mann

state: Quebec

address: 3755 Cote Ste Catherine

institute: Lady Davis Institute

description: gene expression in patient 7

hyb_protocol: The labeled cRNA was then normalized at 600ng, fragmented and hybridized on Human GE Microarray 8X60K. The arrays were incubated in an Agilent Hybridization oven at 650C for 17 hours at 10 rpm.

scan_protocol: They were washed and scanned on an Agilent DNA Microarray Scanner C.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Patient 7 biopsy pre-panobinostat therapy

label_protocol: Cyanine 3-labeled CTP cRNA was produced with 25ng of total RNA using the Low Input Quick Amp Labeling Kit, according to manufacturer’s instructions (Agilent Technologies, Inc)

extract_protocol: Three needle core biopsies were collected and combined in a single-cell suspension. Tumor cells were isolated using a magnetic bead-negative selection technique (Human B Cell Enrichment Cocktail without CD43; Stem Cell Technologies).  RNA was extracted from the isolated tumor cells using All-Prep RNA/DNA (Qiagen) kit.

treatment_protocol: Patients were treated with panobinostat (35 mg, 3 times per week; MWF) +/- rituximab (375 mg/m2 daily).

value: biopsy

tag: cell type

value: diffuse large B cell lymphoma (DLBCL)

tag: panobinostat treatment

value: no


title: Cdx2/IL-1B 52540

description: SCJ intestinal metaplasia nodule


title: sc_6000

description: Female adipose tissue.

tag: gender


title: Cdx2/IL-1B 52541

description: SCJ intestinal metaplasia nodule


title: P.7.Post 15d

description: gene expression in patient 7 after 15 days panobinostat therapy

source_name: Patient 7 biopsy 15 days post-panobinostat therapy

value: yes


title: sc_5991

description: Female adipose tissue.

tag: phenotype


title: IL-1B 52543

description: SCJ intestinal metaplasia nodule


title: IV-11 polyp1

source_name: Patient IV-11- Polyp number 1


title: sc_6028

description: Female adipose tissue.

source_name: obese female, subcutaneous adipose tissue, insulin resistant

tag: insulin resistance

value: resistant


title: IV-4 polyp1

source_name: Patient IV-4 - Polyp number 1


title: SW480 ADH SPRY2 Y55F Rep3

city: Madrid

first: Antonio

last: Barbachano

state: Madrid

address: c/ Arturo Duperier 4

country: Spain

institute: Instituto de Investigaciones Biomédicas "Alberto Sols"

hyb_protocol: Following Affymetrix protocols, labeled RNAs were hybridized to Human Gene 1.0 ST Array (Affymetrix)

scan_protocol: Scanning was performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The RMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data. The probes were mapped to GENE LOCi by the CDF built by GATExplorer, which can be found at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php.

source_name: SW480 ADH SPRY2 Y55F Rep3

label_protocol: Labeling was performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Expression Kit  (Ambion).

growth_protocol: SW480 ADH cells were cultured in Dulbecco´s modified Eagle´s medium plus 10% fetal bovine serum, during 72 h.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions. (Macherey-Nagel, Germany, Ref:740971.250). RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA)

tag: tumor stage

value: Duke´s type B

tag: cell line

value: SW480 ADH


title: sc_5987

description: Female adipose tissue.

tag: tissue

tag: individual identifier


title: III-26 polyp3

source_name: Patient III-26- Polyp number 3


title: sc_5985

description: Female adipose tissue.


title: sc_6040

description: Female adipose tissue.


title: SW480 ADH SPRY2 Y55F Rep2

source_name: SW480 ADH SPRY2 Y55F Rep2


title: SW480 ADH SPRY2 Y55F Rep1

source_name: SW480 ADH SPRY2 Y55F Rep1


title: III-26 polyp2

source_name: Patient III-26- Polyp number 2


title: III-26 polyp1

source_name: Patient III-26- Polyp number 1


title: MEF-N4, biological rep3

city: Bethesda

first: Yuri

last: Postnikov

address: 37 Convent Dr

institute: NIH

description: Gene expression data from mouse embryonic fibroblasts

hyb_protocol: Biotininylated probes were hybridized to Affymetrix Mouse Gene 1.0 ST arrays using Affymetrix Fluidics Station.

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

data_processing: Data were analyzed by BRB Array Tools, GeneSpring GX 12.6 (Agilent Technologies) and Partek Genomics Suite 6.5 software

source_name: Mouse embryonic fibroblasts expressing human HMGN4 (MEF-N4)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: SV40-immortalized mouse embryonic fibroblast (ATCC) cell lines were maintained in Dulbecco's modified Eagle's medium, supplemented with 10% fetal calf serum, at 37˚C and 5% CO2.

treatment_protocol: Cells were harvested by trypsinization

value: embryonic fibroblasts

value: SV40-immortalized (ATCC, CRL-2907)

tag: vector

value: human HMGN4 (MEF-N4)


title: sc_5857

description: Female adipose tissue.


title: III-7 polyp2

source_name: Patient III-7 - Polyp number 2

value: fundic gland polyps


title: SW480 ADH SPRY2 S112A Rep2

source_name: SW480 ADH SPRY2 S112A Rep2


title: SW480 ADH SPRY2 S112A Rep3

source_name: SW480 ADH SPRY2 S112A Rep3


title: sc_5859

description: Female adipose tissue.

source_name: obese female, subcutaneous adipose tissue, insulin sensitive

value: subcutaneous adipose tissue


title: SW480 ADH SPRY2 S112A Rep1

source_name: SW480 ADH SPRY2 S112A Rep1


title: sc_5834

description: Female adipose tissue.

value: female


title: sc_5849

description: Female adipose tissue.

value: obese


title: MEF-N4, biological rep2


title: III-7polyp1

source_name: Patient III-7 - Polyp number 1


title: sc_5876

description: Female adipose tissue.


title: MEF-N4, biological rep1


title: SW480 ADH SPRY2 WT Rep3

source_name: SW480 ADH SPRY2 WT Rep3


title: SW480 ADH SPRY2 WT Rep2

source_name: SW480 ADH SPRY2 WT Rep2


title: sc_5861

description: Female adipose tissue.

value: no systemic insulin resistance


title: sc_5828

description: Female adipose tissue.


title: MEF-N2, biological rep3

source_name: Mouse embryonic fibroblasts expressing human HMGN2 (MEF-N2)

value: human HMGN2 (MEF-N2)


title: sc_5829

description: Female adipose tissue.

value: sensitive


title: sc_5811

description: Female adipose tissue.


title: SW480 ADH Mock Rep3

source_name: SW480 ADH Mock Rep3


title: sc_5810

description: Female adipose tissue.

source_name: obese female, subcutaneous adipose tissue, insulin resistant

value: systemic insulin resistance


title: Torin-treated group sample#3

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

description:
Transcriptional active cumulus and Transcriptional silent oocytes
160346C_Torin-2

hyb_protocol: Fragmented and biotin-labeled cDNA from each sample were then hybridized toAffymetrix® Mouse Gene 2.1 ST Array Strip) for 16 h at 45°C. Post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix

scan_protocol: The arrays were scanned with a GeneChip™3000 laser confocal slide scanner (Affymetrix) and the images were quantified using Gene Chip Operating Software version 1.2 (GCOS, Affymetrix).

data_processing: After the post-hybridization staining and washing, the arrays were scanned with a GeneChip™3000 laser confocal slide scanner (Affymetrix) and the images were quantified using Gene Chip Operating Software version 1.2 (GCOS, Affymetrix).  Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction, summarization based on a multi-array model fit robustly using the median polish algorithm, and sketch-quantile normalization. For this experiment, one pairwise comparison was used to statistically resolve gene expression differences between Type levels using the R/maanova analysis package40 (Wu et al. 2003). Specifically, differentially expressed genes will be detected by using Fs, a modified F-statistic incorporating shrinkage estimate of variance components from within the R/maanova package40-41. Statistical significance levels of the pairwise comparison wase calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method42. Differentially expressed genes are declared at an FDR q-value threshold of 0.05.

source_name: COC treated with Torin-5uM for 14h

label_protocol: RNA samples were subjected to cDNA synthesis and amplification using the Nugen Ovation Pico WTA System (NuGEN Technologies, Inc, San Carlos, CA). The resulting cDNAs were then fragmented and biotin-labeled using the Encore™ Biotin Module (NuGEN Technologies, Inc).

growth_protocol: 21-day old female mice were primed with eCG (5IU/mouse) for 46 hours to stimulate follicle development. Cumulus-oocyte complexes (COCs) were released by puncturing large antral follicles on ovarian surface with a pair of 26 gauge needles. Released COCs were collected and washed for three times by passing through 3 dishes of medium. 100 COCs per group were cultured in MEM-alpha medium supplemented with 3mg/ml of BSA and treated with 5uM of Torin1 or DMSO for 16 hours. After 16-h culture, COCs were collected into a 1.5 ml eppendorf centrifuge tube and re-suspended in 350 µl of RLT buffer (Qiagen, Valencia, CA). After brief vortexing, the COC lysate was snap frozen in liquid nitrogen and temporarily stored at -80°C until RNA isolation.  Three sets of DMSO-treated (Control group) and Torin-treated (treated group) of COC samples were collected and employed in microarray study.  Medium used for oocyte isolation was MEM-α (Invitrogen Corporation, Grand Island, NY) supplemented with 3 mg/ml of crystallized lyophilized bovine serum albumin (Sigma, St. Louis, MO), 75 mg/liter of penicillin G (Sigma) and 50 mg/liter streptomycin sulfate (Sigma). Milrinone (Sigma), a selective inhibitor of oocyte-specific phosphodiesterase (PDE3), was added into the medium at the concentration of 5 µM to prevent the GV-stage oocytes from undergoing maturation during the process of culture.

extract_protocol: Total RNA was extracted from COCs using the RNAeasy micro kit purchased from Qiagen (Valencia, CA) according to the manufacturer's instruction. The quality and quantity of RNA were measured by the Bioanalyzer 2100 and RNA 6000 Pico LabChip assay (Agilent Technologies Inc, Palo Alto, CA) according to supplied protocols (Invitrogen, Carlsbad, CA).

treatment_protocol: no additional treatments were carried out

value: Wildtype

value: cumulus-oocyte complexes (COC)

tag: protocol

value: COCs isolated from 23-d eCG-primed WT mice

tag: treatment

value: COCs treated with Torin


title: SW480 ADH SPRY2 WT Rep1

source_name: SW480 ADH SPRY2 WT Rep1

value: Duke´s type B


title: Torin-treated group sample#2

description:
Transcriptional active cumulus and Transcriptional silent oocytes
Torin-2


title: MEF-N2, biological rep2


title: Torin-treated group sample#1

description:
Transcriptional active cumulus and Transcriptional silent oocytes
Torin-1


title: SW480 ADH Mock Rep2

source_name: SW480 ADH Mock Rep2

value: SW480 ADH


title: SW480 ADH Mock Rep1

source_name: SW480 ADH Mock Rep1


title: MEF-V, biological rep3

source_name: Mouse embryonic fibroblasts expressing empty expression vector (MEF-V)

value: embryonic fibroblasts

value: empty expression vector (MEF-V)


title: sc_5794

description: Female adipose tissue.

tag: disease state


title: DMSO-treated control group sample#3

description:
Transcriptional active cumulus and Transcriptional silent oocytes
DMSO-3

source_name: COC treated with DMSO-5uM for 14h

value: COCs treated with control


title: om_6466

description: Female adipose tissue.

source_name: obese female, omental adipose tissue, insulin sensitive

value: omental adipose tissue


title: sc_5803

description: Female adipose tissue.

value: subcutaneous adipose tissue


title: DMSO-treated control group sample#2

description:
Transcriptional active cumulus and Transcriptional silent oocytes
DMSO-2


title: MEF-N2, biological rep1

value: SV40-immortalized (ATCC, CRL-2907)


title: DMSO-treated control group sample#1

description:
Transcriptional active cumulus and Transcriptional silent oocytes
DMSO-1


title: om_6444

description: Female adipose tissue.

value: female

value: obese


title: MEF-V, biological rep2


title: om_6455

description: Female adipose tissue.

source_name: obese female, omental adipose tissue, insulin resistant

value: resistant


title: om_6446

description: Female adipose tissue.


title: Control 3

city: Vienna

first: Constantin

last: Aschauer

address: Waehringer Gürtel 18-20, 1090 Wien

country: Austria

institute: Medical University of Vienna

hyb_protocol: Protocols for RNA extraction, RNA labeling, hybridization and washing of microarrays can   Be found on our website (http://www.meduniwien.ac.at/nephrogene/)

scan_protocol: Affymetrix GeneChip Scanner 7G Plus

data_processing:
The oligo R package was used for pre-processing and normalization of expression data (RMAnormalized in log2 scale)
the TIGR MultiExperimentViewer was used in order to identify differentially regulated transcripts

source_name: human mesangial cells-in vitro_control

growth_protocol: cultured in MCDB-131 media (Gibco-invitrogen), supplemented with 10% FBS, 100U penicillin/ml 100ug/ml streptomycin and 2mmol L-Glutamine (all supplied from Gibco-Invitrogen) at 37°C in humid atmosphere with 5%CO2 in air

extract_protocol: Trizol and chloroform reagent was used to purify RNA

treatment_protocol: cultured in serum free media and FK 506 (Abcam) dissolved in DMSO (Sigma) in a final concentration of 1 µM for 24h

value: human mesangial cells

tag: treated with

value: DMSO (control)


title: om_6453

description: Female adipose tissue.

value: no systemic insulin resistance

value: sensitive


title: Control 1

label_protocol: Protocols for RNA extraction, RNA labeling, hybridization and washing of microarrays can   Be found on our website (http://www.meduniwien.ac.at/nephrogene/)


title: om_6443

description: Female adipose tissue.

value: systemic insulin resistance


title: Control 4


title: Control 2