title: LP S3

city: Melbourne

first: TANJINA

last: KADER

state: VIC

address: 305 Grattan Street

department: Cancer Genomics

institute: The Sir Peter MacCallum Cancer Centre

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: Copy number values were obtained against a baseline of normal DNA samples. Raw data is only available for the single file run on OncoScan v3. The rest are available in 2 matrix files, and have slightly different numbers of probes. Each sample has 5 columns: Copy A, Copy B, Copy number, Allele ratio and Allelic difference. P1 and P2 was run on OncoScan v2.

source_name: Invasive breast cancer FFPE tissue

label_protocol: standard affymetrix protocol

extract_protocol: up to 40x 10 micron FFPE sections were needle microdissected for epithelial cells. Total genomic DNA was isolated using the DNeasy Blood and Tissue Kit (Qiagen) using a modified protocol: Wu L, Patten N, Yamashiro CT, Chui B (2002) Extraction and amplification of DNA from formalin-fixed, paraffin-embedded tissues. Appl Immunohistochem Mol Morphol 10 (3):269-274

treatment_protocol: retrospective cases received standard care

value: Invasive breast cancer FFPE tissue

tag: grade

tag: er status

value: Positive

tag: recurrence status

value: IDC

tag: her2 copy number status

value: Negative

tag: size (mm)


title: LP S4

status: Public on Aug 02 2016

type: genomic

country: Australia

label: biotin

molecule: genomic DNA

organism: Homo sapiens

tag: tissue


title: LP S2


title: Effector Memory CD8 T cells rep1

type: RNA

city: New Haven

first: Rakesh

last: Verma

state: CT

address: 333 Cedar St.

department: Yale Cancer Center

country: USA

institute: Yale University

description: Gene expression data from sorted EM CD8 T cells of healthy donor-Peripheral blood mononuclear cells (PBMCs), REPLICATE 1

hyb_protocol: RNA was amplified, labeled, and hybridized on the Affymetrix Human Genome U133 Plus 2.0 microarray chips at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

data_processing: The data sets were analyzed using GeneSpring GX 12.5 (Agilent Technologies)

molecule: total RNA

source_name: Sorted EM CD8 T cells from Peripheral blood mononuclear cells (PBMCs) of healthy donors

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

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

treatment_protocol: CD8 TSP cells:  Hoechst staining was performed on single cell suspension of human peripheral blood mono nucleated cells. In brief, the cells were incubated with Hoechst 33342 (5?g/ml) (Sigma- Aldrich) in 2% FCS, 1mM HEPES with or without Verapamil (50?M) (Sigma- Aldrich) for 90 min at 37o C incubator in darkness with intermittent shaking. The cells were then washed in ice- cold Hoechst wash buffer and stained with Flurochrome labeled CD3 and CD8 for 30min on ice. CD3+ CD8+ T cells with Hoechst low Side population phenotype expressing cells were sorted on BD FACS Aria.     Naïve CD8 T cells:   Human peripheral blood mono nucleated cells were stained with Flurochrome labeled CD3, CD8, CD45RA, CD45RO and CD62L for 30min on ice. The Cells were washed twice with buffer and sorted for Naïve CD8 T cells that are CD3+, CD8+, CD45RA+ CD62L+ and are negative for CD45RO.     EM CD8 T cells:   Human peripheral blood mono nucleated cells were stained with Flurochrome labeled CD3, CD8, CD45RA, CD45RO and CD62L for 30min on ice. The Cells were washed twice with buffer and sorted for Effector Memory CD8 T cells that are CD3+, CD8+, CD45RO+ and are negative for CD62L and CD45RA.    CM CD8 T cells:   Human peripheral blood mono nucleated cells were stained with Flurochrome labeled CD3, CD8, CD45RA, CD45RO and CD62L for 30min on ice. The Cells were washed twice with buffer and sorted for Central Memory CD8 T cells that are CD3+, CD8+, CD45RO+ CD62L+ and are negative for CD45RA.

value: Peripheral blood mononuclear cells (PBMCs) from healthy donors

tag: cell type

value: EM CD8 T cells


title: ileum control rep1

status: Public on Aug 03 2016

city: Tsukuba

first: Chise

last: Suzuki

state: Ibaraki

address: 2 Ikenodai

department: Animal Products Res. Division

country: Japan

institute: NARO Institute of Livestock and Grassland Science

description: Gene expression data from ileum of unstressed control mouse

hyb_protocol: Fragmented cRNA was hybridised to mouse 430 2.0 arrays (Affymetrix) during 16 h at 45°C.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.4 (Affymetrix).

data_processing: The microarray data were analyzed using R. Affymetrix CEL files were quantified by the RMA summarization.

organism: Mus musculus

source_name: teminal ileum of unstressed mouse

label_protocol: cRNA was prepared using the Affymetrix GeneChip 3’IVT Epess kit, using 100 ng total RNA as starting material.

growth_protocol: Male C57BL/6JJmsSlc (B6) mice (7 weeks of age; 21-23 g) for intruders and male Slc:ICR (ICR) mice (retired, older than 5 months of age) for residents (purchased from SLC Japan, Shizuoka, Japan) were used. First, these mice were housed individually in single cages (cage size 143 mm × 293 mm × 148 mm; Charles River Laboratories Japan, Kanagawa, Japan) with wood-shaving bedding and were habituated to their environments for a week. AIN-93G diet (Oriental Yeast, Tokyo, Japan) was fed to B6 mice, and standard laboratory diet (MF diet; Oriental Yeast) was fed to ICR mice. Food and water were available ad libitum. Animals were maintained at constant temperature (23 ± 1°C) and humidity (61 ± 1%) under a 12 h light-dark cycle (light on 8:00 am).

extract_protocol: After 3 hr fasting, the lower small intestines were taken and immediately kept in RNAlater (Qiagen). RNA was prepared by RNeasy kit (Qiagen).

treatment_protocol: The sCSDS paradigm was performed in the afternoon (14:00 pm-16:00 pm). The duration of physical contacts was set at 5 min after the first attack bite at Day 1, and then was reduced 0.5 min per day from Day 2 to Day 10. Thus, 0.5 min of physical contact was carried out at Day 10.

tag: strain

tag: treatment

value: control

value: teminal ileum


title: CD8 T Side Population cells rep2

description: Gene expression data from sorted CD8 TSP cells of healthy donor-Peripheral blood mononuclear cells (PBMCs), REPLICATE 2

source_name: Sorted CD8 T SP cells from Peripheral blood mononuclear cells (PBMCs) of healthy donors

value: CD8 TSP cells


title: Sample 5 Fetal Brain (Frontal) - Trisomy

city: Würzburg

first: Marcus

last: Dittrich

address: Biozentrum, Am Hubland

department: Biozentrum

country: Germany

institute: University of Würzburg

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: R (version 3.2.0) and Bioconductor (version 3.1)

label: Cy5 and Cy3

source_name: Fetal Brain (Frontal) - Trisomy

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Illumina Protocol

value: frontal fetal brain

tag: disease state

value: trisomy

tag: gender

value: female


title: Sample 2 Fetal Brain (Frontal) - Normal

source_name: Fetal Brain (Frontal) - Normal

value: normal

value: male


title: Naïve CD8 T cells rep2

description: Gene expression data from sorted Naïve CD8 T cells of healthy donor-Peripheral blood mononuclear cells (PBMCs), REPLICATE 2

source_name: Sorted Naïve CD8 T cells from Peripheral blood mononuclear cells (PBMCs) of healthy donors

value: Naive CD8 T cells


title: wt_ctrl_rep1

city: Huddinge

first: Rune

last: Toftgård

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: expression data of controls

hyb_protocol: affymetrix standard protocols were used for hybridization

scan_protocol: affymetrix standard protocols were used for scanning

data_processing: Affymetrix Eexpression Console was used for analysis with following settings: med-polish (rma-bg,quant-norm, sketch=-1, bioc=true, lowprecision=false, usepm=true, target=0, doavg=false)

source_name: colon of control mouse

label_protocol: affymetrix standard protocols were used for labeling

extract_protocol: Qiagen Rneasy mini extraction kits were used according to the manufacturer's instructions.

treatment_protocol: Tamoxifen was diluted at 20mg/ml in corn oil, sonicated at 37°C for 30 min and injected at 5 mg/25 g mouse i.p. One week later, mice were sacrificed, the colon extracted and a 1 cm piece starting 1.5 cm from the anus immediately frozen in liquid nitrogen.

value: colon

tag: Sex

tag: genotype


title: wt_ctrl_rep2

description: expression data of controls


title: Sample 3 Fetal Brain (Frontal) - Trisomy


title: CD8 T Side Population cells rep1

description: Gene expression data from sorted CD8 TSP cells of healthy donor-Peripheral blood mononuclear cells (PBMCs), REPLICATE 1


title: ileum control rep2


title: Hh activation_rep1

description: expression data after Hh activation

source_name: colon of a mouse with Hh activation


title: Hh activation_rep3

description: expression data after Hh activation

value: Col1a2CreER; Ptch1fl/fl


title: LP S1

value: Invasive breast cancer FFPE tissue


title: Naïve CD8 T cells rep1

description: Gene expression data from sorted Naïve CD8 T cells of healthy donor-Peripheral blood mononuclear cells (PBMCs), REPLICATE 1


title: Central Memory CD8 T cells

description: Gene expression data from sorted CM CD8 T cells of healthy donor-Peripheral blood mononuclear cells (PBMCs)

source_name: Sorted CM CD8 T cells from Peripheral blood mononuclear cells (PBMCs) of healthy donors

value: CM CD8 T cells


title: Effector Memory CD8 T cells rep2

description: Gene expression data from sorted EM CD8 T cells of healthy donor-Peripheral blood mononuclear cells (PBMCs), REPLICATE 2


city: Lisbon

first: Rita

middle: Maria

last: Batista

address: Av Padre Cruz

department: Food safety and nutrition

country: Portugal

institute: Instituto Nacional de Saude Dr. Ricardo Jorge

description: Gene expression data from Generation F4, Control seedlings , biological rep2

hyb_protocol: End-labeled, fragmented cDNA (3.5 µg) was used in a 150-µL hybridization cocktail containing hybridization controls (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix), of which 120 µL were hybridized on array strips for 20 h at 48°C.

scan_protocol: Standard post hybridization wash and double-stain protocols (GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips, Affymetrix) were used on an Affymetrix GeneAtlas system, followed by scanning of the array strips.

data_processing: Gene level normalization (RMA-sketch) and signal summarization was performed on Affymetrix Expression Console Software. Chipster software was used for gene filter by standard deviation (Bayes t-test, p value<0.05) and for Benjamini and Hochberg’s false discovery rate test (0.05 threshold) of filtered data.

organism: Oryza sativa

source_name: Generation F4, Nipponbare Control seedlings

label_protocol: RNA was processed for use on Affymetrix GeneChip RUSGene 1.1ST ArrayStrips, according to the manufacturer’s GeneChip WT PLUS Reagent Kit. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls  was used in a reverse transcription reaction to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA . 15 ug of this cRNA was used for a second cycle of first-strand cDNA synthesis. Single stranded cDNA (5.5 µg) was fragmented and end-labeled using GeneChip WT Terminal Labeling Kit (Affymetrix) and following the manufacturer’s instruction.

growth_protocol: Rice seeds were treated at 50ºC in 0.1% Carbendazim (fungicide) for 30 min, and surface disinfected using standard procedures. Seeds were germinated in darkness, for two days at 28ºC. Seedlings were grown for 13 days in Yoshida medium at 28ºC/24ºC (light/night), 12h photoperiod; 70% relative humidity. Salinity stress (12 dS/m final concentration) was imposed on half of the seedlings (C, Ta and NSb) in F6 generation. Fifteen days-old seedlings were collected after 12 days of salinity stress imposition. From F6 generation onwards, we worked with six rice lines (C, Csalt, Ta, Tasalt, NSb, NSbsalt).

extract_protocol: RNA from three pools of 10 whole-seedlings was isolated using RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Fifteen days-old seedlings were frozen in liquid nitrogen and kept at -80ºC until RNA extractions.

value: pool of 10 whole-seedlings

value: Oryza sativa L. ssp. japonica cv. Nipponbare

tag: age

value: Fifteen days-old


title: wt_ctrl_rep4

description: expression data of controls


title: Hh activation_rep4

description: expression data after Hh activation


title: Tim3+_CD8_3

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

hyb_protocol: Manufacturers instruction

scan_protocol: Manufacturers instruction

data_processing: Data was normalized using RMAExpress.

label_protocol: Manufacturers instruction

growth_protocol: Mice were depleted of CD4 T-cells using the GK1.5 antibody, and infected the the LCMV Clone 13 virus. 45+ days after infection, gp33 tetramer positive T-cells were isolated from the spleens of these mice.

extract_protocol: RNA was extracted using Qiagen RNA extraction kits

tag: strain background

value: Female

tag: disease model

value: LCMV Clone 13, GK1.5

tag: time point

value: 45+ days after infection

value: spleen

value: CD8 T-cells

tag: cell subtype


title: Tim3+_CD8_2


title: Tim3+_CD8_1


title: CXCR5+_CD8_3


title: Naïve_CD8_2

value: naïve


title: CXCR5+_CD8_2


title: Naïve_CD8_1


title: HNSCC_136_cells_transduced_pLVUT_GFP_time1

city: LYON

first: FLORENCE

last: LE CALVEZ-KELM

address: 150 Cours Albert Thomas

department: Genetics

country: France

institute: International Agency for Research on Cancer

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed using log transformation and quantile normalisation with BRBArrayTools and R packages

label_protocol: 500ng of mRNA was amplified into cRNA and biotinylated cRNA using Illumina® TotalPrep™-24 RNA Amplification Kit (Life Technologies).

extract_protocol: RNA was extracted withTotal RNA Isolation NucleoSpin® RNA II kit (Macherey Nagel) in accordance with the prescribed protocol provided with the kit. Quality control was performed withAgilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: HNSCC 136

value: Head and Neck SCC cell line

tag: tranduced with

value: pLVUT GFP as control

tag: treated with

value: doxycyline for 36hrs


title: HNSCC_136_cells_transduced_pLVUT_GFP_time1_rep


city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: CTRL Biopsy Liver sample: N26_.miRNA.3_0..CEL

hyb_protocol: Complex probes were hybridized to each GeneChip® miRNA 3.0 array according to the manufacturer's recommendations (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Scanned images of microarray chips were analyzed using Expression Console (Affymetrix) with the default settings. Raw data were processed using different algorithms. Detected Above Background algorithm (DABD) and RMA Background Adjustment algorithm were performed in order to remove the background value.

source_name: Liver sample

label_protocol: Biotin

extract_protocol: RNA was extracted from liver tissues using Trizol and following manufacter’s manual instructions (Life Tecnologies, Carlsbad, CA). miRNA quantification was performed using the commercial kit Mir-X miRNA First-Strand Synthesis Kit doing as manufacter’s manual instructions (Takara Bio Europe/Clontech, Saint-Germain-en-Laye, France).

tag: immunotolerance group

value: CTRL

value: control

value: liver


title: HNSCC_136_cells_transduced_pLVUT_TLR9_time1_rep

value: pLVUT TLR9


title: HNSCC_136_cells_transduced_pLVUT_TLR9_time1

value: pLVUT’ TLR9


description: ALD-CH Biopsy Liver sample: LM72_.miRNA.3_0..CEL

value: ALD-CH

value: alcohol liver disease-induced cirrhosis

tag: tissue


description: CTRL Biopsy Liver sample: N.17_.miRNA.3_0..CEL


title: Hh activation_rep2

description: expression data after Hh activation

value: colon

value: female


description: CTRL Biopsy Liver sample: N.53_.miRNA.3_0..CEL


description: NASH-CH Biopsy Liver sample: LMCC5_.miRNA.3_0..CEL

value: NASH-CH

value: nonalcoholic steatohepatitis induced cirrhosis


description: CTRL Biopsy Liver sample: N.7_.miRNA.3_0..CEL


description: NASH-CH Biopsy Liver sample: LMCC6_.miRNA.3_0..CEL


description: NASH-CH Biopsy Liver sample: LMH8_.miRNA.3_0..CEL


description: ALD-CH Biopsy Liver sample: LM51_.miRNA.3_0..CEL


description: CTRL Biopsy Liver sample: N23_.miRNA.3_0..CEL


description: ALD-CH Biopsy Liver sample: LM14_.miRNA.3_0..CEL


description: CTRL Biopsy Liver sample: N.54_.miRNA.3_0..CEL


description: NASH-CH Biopsy Liver sample: LMH7_.miRNA.3_0..CEL


description: ALD-CH Biopsy Liver sample: LM12_.miRNA.3_0..CEL


description: HVC-CH Biopsy Liver sample: JMM_.miRNA.3_0._2.CEL

value: HVC-CH

value: HCV-induced cirrhosis


description: NASH-CH Biopsy Liver sample: LMCC4_.miRNA.3_0..CEL


description: HVC-CH Biopsy Liver sample: FSR_.miRNA.3_0..CEL


description: ALD-CH Biopsy Liver sample: LM13._.miRNA.3_0..CEL


description: AH Biopsy Liver sample: CA.82_.miRNA.3_0..CEL

value: AH

value: Alcoholic hepatitis


description: HVC-CH Biopsy Liver sample: FBS_.miRNA.3_0..CEL


description: AH Biopsy Liver sample: CA.92_.miRNA.3_0..CEL


description: HVC-CH Biopsy Liver sample: FSM_.miRNA.3_0..CEL


title: CXCR5+_CD8_1

value: Female

value: LCMV Clone 13, GK1.5

value: 45+ days after infection

value: spleen

tag: cell type

value: CD8 T-cells


description: AH Biopsy Liver sample: CA.77_.miRNA.3_0..CEL

value: liver


description: AH Biopsy Liver sample: CA.8_.miRNA.3_0..CEL


title: 79-VHE 04/009 T1

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: batch "16"

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix' PrimeView Human Gene Expression arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.40.0) of Bioconductor. Expression values are represented on a log2-scale.

source_name: rectal biopsy

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

extract_protocol: Rneasy kit (Qiagen)

treatment_protocol: Tumor, pretreatment

tag: patient

value: VHE

tag: treatment response

value: Non-responder (NR)

value: Tumor

tag: timepoint

value: pretreatment


title: 75-DM 03/007 M

description: batch "16"

treatment_protocol: Mucosa, pretreatment

value: DM

tag: gender

value: Mucosa


title: 73-RM 09/010 T1

description: batch "16"

value: RM


title: 80-VHE 04/006 W3

description: batch "16"

treatment_protocol: Week 3, treatment tumor tissue

value: 3 weeks after start of treatment


title: 77-DM 03/007 W3

description: batch "16"


description: AH Biopsy Liver sample: CA.45_.miRNA.3_0..CEL

tag: disease state


description: AH Biopsy Liver sample: CA.76_.miRNA.3_0..CEL


title: E13R006c02

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

description: LSK sorted from wild type (Mll5+/+) mice; with NAC administration

hyb_protocol: 2.5 ug of labeled and fragmented cRNA was hybridized to Mouse Gene2.0ST GeneChip arrays (Affymetrix Inc., Sanata Clara, CA)

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Probe set normalization was performed using Affymetrix Power Tools (APT) -Robust Multiarray Average (RMA) normalization

label: Biotin

source_name: LSK sorted from mouse bone marrow

label_protocol: Encore Biotin Module (NuGEN Technologies)

growth_protocol: Cells were not cultured; LSK cells sorted from mouse bone marrow cells and directly used in downstream assays

extract_protocol: RNeasy micro kit (Qiagen)

treatment_protocol: Mice were provided with drinking water supplemented with 1g/liter N-Acetyl-L-Cyteine (NAC, LKT-Laboratories Inc., #A0918). Drinking bottles with freshly prepared NAC-supplemented water were exchanged every second day. NAC-treatment was started at the time of mating Mll5+/- parents, and was continued throughout pregnancy and life time of progeny, which were used for experiments.

value: bone marrow

tag: strain

value: LSK

tag: knockout

value: WT

tag: treatment

value: NAC


title: 72-RM 09/010 M

description: batch "16"

value: Female

tag: age


title: E13R006c03


title: 74- RM 09/010 W3

description: batch "16"


description: AH Biopsy Liver sample: CA.64_.miRNA.3_0..CEL

value: AH

value: Alcoholic hepatitis


title: E13R006c01


title: E13R006d03

description: LSK sorted from Mll5 knockout (Mll5-/-) mice; with NAC administration


title: 69-NK 07/006 M

description: batch "16"

value: NK

value: Male

value: Responder (R)


title: 68-LA 12/004 W3

description: batch "16"

value: LA


title: 70-NK 07/006 T1

description: batch "16"

value: Tumor


description: AH Biopsy Liver sample: CA.5_.miRNA.3_0..CEL

value: liver


title: E13R006d02


description: AH Biopsy Liver sample: CA.16_.miRNA.3_0..CEL


title: E13R006a03

description: LSK sorted from wild type (Mll5+/+) mice; without NAC administration (mock)

value: mock


description: AH Biopsy Liver sample: CA.37_.miRNA.3_0..CEL


title: 66-LA 12/004 M

description: batch "16"

value: Mucosa

value: pretreatment


title: 61-AL 04/008 T1

description: batch "16"

value: AL

value: Non-responder (NR)


title: E13R006d01

value: bone marrow

value: LSK


description: AH Biopsy Liver sample: CA.12_.miRNA.3_0..CEL


title: 67-LA 12/004 T1

description: batch "16"


description: AH Biopsy Liver sample: CA.51_.miRNA.3_0..CEL


title: E13R006a02

value: WT


description: AH Biopsy Liver sample: CA.39_.miRNA.3_0..CEL


title: E13R006a01


title: E13R006b03

description: LSK sorted from Mll5 knockout (Mll5-/-) mice; without NAC administration (mock)


title: 59-WL 12/001 W3

description: batch "16"

value: WL

value: Female

value: 3 weeks after start of treatment


title: E13R006b01


title: 56-DF 04/006 W3

description: batch "16"

value: DF


title: 64-MA 02/005 T1

description: batch "16"

value: MA


title: 57-WL 12/001 M

description: batch "16"

value: Responder (R)


title: 60-AL 04/008 M

description: batch "16"


title: 58-WL 12/001 T1

description: batch "16"


title: E13R006b02


title: 35-WR 09/003 T1

description: batch "16"

value: WR


title: 28-NJ 04/003 W3-rep2

description: batch "16"

value: NJ

value: Tumor


title: 54-DF 04/006 M

description: batch "16"


title: 52-VJ 02/004 M

description: batch "16"

value: VJ

value: Male


title: 53-VJ 02/004 T1

description: batch "16"

value: pretreatment


title: 43-GWE 01/006 M

description: batch "16"

value: GWE

value: Mucosa


title: 26-RVS 09/002 M-rep2

description: batch "16"

value: RVS

value: Non-responder (NR)


title: 34-WR 09/003 M

description: batch "16"


title: 17-NJ 04/003 T1-rep2

description: batch "16"


title: 11-IP 01/007 T1

description: batch "15"

value: IP


title: 7-LMC 02/002 M

description: batch "15"

value: LMC


title: 29-EVR 01/003 T1

description: batch "15"

value: EVR

value: Female


title: 17-NJ 04/003 T1-rep1

description: batch "15"


title: 21-VM 03/003 W3

description: batch "15"

value: VM

value: 3 weeks after start of treatment


title: 20-VM 03/003 T1

description: batch "15"

value: Responder (R)


title: 27-LMC 02/002 T1

description: batch "15"


title: 10-IP 01/007 M

description: batch "15"


title: 30-EVR 01/003 W3

description: batch "15"


title: 19-VM 03/003 M

description: batch "15"


title: Sediment-site C-Replicate 2

city: Changsha

first: Shiqi

last: Jie

state: Hunan

address: Lushan South Road 932

country: China

institute: Central South University

description: Microbial functional gene structure in sediment with heavy metal contamination

hyb_protocol: DNA was resuspended into 27.5μl of DNase/RNase-free distilled water, and mixed with 42μl hybridization buffer which contains 1× Acgh blocking, 1× HI-RPM hybridization buffer, 10 pM universal standard DNA, 0.05μg/μl Cot-1 DNA, and 10% formamide, then incubated at 95 °C for 3 min, and kept in 37°C for 30min. Hybridizations process was implemented in GeoChip 5.0 arrays (60 K) at 67 °C in a Agilent hybridization oven for 24 h.

scan_protocol: Slides were washed by Agilent Wash Buffers at room temperature. Then the arrays using NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Inc., Madison, WI, USA) at 633 nm by a laser power of 100% and 75% a photomultiplier tube (PMT).

data_processing: Scanned images were quantified with the help of ImaGene® version 6.0 (BioDiscovery, Inc., Los Angeles, CA, USA). The mean signal intensity was determinted for each spot, and local background signals were automatically ducted.

organism: uncultured bacterium

source_name: Microorganism in sediment from site C

label_protocol: The DNA was labeled with fluorescent dye Cy3 (GE Healthcare) by random primer, then purified with a QIAquick purification kit (Qiagen), and dried in a SpeedVac (45°C, 45 min: ThermoSavant, Milford, MA, USA).

growth_protocol: Sediment

extract_protocol: Given that high concentration of divalent metal ion may result in premature DNA precipitation during extraction, the sediment samples were pre-washed with 40mM EDTA (pH 7.2). The community DNA was extracted using the Soil DNA Kit (D5625-01; Omega Bioservices, Norcross, GA, USA) according to the manufacturer's instructions. Then DNA quality was checked by the absorbance ratios at A260/A280 and A260/A230 using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE). Only when the A260/A280 ratio is larger than 1.7 and the A260/A230 ratio is more than 1.8, can the DNA be used for further analysis.

treatment_protocol: All samples were maintained on ice after collected, then stored at -80°C for further analysis.

tag: site

value: Site C

tag: level of heavy metal contamination

value: Slight


title: 16-NJ 04/003 M

description: batch "15"

value: NJ


title: 28-NJ 04/003 W3-rep1

description: batch "15"

value: Tumor


title: 14-HT 09/004 T1

description: batch "15"

value: HT


title: 6-RVS 09/002 W3

description: batch "15"


title: 26-RVS 09/002 M-rep1

description: batch "15"

value: pretreatment


title: 9-LMC 02/002 W3

description: batch "15"

value: Male


title: 13-HT 09/004 M

description: batch "15"

value: Mucosa


title: Sediment-site C-Replicate 3


title: P2

description:
0004626_B04
processed data file: P1_P2.txt

source_name: Papilloma FFPE tissue

value: Papilloma FFPE tissue

tag: grade

tag: recurrence status

value: Papilloma


title: P1

description:
0004626_A10
processed data file: P1_P2.txt

value: Papilloma-atypical

tag: size (mm)


title: 15-HT 09/004 W3

description: batch "15"


title: Sediment-site C-Replicate 1


title: 22-EVR 01/003 M

description: batch "15"

value: Non-responder (NR)


title: Sediment-site B-Replicate 3

source_name: Microorganism in sediment from site B

value: Site B

value: Moderate


title: Sediment-site B-Replicate 2


title: PBMC_ASD_rep4

status: Public on Aug 01 2016

city: Kyoto

first: Ryo

last: Inoue

address: 1-5, Hangi-cho, shimogamo

institute: Kyoto Prefectural University

hyb_protocol: Slide was hybridized with 1.65 μg Cy3-labeled cDNA using a Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, USA) in a hybridization oven.

scan_protocol: After 17 h of hybridization at 65 °C, the slide was washed with a Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, USA), according to the manufacturer’s instructions. Slides were scanned  after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The intensity signals was imported to CLC Main workbench 6.0 and normalized by the quartile normalization method and log2 transformed.

source_name: PBMC, autistic infant, replicate 4

label_protocol: Complementary DNA amplification was carried out from 35 ng of total RNA using an Ovation PicoSL WTA System V2. After amplification, cDNA samples were labeled with Cy3 using Klenow polymerase.

growth_protocol: PBMC was isolated by density gradient centrifugation on Percoll (d = 1.077) .

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and purified by RNeasy MinElute Cleanup kit.

tag: diagnosis

value: autism

value: whole blood

value: PBMC


title: Sediment-site A-Replicate 2

source_name: Microorganism in sediment from site A

value: Site A

value: Heavy


title: 3-VC 06/005 W3

description: batch "15"

value: VC

tag: tissue

value: 3 weeks after start of treatment


title: PBMC_ASD_rep3

source_name: PBMC, autistic infant, replicate 3

tag: cell type


title: Sediment-site A-Replicate 3


title: PBMC_control_rep4

source_name: PBMC, healthy infant, replicate 4

value: healthy


title: PBMC_ASD_rep2

source_name: PBMC, autistic infant, replicate 2


title: PBMC_control_rep3

source_name: PBMC, healthy infant, replicate 3


title: PBMC_ASD_rep1

source_name: PBMC, autistic infant, replicate 1


title: 253949410922-2-3 [MV4-11-R]

city: Guangzhou

first: Amin

last: Huang

address: 651 Dongfengdong East Rd

institute: Sun Yat-sen University Cancer Center

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Sorafenib-resistant MV4-11 cells

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: MV4-11 were cultured in RPMI 1640 medium with 10% Fetal Bovine Serum and MV4-11-R cells were maintained in RPMI 1640 medium and 10%FBS supplement with 500 nM sorafenib.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: MV4-11-R cells were established by culturing in increasing concentrations of sorafenib with initial concentration of 1 nM until both cell lines survived the concentration of 500 nM after 3 months

tag: cell line source

value: Sorafenib-resistant MV4-11 cells

tag: tissue source

value: peripheral blood cells

tag: disease

value: biphenotypic B myelomonocytic


title: Sediment-site B-Replicate 1


title: PBMC_control_rep1

source_name: PBMC, healthy infant, replicate 1


title: 253949410922-1-2 [MV4-11]

source_name: parental MV4-11 cells

value: parental MV4-11 cells


title: 253949410922-2-1 [MV4-11-R]


title: 253949410922-1-3 [MV4-11]


title: 253949410922-2-2 [MV4-11-R]


title: 25-VC (BO) 06/005 M

description: batch "15"

tag: patient

tag: gender

value: Male

tag: treatment response

value: Mucosa

tag: timepoint

value: pretreatment


title: 253949410922-1-1 [MV4-11]


title: 296-4

city: Chia-Yi

first: Hui

middle: Chun

last: Yu

address: No. 2, Min-Sheng Rd, Dalin Town

department: Medical research

country: Taiwan

institute: Dalin Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation

description: Gene expression after 24hr in Jurket cells co-cultured with ionomycin and phorbol 12-myristate 13-acetate

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human V2 GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA),

data_processing: An image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: Jurkat cells co-cultured with ionomycin and phorbol 12-myristate 13-acetate

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

growth_protocol: Jurkat cells (1×106/mL) were cultured in RPMI-1640 containing heat-inactivated fetal bovine serum (10%), L-glutamine (2 mmol/L), penicillin (100 U/mL) and streptomycin (100 mg/mL)

extract_protocol: Total RNA was extracted from purified T cells or Jurkat cells using the Quick-RNA MiniPrep kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s protocol. The RNA concentration was quantified using a spectrophotometer (NanoDrop 1000, Thermo Fisher Scientific, Waltham, MA, USA).

treatment_protocol: Jurkat cells co-cultured with 10 ng/mL phorbol 12-myristate 13-acetate (PMA) and 500 ng/mL ionomycin 24 h at 37ºC.

value: Jurkat cells

tag: treatment


title: Neg-1

description: Gene expression after 24hr in Jurket cells co-cultured without ionomycin and phorbol 12-myristate 13-acetate

source_name: Jurkat cells co-cultured without ionomycin and phorbol 12-myristate 13-acetate


title: Neg-2

value: co-cultured without ionomycin and phorbol 12-myristate 13-acetate


title: PBMC_control_rep2

source_name: PBMC, healthy infant, replicate 2


title: 296-3

value: co-cultured with ionomycin and phorbol 12-myristate 13-acetate


title: Pig 403 CSF1-Fc

city: Roslin

first: Kristin

last: Sauter

address: Easter Bush, Midlothian

country: United Kingdom

institute: Roslin Institute/The University of Edinburgh

hyb_protocol: Samples were hybridised according to the standard protocol for Affymetrix Gene Titan hybridisation, using the Affymetrix Gene Titan Hybridization Wash & Stain Kit for WT Array Plates (PN 901622)

scan_protocol: Arrays were scanned with the GeneTitan scanner

data_processing:
Data were processed using the Affymetrix Expression Console software version 1.1
PorGene-1_1-st.pgf
PorGene-1_1-st.mps

organism: Sus scrofa

source_name: liver

label_protocol: Samples were Amplified using the Ambion® WT Expression  labelling kit using the standard protocol

growth_protocol: Pig livers dissected from 9 week old pigs

extract_protocol: All liver samples were dissected and stored in RNA later prior to preparation of RNA with Trizol

treatment_protocol: Pigs were sc injected three consecutive days with PBS or 0.75mg/kg CSF1-Fc before cull 24h post final injection

value: liver


title: Pig 401 CSF1-Fc


title: Pig 402 PBS


title: Pig 395 PBS


title: Pig 400 PBS


title: P.20.Post

city: Montreal

first: Koren

last: Mann

state: Quebec

address: 3755 Cote Ste Catherine

country: Canada

institute: Lady Davis Institute

description: gene expression in patient 20 after 15 days panobinostat therapy

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 20 biopsy 15 days post-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).

tag: tissue type

value: biopsy

value: diffuse large B cell lymphoma (DLBCL)

tag: panobinostat treatment

value: yes


title: P.20.Pre

description: gene expression in patient 20

source_name: Patient 20 biopsy pre-panobinostat therapy

value: no


title: Pig 397 PBS


title: Neg-3


title: P.19.Pre

description: gene expression in patient 19

source_name: Patient 19 biopsy pre-panobinostat therapy


title: Pig 399 PBS


title: 296-2


title: P.19.Post

description: gene expression in patient 19 after 15 days panobinostat therapy

source_name: Patient 19 biopsy 15 days post-panobinostat therapy


title: Pig 398 CSF1-Fc


title: Pig 393 CSF1-Fc


title: PM43

city: VILLEJUIF

first: Bastien

last: Job

address: 39 rue Camille Desmoulins

institute: Institut Gustave Roussy

description: primary melanoma 43

hyb_protocol: Pooled test and reference labeled DNA samples were hybridized for 40 hours at 65°C on Agilent 244K high density oligo microarrays (G4411B, AMADID 014693), and washed with Agilent Wash Buffers 1 & 2.

scan_protocol: Washed arrays were dried using a nitrogen pulse gun and scanned on an Agilent G2565BA scanner (Agilent, Palo Alto, CA) using a resolution of 5µm per pixel and 100% of the photomultiplicator for both signals.

data_processing: Intensity aquisition and data normalization and transformation were performed using Feature Extraction v9.1.3.1 (Agilent Sotware) using default protocol. In-house filtering discarding 3993 probes known for their erratic behavior was applied.

source_name: melanoma tumor

label_protocol: DNA was digested with AluI and RsaI restriction enzymes. DNA was labeled with Cy5-dUTP (Cy3-dUTP used for sex-matched normal reference DNA).

extract_protocol: DNA extraction was performed simultaneously with RNA extraction, using the RNEasy Mini Kit (Qiagen). DNA collected from the flow-through phase of the RNA extraction. DNA was purified using the ChargeSwitch Forensic DNA Purification Kit (Invitrogen, Carlsberg, CA). Concentration and purity of DNA was determined using NanoDrop 100ND-1000 (Thermo-Scientific).

treatment_protocol: Samples were snap frozen in liquid nitrogen iso-pendatne at -80°C after surgery.

tag: breslow (mm)

tag: age (year)

value: female

tag: tumor regression

tag: pt

tag: stage at diagnosis

tag: overall survival (year)

tag: time to metastasis (year)

tag: distant metastasis-free survival

value: false

tag: alive status

value: alive

tag: braf mutational status

value: wt

tag: nras mutational status

source_name: Promega commercial normal DNA, sex-matched


title: PM44

description: primary melanoma 44

tag: gender


title: 2-VC (BO) 06/005 T1

description: batch "15"

source_name: rectal biopsy

tag: patient

value: VC

tag: age

tag: treatment response

value: Non-responder (NR)

tag: tissue

value: Tumor


title: PM47

description: primary melanoma 47


title: PM42

description: primary melanoma 42

value: true

value: dead

value: mut


title: PM48

description: primary melanoma 48


title: PM49

description: primary melanoma 49

value: male


title: PM46

description: primary melanoma 46


title: PM38

description: primary melanoma 38


title: PM45

description: primary melanoma 45


title: PM40

description: primary melanoma 40


title: PM32

description: primary melanoma 32


title: PM41

description: primary melanoma 41


title: PM29

description: primary melanoma 29


title: PM26

description: primary melanoma 26


title: PM31

description: primary melanoma 31


title: PM27

description: primary melanoma 27


title: PM34

description: primary melanoma 34


title: PM37

description: primary melanoma 37


title: PM35

description: primary melanoma 35


title: PM22

description: primary melanoma 22


title: PM24

description: primary melanoma 24


title: PM36

description: primary melanoma 36


title: PM39

description: primary melanoma 39


title: PM28

description: primary melanoma 28


title: PM25

description: primary melanoma 25


title: PM23

description: primary melanoma 23


title: PM33

description: primary melanoma 33


title: PM19

description: primary melanoma 19


title: PM21

description: primary melanoma 21


title: PM30

description: primary melanoma 30


title: PM20

description: primary melanoma 20


title: PM18

description: primary melanoma 18


title: PM13

description: primary melanoma 13


title: PM17

description: primary melanoma 17


title: Sediment-site A-Replicate 1

source_name: Microorganism in sediment from site A

tag: site

value: Site A

tag: level of heavy metal contamination

value: Heavy


title: PM16

description: primary melanoma 16

tag: breslow (mm)

tag: age (year)


title: PM14

description: primary melanoma 14

tag: tumor regression

tag: pt


title: PM15

description: primary melanoma 15

tag: stage at diagnosis

tag: overall survival (year)


title: PM11

description: primary melanoma 11

tag: time to metastasis (year)

tag: distant metastasis-free survival


title: Seedlings of the PrSnRK2.7 overexpressor_mock treatment_rep3

city: Ikoma

first: Misato

last: Ohtani

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

institute: NAIST

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. All signals were divided by median value of all probe sets.
Ln value of MAS5.0 signal intensity divided by median value of all non-control probe sets.

organism: Arabidopsis thaliana

source_name: Seven-day old seedlings of the PrSnRK2.7 overexpressors were mock-treated for 2 days, rep3

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

growth_protocol: Seedlings were were grown at 22°C under the LD condition (16 h light/8 h dark) on the 1/2 strength MS medium.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen) following instruction.

treatment_protocol: Seven-day-old plants were transferred to the 1/2 MS medium plates with or without NaCl, and cultured for additional 2 days.

value: Whole seedlings

value: Nine-day old

tag: genotype

value: 35S:PtSnRK2.7:NOS, Columbia strain

tag: treatment

value: Seven-day-old plants grown in the 1/2 strength MS medium were transferred to the 1/2 MS medium plates, and then cultured for additional 2 days.


title: Seedlings of the PrSnRK2.7 overexpressor_Salt treatment_rep2

source_name: Seven-day old seedlings of the PtSnRK2.7 overexpressors were treated with 200 mM NaCl for 2 days, rep2

value: Seven-day-old plants grown in the 1/2 strength MS medium were transferred to the 1/2 MS medium plates with 200 mM NaCl, and then cultured for additional 2 days.


title: Seedlings of the PrSnRK2.7 overexpressor_Salt treatment_rep3

source_name: Seven-day old seedlings of the PtSnRK2.7 overexpressors were treated with 200 mM NaCl for 2 days, rep3


title: PM05

description: primary melanoma 05

tag: gender

value: female

value: no

tag: alive status

tag: braf mutational status

tag: nras mutational status


title: PM10

description: primary melanoma 10

value: yes

value: wt


title: PM06

description: primary melanoma 06


title: PM09

description: primary melanoma 09

value: false

value: alive


title: Seedlings of the PrSnRK2.7 overexpressor_Salt treatment_rep1

source_name: Seven-day old seedlings of the PtSnRK2.7 overexpressors were treated with 200 mM NaCl for 2 days, rep1

tag: tissue

tag: age


title: PM07

description: primary melanoma 07


title: Seedlings of the wild type_Salt treatment_rep3

source_name: Seven-day old seedlings of the wild type were treated with 200 mM NaCl for 2 days, rep3

value: wild type, Columbia strain


title: Seedlings of the PrSnRK2.7 overexpressor_mock treatment_rep2

source_name: Seven-day old seedlings of the PrSnRK2.7 overexpressors were mock-treated for 2 days, rep2


title: Seedlings of the PrSnRK2.7 overexpressor_mock treatment_rep1

source_name: Seven-day old seedlings of the PrSnRK2.7 overexpressors were mock-treated for 2 days, rep1


title: Seedlings of the wild type_Salt treatment_rep2

source_name: Seven-day old seedlings of the wild type were treated with 200 mM NaCl for 2 days, rep2


title: Seedlings of the wild type_Salt treatment_rep1

source_name: Seven-day old seedlings of the wild type were treated with 200 mM NaCl for 2 days, rep1


title: PM12

description: primary melanoma 12

value: true


title: PM03

description: primary melanoma 03

value: mut


title: PM04

description: primary melanoma 04

value: dead


title: PM02

description: primary melanoma 02


title: Seedlings of the wild type_mock treatment_rep2

source_name: Seven-day old seedlings of the wild type were mock-treated for 2 days, rep2


title: PM01

description: primary melanoma 01


title: Seedlings of the wild type_mock treatment_rep1

source_name: Seven-day old seedlings of the wild type were mock-treated for 2 days, rep1


title: Seedlings of the wild type_mock treatment_rep3

source_name: Seven-day old seedlings of the wild type were mock-treated for 2 days, rep3


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS364F)

city: Exeter

first: Rebecca

middle: Georgina

last: Smith

state: Devon

address: RILD, RD and E

department: Medical School

institute: University of Exeter

description:
Sample name: MS364F
Superior temporal gyrus AD

hyb_protocol: Illumina Infinium protocol.

scan_protocol: Illumina Infinium protocol scanned using Illumina HiScan System.

data_processing: Data loaded into R using methylumi, quantile normalised using Dasen function within wateRmelon (version 1.4.0).

label: Cy3, Cy5

source_name: Superior temporal gyrus, female, Alzheimer's disease

label_protocol: Illumina Infinium protocol.

extract_protocol: Phenol-chloroform DNA extraction.

value: superior temporal gyrus

tag: disease status

value: Alzheimer's disease

tag: braak stage

tag: age (yr)

tag: donor id

tag: sentrix id


title: Superior Temporal Gyrus Male Control (MS1329F)

description:
Sample name: MS1329F
Superior temporal gyrus NL

source_name: Superior temporal gyrus, male, control

value: control

value: male


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS340F)

description:
Sample name: MS340F
Superior temporal gyrus AD

source_name: Superior temporal gyrus, male, Alzheimer's disease


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS52F)

description:
Sample name: MS52F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS233F)

description:
Sample name: MS233F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1076F)

description:
Sample name: MS1076F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS1534F)

description:
Sample name: MS1534F
Superior temporal gyrus NL

source_name: Superior temporal gyrus, female, control


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS1280F)

description:
Sample name: MS1280F
Superior temporal gyrus AD


title: PM08

description: primary melanoma 08

source_name: melanoma tumor

tag: breslow (mm)

tag: age (year)

tag: tumor regression

tag: pt

tag: stage at diagnosis

source_name: Promega commercial normal DNA, sex-matched


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS197F)

description:
Sample name: MS197F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS101F)

description:
Sample name: MS101F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1205F)

description:
Sample name: MS1205F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS161F)

description:
Sample name: MS161F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS580F)

description:
Sample name: MS580F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1163F)

description:
Sample name: MS1163F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS339F)

description:
Sample name: MS339F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1308F)

description:
Sample name: MS1308F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS1208F)

description:
Sample name: MS1208F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS112F)

description:
Sample name: MS112F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS884F)

description:
Sample name: MS884F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS869F)

description:
Sample name: MS869F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS1263F)

description:
Sample name: MS1263F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1049F)

description:
Sample name: MS1049F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1358F)

description:
Sample name: MS1358F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1144F)

description:
Sample name: MS1144F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1537F)

description:
Sample name: MS1537F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1279F)

description:
Sample name: MS1279F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS650F)

description:
Sample name: MS650F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS712F)

description:
Sample name: MS712F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS611F)

description:
Sample name: MS611F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS882F)

description:
Sample name: MS882F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS709F)

description:
Sample name: MS709F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS629F)

description:
Sample name: MS629F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS968F)

description:
Sample name: MS968F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS1381F)

description:
Sample name: MS1381F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS899F)

description:
Sample name: MS899F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS124F)

description:
Sample name: MS124F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS1525F)

description:
Sample name: MS1525F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS1033F)

description:
Sample name: MS1033F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS451F)

description:
Sample name: MS451F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS697F)

description:
Sample name: MS697F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1012F)

description:
Sample name: MS1012F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS82F)

description:
Sample name: MS82F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS434F)

description:
Sample name: MS434F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS482F)

description:
Sample name: MS482F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS963F)

description:
Sample name: MS963F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS1054F)

description:
Sample name: MS1054F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS176F)

description:
Sample name: MS176F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS625F)

description:
Sample name: MS625F
Superior temporal gyrus NL


title: Prefrontal Cortex Male Control (MS978AC)

description:
Sample name: MS978AC
Prefrontal Cortex NL

source_name: Prefrontal cortex, male, control

value: prefrontal cortex


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS216F)

description:
Sample name: MS216F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS66F)

description:
Sample name: MS66F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1086F)

description:
Sample name: MS1086F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS1555F)

description:
Sample name: MS1555F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1250F)

description:
Sample name: MS1250F
Superior temporal gyrus NL


title: Prefrontal Cortex Female Control (MS900AC)

description:
Sample name: MS900AC
Prefrontal Cortex NL

source_name: Prefrontal cortex, female, control


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1175F)

description:
Sample name: MS1175F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS1124F)

description:
Sample name: MS1124F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1414F)

description:
Sample name: MS1414F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1131F)

description:
Sample name: MS1131F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1180F)

description:
Sample name: MS1180F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS467F)

description:
Sample name: MS467F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1187F)

description:
Sample name: MS1187F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS1036F)

description:
Sample name: MS1036F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS343F)

description:
Sample name: MS343F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS79F)

description:
Sample name: MS79F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Control (MS1163AC)

description:
Sample name: MS1163AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS1358AC)

description:
Sample name: MS1358AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Alzheimer's Disease (MS462AC)

description:
Sample name: MS462AC
Prefrontal Cortex AD

source_name: Prefrontal cortex, male, Alzheimer's disease


title: Prefrontal Cortex Female Alzheimer's Disease (MS364AC)

description:
Sample name: MS364AC
Prefrontal Cortex AD

source_name: Prefrontal cortex, female, Alzheimer's disease


title: Prefrontal Cortex Female Alzheimer's Disease (MS216AC)

description:
Sample name: MS216AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS1124AC)

description:
Sample name: MS1124AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS1076AC)

description:
Sample name: MS1076AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS1012AC)

description:
Sample name: MS1012AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Alzheimer's Disease (MS340AC)

description:
Sample name: MS340AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS1454AC)

description:
Sample name: MS1454AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS640AC)

description:
Sample name: MS640AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Alzheimer's Disease (MS1017AC)

description:
Sample name: MS1017AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS339AC)

description:
Sample name: MS339AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS1329AC)

description:
Sample name: MS1329AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS1414AC)

description:
Sample name: MS1414AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Alzheimer's Disease (MS1390AC)

description:
Sample name: MS1390AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS1039AC)

description:
Sample name: MS1039AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS19AC)

description:
Sample name: MS19AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS444AC)

description:
Sample name: MS444AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS1291AC)

description:
Sample name: MS1291AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS1279AC)

description:
Sample name: MS1279AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS1024AC)

description:
Sample name: MS1024AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Alzheimer's Disease (MS112AC)

description:
Sample name: MS112AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS1283AC)

description:
Sample name: MS1283AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS1086AC)

description:
Sample name: MS1086AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS1510AC)

description:
Sample name: MS1510AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS1040AC)

description:
Sample name: MS1040AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS1387AC)

description:
Sample name: MS1387AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS124AC)

description:
Sample name: MS124AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS1180AC)

description:
Sample name: MS1180AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS176AC)

description:
Sample name: MS176AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS122AC)

description:
Sample name: MS122AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS404AC)

description:
Sample name: MS404AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS1144AC)

description:
Sample name: MS1144AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Alzheimer's Disease (MS1280AC)

description:
Sample name: MS1280AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS1229AC)

description:
Sample name: MS1229AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS1004AC)

description:
Sample name: MS1004AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS1350AC)

description:
Sample name: MS1350AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS1049AC)

description:
Sample name: MS1049AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS629AC)

description:
Sample name: MS629AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS101AC)

description:
Sample name: MS101AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS1187AC)

description:
Sample name: MS1187AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS1248AC)

description:
Sample name: MS1248AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS1088AC)

description:
Sample name: MS1088AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS1507AC)

description:
Sample name: MS1507AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS1036AC)

description:
Sample name: MS1036AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS1534AC)

description:
Sample name: MS1534AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS1134AC)

description:
Sample name: MS1134AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS1322AC)

description:
Sample name: MS1322AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS607AC)

description:
Sample name: MS607AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Alzheimer's Disease (MS38AC)

description:
Sample name: MS38AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS1409AC)

description:
Sample name: MS1409AC
Prefrontal Cortex NL


title: Superior Temporal Gyrus Female Control (MS800F)

description:
Sample name: MS800F
Superior temporal gyrus NL


title: Prefrontal Cortex Female Control (MS1217AC)

description:
Sample name: MS1217AC
Prefrontal Cortex NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS675F)

description:
Sample name: MS675F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Control (MS1263AC)

description:
Sample name: MS1263AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS518AC)

description:
Sample name: MS518AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS1054AC)

description:
Sample name: MS1054AC
Prefrontal Cortex NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS831F)

description:
Sample name: MS831F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS230F)

description:
Sample name: MS230F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS989F)

description:
Sample name: MS989F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS752F)

description:
Sample name: MS752F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS806F)

description:
Sample name: MS806F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS504F)

description:
Sample name: MS504F
Superior temporal gyrus AD


title: Prefrontal Cortex Male Alzheimer's Disease (MS1033AC)

description:
Sample name: MS1033AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Male Control (MS46F)

description:
Sample name: MS46F
Superior temporal gyrus NL


title: Prefrontal Cortex Male Control (MS1250AC)

description:
Sample name: MS1250AC
Prefrontal Cortex NL


title: Superior Temporal Gyrus Male Control (MS768F)

description:
Sample name: MS768F
Superior temporal gyrus NL


title: Prefrontal Cortex Male Control (MS1220AC)

description:
Sample name: MS1220AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Alzheimer's Disease (MS370AC)

description:
Sample name: MS370AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS197AC)

description:
Sample name: MS197AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS698F)

description:
Sample name: MS698F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS1273F)

description:
Sample name: MS1273F
Superior temporal gyrus NL


title: Prefrontal Cortex Male Control (MS1028AC)

description:
Sample name: MS1028AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS233AC)

description:
Sample name: MS233AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Male Control (MS1220F)

description:
Sample name: MS1220F
Superior temporal gyrus NL


title: Prefrontal Cortex Male Alzheimer's Disease (MS1172AC)

description:
Sample name: MS1172AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS370F)

description:
Sample name: MS370F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS1387F)

description:
Sample name: MS1387F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1291F)

description:
Sample name: MS1291F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1466F)

description:
Sample name: MS1466F
Superior temporal gyrus NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS280AC)

description:
Sample name: MS280AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS350F)

description:
Sample name: MS350F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS350AC)

description:
Sample name: MS350AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS280F)

description:
Sample name: MS280F
Superior temporal gyrus AD


title: Prefrontal Cortex Male Control (MS1042AC)

description:
Sample name: MS1042AC
Prefrontal Cortex NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS122F)

description:
Sample name: MS122F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS369F)

description:
Sample name: MS369F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Control (MS192AC)

description:
Sample name: MS192AC
Prefrontal Cortex NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS19F)

description:
Sample name: MS19F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS1028F)

description:
Sample name: MS1028F
Superior temporal gyrus NL


title: Prefrontal Cortex Male Alzheimer's Disease (MS343AC)

description:
Sample name: MS343AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Alzheimer's Disease (MS467AC)

description:
Sample name: MS467AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS400AC)

description:
Sample name: MS400AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS369AC)

description:
Sample name: MS369AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS1208AC)

description:
Sample name: MS1208AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS1525AC)

description:
Sample name: MS1525AC
Prefrontal Cortex NL


title: Superior Temporal Gyrus Female Control (MS1510F)

description:
Sample name: MS1510F
Superior temporal gyrus NL


title: Prefrontal Cortex Male Control (MS1273AC)

description:
Sample name: MS1273AC
Prefrontal Cortex NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1225F)

description:
Sample name: MS1225F
Superior temporal gyrus AD


title: Prefrontal Cortex Male Control (MS1213AC)

description:
Sample name: MS1213AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS161AC)

description:
Sample name: MS161AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS95F)

description:
Sample name: MS95F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS611AC)

description:
Sample name: MS611AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1283F)

description:
Sample name: MS1283F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS1475F)

description:
Sample name: MS1475F
Superior temporal gyrus NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS434AC)

description:
Sample name: MS434AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS52AC)

description:
Sample name: MS52AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS518F)

description:
Sample name: MS518F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS39AC)

description:
Sample name: MS39AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Female Control (MS1507F)

description:
Sample name: MS1507F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1248F)

description:
Sample name: MS1248F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1409F)

description:
Sample name: MS1409F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS39F)

description:
Sample name: MS39F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS38F)

description:
Sample name: MS38F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS482AC)

description:
Sample name: MS482AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS1555AC)

description:
Sample name: MS1555AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS1175AC)

description:
Sample name: MS1175AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS1381AC)

description:
Sample name: MS1381AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS1225AC)

description:
Sample name: MS1225AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS1191AC)

description:
Sample name: MS1191AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS1466AC)

description:
Sample name: MS1466AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS1308AC)

description:
Sample name: MS1308AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS642AC)

description:
Sample name: MS642AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Male Control (MS1477F)

description:
Sample name: MS1477F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1024F)

description:
Sample name: MS1024F
Superior temporal gyrus NL


title: Prefrontal Cortex Female Control (MS1070AC)

description:
Sample name: MS1070AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS1131AC)

description:
Sample name: MS1131AC
Prefrontal Cortex NL


title: Superior Temporal Gyrus Male Control (MS1454F)

description:
Sample name: MS1454F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1134F)

description:
Sample name: MS1134F
Superior temporal gyrus AD


title: Prefrontal Cortex Male Alzheimer's Disease (MS451AC)

description:
Sample name: MS451AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Male Control (MS1039F)

description:
Sample name: MS1039F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1217F)

description:
Sample name: MS1217F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1191F)

description:
Sample name: MS1191F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS444F)

description:
Sample name: MS444F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS1205AC)

description:
Sample name: MS1205AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Female Control (MS1229F)

description:
Sample name: MS1229F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1088F)

description:
Sample name: MS1088F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS404F)

description:
Sample name: MS404F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS1350F)

description:
Sample name: MS1350F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS1040F)

description:
Sample name: MS1040F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS462F)

description:
Sample name: MS462F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS1004F)

description:
Sample name: MS1004F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS1172F)

description:
Sample name: MS1172F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS1017F)

description:
Sample name: MS1017F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS1070F)

description:
Sample name: MS1070F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS1213F)

description:
Sample name: MS1213F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS1322F)

description:
Sample name: MS1322F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS232F)

description:
Sample name: MS232F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS400F)

description:
Sample name: MS400F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS2010F)

description:
Sample name: MS2010F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS872F)

description:
Sample name: MS872F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS192F)

description:
Sample name: MS192F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS790F)

description:
Sample name: MS790F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS25F)

description:
Sample name: MS25F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS972F)

description:
Sample name: MS972F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS1390F)

description:
Sample name: MS1390F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS684F)

description:
Sample name: MS684F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS776F)

description:
Sample name: MS776F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS484F)

description:
Sample name: MS484F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS842F)

description:
Sample name: MS842F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS798F)

description:
Sample name: MS798F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS607F)

description:
Sample name: MS607F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Control (MS872AC)

description:
Sample name: MS872AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS831AC)

description:
Sample name: MS831AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS642F)

description:
Sample name: MS642F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS79AC)

description:
Sample name: MS79AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Male Control (MS978F)

description:
Sample name: MS978F
Superior temporal gyrus NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS882AC)

description:
Sample name: MS882AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS640F)

description:
Sample name: MS640F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Female Control (MS673F)

description:
Sample name: MS673F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS543F)

description:
Sample name: MS543F
Superior temporal gyrus AD


title: Prefrontal Cortex Male Alzheimer's Disease (MS543AC)

description:
Sample name: MS543AC
Prefrontal Cortex AD


title: Superior Temporal Gyrus Male Control (MS915F)

description:
Sample name: MS915F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Alzheimer's Disease (MS755F)

description:
Sample name: MS755F
Superior temporal gyrus AD


title: Superior Temporal Gyrus Male Control (MS94F)

description:
Sample name: MS94F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS546F)

description:
Sample name: MS546F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Control (MS900F)

description:
Sample name: MS900F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Male Control (MS678F)

description:
Sample name: MS678F
Superior temporal gyrus NL


title: Superior Temporal Gyrus Female Alzheimer's Disease (MS711F)

description:
Sample name: MS711F
Superior temporal gyrus AD


title: Prefrontal Cortex Female Control (MS230AC)

description:
Sample name: MS230AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Alzheimer's Disease (MS698AC)

description:
Sample name: MS698AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS768AC)

description:
Sample name: MS768AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS1537AC)

description:
Sample name: MS1537AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS94AC)

description:
Sample name: MS94AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS684AC)

description:
Sample name: MS684AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS675AC)

description:
Sample name: MS675AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS776AC)

description:
Sample name: MS776AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS95AC)

description:
Sample name: MS95AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS972AC)

description:
Sample name: MS972AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS711AC)

description:
Sample name: MS711AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Control (MS678AC)

description:
Sample name: MS678AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS484AC)

description:
Sample name: MS484AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Control (MS1475AC)

description:
Sample name: MS1475AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS232AC)

description:
Sample name: MS232AC
Prefrontal Cortex NL


title: Prefrontal Cortex Male Alzheimer's Disease (MS989AC)

description:
Sample name: MS989AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS800AC)

description:
Sample name: MS800AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Control (MS673AC)

description:
Sample name: MS673AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS899AC)

description:
Sample name: MS899AC
Prefrontal Cortex AD


title: Prefrontal Cortex Male Alzheimer's Disease (MS712AC)

description:
Sample name: MS712AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS806AC)

description:
Sample name: MS806AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS580AC)

description:
Sample name: MS580AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS798AC)

description:
Sample name: MS798AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS884AC)

description:
Sample name: MS884AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS790AC)

description:
Sample name: MS790AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Control (MS842AC)

description:
Sample name: MS842AC
Prefrontal Cortex NL


title: Prefrontal Cortex Female Alzheimer's Disease (MS869AC)

description:
Sample name: MS869AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS9AC)

description:
Sample name: MS9AC
Prefrontal Cortex AD


title: Prefrontal Cortex Female Alzheimer's Disease (MS697AC)

description:
Sample name: MS697AC
Prefrontal Cortex AD


title: 00S067

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

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.

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: M

value: whole blood


title: 00S070

value: F


title: 0S2300


title: 0S2269


title: Prefrontal Cortex Male Alzheimer's Disease (MS755AC)

description:
Sample name: MS755AC
Prefrontal Cortex AD

tag: gender


title: 0S2210


title: Prefrontal Cortex Female Alzheimer's Disease (MS963AC)

description:
Sample name: MS963AC
Prefrontal Cortex AD

value: female


title: 0S2291


title: 00S156


title: 00S300


title: 0S2352


title: 0S2171


title: 0S2234


title: 0S2190


title: 00S224


title: 0S2175


title: Prefrontal Cortex Male Control (MS1477AC)

description:
Sample name: MS1477AC
Prefrontal Cortex NL


title: 00S051


title: 00S149


title: 00S064


title: 0S2298


title: 00S212


title: 00S251


title: 00S296


title: 00S049


title: 00S027


title: 00S326


title: 0S2207


title: 0S2286


title: 00S273


title: 0S2126


title: 0S2136


title: 0S2316


title: Prefrontal Cortex Male Control (MS915AC)

description:
Sample name: MS915AC
Prefrontal Cortex NL


title: 0S2325


title: 0S2152


title: 0S2321


title: Prefrontal Cortex Female Alzheimer's Disease (MS650AC)

description:
Sample name: MS650AC
Prefrontal Cortex AD


title: 00S215


title: 00S272


title: 0S2185


title: 00S295


title: 0S2247


title: 0S2296


title: 00S302


title: 0S2287


title: 00S655


title: 0S2109


title: Prefrontal Cortex Male Alzheimer's Disease (MS504AC)

description:
Sample name: MS504AC
Prefrontal Cortex AD


title: 0S2305


title: 00S163


title: 00S332


title: Prefrontal Cortex Female Alzheimer's Disease (MS752AC)

description:
Sample name: MS752AC
Prefrontal Cortex AD


title: 00S062


title: 00S075


title: 0S2137


title: 0S2169


title: 00S324


title: 0S2194


title: 0S2131


title: 00S231


title: 0S2228


title: Prefrontal Cortex Male Control (MS1549AC)

description:
Sample name: MS1549AC
Prefrontal Cortex NL


title: 00S203


title: 00S150


title: 00S143


title: 0S2113


title: 0S2326


title: 00S258


title: 00S301


title: 00S161


title: Prefrontal Cortex Female Control (MS546AC)

description:
Sample name: MS546AC
Prefrontal Cortex NL


title: 0S2311


title: 0S2274


title: 00S169


title: 00S047


title: Group2_LowSleep

city: New Haven

first: Yong

last: Zhu

state: Connecticut

address: 60 College St

institute: Yale School of Public Health

description: CESD-H; TST-L subjects, pooled DNA (n=8)

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

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

data_processing: GenomeStudio v 2011.1

source_name: Pooled genomic DNA (n=8)

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from each of 16 subjects using the Qiagen DNEasy Blood and Tissue Kit

tag: sleep

value: Low


title: Group1_HighSleep

description: CESD-H; TST-H subjects, pooled DNA (n=8)

value: High


title: 0S2357


title: 00S118


title: 00S012


title: 00S154


title: 00S032


title: 0S2199


title: 0S2330


title: 00S081


title: Prefrontal Cortex Female Alzheimer's Disease (MS709AC)

description:
Sample name: MS709AC
Prefrontal Cortex AD


title: 0S2154


title: Prefrontal Cortex Female Control (MS82AC)

description:
Sample name: MS82AC
Prefrontal Cortex NL


title: 0S2107


title: 0S2142


title: 00S238


title: 00S204


title: 00S019


title: 00S071


title: 00S283


title: 0S2241


title: S0046


title: 0S2239


title: 00S255


title: 00S119


title: 00S095


title: Prefrontal Cortex Male Alzheimer's Disease (MS66AC)

description:
Sample name: MS66AC
Prefrontal Cortex AD


title: 00S086


title: 0S2295


title: 0S2310


title: 0S2345


title: 00S205


title: S2342


title: 0S2155


title: 00S299


title: 00S292


title: S0234


title: 00S995


title: 0S2222


title: 0S2102


title: 0S2333


title: 00S279


title: 00S077


title: 0S2162


title: 0S2110


title: 00S060


title: 00S137


title: 00S041


title: 0S2130


title: 0S2221


title: 00S155


title: 0S2168


title: 00S266


title: 00S345


title: 00S167


title: 00S098


title: 0S2196


title: 0S2359


title: 0S2170


title: 00S165


title: 00S241


title: 0S2344


title: 0S2128


title: 00S166


title: 0S2327


title: 00S325


title: 0S2139


title: 00S158


title: 00S125


title: 00S236


title: 0S2276


title: 00S275


title: 00S084


title: 00S276


title: 00S090


title: 0S2174


title: S2238


title: 0S2339


title: 0S2275


title: 00S235


title: 00S022


title: 0S2204


title: 00S271


title: 00S983


title: 00S157


title: 0S2165


title: 00S153


title: 00S285


title: 0S2172


title: 00S282


title: 0S2337


title: 00S248


title: 00S072


title: 0S2306


title: 0S2141


title: 00S103


title: 0S2176


title: 00S025


title: 00S066


title: 00S159


title: 0S2193


title: 0S2246


title: F621-03


title: 00S034


title: 00S029


title: 0S2159


title: F366-06


title: 0S2285


title: 00S649


title: 0S2249


title: 00S202


title: 0S2293


title: 00S256


title: 00S208


title: S2264


title: 0S2209


title: 00S253


title: 00S206


title: 00S213


title: 00S307


title: 0S2180


title: 00S044


title: 00S128


title: 00S078


title: 0S2279


title: 0S2358


title: F074-06


title: 0S2135


title: 0S2146


title: 00S080


title: 00S230


title: F158-03


title: 00S659


title: 0S2351


title: 0S2307


title: 0S2114


title: 0S2350


title: 00S270


title: 00S284


title: 00S054


title: 00S005


title: 00S310


title: 00S146


title: 0S2177


title: F552-01


title: 00S239


title: 0S2184


title: 0S2322


title: 0S2117


title: 0S2133


title: 00S229


title: 0S2331


title: 0S2232


title: 00S322


title: 0S2195


title: 00S265


title: 0S2173


title: 00S329


title: 0S2353


title: 0S2118


title: 0S2267


title: 0S2220


title: 0S2179


title: 00S083


title: 00S020


title: 00S259


title: 00S220


title: S2324


title: 00S024


title: 0S2167


title: 0S2304


title: 00S304


title: 0S2100


title: 0S2202


title: 00S122


title: S2121


title: 00S061


title: 00S033


title: 00S057


title: 00S073


title: 00S160


title: S0233


title: 00S141


title: 0S2164


title: S2260


title: 0S2127


title: 00S281


title: 0S2197


title: 0S2256


title: 00S039


title: 00S109


title: 0S2178


title: 00S305


title: 00S108


title: 00S331


title: 0S2255


title: 0S2254


title: 00S082


title: 0S2320


title: 0S2328


title: No.8-fr5-n2

city: Koto

first: Kiyotaka

last: Shiba

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation for Cancer Research

description:
SAMPLE 186
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

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 8

tag: ev source

value: whole saliva

tag: ev fraction

tag: technical replicate


title: No.8-fr6-n1

description:
SAMPLE 189
test


title: No.8-fr6-n4

description:
SAMPLE 192
test


title: No.8-fr5-n3

description:
SAMPLE 187
test


title: No.8-fr6-n3

description:
SAMPLE 191
test


title: No.8-fr6-n2

description:
SAMPLE 190
test


title: No.8-fr5-n4

description:
SAMPLE 188
test


title: No.8-fr5-n1

description:
SAMPLE 185
test


title: 0S2119

tag: age

tag: disease status

tag: tissue


title: 0S2245


title: No.8-fr4-n1

description:
SAMPLE 181
test


title: No.8-fr4-n2

description:
SAMPLE 182
test


title: No.8-fr4-n4

description:
SAMPLE 184
test


title: No.8-fr4-n3

description:
SAMPLE 183
test


title: 00S037


title: 0S2129


title: 0S2215


title: 00S100


title: 00S162


title: No.8-fr3-n1

description:
SAMPLE 177
test


title: No.8-fr2-n4

description:
SAMPLE 176
test


title: No.8-fr3-n4

description:
SAMPLE 180
test


title: No.8-fr3-n2

description:
SAMPLE 178
test


title: No.8-fr3-n3

description:
SAMPLE 179
test


title: 0S2341


title: 0S2140


title: 00S035


title: No.8-fr2-n1

description:
SAMPLE 173
test


title: S2259


title: 0S2150


title: 0S2181


title: 00S092


title: 0S2223


title: No.8-fr1-n3

description:
SAMPLE 171
test


title: No.8-fr1-n4

description:
SAMPLE 172
test


title: No.8-fr1-n2

description:
SAMPLE 170
test


title: No.8-fr1-n1

description:
SAMPLE 169
test


title: F250-02


title: No.7-fr6-n4

description:
SAMPLE 168
test

value: Healthy volunteer 7


title: No.7-fr6-n1

description:
SAMPLE 165
test


title: No.7-fr6-n3

description:
SAMPLE 167
test


title: 0S2312


title: 0S2151


title: 00S207


title: No.7-fr6-n2

description:
SAMPLE 166
test


title: No.8-fr2-n3

description:
SAMPLE 175
test


title: No.7-fr5-n4

description:
SAMPLE 164
test


title: 00S221


title: 0S2125


title: 0S2240


title: 00S996


title: No.8-fr2-n2

description:
SAMPLE 174
test


title: 0S2183


title: No.7-fr5-n3

description:
SAMPLE 163
test


title: No.7-fr5-n2

description:
SAMPLE 162
test


title: No.7-fr5-n1

description:
SAMPLE 161
test


title: 0S2217


title: 00S274


title: 0S2156


title: 00S145


title: 0S2166


title: 0S2280


title: No.7-fr4-n2

description:
SAMPLE 158
test


title: No.7-fr4-n1

description:
SAMPLE 157
test


title: 00S003


title: No.7-fr4-n3

description:
SAMPLE 159
test


title: No.7-fr4-n4

description:
SAMPLE 160
test


title: No.7-fr3-n4

description:
SAMPLE 156
test


title: S2218


title: No.7-fr3-n1

description:
SAMPLE 153
test


title: No.7-fr3-n3

description:
SAMPLE 155
test


title: No.7-fr3-n2

description:
SAMPLE 154
test


title: No.7-fr2-n4

description:
SAMPLE 152
test


title: 00S117


title: No.7-fr2-n2

description:
SAMPLE 150
test


title: No.7-fr2-n3

description:
SAMPLE 151
test


title: 0S2147


title: 00S333


title: No.7-fr2-n1

description:
SAMPLE 149
test


title: No.7-fr1-n4

description:
SAMPLE 148
test


title: 0S2187


title: 00S097


title: No.7-fr1-n3

description:
SAMPLE 147
test


title: No.7-fr1-n2

description:
SAMPLE 146
test


title: 0S2219


title: 00S262


title: 00S263


title: 0S2134


title: No.7-fr1-n1

description:
SAMPLE 145
test


title: No.6-fr6-n4

description:
SAMPLE 144
test

value: Healthy volunteer 6


title: F394-03


title: 00S223


title: 0S2115


title: 00S170


title: No.6-fr6-n3

description:
SAMPLE 143
test


title: No.6-fr5-n4

description:
SAMPLE 140
test


title: No.6-fr6-n1

description:
SAMPLE 141
test


title: 0S2200


title: 00S068


title: 0S2319


title: No.6-fr5-n3

description:
SAMPLE 139
test


title: 00S994


title: No.6-fr4-n4

description:
SAMPLE 136
test


title: No.6-fr5-n1

description:
SAMPLE 137
test


title: No.6-fr5-n2

description:
SAMPLE 138
test


title: 0S2332


title: No.6-fr4-n3

description:
SAMPLE 135
test


title: No.6-fr4-n2

description:
SAMPLE 134
test


title: 00S237


title: 0S2198


title: 00S319


title: 00S004


title: No.6-fr3-n3

description:
SAMPLE 131
test


title: No.6-fr6-n2

description:
SAMPLE 142
test


title: No.6-fr3-n4

description:
SAMPLE 132
test


title: 00S085


title: No.6-fr3-n2

description:
SAMPLE 130
test


title: 00S058


title: No.6-fr3-n1

description:
SAMPLE 129
test


title: 00S038


title: No.6-fr2-n3

description:
SAMPLE 127
test


title: No.6-fr2-n4

description:
SAMPLE 128
test


title: 0S2288


title: No.6-fr2-n2

description:
SAMPLE 126
test


title: 0S2268


title: 00S028


title: 00S201


title: No.6-fr2-n1

description:
SAMPLE 125
test


title: 00S269


title: 00S341


title: 00S088


title: F101-01


title: No.6-fr4-n1

description:
SAMPLE 133
test


title: No.6-fr1-n3

description:
SAMPLE 123
test


title: No.6-fr1-n4

description:
SAMPLE 124
test


title: No.6-fr1-n2

description:
SAMPLE 122
test


title: 0S2257


title: No.5-fr6-n4

description:
SAMPLE 120
test

value: Healthy volunteer 5


title: No.5-fr6-n3

description:
SAMPLE 119
test


title: No.6-fr1-n1

description:
SAMPLE 121
test


title: 00S063


title: 0S2252


title: 00S096


title: No.5-fr6-n2

description:
SAMPLE 118
test


title: No.5-fr5-n3

description:
SAMPLE 115
test


title: No.5-fr6-n1

description:
SAMPLE 117
test


title: No.5-fr5-n1

description:
SAMPLE 113
test


title: 00S249


title: No.5-fr5-n4

description:
SAMPLE 116
test


title: 0S2158


title: 0S2160


title: 00S990


title: 0S2231


title: No.5-fr4-n2

description:
SAMPLE 110
test


title: No.5-fr4-n3

description:
SAMPLE 111
test


title: 0S2201


title: No.5-fr4-n1

description:
SAMPLE 109
test


title: 00S209


title: 0S2203


title: 00S247


title: No.5-fr4-n4

description:
SAMPLE 112
test


title: 0S2186


title: 0S2144


title: No.5-fr5-n2

description:
SAMPLE 114
test


title: 00S980


title: No.5-fr3-n2

description:
SAMPLE 106
test


title: No.5-fr3-n3

description:
SAMPLE 107
test


title: No.5-fr3-n1

description:
SAMPLE 105
test


title: No.5-fr3-n4

description:
SAMPLE 108
test


title: 0S2103


title: No.5-fr2-n4

description:
SAMPLE 104
test


title: 00S291


title: 0S2157


title: 0S2323


title: No.5-fr1-n2

description:
SAMPLE 98
test


title: No.5-fr1-n3

description:
SAMPLE 99
test