title: Microaerobic-xylose cy3-2

source_name: Microaerobic-xylose cy3

source_name: Microaerobic-glucose cy5


title: Genomic DNA from 066042A10_N

status: Public on Jan 01 2016

type: genomic

city: London

first: Andrew

last: Feber

address: Division of Surgery & Interventional Science, Charles Bell House, 43-45 Foley Street

country: United Kingdom

institute: University College London

description:
normal liver
9247377041

hyb_protocol: Illumina HumMeth 450K protocol

scan_protocol: Illumina HumMeth 450K protocol

data_processing: The ChAmp pipeline (Bioconductor). Normalisation with BMIQ and batch correction with ComBat as part of the ChAmp pipeline.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: normal

label_protocol: Illumina HumMeth 450K protocol

extract_protocol: DNA was extracted using the Qiagen QIAamp DNA mini kit

tag: lesion

value: normal

tag: sample site

value: liver

tag: primary site

value: small intestine

tag: grade

tag: source tissue type

value: FFPE

tag: gender

value: M

tag: age


title: Δpgm vs. Δpgm ΔyspI at 30C rep1

type: RNA

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

country: USA

institute: Iowa State University

description: The strain Δpgm is the Y.pestis CO92 pigmentation-negative mutant R88.

hyb_protocol: Corresponding equal amounts (1.5 µg) of Alexa 555- or Alexa 647-labelled cDNA targets were mixed and dried using a Thermo Scientific Savant DNA SpeedVac Concentrator. Targets were suspended in 60 µl hybridization buffer (40% formamide, 5x SSC, 0.1% SDS, 0.6 µg/µl Salmon Sperm DNA), incubated at 95°C for 5 min, centrifuged (10,000 x g, 4 min), and kept at room temperature until placed in a hybridization chamber. Hybridization lasted for 16 h at 42°C and washed in a series of wash buffers (2x saline-sodium citrate (SSC) - 0.1% SDS; 0.1x SSC – 0.1% SDS, and 0.1x SSC) and dried by centrifugation at 1500 x g for 30 s.

scan_protocol: Arrays scanned on a ProScanArray HT scanner (Perkin Elmer, Wellesley, MA) three times with varying photomultiplier tube gain and laser power settings.

data_processing: Data acquisition, normalization and data analysis have been described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102).

molecule: total RNA

organism: Yersinia pestis

source_name: Δpgm

label_protocol: Target generation and labeling were performed as described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102).

growth_protocol: An overnight culture was diluted 1:100 and grown at 30°C in HIB broth until an optical density 600 nm of 1.0 is reached.

extract_protocol: Cells were pelleted and immediately resuspended in 1 ml of Trizol (Ambion) and were then frozen. RNA was extracted from frozen cell pellets using the Trizol reagent protocol. The RNA was treated with DNase I (Ambion) at 37°C for 30 min to remove contaminating genomic DNA. The RNA was purified and concentrated by Microcon Ultracel/YM 30.

treatment_protocol: Microarray studies were performed by comparing strains R88 and Δpgm ΔyspI grown at a mid logarithmic phase.

tag: genotype/variation

value: Δpgm

tag: strain

source_name: Δpgm ΔyspI

value: Δpgm ΔyspI


title: Δpgm vs. Δpgm ΔyspI at 37C rep6

growth_protocol: An overnight culture was diluted 1:100 and grown at 37°C in HIB broth until an optical density 600 nm of 1.0 is reached.


title: Microaerobic-xylose cy5-1

city: Daejeon

first: Oh Cheol

last: Kim

address: Gwahakro 125

country: South Korea

institute: KRIBB

description: The transcriptomes of Hansenula polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions

hyb_protocol: The fluorescent-labeled cDNA was concentrated under a vacuum and resuspended in 15 µl of preheated hybridization buffer (25% formamide, 5x SSC, 0.1% SDS). The pairs of Cys3 and Cys5-labeled samples were mixed and applied to a post-processing H. polymorpha microarray chip.

scan_protocol: After incubation in the dark at 42°C for 16 – 18 h, the slide was washed, dried, and scanned for Cy5(635 nm) and Cy3(532 nm) signals using a GenePix4000B scanner (Axon Instruments)

data_processing:
Spot identification and fluorescent signal quantitation were conducted using GenePix Pro v6.0 software, where any flagged, not found, saturated, or bad signal spot was automatically and manually eliminated.
Data processing and normalization were performed with the Arraynorm program. This data has the Matrix worksheet in your submission contains the normalized data that was generated by the Arraynorm software.

organism: Ogataea angusta

source_name: Microaerobic-xylose cy5

label_protocol: 30 µg total RNA of each samples was used for first-strand cDNA synthesis using SuperScript III reverse transcriptase (Invitrogen, USA) with the oligo dT primer. The cDNA labeling was performed using an Aminoallyl post-DNA labeling kit (GeneChem, Korea) following the manufacturer’s protocol with some modifications.

extract_protocol: To grow the cells aerobically, 500 ml Erlenmeyer flasks containing 50 ml of the medium were inoculated at an initial OD600 of 0.3 units with overnight pre-cultures and incubated at 37°C while shaking at 180 rpm in an orbital shaker. For microaerobic growth, 250 ml Erlenmeyer flasks containing 100 ml of the medium were inoculated at an initial OD600 of 0.3 units with overnight pre-cultures and were incubated at 37°C while shaking at 100 rpm in an orbital shaker. Cell growth was monitored by determining the optical density (OD600) with a SHIMADZU UV-2550 Spectrophotometer. The total RNA was extracted by a hot phenol method followed by purification using an RNeasy column kit (Qiagen)

source_name: Microaerobic-glucose cy3


title: Microaerobic-xylose cy5-2


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep5

description: The strain Δpgm is the Y.pestis CO92 pigmentation-negative mutant R88. The Δpgm ΔypeIR ΔyspIR is R114 strain.

source_name: Δpgm ΔypeIR ΔyspIR

treatment_protocol: Microarray studies were performed by comparing strains R88 and R114 grown at a mid logarithmic phase.

value: Δpgm ΔypeIR ΔyspIR


title: Genomic DNA from 066042A6_T

description:
metastasis liver
9247377041

source_name: metastasis

value: metastasis


title: Genomic DNA from 066042A5_T

description:
metastasis liver
9247377041


title: Δpgm vs. Δpgm ΔyspI at 37C rep5


title: Genomic DNA from 066042A2_T

description:
metastasis liver
9247377041


title: Microaerobic-xylose cy3-1


title: Δpgm vs. Δpgm ΔyspI at 37C rep3


title: Δpgm vs. Δpgm ΔyspI at 37C rep4


title: Genomic DNA from 08S016176A7_T

description:
primary small intestine
9370847109

source_name: primary

value: primary

value: F


title: Genomic DNA from 08C10646269_T

description:
primary small intestine
9374342114


title: Genomic DNA from 068279A17_N

description:
normal small intestine
9370847109


title: Genomic DNA from 0612608A4_T

description:
metastasis mes_omentum
9247377041


title: Δpgm vs. Δpgm ΔyspI at 37C rep2


title: Genomic DNA from 0612608A8_N

description:
normal small intestine
9266441100


title: Δpgm vs. Δpgm ΔyspI at 37C rep1


title: Genomic DNA from 066042A1_T

description:
metastasis liver
9247377041


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep6

growth_protocol: An overnight culture was diluted 1:100 and grown for 9 h at 30°C in HIB broth at which time an optical density 600 nm of 1.0 is reached.


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep5


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep4


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep3


title: Genomic DNA from 0918157B11_N

description:
normal small intestine
7973219119


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep2


title: Δpgm vs. Δpgm ΔypeIR ΔyspIR rep1


title: Crizotinib and Starvation, replicate 4

city: Trento

first: Alessandro

last: Provenzani

address: via delle regole 101

department: CIBIO

country: Italy

institute: University of Trento

hyb_protocol: On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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: Crizotinib treated during starvation H3122 cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained in RPMI1640 medium supplemented with 10% FBS, penicillin (50 units/ml), and streptomycin (50 μg/ml) (LifeTechnologies, Italy)

extract_protocol: Total RNA isolation: cells were lysed in RLT buffer and RNA was isolated with the RNeasy Mini Kit according to the manufacturer's instructions (Quiagen, GmbH Hilden, Germany)

treatment_protocol: H3122 cells were plated in regular medium containing 10% FBS. 24 h later, the cell medium was removed, cells were washed twice with PBS and then incubated either in the same medium or in starvation medium (1% FBS, 0.5 g/l glucose and antibiotics). 24 h later cells were stimulated (or not) with crizotinib. RNA was extracted 72 h later.

tag: cell line

tag: tissue source

value: lung

tag: cell type

value: non small cell adenocarcinoma cell line

tag: growth condition

value: 72 hrs of 400 nM Crizotinib treatment and starvation


title: Genomic DNA from 05466A3_T

description:
primary NA
9370847111


title: Genomic DNA from 060715B04_T

description:
primary small intestine
9370847143


title: Crizotinib and Starvation, replicate 3


title: Genomic DNA from 0414821A4_T

description:
primary small intestine
9370847143

value: unk


title: Crizotinib and Starvation, replicate 2


title: Genomic DNA from 0519934A2_T

description:
primary appendix
7973219126

value: appendix


title: Genomic DNA from 05466A1_N

description:
normal normal
9370847111


title: Crizotinib and Starvation, replicate 1


title: Genomic DNA from 0414821A4_N

description:
normal small intestine
9370847144


title: Crizotinib, replicate 4

source_name: Crizotinib treated H3122 cell

value: 72 hrs of 400 nM Crizotinib treatment


title: Genomic DNA from 0513133B81_N

description:
normal small intestine
7973219096

value: normal


title: Genomic DNA from 0513133B82_T

description:
primary small intestine
7973219096


title: Crizotinib, replicate 1


title: Crizotinib, replicate 3


title: genomic DNA from NPC (NPC_T25)

city: Hong Kong

first: Maria

middle: Li

last: Lung

address: 21 Sassoon Road

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

description:
Sample name: NPC_T25
NPC tumor sample

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

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

data_processing: BeadStudio software v3.2

source_name: NPC tumor tissue

label_protocol: Standard Illumina protocol

extract_protocol: All specimens were extracted using AllPrep DNA/RNA Micro Kit (Qiagen). The quality and quantity of the DNA samples was measured by NanoDrop and Qubit

treatment_protocol: Genomic DNA was bisulphite converted using EZ-96 DNA Methylation Kit (Zymo Research)

tag: disease status

value: Nasopharyngeal Carcinoma

tag: tissue

value: tumor

tag: sample name


title: Crizotinib, replicate 2


title: Control, replicate 3

source_name: Regular medium H3122 cells

value: in normal growth medium


title: Genomic DNA from 033349CT1_T

description:
primary small intestine
9266441100

value: small intestine

value: FFPE


title: Genomic DNA from 0414821A1_N

description:
normal small intestine
9370847143


title: genomic DNA from NPC (NPC_T23)

description:
Sample name: NPC_T23
NPC tumor sample


title: genomic DNA from control (NPC_N25)

description:
Sample name: NPC_N25
Normal NP sample

source_name: NP non-tumor tissue

value: normal (non-tumor tissue)


title: genomic DNA from control (NPC_N24)

description:
Sample name: NPC_N24
Normal NP sample


title: Control, replicate 4


title: genomic DNA from NPC (NPC_T22)

description:
Sample name: NPC_T22
NPC tumor sample


title: Starvation, replicate 4

source_name: Starved H3122 cells

value: 96 hrs of starvation


title: Control, replicate 1


title: genomic DNA from control (NPC_N20)

description:
Sample name: NPC_N20
Normal NP sample


title: Starvation, replicate 3


title: genomic DNA from NPC (NPC_T21)

description:
Sample name: NPC_T21
NPC tumor sample


title: genomic DNA from NPC (NPC_T19)

description:
Sample name: NPC_T19
NPC tumor sample


title: Preneoplastic foci_6033081014_L

city: CAGLIARI

first: AMEDEO

last: COLUMBANO

state: CA

address: VIA PORVELL 4

department: DIPARTIMENTO DI SCIENZE BIOMEDICHE

institute: UNIVERSITA' DEGLI STUDI DI CAGLIARI

description:
6033081014_L
replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina BeadStudio 3.0.19.0 software (Illumina Inc) and BRB Array Tools (Version 4.2.0)

label: biotin

organism: Rattus norvegicus

source_name: Preneoplastic foci

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

extract_protocol: RNA was extracted with Trizol reagent  and Mirvana Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Liver

value: Preneoplastic foci


title: genomic DNA from control (NPC_N22)

description:
Sample name: NPC_N22
Normal NP sample


title: Preneoplastic foci_6033081014_K

description:
6033081014_K
replicate 4


title: genomic DNA from control (NPC_N23)

description:
Sample name: NPC_N23
Normal NP sample


title: Genomic DNA from 0165092_T

description:
primary small intestine
7973219126

value: primary

value: M


title: Starvation, replicate 1

value: lung

value: non small cell adenocarcinoma cell line


title: Starvation, replicate 2


title: genomic DNA from control (NPC_N21)

description:
Sample name: NPC_N21
Normal NP sample


title: Genomic DNA from 0113851A9_T

description:
metastasis mes_omentum
7973219119

value: metastasis

value: colon


title: genomic DNA from control (NPC_N19)

description:
Sample name: NPC_N19
Normal NP sample


title: Preneoplastic foci_6033081014_J

description:
6033081014_J
replicate 4


title: genomic DNA from NPC (NPC_T20)

description:
Sample name: NPC_T20
NPC tumor sample


title: Preneoplastic foci_6033081014_H

description:
6033081014_H
replicate 4


title: Preneoplastic foci_6033081014_I

description:
6033081014_I
replicate 4


title: genomic DNA from NPC (NPC_T17)

description:
Sample name: NPC_T17
NPC tumor sample


title: genomic DNA from control (NPC_N17)

description:
Sample name: NPC_N17
Normal NP sample


title: genomic DNA from control (NPC_N18)

description:
Sample name: NPC_N18
Normal NP sample


title: Genomic DNA from 0113851A5_N

description:
normal colon
7973219155


title: CK-19-positive preneoplastic nodules_5630141062_D

description:
5630141062_D
replicate 3

source_name: CK-19-positive preneoplastic nodules

value: CK-19-positive preneoplastic nodules


title: genomic DNA from control (NPC_N16)

description:
Sample name: NPC_N16
Normal NP sample


title: CK-19-positive preneoplastic nodules_5630141062_C

description:
5630141062_C
replicate 3


title: genomic DNA from NPC (NPC_T24)

description:
Sample name: NPC_T24
NPC tumor sample


title: CK-19-positive preneoplastic nodules_5630141062_B

description:
5630141062_B
replicate 3


title: genomic DNA from NPC (NPC_T15)

description:
Sample name: NPC_T15
NPC tumor sample


title: CK-19-positive preneoplastic nodules_5630141062_A

description:
5630141062_A
replicate 3


title: Control, replicate 2


title: CK-19-negative preneoplastic nodules_5630141062_F

description:
5630141062_F
replicate 2

source_name: CK-19-negative preneoplastic nodules

value: CK-19-negative preneoplastic nodules


title: genomic DNA from control (NPC_N15)

description:
Sample name: NPC_N15
Normal NP sample

value: Nasopharyngeal Carcinoma


title: CK-19-negative preneoplastic nodules_5665167013_I

description:
5665167013_I
replicate 2


title: CK-19-negative preneoplastic nodules_5665167013_H

description:
5665167013_H
replicate 2


title: CK-19-negative preneoplastic nodules_5665167013_J

description:
5665167013_J
replicate 2


title: genomic DNA from NPC (NPC_T16)

description:
Sample name: NPC_T16
NPC tumor sample

value: tumor


title: genomic DNA from control (NPC_N14)

description:
Sample name: NPC_N14
Normal NP sample


title: CK-19-negative preneoplastic nodules_5665167013_L

description:
5665167013_L
replicate 2


title: Control_5842741071_B

description:
5842741071_B
replicate 1

source_name: Control

value: hepatocytes


title: Control_5665167013_A

description:
5665167013_A
replicate 1


title: Control_5842741071_A

description:
5842741071_A
replicate 1


title: Control_5630141062_L

description:
5630141062_L
replicate 1


title: genomic DNA from control (NPC_N11)

description:
Sample name: NPC_N11
Normal NP sample


title: Control_5630141062_K

description:
5630141062_K
replicate 1


title: genomic DNA from control (NPC_N13)

description:
Sample name: NPC_N13
Normal NP sample


title: genomic DNA from NPC (NPC_T10)

description:
Sample name: NPC_T10
NPC tumor sample


title: genomic DNA from NPC (NPC_T11)

description:
Sample name: NPC_T11
NPC tumor sample


title: Preneoplastic foci_6033081014_K (I)

description:
6033081014_K
replicate 3


title: genomic DNA from NPC (NPC_T18)

description:
Sample name: NPC_T18
NPC tumor sample


title: Preneoplastic foci_6033081014_L (I)

description:
6033081014_L
replicate 3


title: genomic DNA from control (NPC_N10)

description:
Sample name: NPC_N10
Normal NP sample


title: Preneoplastic foci_6033081014_I (I)

description:
6033081014_I
replicate 3


title: genomic DNA from control (NPC_N9)

description:
Sample name: NPC_N9
Normal NP sample


title: genomic DNA from NPC (NPC_T9)

description:
Sample name: NPC_T9
NPC tumor sample


title: Preneoplastic foci_6033081014_H (I)

description:
6033081014_H
replicate 3


title: genomic DNA from control (NPC_N7)

description:
Sample name: NPC_N7
Normal NP sample


title: Oval cells_5842741071_F (I)

description:
5842741071_F
replicate 2

source_name: Oval cells

value: Oval cells (liver cancer progenitor cells)


title: Oval cells_5842741071_D (I)

description:
5842741071_D
replicate 2


title: genomic DNA from NPC (NPC_T7)

description:
Sample name: NPC_T7
NPC tumor sample


title: CK-19-positive preneoplastic nodules_5630141062_E

description:
5630141062_E
replicate 3


title: genomic DNA from NPC (NPC_T6)

description:
Sample name: NPC_T6
NPC tumor sample


title: genomic DNA from control (NPC_N6)

description:
Sample name: NPC_N6
Normal NP sample


title: Preneoplastic foci_6033081014_J (I)

description:
6033081014_J
replicate 3


title: Oval cells_5842741071_C (I)

description:
5842741071_C
replicate 2


title: genomic DNA from NPC (NPC_T12)

description:
Sample name: NPC_T12
NPC tumor sample


title: genomic DNA from NPC (NPC_T3)

description:
Sample name: NPC_T3
NPC tumor sample


title: genomic DNA from control (NPC_N4)

description:
Sample name: NPC_N4
Normal NP sample


title: genomic DNA from control (NPC_N8)

description:
Sample name: NPC_N8
Normal NP sample


title: genomic DNA from control (NPC_N5)

description:
Sample name: NPC_N5
Normal NP sample


title: genomic DNA from NPC (NPC_T4)

description:
Sample name: NPC_T4
NPC tumor sample


title: Oval cells_5842741071_E (I)

description:
5842741071_E
replicate 2


title: genomic DNA from NPC (NPC_T8)

description:
Sample name: NPC_T8
NPC tumor sample


title: Oval cells_5842741071_H (I)

description:
5842741071_H
replicate 2


title: Control_5842741071_B (I)

description:
5842741071_B
replicate 1


title: genomic DNA from NPC (NPC_T14)

description:
Sample name: NPC_T14
NPC tumor sample


title: genomic DNA from control (NPC_N12)

description:
Sample name: NPC_N12
Normal NP sample


title: genomic DNA from control (NPC_N3)

description:
Sample name: NPC_N3
Normal NP sample


title: Control_5842741071_A (I)

description:
5842741071_A
replicate 1


title: genomic DNA from NPC (NPC_T2)

description:
Sample name: NPC_T2
NPC tumor sample


title: genomic DNA from NPC (NPC_T5)

description:
Sample name: NPC_T5
NPC tumor sample


title: Pancreas_sitag_rep3

city: Urbana

first: Diego

middle: Armando

last: Luna-Vital

state: ILLINOIS

address: 228 ERML MC 051, 1201 W Gregory Dr

data_processing: The data were processed in R 3.1.2) using limma (3.22.1) using the neqc function, which does a normexp background correction using negative control probes, quantile normalization using negative and positive control probes and log2 transformation.

organism: Mus musculus

source_name: Mice pancreatic tissue

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit according to manufacturer's instructions

growth_protocol: Animal use was conducted in accordance with Institutional Animal Care and Use Committee approved protocols (#14060) at the University of Illinois at Urbana-Champaign. Male C57BL/6J mice 3 weeks old were purchased from Jackson Laboratory (Bar Harbor, Maine), housed in standardized conditions with a reversed 12 h light/dark cycle, kept in a room maintained at 23°C in individual caging systems (singly) in order to accurately determine feed and water intake, and acclimated for one week upon arrival.

extract_protocol: RNA was extracted with the QIAGEN RNeasy mini kit according to the manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: All six treatment groups received a standard 22/4 rodent diet (TD.8640) for weeks 1 and 2 before switching in week 3 to a high-fat diet (TD.06414: 60% fat, 21% carbohydrate, 18% protein, Harlan Laboratories, Madison, WI). Food was provided ad libitum and intake recorded bi weekly. After baseline blood glucose measures, the mice were randomized into 6 groups (n=12/group) to receive ad libitum, instead of water, 6 different treatments including an alcohol free fermented beverage (AFFB), three doses of phenolic compounds from AFFB (PAE), and a commercial DPP-IV inhibitor as an admix also provided in the water (n = 12/group), as follows: (a) AFFB (70%blackberry-30% blueberry, 8.4 mg/kg BW/d); dose 0.1X PAE, 1.1 mg/kg BW/d; (c) dose 1X PAE, 9.0 mg/kg BW/d; (d) dose 2X PAE, 18.9 mg/kg BW/d; where X is the equivalent dose of ANC found in fermented beverage group (AFFB); (e) water as negative control; and (f) sitagliptin phosphate at 150 mg/L in water as hypoglycemic control commonly used to control hyperglycemia in obese patients with type-2 diabetes.

value: 3 weeks

value: Male

value: Pancreas


title: genomic DNA from NPC (NPC_T1)

description:
Sample name: NPC_T1
NPC tumor sample


title: Pancreas_sitag_rep1

institute: University of Illinois at Urbana-Champaign


title: genomic DNA from control (NPC_N1)

description:
Sample name: NPC_N1
Normal NP sample

value: normal (non-tumor tissue)


title: genomic DNA from NPC (NPC_T13)

description:
Sample name: NPC_T13
NPC tumor sample


title: Oval cells_5842741071_G (I)

description:
5842741071_G
replicate 2

value: Liver


title: Pancreas_sitag_rep2


title: DNA-methylation in PJ-34 treated cells

city: Grand Rapids

first: Yvonne

middle: Nsokika

last: Fondufe-Mittendorf

state: MI

address: 333 Bostwick Ave NE

department: Epigenetics

institute: Van Andel Institute

description: Sample name: MCF7-PJ34

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium Human Methylation450 Beadchip using the standard Illumina protocol

scan_protocol: Arrays were imaged using the HiScan with the standard recommended settings

data_processing: GenomeStudio v.2011.1

source_name: Breast cancer cell line

label_protocol: Standard Illumina Protocol

growth_protocol: Cell cultures were incubated at 37 degree with humidified air and 5% CO2. Cells were harvested after each treatment. Cells were grown ensuring that 95% of the cells were viable. Harvested cells were centrifuged for five minutes at 200 X g.

extract_protocol: Genomic DNA was extracted using Qiagen Dneasykit according to manusfacturers instructions.

treatment_protocol: MCF7 cells were then treated with vehicle and PJ34 for 2hours respectively.

tag: agent


title: Pancreas_H2O_rep4


title: DNA methylation in NT cells

description: Sample name: MCF7

value: control


title: Pancreas_H2O_rep2


title: Pancreas_H2O_rep1


title: Pancreas_3X_rep2


title: genomic DNA from control (NPC_N2)

description:
Sample name: NPC_N2
Normal NP sample


title: Pancreas_3X_rep3


title: Pancreas_3X_rep1


title: quality control (QC_5935534023.RO5C02)

city: athens

first: panagiotis

last: georgiadis

state: Greece

address: 48 vas costantinou

department: IBMCB

country: Greece

institute: NHRF

description: genomic DNA from buffy coat

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450K  Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2 and  a novel intensity-based normalization method using technical quality controls (see ralated publication)

source_name: TQC 18 buffy coat

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: quality control

value: blood

tag: tissue fraction

value: buffy coat


title: Pancreas_1X_rep4


title: Pancreas_1X_rep3


title: quality control (QC_5773184005.RO5C01)

description: genomic DNA from buffy coat

source_name: TQC 10 buffy coat


title: quality control (QC_5773184012.RO1C01)

description: genomic DNA from buffy coat

source_name: TQC 11 buffy coat


title: Pancreas_3X_rep4


title: quality control (QC_5773184005.RO4C02)

description: genomic DNA from buffy coat

source_name: TQC 9 buffy coat


title: Pancreas_sitag_rep4


title: Pancreas_0.1X_rep4


title: Pancreas_1X_rep1


title: quality control (QC_5957881012.RO5C01)

description: genomic DNA from buffy coat

source_name: TQC 6 buffy coat


title: Pancreas_0.1X_rep3


title: quality control (QC_5935294023.RO4C01)

description: genomic DNA from buffy coat

source_name: TQC 14 buffy coat


title: Pancreas_1X_rep2


title: quality control (QC_5957881015.RO4C02)

description: genomic DNA from buffy coat

source_name: TQC 7 buffy coat


title: Pancreas_0.1X_rep2


title: Pancreas_H2O_rep3


title: quality control (QC_5957961013.RO6C02)

description: genomic DNA from buffy coat

source_name: TQC 8 buffy coat


title: Pancreas_0.1X_rep1


title: quality control (QC_5957881009.RO2C02)

description: genomic DNA from buffy coat

source_name: TQC 5 buffy coat


title: quality control (QC_5957881002.RO4C01)

description: genomic DNA from buffy coat

source_name: TQC 3 buffy coat


title: quality control (QC_5773184013.RO6C02)

description: genomic DNA from buffy coat

source_name: TQC 13 buffy coat


title: quality control (QC_5957881001.RO3C02)

description: genomic DNA from buffy coat

source_name: TQC 2 buffy coat


title: Pancreas_AFFB_rep2


title: quality control (QC_5957881005.RO1C01)

description: genomic DNA from buffy coat

source_name: TQC 4 buffy coat


title: Pancreas_AFFB_rep3


title: cardiomyocytes 26 day after proton radiation exposure rep2

city: Livermore

first: Matthew

last: Coleman

address: 7000 East Ave.

institute: Lawrence Livermore National Laboratory

hyb_protocol: Follow manufacturor Affymetrix standard procedure

scan_protocol: Scanned with Affymetrix GeneChip imager

data_processing: MAS5.0 signal intensities analyzed using Dchip in Webarray

source_name: left ventricular murine cardiomyocytes to 90 cGy,  1 GeV proton (1H) 26 day after exposure

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

extract_protocol: Cardiac Cell Isolation – Primary left ventricular cardiac cells from 8-9 months old C57Bl/6NT mice were isolated using standard preparation protocol that includes cannulation of the aorta and collagenase digestion followed by a Ca2+ gradient selection (22, 25, 26, 33). This procedure yielded >90% of Ca2+ tolerant cardiomyocytes (CMs). The resulting cell suspension could contain a small population of inflammatory and/or endothelial cells. Following isolation of CMs, RNA was extracted via TRIzol (Life Technologies, Grand Island, NY) according to the manufactures instructions.  RNA quality and quantity was assessed using the 2100 Bioanalyzer (Agilent Tech., Santa Clara, CA).

treatment_protocol: Irradiation and Dosimetry – Whole body irradiation of adult (8-9 months old) male C57Bl/6NT (Taconic) mice was performed at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (Upton, NY).  Using dose-rates between 0.05 Gy/min and 0.17 Gy/min, iron and proton, respectively; 0.15 Gy was delivered using 1 GeV/nucleon iron ions (LET ~151 keV per µm) or 0.9 Gy at 1 GeV energy protons (LET ~0.22 keV per µm).

value: left ventricular murine cardiomyocytes

tag: Sex

value: male

value: adult (8-9 months old)


title: quality control (QC_5935534033.RO6C01)

description: genomic DNA from buffy coat

source_name: TQC 1 buffy coat


title: cardiomyocytes 1 day after sham radiation exposure rep1 (proton)

source_name: left ventricular murine cardiomyocytes 1 day after sham radiation exposure


title: quality control (QC_5935534021.RO1C02)

description: genomic DNA from buffy coat

source_name: TQC 17 buffy coat


title: cardiomyocytes 1 day after sham radiation exposure rep2 (proton)


title: diseased (E_BC_CA_098_5935294023.RO3C01)

description: genomic DNA from buffy coat

source_name: 95 buffy coat

value: diseased (case, breast cancer)


title: diseased (E_BC_CA_099_5935294023.RO5C01)

description: genomic DNA from buffy coat

source_name: 96 buffy coat


title: quality control (QC_5773184012.RO6C02)

description: genomic DNA from buffy coat

source_name: TQC 12 buffy coat


title: cardiomyocytes 3 days after sham radiation exposure (proton)

source_name: left ventricular murine cardiomyocytes 3 days after sham radiation exposure


title: cardiomyocytes 26 day after proton radiation exposure rep1


title: quality control (QC_5935294023.RO5C02)

description: genomic DNA from buffy coat

source_name: TQC 15 buffy coat


title: diseased (E_BC_CA_094_5935294033.RO5C02)

description: genomic DNA from buffy coat

source_name: 93 buffy coat


title: diseased (E_BC_CA_095_5935294033.RO6C02)

description: genomic DNA from buffy coat

source_name: 94 buffy coat


title: cardiomyocytes 12 day after proton radiation exposure rep2

source_name: left ventricular murine cardiomyocytes to 90 cGy,  1 GeV proton (1H) 12 day after exposure


title: quality control (QC_5935294032.RO2C01)

description: genomic DNA from buffy coat

source_name: TQC 16 buffy coat


title: diseased (E_BC_CA_085_5935294033.RO2C01)

description: genomic DNA from buffy coat

source_name: 89 buffy coat


title: diseased (E_BC_CA_088_5957881012.RO1C01)

description: genomic DNA from buffy coat

source_name: 90 buffy coat


title: Pancreas_AFFB_rep1

source_name: Mice pancreatic tissue


title: Pancreas_AFFB_rep4


title: cardiomyocytes 12 day after proton radiation exposure rep1


title: cardiomyocytes 5 day after proton radiation exposure rep3

source_name: left ventricular murine cardiomyocytes to 90 cGy,  1 GeV proton (1H) 5 day after exposure


title: diseased (E_BC_CA_080_5935294029.RO2C02)

description: genomic DNA from buffy coat

source_name: 86 buffy coat


title: diseased (E_BC_CA_089_5935294033.RO6C01)

description: genomic DNA from buffy coat

source_name: 91 buffy coat


title: cardiomyocytes 5 day after proton radiation exposure rep1


title: cardiomyocytes 5 day after proton radiation exposure rep2


title: diseased (E_BC_CA_078_5935294029.RO6C01)

description: genomic DNA from buffy coat

source_name: 85 buffy coat


title: cardiomyocytes 3 day after proton radiation exposure rep3

source_name: left ventricular murine cardiomyocytes to 90 cGy,  1 GeV proton (1H) 3 day after exposure


title: diseased (E_BC_CA_082_5935294029.RO4C02)

description: genomic DNA from buffy coat

source_name: 87 buffy coat


title: cardiomyocytes 3 day after proton radiation exposure rep2


title: diseased (E_BC_CA_091_5935294033.RO2C02)

description: genomic DNA from buffy coat

source_name: 92 buffy coat


title: diseased (E_BC_CA_084_5935294033.RO1C01)

description: genomic DNA from buffy coat

source_name: 88 buffy coat


title: cardiomyocytes 1 day after proton radiation exposure rep1

source_name: left ventricular murine cardiomyocytes to 90 cGy,  1 GeV proton (1H) 1 day after exposure


source_name: left ventricular murine cardiomyocytes 3 days after sham radiation exposure


title: cardiomyocytes 1 day after sham radiation exposure rep2

source_name: left ventricular murine cardiomyocytes 1 day after sham radiation exposure


title: cardiomyocytes 1 day after proton radiation exposure rep2


title: diseased (E_BC_CA_070_5957881012.RO4C01)

description: genomic DNA from buffy coat

source_name: 81 buffy coat


title: cardiomyocytes 3 day after proton radiation exposure rep1


title: Cervical swab_HPV16-persistent_with progression_rep20

city: Tuebingen

first: Frank

last: Stubenrauch

address: Elfriede-Aulhorn-Str. 6

department: Institute for Medical Virology

country: Germany

institute: University Hospital Tuebingen

hyb_protocol: Performed following standard Affymetrix procedures.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and condensed with GC-RMA CEL condensor 1.0. The logarithmized gene expression values from the microarray analyses were normalized by locally weighted scatterplot smoothing (LOWESS) [26] and by shifting the medians of each experiment to a value of 10,000. In order to eliminate possible batch effects, expression values were divided by the medians of the corresponding HPV-negative control group.

source_name: Cervical swab, HPV-16 persisters with progression

label_protocol: RNA amplification and hybridization to Affymetrix Human Genome U133 Plus 2.0 arrays were performed following standard Affymetrix procedures.

extract_protocol: RNA was extracted from cervical swab samples. Extraction was done using the RNeasy Mini Kit (Qiagen, Hilden, Germany), and the RNA was stored at –80°C. RNA quality was determined using an Agilent Bioanalyzer 2100.

value: cervix

tag: category (0 = normal, 1 = hpv without progression, 2 = hpv with progression)

tag: hpv status

value: moderate dysplasia


title: cardiomyocytes 28 day after iron radiation exposure rep2

source_name: left ventricular murine cardiomyocytes to 15 cGy,  1 GeV/nucleon (n) iron (56Fe) particles 28 days after exposure


title: diseased (E_BC_CA_073_5935294029.RO1C01)

description: genomic DNA from buffy coat

source_name: 83 buffy coat


title: diseased (E_BC_CA_075_5935294029.RO3C01)

description: genomic DNA from buffy coat

source_name: 84 buffy coat


title: diseased (E_BC_CA_072_5935294032.RO5C02)

description: genomic DNA from buffy coat

source_name: 82 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep19

scan_protocol: Performed following standard Affymetrix procedures.

value: severe dysplasia


title: diseased (E_BC_CA_065_5935294032.RO3C01)

description: genomic DNA from buffy coat

source_name: 79 buffy coat


title: diseased (E_BC_CA_058_5957881015.RO1C02)

description: genomic DNA from buffy coat

source_name: 76 buffy coat


title: diseased (E_BC_CA_064_5957881012.RO2C01)

description: genomic DNA from buffy coat

source_name: 78 buffy coat


title: diseased (E_BC_CA_067_5935294032.RO5C01)

description: genomic DNA from buffy coat

source_name: 80 buffy coat


title: diseased (E_BC_CA_062_5957881009.RO5C02)

description: genomic DNA from buffy coat

source_name: 77 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep17

value: CIS


title: diseased (E_BC_CA_054_5957881015.RO3C01)

description: genomic DNA from buffy coat

source_name: 74 buffy coat


title: diseased (E_BC_CA_046_5957881001.RO6C01)

description: genomic DNA from buffy coat

source_name: 70 buffy coat


title: cardiomyocytes 14 day after iron radiation exposure rep1

source_name: left ventricular murine cardiomyocytes to 15 cGy,  1 GeV/nucleon (n) iron (56Fe) particles 14 days after exposure


title: diseased (E_BC_CA_051_5957881009.RO3C02)

description: genomic DNA from buffy coat

source_name: 73 buffy coat


title: cardiomyocytes 7 day after iron radiation exposure rep1

source_name: left ventricular murine cardiomyocytes to 15 cGy,  1 GeV/nucleon (n) iron (56Fe) particles 7 days after exposure


title: cardiomyocytes 14 day after iron radiation exposure rep2


title: Cervical swab_HPV16-persistent_with progression_rep16


title: Cervical swab_HPV16-persistent_with progression_rep15


title: diseased (E_BC_CA_055_5957881015.RO4C01)

description: genomic DNA from buffy coat

source_name: 75 buffy coat


title: diseased (E_BC_CA_048_5957881001.RO2C02)

description: genomic DNA from buffy coat

source_name: 71 buffy coat


title: diseased (E_BC_CA_044_5957881001.RO4C01)

description: genomic DNA from buffy coat

source_name: 69 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep14

source_name: Cervical swab, HPV-16 persisters with progression


title: cardiomyocytes 28 day after iron radiation exposure rep1

source_name: left ventricular murine cardiomyocytes to 15 cGy,  1 GeV/nucleon (n) iron (56Fe) particles 28 days after exposure


title: Cervical swab_HPV16-persistent_without progression_rep10

source_name: Cervical swab, HPV-16 persisters without progression


title: cardiomyocytes 3 day after iron radiation exposure rep1

source_name: left ventricular murine cardiomyocytes to 15 cGy,  1 GeV/nucleon (n) iron (56Fe) particles 3 days after exposure


title: cardiomyocytes 1 day after iron radiation exposure rep3

source_name: left ventricular murine cardiomyocytes to 15 cGy,  1 GeV/nucleon (n) iron (56Fe) particles 1 day after exposure


title: Cervical swab_HPV16-persistent_with progression_rep12


title: cardiomyocytes 3 day after iron radiation exposure rep3


title: cardiomyocytes 3 day after iron radiation exposure rep2


title: diseased (E_BC_CA_042_5957881009.RO4C01)

description: genomic DNA from buffy coat

source_name: 68 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep13


title: Cervical swab_HPV16-persistent_with progression_rep18


title: diseased (E_BC_CA_033_5957881002.RO5C01)

description: genomic DNA from buffy coat

source_name: 65 buffy coat


title: diseased (E_BC_CA_032_5957881002.RO3C01)

description: genomic DNA from buffy coat

source_name: 64 buffy coat


title: cardiomyocytes 1 day after iron radiation exposure rep2


title: diseased (E_BC_CA_049_5957881009.RO1C02)

description: genomic DNA from buffy coat

source_name: 72 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep11

value: cancer


title: diseased (E_BC_CA_027_5935534023.RO3C02)

description: genomic DNA from buffy coat

source_name: 62 buffy coat


title: WT_d144-02O

city: Neuherberg

first: Philipp

last: Bruns

address: Ingolstädter Landstr. 1

department: ICB

institute: Helmholtz Zentrum München

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was processed with Bioconductor/R using the affy package, rma normalization and nsFilter for filtering out non-significantly expressed probes.

source_name: wild-type pancreas, d14 after caerulein injection

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Tissues were processed according to instructions provided in the RNeasy mini kit (Qiagen, Venlo, Netherlands) using 50 µl of β-mercaptopurinol in 1 ml RLT Buffer. The extracted RNA was eluted in purified water and shock-frozen in liquid nitrogen. Samples were stored at -80°C.

treatment_protocol: Acute pancreatitis in WT and KrasG12D mice was induced at eight to nine weeks of age by administering caerulein according to the previously described “consecutive” protocol (14). Control animals were treated with 0.9% sodium chloride. The last injection was considered “hour 0” or “day 0”. Mice were sacrificed at several time points between 3h and 14 days after injections

tag: tissue type

value: pancreas

value: wild-type

tag: time


title: cardiomyocytes 1 day after sham radiation exposure rep1

source_name: left ventricular murine cardiomyocytes 1 day after sham radiation exposure

tag: age


title: Cervical swab_HPV16-persistent_with progression_rep10


title: diseased (E_BC_CA_038_5957881002.RO4C02)

description: genomic DNA from buffy coat

source_name: 67 buffy coat


title: diseased (E_BC_CA_024_5935534023.RO6C01)

description: genomic DNA from buffy coat

source_name: 60 buffy coat


title: WT_d142-02P

tag: genotype/variation


title: cardiomyocytes 1 day after iron radiation exposure rep1

tag: strain


title: WT_d142-01O


title: WT_d74-307-04F

source_name: wild-type pancreas, d7 after caerulein injection


title: WT_d141-01P


title: Cervical swab_HPV16-persistent_with progression_rep7


title: Cervical swab_HPV16-persistent_with progression_rep8


title: diseased (E_BC_CA_026_5935534023.RO2C02)

description: genomic DNA from buffy coat

source_name: 61 buffy coat


title: Cervical swab_HPV16-persistent_without progression_rep9


title: Cervical swab_HPV16-persistent_without progression_rep8


title: diseased (E_BC_CA_030_5957881002.RO1C01)

description: genomic DNA from buffy coat

source_name: 63 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep9

source_name: Cervical swab, HPV-16 persisters with progression


title: cardiomyocytes 7 day after iron radiation exposure rep2

source_name: left ventricular murine cardiomyocytes to 15 cGy,  1 GeV/nucleon (n) iron (56Fe) particles 7 days after exposure


title: WT_d71-307-07F


title: Cervical swab_HPV16-persistent_without progression_rep7

source_name: Cervical swab, HPV-16 persisters without progression


title: WT_d73-307-05F


title: WT_d54-41C

source_name: wild-type pancreas, d5 after caerulein injection


title: diseased (E_BC_CA_022_5935534023.RO4C01)

description: genomic DNA from buffy coat

source_name: 59 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep6


title: WT_d52-07O


title: diseased (E_BC_CA_035_5957881002.RO1C02)

description: genomic DNA from buffy coat

source_name: 66 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep5


title: diseased (E_BC_CA_013_5935534033.RO1C02)

description: genomic DNA from buffy coat

source_name: 55 buffy coat


title: diseased (E_BC_CA_018_5935534033.RO6C02)

description: genomic DNA from buffy coat

source_name: 57 buffy coat


title: WT_d53-40C


title: WT_d51-06O


title: diseased (E_BC_CA_019_5935534023.RO1C01)

description: genomic DNA from buffy coat

source_name: 58 buffy coat


title: diseased (E_BC_CA_011_5935534033.RO4C01)

description: genomic DNA from buffy coat

source_name: 54 buffy coat


title: Cervical swab_HPV16-persistent_without progression_rep6


title: WT_96h4-38C

source_name: wild-type pancreas, 96h after caerulein injection


title: Cervical swab_normal_rep11

source_name: Cervical swab, Normal (no HPV and no-disease in follow-up)


title: WT_84h4-27A

source_name: wild-type pancreas, 84h after caerulein injection


title: diseased (E_BC_CA_009_5935534033.RO2C01)

description: genomic DNA from buffy coat

source_name: 53 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep4


title: Cervical swab_HPV16-persistent_without progression_rep5


title: diseased (E_BC_CA_004_5935534021.RO3C02)

description: genomic DNA from buffy coat

source_name: 50 buffy coat


title: Cervical swab_normal_rep9


title: WT_96h3-37C


title: WT_96h2-36C


title: WT_84h2-25A


title: Cervical swab_normal_rep10


title: diseased (E_BC_CA_006_5935534021.RO5C02)

description: genomic DNA from buffy coat

source_name: 51 buffy coat


title: WT_84h3-26A


title: Cervical swab_normal_rep7


title: Cervical swab_normal_rep6


title: Cervical swab_HPV16-persistent_without progression_rep4


title: WT_72h2-130210-06P

source_name: wild-type pancreas, 72h after caerulein injection


title: Cervical swab_normal_rep8


title: normal (E_BC_CO_097_5935294023.RO2C01)

description: genomic DNA from buffy coat

source_name: 47 buffy coat

value: normal (control)


title: WT_72h2-05O


title: diseased (E_BC_CA_015_5935534033.RO3C02)

description: genomic DNA from buffy coat

source_name: 56 buffy coat


title: Cervical swab_HPV16-persistent_with progression_rep3

source_name: Cervical swab, HPV-16 persisters with progression


title: normal (E_BC_CO_096_5935294023.RO1C01)

description: genomic DNA from buffy coat

source_name: 46 buffy coat


title: WT_72h1-130210-05P


title: WT_72h1-31C


title: diseased (E_BC_CA_002_5935534021.RO6C01)

description: genomic DNA from buffy coat

source_name: 49 buffy coat


title: Cervical swab_normal_rep5


title: Cervical swab_HPV16-persistent_with progression_rep2


title: WT_60h2-19A

source_name: wild-type pancreas, 60h after caerulein injection


title: WT_60h3-20A


title: Cervical swab_HPV16-persistent_without progression_rep3

source_name: Cervical swab, HPV-16 persisters without progression


title: WT_48h3-29C

source_name: wild-type pancreas, 48h after caerulein injection


title: Cervical swab_HPV16-persistent_without progression_rep2


title: Cervical swab_HPV16-persistent_with progression_rep1


title: Cervical swab_HPV16-persistent_without progression_rep1


title: normal (E_BC_CO_087_5957881009.RO6C02)

description: genomic DNA from buffy coat

source_name: 42 buffy coat


title: normal (E_BC_CO_100_5935294023.RO6C01)

description: genomic DNA from buffy coat

source_name: 48 buffy coat


title: WT_60h4-21A


title: normal (E_BC_CO_093_5935294033.RO4C02)

description: genomic DNA from buffy coat

source_name: 45 buffy coat


title: Cervical swab_normal_rep4

source_name: Cervical swab, Normal (no HPV and no-disease in follow-up)


title: normal (E_BC_CO_092_5935294033.RO3C02)

description: genomic DNA from buffy coat

source_name: 44 buffy coat


title: WT_48h1-03O


title: normal (E_BC_CO_086_5935294033.RO3C01)

description: genomic DNA from buffy coat

source_name: 41 buffy coat


title: Cervical swab_normal_rep3


title: normal (E_BC_CO_090_5935294033.RO1C02)

description: genomic DNA from buffy coat

source_name: 43 buffy coat


title: WT_36h4-15A

source_name: wild-type pancreas, 36h after caerulein injection


title: WT_48h1-27C


title: Cervical swab_normal_rep1


title: normal (E_BC_CO_077_5935294029.RO5C01)

description: genomic DNA from buffy coat

source_name: 38 buffy coat


title: normal (E_BC_CO_081_5935294029.RO3C02)

description: genomic DNA from buffy coat

source_name: 39 buffy coat


title: WT_36h3-14A


title: WT_24h4-158-01F

source_name: wild-type pancreas, 24h after caerulein injection


title: normal (E_BC_CO_074_5935294029.RO2C01)

description: genomic DNA from buffy coat

source_name: 36 buffy coat


title: Volunteer_10_rechallenge_2

city: Copenhagen N

first: Atul

last: Anand

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Department of Pathology

country: Denmark

institute: Rigshospitalet

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45 degrees celsius on Affymetrix Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Probe cell intensity data was analyzed in the Expression Console™ software application (Affymetrix® 2013) using the RMA algorithm to create CHP files. The RMA workflow includes quantile normalization and general background correction.

source_name: Inner upper-arm

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3´ IVT Express Kit, 2008-2010 - Revision 8, Affymetrix).

extract_protocol: Total RNA was purified and extracted with the RNeasy Micro Kit according to the manufacturers instructions.

treatment_protocol: Punch biopsies were snap-frozen in liquid nitrogen followed by sample storage in freezer (-80 degree celsius).

value: 4 mm skin sample

tag: volunteer id

tag: protocol


title: WT_36h2-13A


title: Volunteer_10_rechallenge_3


title: WT_24h3-158-02F


title: Volunteer_10_rechallenge_4


title: normal (E_BC_CO_076_5957881012.RO1C02)

description: genomic DNA from buffy coat

source_name: 37 buffy coat


title: normal (E_BC_CO_068_5957881012.RO3C01)

description: genomic DNA from buffy coat

source_name: 33 buffy coat


title: diseased (E_BC_CA_008_5935534033.RO1C01)

description: genomic DNA from buffy coat

source_name: 52 buffy coat


title: Cervical swab_normal_rep2


title: normal (E_BC_CO_069_5935294032.RO1C02)

description: genomic DNA from buffy coat

source_name: 34 buffy coat


title: normal (E_BC_CO_071_5935294032.RO4C02)

description: genomic DNA from buffy coat

source_name: 35 buffy coat


title: WT_12h3-09A

source_name: wild-type pancreas, 12h after caerulein injection


title: WT_24h2-158-03F


title: normal (E_BC_CO_066_5935294032.RO4C01)

description: genomic DNA from buffy coat

source_name: 32 buffy coat


title: Volunteer_9_rechallenge_4


title: WT_12h2-08A


title: Volunteer_9_rechallenge_1


title: normal (E_BC_CO_083_5957881009.RO6C01)

description: genomic DNA from buffy coat

source_name: 40 buffy coat


title: Volunteer_10_rechallenge_1


title: normal (E_BC_CO_057_5957881015.RO6C01)

description: genomic DNA from buffy coat

source_name: 28 buffy coat


title: Volunteer_10_vehicle_control


title: WT_03h3-05A

source_name: wild-type pancreas, 3h after caerulein injection


title: WT_03h2-23C


title: WT_03h1-04A


title: Volunteer_9_rechallenge_3


title: Volunteer_9_rechallenge_2


title: Volunteer_9_initial_elicitation_challenge


title: normal (E_BC_CO_056_5957881015.RO5C01)

description: genomic DNA from buffy coat

source_name: 27 buffy coat


title: normal (E_BC_CO_059_5957881015.RO2C02)

description: genomic DNA from buffy coat

source_name: 29 buffy coat


title: normal (E_BC_CO_052_5957881015.RO1C01)

description: genomic DNA from buffy coat

source_name: 25 buffy coat


title: normal (E_BC_CO_063_5935294032.RO1C01)

description: genomic DNA from buffy coat

source_name: 31 buffy coat


title: WT_00h3-02A

source_name: wild-type pancreas, NaCl-treated control

value: NaCl-treated control


title: Volunteer_9_vehicle_control


title: normal (E_BC_CO_045_5957881001.RO5C01)

description: genomic DNA from buffy coat

source_name: 22 buffy coat


title: normal (E_BC_CO_053_5957881015.RO2C01)

description: genomic DNA from buffy coat

source_name: 26 buffy coat


title: WT_00h2-05R


title: WT_00h1-04R


title: WT_00h2-01A


title: normal (E_BC_CO_043_5957881001.RO3C01)

description: genomic DNA from buffy coat

source_name: 21 buffy coat


title: Volunteer_8_rechallenge_4

source_name: Inner upper-arm


title: Volunteer_8_rechallenge_3


title: Volunteer_8_rechallenge_1


title: P48Kras_d143-307-20G

source_name: KrasG12D pancreas, d14 after caerulein injection


title: normal (E_BC_CO_047_5957881001.RO1C02)

description: genomic DNA from buffy coat

source_name: 23 buffy coat


title: P48Kras_d142-307-19G


title: Volunteer_8_rechallenge_2


title: normal (E_BC_CO_041_5957881001.RO1C01)

description: genomic DNA from buffy coat

source_name: 20 buffy coat


title: normal (E_BC_CO_061_5957881015.RO5C02)

description: genomic DNA from buffy coat

source_name: 30 buffy coat


title: Volunteer_8_initial_elicitation_challenge


title: normal (E_BC_CO_050_5957881001.RO5C02)

description: genomic DNA from buffy coat

source_name: 24 buffy coat


title: P48Kras_d141-137-17G


title: normal (E_BC_CO_037_5957881002.RO3C02)

description: genomic DNA from buffy coat

source_name: 19 buffy coat


title: Volunteer_8_vehicle_control


title: normal (E_BC_CO_036_5957881002.RO2C02)

description: genomic DNA from buffy coat

source_name: 18 buffy coat


title: normal (E_BC_CO_034_5957881002.RO6C01)

description: genomic DNA from buffy coat

source_name: 17 buffy coat


title: P48Kras_d73-307-16G

source_name: KrasG12D pancreas, d7 after caerulein injection


title: Volunteer_7_rechallenge_5


title: Volunteer_7_rechallenge_4


title: WT_12h1-07A

source_name: wild-type pancreas, 12h after caerulein injection


title: WT_00h3-06R


title: normal (E_BC_CO_029_5935534023.RO6C02)

description: genomic DNA from buffy coat

source_name: 15 buffy coat


title: Volunteer_7_rechallenge_3


title: P48Kras_84h2-35-19E

source_name: KrasG12D pancreas, 84h after caerulein injection


title: P48Kras_84h1-130210-03Q


title: normal (E_BC_CO_028_5935534023.RO4C02)

description: genomic DNA from buffy coat

source_name: 14 buffy coat


title: Volunteer_7_rechallenge_2


title: P48Kras_60h2-130210-02Q

source_name: KrasG12D pancreas, 60h after caerulein injection


title: Volunteer_7_rechallenge_1


title: normal (E_BC_CO_025_5935534023.RO1C02)

description: genomic DNA from buffy coat

source_name: 13 buffy coat


title: P48Kras_d72-37-15G


title: P48Kras_60h3-35-16E


title: Volunteer_7_initial_elicitation_challenge


title: normal (E_BC_CO_023_5935534023.RO5C01)

description: genomic DNA from buffy coat

source_name: 12 buffy coat


title: normal (E_BC_CO_021_5935534023.RO3C01)

description: genomic DNA from buffy coat

source_name: 11 buffy coat


title: P48Kras_48h1-145-14E

source_name: KrasG12D pancreas, 48h after caerulein injection


title: Volunteer_6_rechallenge_5

source_name: Inner upper-arm


title: P48Kras_60h1-07D


title: P48Kras_36h2-39-03J

source_name: KrasG12D pancreas, 36h after caerulein injection


title: Volunteer_10_initial_elicitation_challenge


title: Volunteer_7_vehicle_control


title: Volunteer_6_rechallenge_3


title: P48Kras_36h1_02J


title: Volunteer_6_rechallenge_1


title: Volunteer_6_rechallenge_4


title: P48Kras_36h1-05D


title: Volunteer_6_rechallenge_2


title: P48Kras_24h1-130210-01Q

source_name: KrasG12D pancreas, 24h after caerulein injection


title: normal (E_BC_CO_017_5935534033.RO5C02)

description: genomic DNA from buffy coat

source_name: 9 buffy coat


title: normal (E_BC_CO_031_5957881002.RO2C01)

description: genomic DNA from buffy coat

source_name: 16 buffy coat


title: Volunteer_6_initial_elicitation_challenge


title: normal (E_BC_CO_020_5935534023.RO2C01)

description: genomic DNA from buffy coat

source_name: 10 buffy coat


title: normal (E_BC_CO_014_5935534033.RO2C02)

description: genomic DNA from buffy coat

source_name: 7 buffy coat


title: Volunteer_6_vehicle_control


title: normal (E_BC_CO_012_5935534033.RO5C01)

description: genomic DNA from buffy coat

source_name: 6 buffy coat


title: P48Kras_24h2-18-14G


title: normal (E_BC_CO_007_5935534021.RO6C02)

description: genomic DNA from buffy coat

source_name: 4 buffy coat


title: Volunteer_5_rechallenge_5


title: P48Kras_24h1-18-13G


title: normal (E_BC_CO_005_5935534021.RO4C02)

description: genomic DNA from buffy coat

source_name: 3 buffy coat


title: P48Kras_24h1-145-09E


title: Volunteer_5_rechallenge_3


title: P48Kras_12h1-39-01J

source_name: KrasG12D pancreas, 12h after caerulein injection


title: normal (E_BC_CO_001_5935534021.RO5C01)

description: genomic DNA from buffy coat

source_name: 1 buffy coat


title: normal (E_BC_CO_003_5935534021.RO2C02)

description: genomic DNA from buffy coat

source_name: 2 buffy coat


title: normal (E_BC_CO_010_5935534033.RO3C01)

description: genomic DNA from buffy coat

source_name: 5 buffy coat


title: Volunteer_5_rechallenge_1


title: P48Kras_03h2-35-04E

source_name: KrasG12D pancreas, 3h after caerulein injection


title: genomic DNA from peripheral blood 109

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

description: peripheral blood given by child born SGA

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

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

data_processing: GenomeStudio software

source_name: peripheral blood 109

extract_protocol: genomic DNA was extracted and purified from peripheral blood samples using Gentra Puregene Blood Kit according to standard instructions

value: SGA


title: Volunteer_5_rechallenge_2


title: genomic DNA from peripheral blood 106

source_name: peripheral blood 106


title: genomic DNA from peripheral blood 110

source_name: peripheral blood 110


title: genomic DNA from peripheral blood 107

source_name: peripheral blood 107


title: P48Kras_12h2-138-12G


title: genomic DNA from peripheral blood 105

source_name: peripheral blood 105


title: normal (E_BC_CO_016_5935534033.RO4C02)

description: genomic DNA from buffy coat

source_name: 8 buffy coat

value: blood


title: Volunteer_4_rechallenge_4

source_name: Inner upper-arm


title: Volunteer_5_initial_elicitation_challenge


title: Volunteer_4_initial_elicitation_challenge


title: P48Kras_00h4-04S

source_name: KrasG12D pancreas, NaCl-treated control


title: P48Kras_03h2-145-06E


title: P48Kras_12h1-138-11G


title: genomic DNA from peripheral blood 103

source_name: peripheral blood 103


title: Volunteer_5_vehicle_control


title: genomic DNA from peripheral blood 108

source_name: peripheral blood 108


title: Volunteer_5_rechallenge_4


title: P48Kras_03h1-145-05E


title: Volunteer_4_rechallenge_3


title: P48Kras_03h1-02D


title: Volunteer_4_rechallenge_1


title: genomic DNA from peripheral blood 104

source_name: peripheral blood 104


title: P48Kras_00h3-03S


title: P48Kras_00h1-01S


title: Volunteer_4_vehicle_control


title: Volunteer_4_rechallenge_2


title: Islet_Pax4R121W/rtTA_-DOX_ Rep1

city: Seville

first: Benoit

middle: Raymond

last: Gauthier

state: Seville

address: Americo Vespucio Avenue

department: Stem Cells

country: Spain

institute: Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)

description: The mouse presented healthy appearance

hyb_protocol: Following fragmentation, 5.5 ug of single-stranded cDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 1,0 ST Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix GCOS software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package of R/Bioconductor project.

source_name: Primary isolated islets from Pax4R121W/rtTA mice untreated

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA Labeling Protocol (The Ambion WT Expression kit for Affymetrix GeneChip® Whole Transcript Expression Arrays, Life Technologies Corporation, 2009).

growth_protocol: Standard feeding

extract_protocol: RNA from approximatelly 200 islets per replicate was isolated using the RNAesay micro kit according to the manufacturer´s protocol (Qiagen).

treatment_protocol: Animals were maintained under standard conditions

value: 2 months old

tag: treatment

value: untreated

value: Primary isolated islets


title: Islet_Pax4R121W/rtTA_-DOX_ Rep3

description: The mouse presented healthy appearance


title: Islet_Pax4R121W/rtTA_+DOX_ Rep3

description: The mouse presented healthy appearance

source_name: Primary isolated islets from Pax4R121W/rtTA mice treated with DOX

value: DOX


title: genomic DNA from peripheral blood 102

source_name: peripheral blood 102


title: Volunteer_3_rechallenge_2


title: Volunteer_3_initial_elicitation_challenge


title: Volunteer_3_rechallenge_4


title: Islet_Pax4R121W/rtTA_-DOX_ Rep2

description: The mouse presented healthy appearance


title: Islet_Pax4R121W/rtTA_+DOX_ Rep2

description: The mouse presented healthy appearance


title: Volunteer_3_rechallenge_3


title: Islet_Pax4R121W/rtTA_+DOX_ Rep1

description: The mouse presented healthy appearance


title: Volunteer_3_rechallenge_1


title: Volunteer_3_vehicle_control


title: Islet_Pax4/rtTA_-DOX_ Rep3

description: The mouse presented healthy appearance

source_name: Primary isolated islets from Pax4/rtTA mice untreated


title: genomic DNA from peripheral blood 97

source_name: peripheral blood 97


title: P48Kras_00h2-02S


title: genomic DNA from peripheral blood 100

source_name: peripheral blood 100


title: Volunteer_2_rechallenge_4


title: Volunteer_2_rechallenge_5


title: genomic DNA from peripheral blood 93

source_name: peripheral blood 93


title: Islet_Pax4/rtTA_-DOX_ Rep2

description: The mouse presented healthy appearance


title: Islet_Pax4/rtTA_-DOX_ Rep1

description: The mouse presented healthy appearance


title: genomic DNA from peripheral blood 94

source_name: peripheral blood 94


title: Islet_Pax4/rtTA_+DOX_ Rep1

description: The mouse presented healthy appearance

source_name: Primary isolated islets from Pax4/rtTA mice treated with DOX


title: genomic DNA from peripheral blood 96

source_name: peripheral blood 96


title: Islet_Pax4/rtTA_+DOX_ Rep3

description: The mouse presented healthy appearance


title: Volunteer_2_rechallenge_3


title: Islet_Pax4/rtTA_+DOX_ Rep2

description: The mouse presented healthy appearance


title: Volunteer_2_initial_elicitation_challenge


title: genomic DNA from peripheral blood 98

source_name: peripheral blood 98


title: Volunteer_2_rechallenge_2


title: genomic DNA from peripheral blood 101

source_name: peripheral blood 101


title: genomic DNA from peripheral blood 92

source_name: peripheral blood 92


title: genomic DNA from peripheral blood 95

source_name: peripheral blood 95


title: Volunteer_2_rechallenge_1

source_name: Inner upper-arm


title: Mouse 59

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

label: Biotin

source_name: adeno-sh Grb14 injection, study at d7

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

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

treatment_protocol: in vivo adenovirus injection

value: liver

value: adeno-sh Grb14 injection


title: genomic DNA from peripheral blood 99

source_name: peripheral blood 99


title: Volunteer_2_vehicle_control


title: Mouse 60


title: genomic DNA from peripheral blood 89

source_name: peripheral blood 89


title: genomic DNA from peripheral blood 91

source_name: peripheral blood 91


title: Volunteer_1_rechallenge_5


title: Mouse 57


title: Mouse 56


title: genomic DNA from peripheral blood 90

source_name: peripheral blood 90


title: genomic DNA from peripheral blood 86

source_name: peripheral blood 86


title: Volunteer_1_rechallenge_3


title: Volunteer_1_rechallenge_4


title: Mouse 58


title: genomic DNA from peripheral blood 88

source_name: peripheral blood 88


title: Volunteer_1_rechallenge_1


title: genomic DNA from peripheral blood 83

source_name: peripheral blood 83


title: Mouse 54

source_name: adeno-sh scramble injection, study at d7

value: adeno-sh scramble injection


title: Volunteer_1_initial_elicitation_challenge


title: Mouse 55


title: Volunteer_1_rechallenge_2


title: Mouse 53


title: genomic DNA from peripheral blood 87

source_name: peripheral blood 87


title: genomic DNA from peripheral blood 82

source_name: peripheral blood 82


title: Mouse 51


title: Mouse 52


title: 24h after 5uM cocaine, biological rep 2

city: Barcelona

first: Noelia

last: Fernandez-Castillo

address: Avda Diagonal 643. Edifici Prevosti 3r pis.

department: Genetics

institute: Universitat de Barcelona

description: gene expression data of differentiated SH-SY5Y 24 hours after a 30-min exposure to 5uM cocaine (non-treated control)

hyb_protocol: Hybridization was performed according to manufacturer's protocol for GeneChip® Human Genome U133 Plus 2.0 Array

scan_protocol: GeneChips were scanned using the GenePix4000B scanner (Molecular Devices) and raw data were obtained using the GenePix Pro 4.0 (Molecular Devices)   and GCOS softwares (Affymetrix).

data_processing: Data was processed using Bioconductor. Background correction, normalization and summarization were performed using the background method, RMA and median polish, respectively. Class comparison was performed using limma package and FDR 10% was used for multiple testing correction

source_name: SH-SY5Y 24 hours after 30 min exposure of 5uM cocaine

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: SH-SY5Y were differentiated with 10 uM of retinoic acid (RA) during 7 days. After differentiation, the medium was replaced with medium without RA for 24 hours before cocaine exposure

extract_protocol: cells were trypsinized, the pellets were homogenized using Qiashredder (Qiagen) and total RNA was isolated using the RNeasy Mini Kit (Qiagen).

treatment_protocol: cells were exposed to cocaine (0, 1 or 5 uM) during 30 min and retrieved at 6 or 24 hours after exposure.

tag: cell line

value: SH-SY5Y differentiated with RA


title: Volunteer_1_vehicle_control

tag: tissue


title: 24h after 5uM cocaine, biological rep 3

value: 24 hours after a 30-min exposure to 5uM cocaine (non-treated control)


title: genomic DNA from peripheral blood 81

source_name: peripheral blood 81


title: genomic DNA from peripheral blood 79

source_name: peripheral blood 79


title: 24h after 1uM cocaine, biological rep 3

description: gene expression data of differentiated SH-SY5Y 24 hours after a 30-min exposure to 1uM cocaine

source_name: SH-SY5Y 24 hours after 30 min exposure of 1uM cocaine


title: 24h after 5uM cocaine, biological rep 1


title: Mouse 50


title: genomic DNA from peripheral blood 76

source_name: peripheral blood 76


title: genomic DNA from peripheral blood 80

source_name: peripheral blood 80


title: genomic DNA from peripheral blood 77

source_name: peripheral blood 77


title: genomic DNA from peripheral blood 78

source_name: peripheral blood 78


title: 24h after 1uM cocaine, biological rep 1

value: 24 hours after a 30-min exposure to 1uM cocaine


title: 24h after 1uM cocaine, biological rep 2


title: MSC IV rep 2

city: Rehovot

first: Sarit

last: Levin

address: 234 Herzel st.

department: Department of Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G plus scanner

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

source_name: Bone marrow mesenchymal stromal cells

growth_protocol: BM MSCs P16-17 were grown in murine MesenCult Basal Media supplemented with 20% murine mesenchymal supplement (StemCell Technologies, Vancouver, Canada), 60 µg/mL penicillin, 100 µg/mL streptomycin and 50 µg/mL kanamycin.

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

tag: gender

value: female


title: genomic DNA from peripheral blood 75

source_name: peripheral blood 75


title: MSC V rep 2

description: Gene expression data

hyb_protocol: According to Affymetrix standard protocols


title: 24h after 0uM cocaine, biological rep 3

description: gene expression data of differentiated SH-SY5Y 24 hours after a 30-min exposure to 0uM cocaine (non-treated control)

source_name: SH-SY5Y 24 hours after 30 min exposure of 0uM cocaine (non-treated control)


title: MSC III rep 2

description: Gene expression data

label_protocol: According to Affymetrix standard protocols


title: 24h after 0uM cocaine, biological rep 1

value: 24 hours after a 30-min exposure to 0uM cocaine (non-treated control)


title: genomic DNA from peripheral blood 74

source_name: peripheral blood 74


title: 6h after 5uM cocaine, biological rep 3

description: gene expression data of differentiated SH-SY5Y 6 hours after a 30-min exposure to 5uM cocaine (non-treated control)

source_name: SH-SY5Y 6 hours after 30 min exposure of 5uM cocaine


title: 24h after 0uM cocaine, biological rep 2


title: MSC I rep 2

description: Gene expression data


title: genomic DNA from peripheral blood 84

source_name: peripheral blood 84


title: MSC V rep 1

description: Gene expression data


title: MSC IV rep 1

description: Gene expression data


title: MSC II rep 2

description: Gene expression data


title: Mouse 49

source_name: adeno-sh scramble injection, study at d7


title: MSC III rep 1

description: Gene expression data


title: genomic DNA from peripheral blood 72

source_name: peripheral blood 72


title: MSC II rep 1

description: Gene expression data


title: 6h after 5uM cocaine, biological rep 2

value: 6 hours after a 30-min exposure to 5uM cocaine (non-treated control)


title: MSC I rep 1

description: Gene expression data


title: 786O HIF2a null, 48 hr PT2399

city: Boston

first: William

middle: G

last: Kaelin

state: MA

address: M457, 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: HIF2a null 786O cells (CRISPR) treated with PT2399 for 48 hrs

hyb_protocol: Targets were hybridized onto Human Gene 1.0ST arrays for 16hr at 45C. Genechips were washed and stained using Fluidics Station 450 using Affymetrix Hybe/Wash/Stain (cat#900720)

scan_protocol: Chips were scanned using GeneChip Scanner 3000 7G

data_processing: Data was analyzed using dChip

source_name: 786O cells HIF2a null

label_protocol: Biotinylated sense-strand DNA targets were synthesized from 100ng total RNA using the Affymetrix GeneChip WT Plus Reagent Kit (Cat#703174)

growth_protocol: HIF2a null 786O cells were cultured in DMEM (with 10% FBS and Penn/Strep) for indicated periods of time either in the presence of DMSO or PT2399

extract_protocol: Total RNA was extracted using Trizol as per the manufacturers instructions

treatment_protocol: Cells were treated with DMSO or PT2399 (2uM) for either 24hrs or 48 hrs, as indicated

tag: cell type

value: Clear Cell Renal Cell Carcinoma cells

value: HIF2a null

tag: treated with

value: 2uM PT2399 for 48 hrs


title: 786O HIF2a null, 24 hr PT2399

description: HIF2a null 786O cells (CRISPR) treated with PT2399 for 24 hrs

value: 2uM PT2399 for 24 hrs


title: 6h after 5uM cocaine, biological rep 1


title: 6h after 1uM cocaine, biological rep 3

description: gene expression data of differentiated SH-SY5Y 6 hours after a 30-min exposure to 1uM cocaine

source_name: SH-SY5Y 6 hours after 30 min exposure of 1uM cocaine


title: genomic DNA from peripheral blood 67

source_name: peripheral blood 67

tag: disease state

value: SGA


title: genomic DNA from peripheral blood 66

source_name: peripheral blood 66


title: genomic DNA from peripheral blood 71

source_name: peripheral blood 71


title: genomic DNA from peripheral blood 70

source_name: peripheral blood 70


title: genomic DNA from peripheral blood 73

source_name: peripheral blood 73


title: genomic DNA from peripheral blood 65

source_name: peripheral blood 65


title: genomic DNA from peripheral blood 68

source_name: peripheral blood 68


title: 786O HIF2a null, 48 hr DMSO

description: HIF2a null 786O cells (CRISPR) treated with DMSO for 48 hrs

value: DMSO for 48hrs


title: 6h after 0uM cocaine, biological rep 2

description: gene expression data of differentiated SH-SY5Y 6 hours after a 30-min exposure to 0uM cocaine (non-treated control)

source_name: SH-SY5Y 6 hours after 30 min exposure of 0uM cocaine (non-treated control)


title: 6h after 1uM cocaine, biological rep 2

value: 6 hours after a 30-min exposure to 1uM cocaine


title: 6h after 0uM cocaine, biological rep 3

value: 6 hours after a 30-min exposure to 0uM cocaine (non-treated control)


title: 786O HIF2a null, 24 hr DMSO

description: HIF2a null 786O cells (CRISPR) treated with DMSO for 24 hrs

value: DMSO for 24hrs


title: genomic DNA from peripheral blood 69

source_name: peripheral blood 69


title: 6h after 0uM cocaine, biological rep 1


title: genomic DNA from peripheral blood 85

source_name: peripheral blood 85


title: 6h after 1uM cocaine, biological rep 1


title: cells_no hsp70 treated_rep1

city: Hangzhou

first: Erman

last: Chen

state: Zhejiang Province

address: No.88, Jiefang road

department: Department of Orthopedics

country: China

institute: Second Affiliated Hospital, School of Medicine, Zhejiang University

description: Gene expression data from hMSCs were osteogenic induced after 3 days

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: hMSCs, no HSP70 treated, 3 days

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions.

treatment_protocol: hMSCs were induced by osteogenic differentiation medium(Cyagen Biosciences Inc, China) in an incubator at 37 ℃with 5% CO2.

value: male

value: mesenchymal stem cells


title: 786O Parental, 48 hr DMSO

description: DMSO treated cells for 48 hrs

source_name: 786O Parental cells

value: parental


title: genomic DNA from peripheral blood 63

source_name: peripheral blood 63


title: genomic DNA from peripheral blood 64

source_name: peripheral blood 64


title: cells_hsp70 treated_rep1

description: Gene expression data from hMSCs were osteogenic induced companying with hsp70 (200ng/ml)after 3 days

source_name: hMSCs, HSP70 treated, 3 days


title: genomic DNA from peripheral blood 62

source_name: peripheral blood 62


title: 786O Parental, 48 hr PT2399

description: PT2399 treated cells for 48 hrs


title: 786O Parental, 24 hr DMSO

description: DMSO treated cells for 24 hrs


title: genomic DNA from peripheral blood 61

source_name: peripheral blood 61


title: 63M_monolayer

city: Itabashi-ku, Tokyo

first: Shigehiro

last: Abe

address: 30-1 Oyaguchikami-cho

department: Oral Surgery

country: Japan

institute: Nihon University

hyb_protocol: 12.5 μg of cRNA was added to a hybridization buffer and hybridized to a GeneChip® Human Genome U133 Plus 2.0 microarray chip (Affymetrix) for 16 hr using standard protocols.

scan_protocol: The chips were washed in the GeneChip® Fluidics Station 450 (Affymetrix) and subsequently scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Raw data were obtained using Affymerrix® GeneChip® Command Console® software and analyzed using Affymetrix® Expression Console® software.

source_name: oral mucosa stromal cells, monolayer cells

label_protocol: Total RNA obtained from three patients was used for microarray analysis. First, 100 ng of total RNA was reverse transcribed into cRNA using the 3′ IVT PLUS Reagent Kit .

growth_protocol: For primary explant culture, oral mucosa tissues were cut into pieces about 2–3 mm in size. Each piece was plated on a culture dish with Isocove’s modified Dulbecco’s medium with 10% fetal bovine serum. After 3 weeks of primary outgrowth culture, Oral mucosa stromal cells (OMSCs) were detached. The cells were then seeded at a density of 2.0 × 104 cells/well on a 6-well culture plate. Enzymatically dissociated OMSCs (2 × 104 cells/well) were grown in 24-well super-hydrophilic plates  in serum-free Dulbecco’s modified Eagle’s medium (DMEM)/F12 (1:1) containing N2 supplements, 20 ng/ml of basic fibroblasts growth factor, and 20 ng/ml epidermal growth factor.

extract_protocol: Total RNA was extracted from OMSCs and oral mucosa sphere-forming cells (OMSFCs) by using an RNeasy Mini Kit.

value: oral mucosa

tag: Sex

value: Male


title: 63M_sphere

source_name: oral mucosa stromal cells, sphere-forming cells


title: NK cells LCD patient LPG-stimulated 6h, biological rep 3

city: Cambridge

first: Madeline

last: Lancaster

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

department: Cell Biology Division

institute: MRC Laboratory of Molecular Biology

description:
Gene expression data from Human NK cells  LPG-stimulated from DCL patient
DCL LPG 3

hyb_protocol: The labeled cDNA product was heated to 95°C and hybridized to the Human Gene 1.0 ST microarray (Affymetrix Inc.) for 17 + 1 hr at 45°C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

scan_protocol: A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature

data_processing: The statistical analyses were performed with R 2.11.0. All samples were normalized and summarized by Robust Multiarray Average (RMA). Times series analysis was carried out using bioconductor timecourse package. Differential expression analysis between NK cells non stimulated and LPG-stimulated was performed using LIMMA. The Benjamini and Hochberg multiple hypothesis testing correction procedure was applied to control the false discovery rate (FDR). Data were filtered to include only genes that had a 2-fold-change difference between the groups and an adjusted p value of 0.05

source_name: Human NK cells from DCL patient LPG-stimulated 20μg/mL 6 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

growth_protocol: All cell cultures were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) in a 37 C humidified incubator containing 5% CO2

extract_protocol: RNA was isolated from human NK cells using TRIZOL (Invitrogen) according to the manufacturer´s directions

treatment_protocol: NK cells were non stimulated or stimulated with LPG 20μg/mL 6 hours then were harvested and washed with cold PBS three times. Cells were resuspended on TRIZOL reagent.

value: DCL

value: Human NK cells from PBMC

value: Leishmania mexicana LPG 20μg/mL 6 hours


title: genomic DNA from peripheral blood 60

source_name: peripheral blood 60


title: genomic DNA from peripheral blood 59

source_name: peripheral blood 59


title: NK cells LCD patient LPG-stimulated 6h, biological rep 2

description:
Gene expression data from Human NK cells  LPG-stimulated from DCL patient
DCL LPG 2


title: genomic DNA from peripheral blood 58

source_name: peripheral blood 58


title: NK cells LCD patient non stimulated, biological rep 3

description:
Gene expression data from Human NK cells non stimulated from DCL patient
DCL NS 3

source_name: Human NK cells from DCL patient non stimulated

value: non stimulated


title: genomic DNA from peripheral blood 56

source_name: peripheral blood 56


title: 42F_monolayer

value: Female


title: NK cells LCD patient LPG-stimulated 6h, biological rep 1

description:
Gene expression data from Human NK cells  LPG-stimulated from DCL patient
DCL LPG 1


title: 42F_sphere


title: 786O Parental, 24 hr PT2399

description: PT2399 treated cells for 24 hrs

value: Clear Cell Renal Cell Carcinoma cells


title: NK cells LCD patient non stimulated, biological rep 1

description:
Gene expression data from Human NK cells non stimulated from DCL patient
DCL NS 1


title: NK cells LCL patient LPG-stimulated 6h, biological rep 2

description:
Gene expression data from Human NK cells LPG-stimulated from LCL patient
LCL LPG 2

source_name: Human NK cells from LCL patient LPG-stimulated 20μg/mL 6 hours

value: LCL


title: genomic DNA from peripheral blood 52

description: peripheral blood given by child born SGA

source_name: peripheral blood 52

value: SGA


title: 20F_monolayer


title: Wild type Hmel, rep2

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description:
WT_2
Wild-type
Gene expression from wild type human melanocytes- Hmel cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Microarray data was normalized by using RMA normalization with the Bioconductor affy package. Data was analyzed using the LIMMA Bioconductor package.

source_name: Wild type Hmel

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were maintained in standard tissue culture conditions (5% CO2 , 37oC).

extract_protocol: RNA was isolated using the RNeasy Kit per manufacturer's instructions. cDNA was prepared using SuperScript III using the manufacturer's instructions. qPCR were performed using SybrGreener (Invitrogen) and Stratagene instrument.

treatment_protocol: Cells were infected with pLenti6.3-RNF2WT or pLenti6.3-GFP lentiviruses, selected with blasticidine (5mg/ml) till control uninfected cells were dead.

value: immortalized melanocytes

tag: overexpression

value: GFP


title: RNF2-overexpressed Hmel, rep2

description:
RNF2_2
RNF2-overexpressed
Gene expression from RNF2-overexpressed human melanocytes - Hmel cells.

source_name: RNF2 overexpressed Hmel


title: NK cells LCD patient non stimulated, biological rep 2

description:
Gene expression data from Human NK cells non stimulated from DCL patient
DCL NS 2


title: Wild type Hmel, rep1

description:
WT_1
Wild-type
Gene expression from wild type human melanocytes- Hmel cells.


title: 20F_sphere


title: genomic DNA from peripheral blood 53

source_name: peripheral blood 53


title: genomic DNA from peripheral blood 57

source_name: peripheral blood 57


title: genomic DNA from peripheral blood 55

source_name: peripheral blood 55


title: NK cells LCL patient non stimulated, biological rep 2

description:
Gene expression data from Human NK cells non stimulated from LCL patient
LCL NS 2

source_name: Human NK cells from LCL patient non stimulated


title: NK cells control LPG-stimulated 6h, biological rep 4

description:
Gene expression data from Human NK cells LPG-stimulated from control
Control LPG 4

source_name: Human NK cells from control LPG-stimulated 20μg/mL 6 hours

value: control


title: genomic DNA from peripheral blood 54

source_name: peripheral blood 54


title: NK cells LCL patient LPG-stimulated 6h, biological rep 1

description:
Gene expression data from Human NK cells LPG-stimulated from LCL patient
LCL LPG 1


title: genomic DNA from peripheral blood 50

source_name: peripheral blood 50


title: NK cells LCL patient non stimulated, biological rep 1

description:
Gene expression data from Human NK cells non stimulated from LCL patient
LCL NS 1


title: NK cells control LPG-stimulated 6h, biological rep 3

description:
Gene expression data from Human NK cells LPG-stimulated from control
Control LPG 3


title: SW620-LATS2

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

description: Gene expression data in SW620 infected with full length LATS2 virus

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix human Genome 133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

source_name: Full length LATS2 overexpression

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA ( Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Cells were grown in humidified 5% CO2 incubator in DMEM supplemented with 10% FBS

extract_protocol: Rneasy kit (Qiagen) extraction of total RNA was performed according to the manufacture's protocol

value: colorectal cancer

value: full length LATS2


title: NK cells control LPG-stimulated 6h, biological rep 1

description:
Gene expression data from Human NK cells LPG-stimulated from control
Control LPG 1


title: genomic DNA from peripheral blood 48

source_name: peripheral blood 48


title: SW620-EV

description: Gene expression data in SW620 infected with control virus

source_name: empty vector control

value: empty vector


title: RNF2-overexpressed Hmel, rep1

description:
RNF2_1
RNF2-overexpressed
Gene expression from RNF2-overexpressed human melanocytes - Hmel cells.


title: NK cells control non stimulated, biological rep 4

description:
Gene expression data from Human NK cells non stimulated from control
Control NS 4

source_name: Human NK cells from control non stimulated


title: NK cells control LPG-stimulated 6h, biological rep 2

description:
Gene expression data from Human NK cells LPG-stimulated from control
Control LPG 2


title: MDD 505

city: San Diego

first: YING

last: DING

address: 10777 Science Center Dr.

department: Computational Biology

institute: Pfizer

description: Gene expression data from human postmotem brain region AMY

hyb_protocol: standard Affymetrix protocol

scan_protocol: Microarrays were scanned and summarized by manufacturers’ defaults

data_processing: Data from Affymetrix arrays were processed by robust multi-array (RMA) method

extract_protocol: unknown

value: M

tag: pair

tag: disease status

value: MDD


title: MDD 1060


title: MDD 513


title: genomic DNA from peripheral blood 46

description: peripheral blood given by child born SGA

source_name: peripheral blood 46


title: NK cells control non stimulated, biological rep 3

description:
Gene expression data from Human NK cells non stimulated from control
Control NS 3


title: genomic DNA from peripheral blood 51

source_name: peripheral blood 51


title: MDD 868


title: genomic DNA from peripheral blood 49

source_name: peripheral blood 49


title: MDD 1049


title: genomic DNA from peripheral blood 47

source_name: peripheral blood 47


title: MDD 1001


title: genomic DNA from peripheral blood 41

source_name: peripheral blood 41


title: SW620-LATS2N

description: Gene expression data in SW620 infected with LATS2N(1-625) virus

source_name: LATS2N(1-625) overexpression


title: NK cells control non stimulated, biological rep 2

description:
Gene expression data from Human NK cells non stimulated from control
Control NS 2


title: WT-CXCR4

city: Jerusalem

first: Shiran

last: Bar

address: Edmond J. Safra Campus, Givat Ram

institute: The Hebrew University, Jerusalem

description: Gene expression data from WT-CXCR4

hyb_protocol: Affymetrix protocol, 11 µg cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console (RMA)

source_name: Control iPS Cells differentiated to endodermal progenitors and sorted using CXCR4

label_protocol: 200 ng total RNA, Affymetrix protocol

extract_protocol: Total RNA was extracted using RNeasy® Mini Kit (QIAGEN).

value: Male


title: genomic DNA from peripheral blood 44

source_name: peripheral blood 44


title: genomic DNA from peripheral blood 42

source_name: peripheral blood 42


title: genomic DNA from peripheral blood 39

source_name: peripheral blood 39


title: Pg-CXCR4

description: Gene expression data from Pg-CXCR4

source_name: Parthenogenetic iPS Cells differentiated to endodermal progenitors and sorted using CXCR4


title: MDD 863


title: MDD 926


title: Pg-NCAM1-2

description: Gene expression data from Pg-NCAM1-2

source_name: Parthenogenetic iPS Cells differentiated to neural progenitors and sorted using NCAM1


title: MDD 809


title: genomic DNA from peripheral blood 40

source_name: peripheral blood 40


title: genomic DNA from peripheral blood 45

source_name: peripheral blood 45


title: genomic DNA from peripheral blood 43

source_name: peripheral blood 43


title: Pg-NCAM1-1

description: Gene expression data from Pg-NCAM1-1


title: MDD 783


title: WT-NCAM1-2

description: Gene expression data from WT-NCAM1-2

source_name: Control iPS Cells differentiated to neural progenitors and sorted using NCAM1


title: MDD 698


title: WT-NCAM1-1

description: Gene expression data from WT-NCAM1-1


title: MDD 943


title: Blood-3.0Gy-1hr-rep2

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: Leukocytes treated with 3.0 Gy radiation, measured 1 hr post-exposure.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45oC to Affymetrix® Human gene 1.0 ST v1 arrays according to the GeneChip® WT Terminal Labeling and Hybridization User Manual from Affymetrix®.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G (Affymetrix) and the GeneChip® Command Console® software version 3.1 (Affymetrix®).

data_processing:
All data analysis was performed in R using bioconductor packages.  CEL files were preprocessed and normalized using robust multichip averaging (RMA) within the oligo package.  Differential expression was performed using Limma.
annotation file: HuGene-1_0-st-v1.na34.1.hg19.transcript.csv

source_name: blood, isolated leukocytes, 3.0 Gy radiation, 1hr post-exposure

label_protocol: Biotinylated cDNA were prepared according to the standard protocol for Affymetrix® GeneChip® WT Expression protocol (Affymetrix® Inc., Santa Clara, CA) (Ambion WT Expression kit followed by GeneChip® WT Terminal Labeling and Hybridization kit) from 100 ng total RNA.

growth_protocol: Whole blood was drawn from four (4) volunteers using a Safety Winged IV blood draw set (Exel International, St. Petersburg, FL) in 7-ml lavender topped Ethylenediaminetetraacetic acid (EDTA) anticoagulant-containing vacutainers.  Blood samples were aliquoted and kept at room temperature throughout the radiation and white blood cell (WBC) isolation process.

extract_protocol: Approximately 30 minutes after completion of the radiation cycle, red blood cells (RBC) were lysed by adding 15ml of NH4Cl red blood cell (RBC) lysis buffer for each ml of whole blood (1:15 v/v dilution) in order to isolate leukocytes.  The tubes were agitated 5 minutes on a rocker platform and centrifuged for 5 minutes at 1,500 RPM at room temperature.  Cells were suspended in 10 ml of phosphate-buffered saline (PBS) and centrifuged again twice for 5 minutes at 1,500 RPM.  White blood cells (WBC) were suspended in 2 ml PBS, equivalent to the initial volume of the whole blood.  WBC were centrifuged 5 min at 1,500 RPM.  Supernatant was discarded and cell pellets were suspended in 600µl RLT lysis buffer (Qiagen, Venlo, The Netherlands) and tubes were vortexed vigorously and stored at -70oC until RNA purification. Purification of total RNA was performed using the RNAeasy Mini Kit (Qiagen).  Optional on-column DNase digestion was performed to eliminate genomic DNA contamination.  Total RNA was eluted in 60 µl of RNase-free water. The quantity analysis of the total RNA was performed with a Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE).  The quality of the total RNA was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc, Santa Clara, CA).

treatment_protocol: Whole blood samples were radiated at the Kentucky Lion Eye Center using a Gammacell 1000 Elite (Cs-137) (Best Theratronics Ltd., Ottawa, Canada) for 0 seconds (control – 0.0 Gy exposure), 3 seconds (0.30 Gy exposure), 16 seconds (1.5 Gy exposure), or 32 seconds (3.0 Gy exposure).

tag: volunteer

tag: radiation dose

tag: time

value: 1 hr

value: blood, isolated leukocytes


title: Blood-3.0Gy-1hr-rep4


title: Blood-3.0Gy-1hr-rep1


title: Blood-3.0Gy-1hr-rep3


title: Control 857

value: Control


title: Control 789


title: MDD 598


title: Control 685


title: Blood-1.5Gy-1hr-rep4

description: Leukocytes treated with 1.5 Gy radiation, measured 1 hr post-exposure.

source_name: blood, isolated leukocytes, 1.5 Gy radiation, 1hr post-exposure


title: Control 604


title: Blood-1.5Gy-1hr-rep3


title: genomic DNA from peripheral blood 33

source_name: peripheral blood 33

label_protocol: Standard Illumina Protocol


title: genomic DNA from peripheral blood 36

source_name: peripheral blood 36


title: genomic DNA from peripheral blood 34

source_name: peripheral blood 34


title: NK cells control non stimulated, biological rep 1

description:
Gene expression data from Human NK cells non stimulated from control
Control NS 1

source_name: Human NK cells from control non stimulated

value: Human NK cells from PBMC

value: non stimulated


title: genomic DNA from peripheral blood 31

source_name: peripheral blood 31


title: Blood-1.5Gy-1hr-rep2


title: genomic DNA from peripheral blood 38

source_name: peripheral blood 38


title: Control 852


title: Control 1047


title: CP_3

city: Tokyo

first: Itsuki

last: Ajioka

address: 1-5-45 Yushima, Bunkyo-ku

department: Center for Brain Integration Research

institute: Tokyo Medical and Dental University

description: manually dissected E16 CP tissue

hyb_protocol: The amplified cRNA (1.5 µg) was hybridized on Agilent Whole mouse Genome Array (4 × 44K) ver 2.0 for 17 hours.

scan_protocol: The Chips were scanned on a Agilent DNA Microarray Scanner using Feature Extraction software ver 10.7.1.1 (Agilent).

data_processing:
Normalized by pergentile shift (75%) and baseline to median of all samples; GeneSpring software ver 11.5.
Entities were filtered based on their signal intensity value (20-100%), and then the standard deviation (< 0.1). Filtered data linked as supplementary file on Series record.

source_name: manually dissected E16 CP tissue

label_protocol: Total RNA was amplified following One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), ver 6.0.

extract_protocol: 100 ng of the total RNA was purified by RNeasy Micro (QIAGEN)

tag: strain

value: ICR

tag: developmental stage

value: CP


title: Blood-1.5Gy-1hr-rep1


title: genomic DNA from peripheral blood 35

source_name: peripheral blood 35

value: SGA


title: CP_2

description: manually dissected E16 CP tissue


title: CP_4

description: manually dissected E16 CP tissue


title: Blood-0.3Gy-1hr-rep4

description: Leukocytes treated with 0.3 Gy radiation, measured 1 hr post-exposure.

source_name: blood, isolated leukocytes, 0.3 Gy radiation, 1hr post-exposure


title: genomic DNA from peripheral blood 30

source_name: peripheral blood 30


title: genomic DNA from peripheral blood 28

source_name: peripheral blood 28


title: genomic DNA from peripheral blood 26

source_name: peripheral blood 26


title: genomic DNA from peripheral blood 27

source_name: peripheral blood 27


title: Blood-0.3Gy-1hr-rep2


title: genomic DNA from peripheral blood 32

source_name: peripheral blood 32


title: Control 1122


title: Blood-0.3Gy-1hr-rep3


title: genomic DNA from peripheral blood 29

source_name: peripheral blood 29


title: Control 1086


title: CP_1

description: manually dissected E16 CP tissue


title: Control 736


title: genomic DNA from peripheral blood 25

source_name: peripheral blood 25


title: Control 1031


title: genomic DNA from peripheral blood 37

source_name: peripheral blood 37


title: genomic DNA from peripheral blood 23

source_name: peripheral blood 23


title: genomic DNA from peripheral blood 24

source_name: peripheral blood 24


title: Control 713


title: Blood-0.3Gy-1hr-rep1


title: Control 795


title: MDD 600


title: Control 615


title: Blood-0.0Gy-1hr-rep4

description: Leukocytes treated with 0.0 Gy radiation, measured 1 hr post-exposure.

source_name: blood, isolated leukocytes, 0.0 Gy radiation, 1hr post-exposure