title: MSUS_&_AS 536437A10

tag: group

tag: phenotype

value: F2 acute stress, after paternal stress in F1 generation

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: Control_&_AS 536437A08

status: Public on Jul 01 2014

type: RNA

city: Basel

first: Guido

last: Steiner

address: Grenzacher Str.

country: Switzerland

institute: F. Hoffmann-La Roche

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Mus musculus

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: C57Bl/6J females and males (2.5 months) or the F1 generation breeding were obtained from Janvier (France) and maintained in a temperature- and humidity-controlled facility on a 12-hour reversed light–dark cycle with food and water ad libitum. All procedures were carried out in accordance with Swiss cantonal regulations for animal experimentation. Mice were killed by cervical dislocation either 45 min (acute stress condition) or 2 weeks (baseline resting condition) after exposure to forced swim stress (6 min, 18°C water). The brain was removed and the hippocampus was rapidly dissected on ice and stored at -80°C until processed.

extract_protocol: RNA was extracted from the hippocampus with Trizol (Invitrogen) and amplified using the Ovation RNA amplification kit V2 (Nugen Technologies).

tag: tissue

value: hippocampus

value: F2 acute stress, after control handling in F1 generation

tag: cage


title: Blood SCD patientA0036

city: Montreal

first: Jacklyn

last: Quinlan

state: Qc

address: 3175 Cote Ste-Catherine

department: Pediatrics

country: Canada

institute: CHU Ste-Justine Hospital

description:
Sample30
globin mRNA-depleted total RNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was log2 transfromed and normalised using quantile normalisation with JMP Genomics

label: Biotin

organism: Homo sapiens

source_name: whole blood

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted from whole blood collected in Tempus tubes using the Tempus Spin RNA Isolation kit (Applied Biosystems). Total RNA was then globin-mRNA-depleted using GlobinClear kit (Ambion). Quality control was performed with Agilent Bioanalyser.

tag: age (years)

tag: clinical status

value: E

tag: severity score

tag: Sex

value: M

tag: hb phenotype

value: SS

tag: white blood cells

tag: mean corpuscular volume

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0035

description:
Sample29
globin mRNA-depleted total RNA

value: SC


title: Blood SCD patientA0033

description:
Sample27
globin mRNA-depleted total RNA

value: FU

value: F


title: Control 536437A06

source_name: Control 536437A06

tag: group

value: Control

tag: phenotype

value: F2 control handling, after control handling in F1 generation

tag: litter


title: NOD pancreas CD8α-DC PBS rep 4

city: Rotterdam

first: Wouter

last: Beumer

address: Dr. Molenwaterplein 50

department: Immunology

country: Netherlands

institute: Erasmus MC

description: Gene expression data from NOD pancreas CD11c+CD8α- DCs at 5 weeks of age in-vitro stimulated with PBS

hyb_protocol: After fragmentation the chips were hybridized for 18h at 45C according to the manufacturers protocol.

scan_protocol: Chips were scanned on a Affymetrix GeneChip Scanner 3000 7G according to the manufacturers protocol using the GeneChip® Command Console® Software (AGCC) v3.2.4

data_processing: Quality analysis of the CEL data was assessed by running a standardized workflow developed at the BiGCaT department of Maastricht University - The Netherlands (http://www.arrayanalysis.org/). The expression data containing .CEL files were imported and processed further with BRB-ArrayTools (R. Simon, http://linus.nci.nih.gov/BRB-ArrayTools.html). Gene expression data was normalized using  RMA (Robust Multichip Average)

label: biotin

source_name: NOD pancreas CD11c+CD8α- DCs at 5 weeks in-vitro after 18h PBS stimulation

label_protocol: The RNA was reverse transcribed, amplified, biotinylated and fragmented with the Ovation Pico WTA v2 and Encore Biotin Module (NuGEN Technologies) and subsequently hybridized on Mouse Genome 430 2.0 Arrays (Affymetrix) according to the manufacturers protocols.

growth_protocol: NA. Cells were obtained from pancreas tissue after 1. enzymatic digestion of tissue, single-cell suspension 2. pre-separation of CD45+ cells with magnetic beads 3. FACS sorting of CD11c+CD8α- DCs

extract_protocol: RNA was iolated and Dnase treated with the PicoPure RNA extraction kit according to the manufacturers protocol (Arcurus, Applied Biosystems)

treatment_protocol: steady-state (no treatment) or in-vitro PBS/LPS stimulation for 18h

value: Pancreas CD11c+CD8α- DCs

tag: gender

value: female

tag: age

value: 5 weeks

tag: treatment

value: in-vitro PBS stimulation 18 hours

tag: strain

value: NOD


title: Control 536437A05

source_name: Control 536437A05

tag: tissue

tag: cage

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: Control_&_AS 536437A07


title: NOD pancreas CD8α-DC PBS rep 2


title: MSUS_&_AS 536437A03


title: Blood SCD patientA0024

description:
Sample20
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

tag: severity score

tag: Sex

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume


title: Control_&_AS 536437A02

tag: group

tag: phenotype

tag: litter


title: MSUS_&_AS 536437A04


title: Blood SCD patientA0031

description:
Sample25
globin mRNA-depleted total RNA

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0032

description:
Sample26
globin mRNA-depleted total RNA


title: NOD pancreas CD8α-DC PBS rep 3

tag: tissue

tag: gender

tag: age

tag: treatment

tag: strain


title: Blood SCD patientA0023

description:
Sample19
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status


title: C57BL6 pancreas CD8α-DC PBS rep 4

description: Gene expression data from C57BL6 pancreas CD11c+CD8α- DCs at 5 weeks of age in-vitro stimulated with PBS

source_name: C57BL6 pancreas CD11c+CD8α- DCs at 5 weeks in-vitro after 18h PBS stimulation


title: C57BL6 pancreas CD8α-DC PBS rep 3


title: Blood SCD patientA0027

description:
Sample21
globin mRNA-depleted total RNA

value: A

tag: severity score

tag: Sex


title: Blood SCD patientA0034

description:
Sample28
globin mRNA-depleted total RNA

tag: hb phenotype

tag: white blood cells


title: Blood SCD patientA0021

description:
Sample17
globin mRNA-depleted total RNA

tag: mean corpuscular volume


title: C57BL6 pancreas CD8α-DC PBS rep 2


title: Control_&_AS 536437A01

tag: group

tag: phenotype

tag: cage

tag: day of sacrifice

tag: sacrifice time

tag: chip average background

tag: genetic background


title: Blood SCD patientA0030

description:
Sample24
globin mRNA-depleted total RNA

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0022

description:
Sample18
globin mRNA-depleted total RNA

tag: age (years)


title: NOD pancreas CD8α-DC PBS rep 1

tag: tissue

tag: gender

tag: age

tag: treatment

tag: strain


title: C57BL6 pancreas CD8α-DC PBS rep 1


title: Blood SCD patientA0019

description:
Sample15
globin mRNA-depleted total RNA

tag: clinical status

tag: severity score

tag: Sex

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume


title: Blood SCD patientA0018

description:
Sample14
globin mRNA-depleted total RNA


title: Blood SCD patientA0028

description:
Sample22
globin mRNA-depleted total RNA


title: Blood SCD patientA0020

description:
Sample16
globin mRNA-depleted total RNA


title: Blood SCD patientA0029

description:
Sample23
globin mRNA-depleted total RNA


title: Control 536436A12

source_name: Control 536436A12

tag: group

tag: phenotype

tag: cage

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background


title: Blood SCD patientA0017

description:
Sample13
globin mRNA-depleted total RNA

tag: age (years)

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Control 536436A11

source_name: Control 536436A11

tag: tissue

tag: genetic background


title: Blood SCD patientA0014

description:
Sample10
globin mRNA-depleted total RNA

tag: clinical status

tag: severity score

tag: Sex


title: Control_&_AS 536436A08


title: Blood SCD patientA0016

description:
Sample12
globin mRNA-depleted total RNA

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume


title: Blood SCD patientA0015

description:
Sample11
globin mRNA-depleted total RNA


title: C57BL6 pancreas  CD8α-DC rep6

description: Gene expression data from C57BL6 pancreas CD11c+CD8α- DCs at 5 weeks of age

source_name: C57BL6  pancreas CD11c+CD8α- DCs at 5 weeks under steady-state conditions

tag: gender

tag: age

tag: treatment

value: steady-state

tag: strain


title: NOD pancreas  CD8α-DC rep4

description: Gene expression data from NOD pancreas CD11c+CD8α- DCs at 5 weeks of age

source_name: NOD  pancreas CD11c+CD8α- DCs at 5 weeks under steady-state conditions


title: Blood SCD patientA0010

description:
Sample6
globin mRNA-depleted total RNA


title: MSUS_&_AS 536436A09

value: hippocampus

tag: group

tag: phenotype

value: F2 acute stress, after paternal stress in F1 generation

tag: cage

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background


title: C57BL6 pancreas  CD8α-DC rep5

tag: tissue


title: Blood SCD patientA0012

description:
Sample8
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

tag: severity score

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0009

description:
Sample5
globin mRNA-depleted total RNA

tag: Sex

tag: hb phenotype

tag: white blood cells

tag: mean corpuscular volume


title: MSUS_&_AS 536436A10

tag: group

tag: phenotype

tag: genetic background


title: NOD pancreas  CD8α-DC rep6

source_name: NOD pancreas CD11c+CD8α- DCs at 5 weeks under steady-state conditions

tag: gender

tag: age

tag: treatment

tag: strain


title: Blood SCD patientA0008

description:
Sample4
globin mRNA-depleted total RNA

tag: age (years)


title: Control_&_AS 536436A07

tag: tissue

value: F2 acute stress, after control handling in F1 generation

tag: cage

tag: litter

tag: day of sacrifice

tag: sacrifice time

tag: chip average background


title: Blood SCD patientA0013

description:
Sample9
globin mRNA-depleted total RNA

tag: clinical status

tag: severity score

tag: Sex

value: M

tag: hb phenotype

tag: red blood cells

tag: genotypic pc1

tag: genotypic pc2


title: Blood SCD patientA0011

description:
Sample7
globin mRNA-depleted total RNA

value: E

value: SS

tag: white blood cells

tag: mean corpuscular volume


title: Blood SCD patientA0007

description:
Sample3
globin mRNA-depleted total RNA


title: Blood SCD patientA0006

description:
Sample2
globin mRNA-depleted total RNA

value: SC


title: C57BL6 pancreas  CD8α-DC rep1

source_name: C57BL6 pancreas CD11c+CD8α- DCs at 5 weeks under steady-state conditions

tag: gender

tag: age

tag: treatment

tag: strain


title: Control 536436A06

source_name: Control 536436A06

tag: tissue

tag: group

tag: phenotype

tag: cage

tag: litter

tag: genetic background


title: Blood SCD patientA0005

description:
Sample1
globin mRNA-depleted total RNA

tag: age (years)

tag: clinical status

tag: severity score

tag: Sex

value: F


title: MSUS_&_AS 536436A04

tag: day of sacrifice

tag: sacrifice time

tag: chip average background


title: Control 536436A05

source_name: Control 536436A05

value: Control


title: C57BL6 pancreas  CD8α-DC rep4

tag: gender


title: NODpancreas  CD8α-DC rep1

tag: age


title: Control_&_AS 536436A02


title: CTX-2d myogenic cells

city: suita

first: so-ichiro

last: fukada

address: 1-6 yamadaoka

country: Japan

institute: osaka University

description:
CTX-2d
Antibody SM/C-2.6 is described in Exp. Cell Res. 2004 296(2); 245-255.
Affymetrix mouse 430A array was used.

hyb_protocol: Following fragmentation, 10 ug of labeled cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array (MOE430A). 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: Affymetrix MAS 5.0 with p-value cuttoffs of 0.04 and 0.06 for present, marginal, and absent.

source_name: Myogenic cells 2d after cardiotoxin injection

label_protocol: GeneChip® Eukaryotic Small Sample Target Labeling Assay Version II.

growth_protocol: These samples were directly isolated from mouse skeletal muscle. Therefore, the cells were not cultured in vitro.

extract_protocol: Used Qiagen RNeasy Mini Kit according to instructions therein.

treatment_protocol: Hind limb muscle was injured by cardiotoxin (CTX).

tag: strain/background

value: 8-12 weeks

tag: treatment

value: cardiotoxin (CTX)

tag: cell type

value: myogenic cells

tag: time post-ctx


title: Control 536435A12

source_name: Control 536435A12

tag: tissue

tag: group

tag: phenotype

value: F2 control handling, after control handling in F1 generation


title: H2A.Z ChIP in wild-type

type: genomic

city: Davis

first: Shajahan

last: Anver

state: CA

address: 1002 LSA, One Shields Av

department: Plant Biology

country: USA

institute: University of California Davis

description: H2A.Z ChIP wt V3

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-1100_Jul11 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization. The enrichment ratios ('enrichment_ratios.txt') were calculated by dividing the normalized ChIP signals by whole cell extract (control) and provided as Series supplementary file.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: M2 FLAG immunoprecipitated DNA

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated by incubation with anti HA affinity matrix (Roche 3F10) or M2 FLAG slurry (Sigma). Recovered DNA was reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C; for Xap5 immunoprecipitation paraformaldehyde fixation was supplemented with DMA (10mM, 45 min, 30˚C) crosslinking.

value: pht1-3xflag cells

tag: growth stage

value: exponentially growing cells

tag: ip method

value: M2 FLAG slurry (Sigma)

source_name: Whole-cell extract DNA


title: Control_&_AS 536436A01

tag: cage

tag: litter

tag: genetic background


title: Xap5-HA-TAP ChIP  in wild-type cells (control for pht1D)

data_processing:
Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-1100_Jul11 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.
Enrichment values were calculated as a ratio of Cy5 processed signal/ Cy3 processed signal.

source_name: log. growing cells

tag: genotype

value: wild type

value: Xap5-HA-TAP cells

tag: sample type

value: Xap5-HA-TAP immunoprecipitated DNA

tag: chip antibody

value: xap5-HA-TAP cells

value: Whole-cell extract DNA

value: input


title: H2A.Z ChIP in xap5D

value: M2 FLAG immunoprecipitated DNA

value: M2 FLAG


title: Xap5-HA-TAP ChIP in wild-type cells

description: Xap5 ChIP wt V3

source_name: Xap5-HA-TAP immunoprecipitated DNA

value: anti HA affinity matrix (Roche 3F10)


title: VCaP-PCAT29-shRNA-1-replicate-1

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: Michigan

address: 1500 E Medical Center Drive

department: Pathology

institute: University of Michigan

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner.Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: 10 ug of total RNA were primed with 2 ul of 100 uM T16N2 DNA primer at 70_C for 10 min, then reversed transcribed at 42_C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 uM each dATP, dTTP, dGTP, with 25 uM dCTP, 25 uM Cy3-label.

growth_protocol: VCaP and LNCaP cells were grown in DMEM-Glutmax (Invitrogen) and RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin respectively.

extract_protocol: Total RNA was isolated using Trizol and an RNeasy Kit (Invitrogen) with DNase I digestion according to the manufacturer_s instructions.

treatment_protocol: Cells were plated in 100mM plates at a desired concentration and infected with shRNA targeting PCAT29 or a non-targetting shRNA. Knockdown efficiency was determined by qPCR.

tag: cell line

value: VCaP

value: prostate cancer cell line

tag: transfected with

value: PCAT29-targeting sRNA 1

value: non-targetting shRNA


title: LNCaP-PCAT29-shRNA-2

value: LNCaP

value: PCAT29-targeting sRNA 2


title: CTX-5d myogenic cells

description:
CTX-5d
Antibody SM/C-2.6 is described in Exp. Cell Res. 2004 296(2); 245-255.
Affymetrix mouse 430A array was used.

source_name: Myogenic cells 5d after cardiotoxin injection

tag: strain/background

tag: age

value: 8-12 weeks

value: cardiotoxin (CTX)

value: myogenic cells


title: VCaP-PCAT29-shRNA-2-replicate-2

tag: cell type


title: H2A.Z ChIP in  wild-type (control for xap5D)

value: wild type

value: pht1-3xflag cells


title: MSUS_&_AS 536435A09

value: hippocampus

value: F2 acute stress, after paternal stress in F1 generation

tag: day of sacrifice

tag: sacrifice time

tag: chip average background


title: Control 536435A11

source_name: Control 536435A11

tag: tissue

tag: group

value: Control

tag: phenotype

value: F2 control handling, after control handling in F1 generation


title: VCaP-PCAT29-shRNA-2-replicate-1


title: MSUS_&_AS 536436A03

tag: cage


title: VCaP-PCAT29-shRNA-1-replicate-2


title: LNCaP-PCAT29-shRNA-1


title: Control_&_AS 536435A08

value: F2 acute stress, after control handling in F1 generation

tag: litter


title: hac1∆(hsf1), biological rep1

city: Göteborg

first: Tobias

last: Österlund

address: Kemivägen 10

department: Dept. of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description:
HH1
Gene expression data from hac1∆(hsf1).

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Yeast Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Washing and straining of the hybridized microarrays were carried out on the Affymetrix Genechip® Fludics Station 450.

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip® 3000 7C Scanner.

data_processing: Affymetrix CEL-data files were analyzed using the R suite and Bioconductor packages. Briefly, data normalization was carried out using the method of Probe Logarithmic Intensity Error (PLIER) with perfect match probe only (PM-only).

organism: Saccharomyces cerevisiae

source_name: hac1∆(hsf1) treated with 2.5 mM DTT

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: The strains were inoculated into SD-URA medium at 30 C and grown in early exponential phase.

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed to cRNA using the GeneChip 3' IVT Express Kit (Affymetrix).

treatment_protocol: 2.5 mM DTT was added into the medium for two hours induction.


title: WT, biological rep3

description:
WT3
Gene expression data from WT.

source_name: WT treated with 2.5 mM DTT

value: WT


title: hac1∆(hsf1), biological rep3

description:
HH3
Gene expression data from hac1∆(hsf1).


title: Control_&_AS 536435A07

tag: genetic background


title: WT(hsf1), biological rep1

description:
HSF1
Gene expression data from WT(hsf1).

source_name: WT(hsf1) treated with 2.5 mM DTT

tag: genotype


title: hac1∆, biological rep1

description:
HAC1
Gene expression data from hac1∆.

source_name: hac1∆ treated with 2.5 mM DTT


title: WT, biological rep1

description:
WT1
Gene expression data from WT.


title: WT, biological rep2

description:
WT2
Gene expression data from WT.


title: hac1∆(hsf1), biological rep2

description:
HH2
Gene expression data from hac1∆(hsf1).


title: Xap5-HA-TAP ChIP  in pht1D cells

value: Xap5-HA-TAP cells

tag: sample type

value: Xap5-HA-TAP immunoprecipitated DNA

value: xap5-HA-TAP cells

value: Whole-cell extract DNA

value: input


title: Control_&_AS 536435A02


title: WT(hsf1), biological rep2

description:
HSF2
Gene expression data from WT(hsf1).


title: Control 536435A06

source_name: Control 536435A06


title: MSUS_&_AS 536435A10


title: WT(hsf1), biological rep3

description:
HSF3
Gene expression data from WT(hsf1).


title: Control_&_AS 536435A01


title: Control 536435A05

source_name: Control 536435A05


title: hac1∆, biological rep2

description:
HAC2
Gene expression data from hac1∆.


title: MSUS_&_AS 536435A04


title: MSUS_&_AS 536435A03


title: hac1∆, biological rep3

description:
HAC3
Gene expression data from hac1∆.


title: 26_Control

growth_protocol: C57Bl/6J females and males (2.5 months) for the F1 generation breeding were obtained from Janvier (France) and maintained in a temperature- and humidity-controlled facility on a 12-hour reversed light–dark cycle with food and water ad libitum. All procedures were carried out in accordance with Swiss cantonal regulations for animal experimentation. Mice were killed by cervical dislocation either 45 min (acute stress condition) or 2 weeks (baseline resting condition) after exposure to forced swim stress (6 min, 18°C water). The brain was removed and the hippocampus was rapidly dissected on ice and stored at -80°C until processed.

value: F2, after control handling in F1 generation

tag: animal number


title: 25_Control


title: 29_MSUS

value: MSUS

value: F2, after paternal stress in F1 generation


title: 23_MSUS


title: Nerve graft harvested  from Balb/c mice w/ nerve isograft at 7 days, rep2

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: group with untreated nerve isografting

hyb_protocol: The pre-hybridization of MRmiOA v2 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on MRmiOA v2 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 580-600 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: The data processing was processed by R program (2.12.1). Import Foreground value of each miRNA probes in triplicates from GPR files, plus the absolute value of minimum value of array to replace the week signal. Filter out probes that ﬂag <0 in all samples. Porbes that passed the criteria were normalized by 75% media scaling between arrays.

source_name: Nerve isograft

label_protocol: Small RNA population were enriched by (Nanosep100k, Pall Corp.) from 2.5 µg of total RNA. NHS-CyDye (Cy5, Amershan) were direct labeled to Guanine (G) by chemical labeling method using ULS™ microRNA Labeling Kit (EA-038, Kreatech).

growth_protocol: No growth protocol

extract_protocol: RNA extraction by RNeasy Protect Animal Blood Kit (QIAGEN Cat. no. 73224). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: Surgical procedures: The mice were anesthetized by intraperitoneal injection of an anesthetic cocktail consisting of 0.1 mg/g ketamine and 0.01 mg/g xylazine. The anesthetized mice were restrained in a supine position on a heated pad to maintain the body temperature at 37°C. Under aseptic conditions, with sterile povidone/iodine preparation and 70% ethanol and sterile instruments and drapes, the skin over the proximal right hindlimb was incised, and the underlying biceps femoris muscle was bluntly dissected to expose the sciatic nerve. An established mouse sciatic nerve allotransplantation model was used. In brief, 1-cm Balb/c or C57BL/6 donor sciatic nerve grafts were transplanted in reverse orientation into 0.5-cm sciatic nerve gaps created in the recipient Balb/c mice. Tension-free repair was then performed under an operating microscope with three 11–0 nylon (Ethicon Inc., Somerville, NJ) interrupted epineurial sutures under 40 magnification. The muscle was closed with 5–0 vicryl sutures, and the skin with interrupted 5–0 nylon sutures. The animals were monitored to ensure appropriate feeding and diet after surgery.

tag: strain

value: Balb/c

tag: gender

value: male

value: nerve allograft

tag: treatment

value: nerve isograft at 7 days


title: Nerve graft harvested  from Balb/c mice w/ nerve isograft at 7 days, rep1

description: group with untreated nerve isografting


title: Nerve graft harvested  from Balb/c mice w/ untreated nerve allograft at 7 days, rep2

description: group with untreated nerve allografting

source_name: Nerve allograft

value: untreated nerve allograft at 7 days


title: KO.htz_53.3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
heterozygote CHD7_KO
whirligig mouse line (Bosman et al. 2005).

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in the Hybridization Oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed.

data_processing: Agilent's Feature Extraction Software Version 10.7.3.1 using default parameters. Data were quantile normalized using R and Bioconductor package limma.

source_name: E9.5 female mouse embryo, Chd7 heterozygote

label_protocol: Microarrays were done using the "Low RNA Input linear Amplification Kit Plus, One Color" protocol (Agilent Technologies, Inc. 2007; Cat. Nr: 5188-5339) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5282) following the manufacturer's standard protocol.

extract_protocol: RNA isolation was performed from four biological replicates from E9.5 wildtype, Chd7Whi/+ and Chd7Whi/Whi female mouse embryos using the Trizol (Invitrogen) method according to the manufacturer's recommendations. Afterwards, the samples were DNase I (Sigma) treated in order to remove DNA contamination. RNA quality was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) microfluidic electrophoresis. Only samples with comparable RNA integrity numbers were selected for microarray analysis.

treatment_protocol: Matings between heterozygous Whirligig males and females were set up. Female Whirligig mice (Chd7Whi/+) were checked daily for the presence of a copulation plug. The day on which the vaginal plug was observed was counted as E0.5. Pregnant female Whirligig mice (Chd7Whi/+) were sacrificed by cervical dislocation, the uterus was removed and the embryos were dissected from the yolk-sacs.

tag: strain/background

value: mixed C3HeB/FeJ

value: female

tag: age

value: embryo


title: KO.htz_53.1


title: 20_Control

value: hippocampus

value: Control


title: 15_Control


title: WT_50.9

description:
WT
whirligig mouse line (Bosman et al. 2005).

source_name: E9.5 female mouse embryo, WT


title: 7_MSUS


title: 10_MSUS


title: KO.htz_50.2


title: Nerve graft harvested  from Balb/c mice w/ nerve allograft + daily 1 mg/kg subcutaneous FK506 treatment for 7 days, rep2

description: group with treated nerve allografting

value: nerve allograft and daily 1 mg/kg subcutaneous FK506 treatment for 7 days


title: 4_Control


title: KO.htz_39.3


title: WT_39.2


title: Nerve graft harvested  from Balb/c mice w/ nerve allograft + daily 1 mg/kg subcutaneous FK506 treatment for 7 days, rep1

description: group with treated nerve allografting


title: KO_33.2

description:
CHD7_KO
whirligig mouse line (Bosman et al. 2005).

source_name: E9.5 female mouse embryo, Chd7 knockout


title: 11_MSUS


title: Nerve graft harvested  from Balb/c mice w/ untreated nerve allograft at 7 days, rep1

description: group with untreated nerve allografting


title: WT_53.2


title: Blood drawn from the Balb/c mice with nerve isograft at 7 days, rep2

description: group with untreated nerve isografting

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 600 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by R program (2.12.1). Import Foreground value of each miRNA probes in triplicates from GPR files, plus the absolute value of minimum value of array to replace the week signal. Filter out probes that ﬂag <0 in all samples. Porbes that passed the criteria were normalized by 75% media scaling between arrays.
The Matrix value is normalized intensities. Based on the normalized intensities, we calculate average ratios and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: whole blood

value: blood


title: KO_69.5


title: 2_Control


title: KO_50.7


title: Blood drawn from the Balb/c mice with nerve isograft at 7 days, rep1

description: group with untreated nerve isografting


title: 6_MSUS


title: KO_53.4


title: Blood drawn from the Balb/c mice with nerve allograft and daily 1 mg/kg subcutaneous FK506 treatment for 7 days, rep2

description: group with treated nerve allografting


title: Blood drawn from the Balb/c mice with untreated nerve allograft at 7 days, rep1

description: group with untreated nerve allografting


title: Blood drawn from the Balb/c mice with nerve allograft and daily 1 mg/kg subcutaneous FK506 treatment for 7 days, rep1

description: group with treated nerve allografting


title: WT_50.6


title: 8 mg/kg bw furan_BrdU_rep5

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

institute: Health Canada

description: Sample 50

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

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

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

source_name: 8 mg/kg bw furan_BrdU_liver

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

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

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

treatment_protocol: Mice were dosed with 1 or 8 mg/kg bw furan via oral gavage for 21 days. Control animals were gavaged with corn oil oil only.  All animals were given BrdU in drinking water for 5 days prior to necropsy. Tissues were collected 4 hours following the final dose.

value: 5-6 weeks

tag: gavaged with

value: 8 mg/kg bw furan for 3wks

tag: treated with

value: BrdU in drinking water for 5 days before sacrifice

tag: sample collection time

value: 4hrs after the final furan exposure

value: liver

source_name: Universal Mouse Reference RNA

value: universal reference


title: 8 mg/kg bw furan_BrdU_rep4

description: Sample 49

tag: tissue


title: 8 mg/kg bw furan_BrdU_rep3

description: Sample 48


title: Blood drawn from the Balb/c mice with untreated nerve allograft at 7 days, rep2

description: group with untreated nerve allografting

value: Balb/c

value: male


title: 8 mg/kg bw furan_BrdU_rep1

description: Sample 46


title: 1 mg/kg bw furan_BrdU_rep4

description: Sample 19

source_name: 1 mg/kg bw furan_BrdU_liver

value: 1 mg/kg bw furan for 3wks


title: 1 mg/kg bw furan_BrdU_rep2

description: Sample 17


title: Control_BrdU_rep4

description: Sample 10

value: corn oil oil only (vehicle control) for 3wks


title: 8 mg/kg bw furan_BrdU_rep2

description: Sample 47


title: Multi-fractionated radiation 24hr 2Gyx5, Rep3 [mRNA]

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent-026652 Whole Human Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction), and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: HCAECs, MF, 24hr

label_protocol: First and second strand cDNA was prepared from the total RNA samples. Labeled cRNA target was prepared from the DNA template and verified on the Bioanalyzer. cRNA was fragmented to uniform size and verified on the Bioanalyzer.

growth_protocol: Cryopreserved human coronary artery endothelial cells (HCAEC) and the media were purchased from Lonza Walkersville Inc. (Walkersville, MD). Cells were thawed and maintained in EBM-2 basal medium supplemented with fetal bovine serum and growth factors (EGM-2 MV BulletKit CC-3202) according to the supplier's instructions. Cells from passages P1 to P3 were used. Cells were plated into T75cm2 flasks (1-1.5 x 10^6 for single-dose radiation and 0.6-0.8 x 10^6 for fractionated radiation).

extract_protocol: Total RNA was extracted and purified using Ribopure (Ambion) RNA isolation and confirmed for quality (Agilent 2100 Bioanalyzer, Agilent Technologies, Inc., Santa Clara, CA) following the manufacturers' instructions.

treatment_protocol: Cells were irradiated in a PANTAK high frequency X-ray generator (Precision X-ray Inc., N. Bedford, CT), operated at 300kV and 10MA. The dose rate was 1.6 Gy per min. Cells were plated into T75cm2 flasks (1-1.5 x 10^6 for single-dose radiation and 0.6-0.8 x 10^6 for fractionated radiation). After 24h, cells were exposed to a total of 10 Gy radiation administered either as a single-dose radiation (SD), or as multi-fractionated radiation of 2 Gy x 5 (MF). These non-isoeffective doses were selected to simulate clinical hypofractionated and conventionally fractionated radiotherapy regimens. For the MF protocol, cells were exposed to 2 Gy radiation twice a day, at 6h interval. The cells were approximately 90% confluent at the time of harvesting. For both protocols, radiation-induced changes were analyzed at 6h and 24h after a SD and 6h and 24h after the final dose of fractionated irradiation. Separate controls were maintained for SD and MF radiation protocols.

tag: cell type

value: human coronary artery endothelial cells (HCAECs)

value: multi-fractionated radiation (2Gyx5)

tag: time point


title: Multi-fractionated radiation 24hr 2Gyx5, Rep2 [mRNA]


title: Multi-fractionated radiation 24hr Control, Rep3 [mRNA]

source_name: HCAECs, control (MF), 24hr

value: control (multi-fractionated radiation)


title: MISS_WT_E2 384

city: Toulouse

first: Francoise

middle: B.

last: LENFANT

address: 1 avenue J. Poulhès

department: Team 9- I2MC

country: France

institute: INSERM U1048

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a weight of 1 for 25 out of 31 microarrays or with a weight of 1 in all 2 microarrays from at least one experimental group. At this step, 46859 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 43753 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: MISS WT E2

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 µg of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

growth_protocol: mice were ovariectomized at 4 weeks of age and maintained in animal facility 3 weeks before treatment on normal chow diet.

extract_protocol: Total RNA was extracted from uterus using TriPure reagent (Roche) and reverse-transcribed (High-Capacity cDNA Reverse Transcription Kit, Applied Biosystems).

treatment_protocol: ovariectomized mice were treated 6 hours with 0 or 8µg/kg of 17b-estradiol injected subcutaneously in castor oil.

value: uterus

value: MISS WT


title: Multi-fractionated radiation 24hr 2Gyx5, Rep1 [mRNA]


title: Multi-fractionated radiation 6hr 2Gyx5, Rep2 [mRNA]

source_name: HCAECs, MF, 6hr


title: AF2_WT_PLB 365a

source_name: AF2 WT PLB

value: AF2 WT

value: placebo


title: Control_BrdU_rep1

description: Sample 7

value: 5-6 weeks

value: female


title: Multi-fractionated radiation 6hr 2Gyx5, Rep3 [mRNA]


title: AF2_KO_E2 159

source_name: AF2 KO E2

value: AF2 KO


title: Multi-fractionated radiation 24hr Control, Rep1 [mRNA]


title: Control_BrdU_rep2

description: Sample 8

value: BrdU in drinking water for 5 days before sacrifice

value: 4hrs after the final furan exposure


title: PreExposure_Sputum_180

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: Sample from human sputum prior to ozone inhalation exposure

hyb_protocol: Following fragmentation, cRNA was hybridized on Agilent Human miRNA Microarray, ver 1

scan_protocol: Microarrays were scanned using Agilent Microarray Scanner

data_processing: Data were normalized by quantile using Partek® Genomics SuiteTM software (version 6.5)

label: Cyanine 3-Cytidine bisphosphate (pCp) reagent

source_name: Sputum sample, before ozone exposure

label_protocol: Labeled cRNA were prepared according to the standard Agilent protocol

growth_protocol: Twenty healthy non-asthmatic adult subjects aged 18 – 37 years, with no history of smoking in the past 10 years, completed the study. All subjects underwent a physical examination, a routine blood panel with complete blood cell count, and differential and allergy skin testing for common allergens. Subjects were required to have a negative methacholine challenge test result. Female subjects were required to have a negative urine pregnancy test result before challenge, and all volunteers were required to be free of chronic cardiorespiratory disease and no acute respiratory illnesses within the previous four to six weeks of ozone challenge. All subjects had FEV1 and forced vital capacity (FVC) values of 80% or greater of predicted value and FEV1/FVC ratios of 75% or greater of predicted normal value for height and age. All subjects were screened for their ability to provide an adequate induced sputum sample during their training session 48 hours prior to exposure and this sample acted as their pre-exposure baseline. Pre and post sputum samples were separated by a minimum of 48 hours.

extract_protocol: Sputum was obtained 6 hours after exposure. In brief, three 7-minute inhalation periods of nebulized hypertonic saline (3%, 4%, and 5%; UltraNeb 99 ultrasonic nebulizer; DeVilbiss, Jackson, TN) were followed by expectoration of sputum into a sterile specimen cup. Cell-rich “plug” material was selected from the raw sample and treated with a dilute (0.1%) solution of dithiothreitol (Sputolysin; Calbiochem, San Diego, CA) in Dulbecco PBS. The cells were treated with 1 ml of TRIzol reagent (Invitrogen Life Technologies, Carlsbad, CA) and frozen at -80 degrees C until RNA extraction. RNA was extracted according to standard TRIzol protocol.

treatment_protocol: The ozone exposures were conducted in an exposure chamber. Each subject was exposed to 0.4 ppm ozone for two hours while performing four 15-minute sessions of intermittent moderate exercise (expiratory minute ventilation, 30–40 L/min) on a treadmill, separated by 15 minutes of seated rest.

value: between 18 and 37 years

tag: exposure


title: AF2_KO_PLB 360

source_name: AF2 KO PLB


title: Multi-fractionated radiation 6hr 2Gyx5, Rep1 [mRNA]


title: AF2_WT_E2 212

source_name: AF2 WT E2


title: Multi-fractionated radiation 24hr Control, Rep2 [mRNA]


title: Multi-fractionated radiation 6hr Control, Rep2 [mRNA]

source_name: HCAECs, control (MF), 6hr


title: 1 mg/kg bw furan_BrdU_rep5

description: Sample 20

value: liver

value: universal reference


title: MISS_KO_PLB 365m

source_name: MISS KO PLB

value: MISS KO


title: 1 mg/kg bw furan_BrdU_rep3

description: Sample 18

value: 1 mg/kg bw furan for 3wks


title: PostExposure_Sputum_180

description: Sample from human sputum after ozone inhalation exposure

source_name: Sputum sample, after ozone exposure

value: male

value: 0.4 ppm ozone for 2 hours


title: MISS_KO_E2 373

source_name: MISS KO E2


title: 1 mg/kg bw furan_BrdU_rep1

description: Sample 16


title: AF2_WT_E2 137


title: MISS_KO_PLB 101


title: Control_BrdU_rep3

description: Sample 9

value: corn oil oil only (vehicle control) for 3wks


title: PreExposure_Sputum_179


title: PostExposure_Sputum_179


title: PostExposure_Sputum_176


title: PreExposure_Sputum_176


title: Multi-fractionated radiation 6hr Control, Rep3 [mRNA]

value: human coronary artery endothelial cells (HCAECs)

value: control (multi-fractionated radiation)


title: AF2_WT_PLB 209

value: uterus

value: AF2 WT


title: MISS_WT_PLB 100

source_name: MISS WT PLB

value: MISS WT

value: placebo


title: PreExposure_Sputum_173

value: female


title: PostExposure_Sputum_173


title: PreExposure_Sputum_170


title: MISS_WT_E2 371


title: Single-dose radiation 24hr 10Gy, Rep3 [mRNA]

source_name: HCAECs, SD, 24hr

value: single-dose radiation (10Gy)


title: PostExposure_Sputum_169


title: AF2_KO_E2 155

value: AF2 KO


title: Multi-fractionated radiation 6hr Control, Rep1 [mRNA]


title: PreExposure_Sputum_168

value: between 18 and 37 years


title: PreExposure_Sputum_169


title: Single-dose radiation 24hr 10Gy, Rep4 [mRNA]


title: MISS_KO_E2 382


title: AF2_KO_PLB 193


title: PostExposure_Sputum_170


title: PostExposure_Sputum_168


title: Single-dose radiation 24hr Control, Rep4 [mRNA]

source_name: HCAECs, control (SD), 24hr

value: control (single-dose radiation)


title: Single-dose radiation 24hr Control, Rep3 [mRNA]


title: PostExposure_Sputum_163


title: PreExposure_Sputum_163


title: PostExposure_Sputum_167


title: Single-dose radiation 24hr Control, Rep1 [mRNA]


title: AF2_KO_PLB 355


title: PreExposure_Sputum_167


title: PreExposure_Sputum_157


title: Single-dose radiation 6hr 10Gy, Rep4 [mRNA]

source_name: HCAECs, SD, 6hr


title: MISS_WT_PLB 367


title: PostExposure_Sputum_157


title: Single-dose radiation 6hr 10Gy, Rep3 [mRNA]


title: AF2_WT_E2 178


title: PreExposure_Sputum_153


title: MISS_WT_PLB 340


title: PreExposure_Sputum_152


title: Single-dose radiation 24hr 10Gy, Rep1 [mRNA]


title: MISS_KO_E2 369


title: PostExposure_Sputum_141


title: PostExposure_Sputum_152


title: PostExposure_Sputum_153


title: PostExposure_Sputum_140


title: Single-dose radiation 6hr 10Gy, Rep1 [mRNA]


title: PreExposure_Sputum_141


title: Single-dose radiation 6hr Control, Rep4 [mRNA]

source_name: HCAECs, control (SD), 6hr


title: PostExposure_Sputum_137


title: AF2_WT_PLB 357


title: PreExposure_Sputum_137


title: PreExposure_Sputum_140


title: PreExposure_Sputum_136


title: PostExposure_Sputum_136


title: Single-dose radiation 6hr Control, Rep3 [mRNA]


title: PreExposure_Sputum_128


title: PostExposure_Sputum_135


title: Single-dose radiation 6hr Control, Rep1 [mRNA]


title: PreExposure_Sputum_127


title: AF2_WT_E2 172


title: PreExposure_Sputum_135


title: MISS_KO_PLB 363


title: MISS_WT_E2 370


title: PostExposure_Sputum_127


title: PostExposure_Sputum_128


title: PreExposure_Sputum_123


title: AF2_KO_E2 185


title: AF2_KO_PLB 358


title: MISS_KO_E2 372


title: PostExposure_Sputum_123


title: MISS_WT_PLB 337


title: MISS_WT_E2 368


title: MISS_KO_PLB 362


title: M368662_IU

city: Burwood

first: phillip

middle: david

last: parker

state: Victoria

address: 221 Burwood Highway

department: Health

country: Australia

institute: Deakin University

description:
US83403541_252206023757_S01_CGH_107_Sep09_2_1_4
uninvolved control tissue for large bowel fistula

hyb_protocol: The fragmented labelled DNA was then prepared for hybridisation to the Agilent 4x180k Human CGH arrays using the aCGH hybridisation kit (Agilent – 5188-5220) where each hybridisation reaction had a final volume of 110ul.  The Agilent hybridisation chambers were prepared according to manufacturer’s instructions.  Each sample was loaded on to the Agilent hybridisation gaskets slide which is placed into a hybridisation chamber.  The 4x180k array slide was carefully lowered onto the gasket to create a sealed array for each sample.  The hybridisation chambers were then placed in a rotating hybridisation oven at 65C for 24 hours.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

source_name: Gastrointestinal Tissue with active Crohn's Fistula

label_protocol: Human gDNA was quality ascertained using the Nanodrop ND-1000 spectrophotometer and standard agarose gel electrophoresis.  A total of 500ng was fragmented and labelled using the ULS cydye (Cy3 or Cy5) coupling method (Agilent – 5190-0419).  The cydye incorporation was determined using the Nanodrop ND-1000 spectrophotometer.

extract_protocol: Total gDNA was extracted and RNase treated with the QIAmp® DNA FFPE kit (Qiagen, Australia) following the manufacturer’s instructions. For each sample approximately 8 FFPE sections (20mm x 20mm x 10µm per section) were used. gDNA was further treated using the MiniElute PCR purification kit (Qiagen, Australia) followed by whole genome amplification (WGA) using the Ovation® WGA FFPE System (Nugen, USA). For each WGA 200 ng of starting material was used. The amplified DNA product was purified using the MiniElute PCR purification kit (Qiagen, Australia). Patient samples were interrogated for CNV using 4 x 180K (60-mer) genome-wide microarrays (Agilent Technologies, USA). Sample Quality Analysis, hybridisation and data generation were performed by the Australian Genome Research Facility (WEHI, Melbourne, Australia).

treatment_protocol: Samples were selected from patients presenting with Crohn’s Disease fistulae at Eastern Health Department of Gastroenterology and Hepatology (Arnold Street, Box Hill, Victoria, Australia). The 8 samples used in this study were formalin-fixed paraffin-embedded (FFPE) specimens resected as part of a surgical intervention to remove fistula tissue. To focus on changes within the individual patient we used tissue taken from the same surgery at an uninvolved region of the intestine.

tag: Sex

value: Male

tag: patient age

tag: clinical comments

value: Large bowel fistula

source_name: Uninvolved Control Gastrointestinal tissue from same individual as test sample


title: AF2_WT_PLB 195

tag: genotype

tag: genetic background


title: B735051_IU

description:
US83403541_252206023757_S01_CGH_107_Sep09_2_1_1
uninvolved control tissue for sigmoid resection with colovesical fistula

value: Female

value: Sigmoid resection with colovesical fistula


title: murine submandibular gland non-stem cell epithelia 1

city: Stanford

first: tori

last: xn

address: 269 Campus Drive

institute: Stanford

description: Gene expression  of Salivary gland non- stem cell epithelia

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (G4112F) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) 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 GE1-107-Sep09 and Grid: 014868-D-20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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.

extract_protocol: RNA was prepared using the RNeasy kit (Qiagen,Germantown MD) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly murine submandibular gland stem cells and non-stem cell epithelia were sorted through FACs.

value: 8-10 weeks

tag: strain


title: Bronchial Epithelial Cells SA biological 2254P

city: Pittsburgh

first: Jadranka

last: Milosevic

state: PA - Pennsylvania

address: 2330 Tilbury Avenue

institute: University of Pittsburgh

description:
Freshly isolated  Bronchial Epithelial Cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011). The bronchial brushings generally comprised >90% epithelial cells and were placed into Trizol for mRNA analysis.

hyb_protocol: Labeled RNA was hybridized for 17 hr at 65C on Agilent gene expression array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides

data_processing: Agilent Feature Extraction v10.7.3.1 default parameters

source_name: Human Fresh Bronchial Epithelial cells

label_protocol: Cy3-CTP  labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA

extract_protocol: Total RNA extracted using Trizol according to the manufacturer's instructions.

tag: disease state

value: Severe Asthma

value: Fresh Bronchial Epithelial Cells

tag: gender


title: Bronchial Epithelial Cells SA biological 2111T

value: male


title: SH-SY5Y_Mock

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

country: China

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of empty vector

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: SH-SY5Y stably transfected with empty vector

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The H2AB expression or empty vectors were transfected into tumor cell, and stable cell lines were screened by administration of neomycin.

value: neuroblastoma

tag: cell line


title: Bronchial Epithelial Cells SA biological 2147O

tag: age


title: Bronchial Epithelial Cells SA biological 2184U


title: Bronchial Epithelial Cells SA biological 2166S


title: SH-SY5Y_H2AB

description: Gene expression after stable transfection of H2AB expression vector

source_name: SH-SY5Y stably transfected with H2AB expression vector


title: murine submandibular gland stem cells 2

description: Gene expression  of Salivary gland stem cells

source_name: submandibular gland stem cells

value: submandibular gland stem cells


title: Bronchial Epithelial Cells SA biological 2118H


title: M112097_IU

description:
US83403541_252206023757_S01_CGH_107_Sep09_2_1_3
uninvolved control tissue for enterovesical fistula

value: Enterovesical fistula


title: murine submandibular gland stem cells 1


title: Bronchial Epithelial Cells SA biological 2016Z


title: Bronchial Epithelial Cells SA biological 2136J


title: B417270_IU

description:
US83403541_252206023756_S01_CGH_107_Sep09_2_1_2
uninvolved control tissue for subtotal colectomy specimen, fistula tracts reported near IC valve

value: Subtotal colectomy specimen, fistula tracts reported near IC valve


title: Bronchial Epithelial Cells SA biological 2177X

value: female


title: B655579_IU

description:
US83403541_252206023756_S01_CGH_107_Sep09_2_1_4
uninvolved control tissue for small bowel resection/ enterocutaneous fistulae

value: Small bowel resection/ enterocutaneous fistulae


title: Bronchial Epithelial Cells SA biological 2102S


title: Bronchial Epithelial Cells SA biological 2030T


title: Bronchial Epithelial Cells SA biological 2047K


title: Bronchial Epithelial Cells SA biological 1998G


title: B596025_IU

description:
US83403541_252206023756_S01_CGH_107_Sep09_2_1_3
uninvolved control tissue for sigmoid and ileal fistulae

value: Sigmoid and ileal fistulae


title: murine submandibular gland non-stem cell epithelia 2


title: Bronchial Epithelial Cells SA biological 2040W


title: B316315_IU

description:
US83403541_252206023756_S01_CGH_107_Sep09_2_1_1
uninvolved control tissue for proctectomy and ileal resection with enteric and anal fistula

value: Proctectomy and ileal resection with enteric and anal fistula


title: M093243_IU

description:
US83403541_252206023757_S01_CGH_107_Sep09_2_1_2
uninvolved control tissue for enterocutaneous fistula resected

value: Enterocutaneous fistula resected


title: Bronchial Epithelial Cells SA biological 1969Z


title: Bronchial Epithelial Cells SA biological 1987B


title: Bronchial Epithelial Cells SA biological 1929N


title: Bronchial Epithelial Cells SA biological 1870G


title: Bronchial Epithelial Cells SA biological 1744B


title: Blood-Standardbred-Airway inflammation 7023

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: For Cy3 28 pmol incorporated dye was fragmented and resuspended in 55ul hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software version 10.1.1.1 (Agilent Technologies).

data_processing: The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v10.1.1.1) . Intensities were base 2 log-transformed. Control probes were removed.

organism: Equus caballus

source_name: Blood-Standardbread-Airway inflammation

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent Technologies).

extract_protocol: PAXgene Blood RNA Kit

tag: organism

value: Equus caballus; Breed:Standardbred; Condition:Airway inflammation; Tissue:Blood


title: Blood-Endurance-Airway inflammation 7025

source_name: Blood-Endurance-Airway inflammation

value: Equus caballus; Breed:Endurance; Condition:Airway inflammation; Tissue:Blood


title: Blood-Standardbred-Healthy 7022

source_name: Blood-Standardbread-Healthy

value: Equus caballus; Breed:Standardbred; Condition:Healthy; Tissue:Blood


title: Blood-Thoroughbred-Healthy 7020

source_name: Blood-Thoroughbread-Healthy

value: Equus caballus; Breed:Thoroughbred; Condition:Healthy; Tissue:Blood


title: Blood-Endurance-Airway inflammation 7019


title: Bronchial Epithelial Cells SA biological 1661X


title: Blood-Endurance-Healthy 7024

source_name: Blood-Endurance-Healthy

value: Equus caballus; Breed:Endurance; Condition:Healthy; Tissue:Blood


title: Blood-Endurance-Healthy 7018


title: Bronchial Epithelial Cells SA biological 1743Z

value: Severe Asthma


title: Bronchial Epithelial Cells SA biological 1970K

value: Fresh Bronchial Epithelial Cells


title: Bronchial Epithelial Cells SA biological 1989F


title: Blood-Standardbred-Healthy 7016


title: Bronchial Epithelial Cells SA biological 1941D


title: Bronchial Epithelial Cells SA biological 1841Z


title: Blood-Standardbred-Airway inflammation 7017


title: Bronchial Epithelial Cells SA biological 1964P


title: Bronchial Epithelial Cells SA biological 1921X


title: Bronchial Epithelial Cells SA biological 1997E


title: Bronchial Epithelial Cells SA biological 1683H


title: Bronchial Epithelial Cells SA biological 1771E


title: Bronchial Epithelial Cells SA biological 1986Z


title: Bronchial Epithelial Cells SA biological 1918I

value: male


title: Bronchial Epithelial Cells SA biological 1628Z


title: Blood-Thoroughbred-Airway inflammation 7021

source_name: Blood-Thoroughbread-Airway inflammation

value: Equus caballus; Breed:Thoroughbred; Condition:Airway inflammation; Tissue:Blood


title: Blood-Thoroughbred-Airway inflammation 7015


title: Bronchial Epithelial Cells SA biological 1623P


title: Bronchial Epithelial Cells SA biological 1578K


title: Bronchial Epithelial Cells SA biological 0658D


title: Blood-Endurance-Airway inflammation 7013


title: Bronchial Epithelial Cells MMA biological 2014V

value: Moderate Asthma


title: Blood-Endurance-Healthy 7012


title: Bronchial Epithelial Cells MMA biological 2128K


title: Bronchial Epithelial Cells MMA biological 1973Q


title: Bronchial Epithelial Cells MMA biological 2156P


title: Bronchial Epithelial Cells SA biological 1568H


title: Bronchial Epithelial Cells SA biological 1566D


title: Blood-Thoroughbred-Healthy 7014


title: 10nM_insulin_45min

city: Fukuoka

first: Hiroyuki

last: Kubota

address: 3-1-1 Maidashi Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

description: Gene expression after 45min in 10nM insulin stimulated Fao cells

hyb_protocol: Samples were then hybridized to the Agilent Rat Whole Genome Microarrays (Agilent Technologies, #G4131F) according to the standard protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with gene spring 12.5 (Agilent) using default parameters.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Fao 10nM insulin 45min

label_protocol: Labelled cRNA was synthesized from 700 ng of total RNA using the standard protocol of the Agilent Low RNA Input Linear Amplification Kit (Agilent Technologies).

growth_protocol: Fao cells were seeded at a density of 1.8×106 cells per 6 cm dish, and then cultured in RPMI 1640 supplemented with 10% (v/v) fetal bovine serum for 2 days before starvation. The cells were starved in the presence of 10 nM of dexamethasone (Wako) in RPMI 1640 for 16 hours.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen).

treatment_protocol: The cells were stimulated by 10nM insulin for indicated time.

value: Fao rat hepatoma


title: Bronchial Epithelial Cells MMA biological 1945L


title: 10nM_insulin_30min

description: Gene expression after 30min in 10nM insulin stimulated Fao cells

source_name: Fao 10nM insulin 30min


title: Bronchial Epithelial Cells MMA biological 1958U


title: Blood-Standardbred-Healthy 7010


title: Bronchial Epithelial Cells MMA biological 1863J


title: Bronchial Epithelial Cells MMA biological 1790I


title: Blood-Standardbred-Airway inflammation 7011


title: 10nM_insulin_0min

description: Gene expression after 0min in 10nM insulin stimulated Fao cells

source_name: Fao 10nM insulin 0min


title: Bronchial Epithelial Cells MMA biological 1784N


title: Blood-Thoroughbred-Healthy 7008


title: Bronchial Epithelial Cells MMA biological 1708X


title: Bronchial Epithelial Cells MMA biological 0667E


title: 10nM_insulin_60min

description: Gene expression after 60min in 10nM insulin stimulated Fao cells

source_name: Fao 10nM insulin 60min


title: Bronchial Epithelial Cells MMA biological 1751Y


title: Blood-Endurance-Airway inflammation 7007


title: 10nM_insulin_15min

description: Gene expression after 15min in 10nM insulin stimulated Fao cells

source_name: Fao 10nM insulin 15min


title: Blood-Thoroughbred-Airway inflammation 7009


title: Bronchial Epithelial Cells MMA biological 2143G


title: Blood-Standardbred-Airway inflammation 7005


title: Bronchial Epithelial Cells MMA biological 2139P


title: Bronchial Epithelial Cells MMA biological 2073L


title: Bronchial Epithelial Cells MMA biological 2048M


title: Blood-Endurance-Healthy 7006


title: Bronchial Epithelial Cells MMA biological 2198F


title: Bronchial Epithelial Cells MMA biological 2130X


title: Blood-Thoroughbred-Airway inflammation 7003


title: Bronchial Epithelial Cells MMA biological 1691G


title: Bronchial Epithelial Cells MMA biological 2079X


title: Bronchial Epithelial Cells MMA biological 1815Y


title: Bronchial Epithelial Cells MMA biological 2065M


title: Bronchial Epithelial Cells MMA biological 0154V


title: Bronchial Epithelial Cells MMA biological 2134F


title: Blood-Thoroughbred-Healthy 7002


title: Bronchial Epithelial Cells MMA biological 1821T


title: Bronchial Epithelial Cells MMA biological 2154L


title: Bronchial Epithelial Cells MMA biological 1780F


title: Bronchial Epithelial Cells MMA biological 2001M


title: Bronchial Epithelial Cells MMA biological 2122Y


title: Blood-Standardbred-Healthy 7004


title: SFA, 162_W7

city: Stockholm

first: Ingrid

last: Dahlman

address: Karolinska Huddinge

institute: Karolinska

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.1 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix, Inc., Santa Clara, CA).

data_processing: Subsequent data analyses were performed using the Affymetrix GeneChip Operating Software (GCOS) Version 1.4. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probe set scaling to target signal 100. # Summarization: PLIER, Background correction: PM-GCBG, Normalization method: Global Median.

source_name: white adipose tissue, SFA, week 7

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol.

extract_protocol: RNA was extracted using the Nucleospin RNA11 kit (Macherey-Nagel, Duren, Germany). RNA samples were treated with RNase-free DNase (Macherey-Nagel).

treatment_protocol: Patients had been fasting over night. An abdominal subcutaneous adipose tissue needle biopsy was obtained under local anesthesia. The biopsy was rapidly rinsed in saline and snap frozen in liquid nitrogen.

value: abdominal subcutaneous adipose tissue

value: 22 yrs

tag: treatment

value: SFA diet

tag: time

value: week 7

tag: individual identifier


title: PUFA, 161_W7

source_name: white adipose tissue, PUFA, week 7

tag: tissue

value: 29 yrs

value: PUFA diet


title: Bronchial Epithelial Cells MMA biological 0828C

source_name: Human Fresh Bronchial Epithelial cells

tag: cell type

value: female


title: Bronchial Epithelial Cells MMA biological 2003Q


title: SFA, 163_W7

value: 21 yrs


title: SFA, 155_W7


title: SFA, 158_W7

value: 20 yrs


title: Bronchial Epithelial Cells MMA biological 1753C


title: Bronchial Epithelial Cells MMA biological 1765J


title: PUFA, 159_W7

value: 30 yrs


title: Bronchial Epithelial Cells MMA biological 2131Z


title: Bronchial Epithelial Cells MMA biological 0211F


title: Bronchial Epithelial Cells MMA biological 0114X


title: PUFA, 151_W7

value: 26 yrs


title: Bronchial Epithelial Cells MMA biological 2163M


title: Bronchial Epithelial Cells MMA biological 2230B


title: PUFA, 139_W7

value: 24 yrs


title: Bronchial Epithelial Cells MMA biological 1908F

value: Fresh Bronchial Epithelial Cells


title: PUFA, 145_W7

value: 25 yrs


title: Bronchial Epithelial Cells MMA biological 2012R


title: SFA, 150_W7

value: male


title: Bronchial Epithelial Cells MMA biological 2119J

value: Moderate Asthma


title: PUFA, 146_W7


title: Bronchial Epithelial Cells MMA biological 2063I


title: Bronchial Epithelial Cells MMA biological 1943H


title: Bronchial Epithelial Cells MMA biological 1926H


title: Bronchial Epithelial Cells MMA biological 1781H


title: Bronchial Epithelial Cells MMA biological 1752A


title: Stroke Paxgene blood VAL-98

city: Sacramento

first: Glen

last: Jickling

description: miRNA expression from human blood cells

hyb_protocol: Affymetrix miRNA GeneChip 3.0 protocol, 45'C 18hr GeneChip Hybridization Oven 645

scan_protocol: Affymetrix GCS3000 Gene Array Scanner

data_processing: Partek Genomics Suite 6.6, RMA normalization, log2 transformation, hsa-miR filter

source_name: Paxgene venous blood

label_protocol: 200ng total RNA labelled with FlashTag Biotin HSR labeling kits (Affymetrix)

growth_protocol: Venous blood draw into PAXgene tube

extract_protocol: PAXgene blood miRNA kit, Pre-AnalytiX, Quantity and quality of RNA was determined by Nano-Drop (Thermo Fisher) and Agilent 2100 Bioanalyzer (Agilent). Samples required A260/A280 absorbance ratio ≥1.8, A260/A230 ≥1.8, 28S/18S rRNA ratio ≥1.8, and an RNA integrity number ≥8.

treatment_protocol: PAXgene tube, frozen -80'C

tag: diagnosis

value: Ischemic Stroke

value: venous blood


title: Bronchial Epithelial Cells MMA biological 1397G


title: Stroke Paxgene blood VAL-54

description: miRNA expression from human blood cells


title: Stroke Paxgene blood VAL-55

description: miRNA expression from human blood cells


title: Bronchial Epithelial Cells MMA biological 0168R


title: Stroke Paxgene blood VAL-53

description: miRNA expression from human blood cells


title: SFA, 138_W7

value: abdominal subcutaneous adipose tissue

value: 31 yrs


title: PUFA, 136_W7

value: week 7


title: Bronchial Epithelial Cells control biological 2096X

value: Control


title: Stroke Paxgene blood VAL-52

description: miRNA expression from human blood cells


title: Bronchial Epithelial Cells control biological 2170J


title: SFA, 133_W7

value: 23 yrs

value: SFA diet


title: Stroke Paxgene blood VAL-50

description: miRNA expression from human blood cells


title: Bronchial Epithelial Cells MMA biological 1142Z

value: female


title: Stroke Paxgene blood VAL-36

description: miRNA expression from human blood cells


title: Bronchial Epithelial Cells MMA biological 1774K


title: Bronchial Epithelial Cells control biological 2129M


title: SFA, 132_W7

value: 27 yrs


title: Bronchial Epithelial Cells control biological 2034B


title: Bronchial Epithelial Cells control biological 1878H


title: SFA, 130_W7

value: 30 yrs


title: Stroke Paxgene blood VAL-30

description: miRNA expression from human blood cells


title: Bronchial Epithelial Cells control biological 1925F


title: SFA, 129_W7


title: Bronchial Epithelial Cells control biological 1902T


title: Bronchial Epithelial Cells control biological 2052D


title: Bronchial Epithelial Cells control biological 1734Y


title: Bronchial Epithelial Cells control biological 1818E


title: Stroke Paxgene blood VAL-25

description: miRNA expression from human blood cells


title: SFA, 126_W7


title: Stroke Paxgene blood VAL-13

description: miRNA expression from human blood cells


title: Bronchial Epithelial Cells control biological 1733W


title: SFA, 127_W7

value: 33 yrs


title: Bronchial Epithelial Cells control biological 1705R


title: SFA, 121_W7

value: 28 yrs


title: Blood

city: Aarhus N

first: Philippe

last: Lamy

address: Brendstrupgårdsvej 100

department: Department of molecular medecine

country: Denmark

institute: MOMA

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a iScan Reader (Illumina).

data_processing: Genomic DNA extracted from bladder tumors was genotyped using Infinium HumanOmni 1-Quad BeadChip (Illumina, San Diego, CA, USA).

label: C-Bio and A-DNP

source_name: Blood

label_protocol: 500 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA from the paired-WGS set was extracted from frozen tumor tissue and blood using the Puregene DNA purification kit (Gentra Systems, Minneapolis, MN, USA). DNA was amplified  using Multiple Displacement Amplification (MDA) (Illustra GenomiPhi V2 DNA Amplification Kit, GE Healthcare)

value: Female

value: Blood


title: Stroke Paxgene blood VAL-18

institute: University of California Davis

description: miRNA expression from human blood cells


title: Stroke Paxgene blood VAL-09

description: miRNA expression from human blood cells


title: Urothelial bladder tumor 2

description: Genomic DNA extracted from bladder tumors was genotyped using Infinium HumanOmni 1-Quad BeadChip (Illumina, San Diego, CA, USA)

source_name: Bladder Carcinoma

value: Urothelial bladder tumor

value: Carcinoma


title: PUFA, 119_W7

value: male

value: PUFA diet


title: Bronchial Epithelial Cells control biological 1656E

value: Fresh Bronchial Epithelial Cells


title: PUFA, 118_W7

value: abdominal subcutaneous adipose tissue

value: 26 yrs


title: Bronchial Epithelial Cells control biological 1624R

value: Control


title: Bronchial Epithelial Cells control biological 1579M


title: Stroke Paxgene blood UCDSS 707

description: miRNA expression from human blood cells

value: Ischemic Stroke

value: venous blood


title: Stroke Paxgene blood UofASS 016

description: miRNA expression from human blood cells


title: SFA, 117_W7

value: SFA diet

value: week 7


title: Bronchial Epithelial Cells control biological 1070A

value: female


title: Bronchial Epithelial Cells control biological 1325H


title: Stroke Paxgene blood UCDSS 660

description: miRNA expression from human blood cells


title: Stroke Paxgene blood UCDSS 683

description: miRNA expression from human blood cells


title: Bronchial Epithelial Cells control biological 1546X


title: Bronchial Epithelial Cells control biological 1619Y


title: PUFA, 116_W7

value: 22 yrs


title: Stroke Paxgene blood UCDSS 542

description: miRNA expression from human blood cells


title: THP-1 exposed to S1 + S2

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

institute: Meiji Pharmaceutical University

description: Gene expression data from THP-1 exposed to S1 + S2 (LPS+, nigericin +)

hyb_protocol: Hybridization was performed at 45℃ for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software (Affymetrix).

label_protocol: Three hundred ng of total RNA was processed for cDNA synthesis, fragmentation, and terminal labeling with the GeneChip Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix).

growth_protocol: THP-1 cells provided by Riken Cell Bank were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 55 microM 2-mercaptoethanol, 2 mM L-glutamine, 100 U/ml penicillin and 100 microgram/ml streptomycin (culture medium).

extract_protocol: Total cellular RNA was isolated by using the TRIZOL Plus RNA Purification kit (Invitrogen). The quality of total RNA was evaluated on Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: To load the Signal 1 (S1), THP-1 cells were incubated for 3 hours in the culture medium with or without inclusion of 0.2 microgram/ml lipopolysaccharide (LPS). To load the Signal 2 (S2), they were incubated further for 2 hours in the culture medium supplemented with 10 microM nigericin sodium salt dissolved in ethanol or the equal v/v% concentration of ethanol (vehicle).

value: human monocyte cell line THP-1


title: PUFA, 113_W7

value: 28 yrs


title: human fetal alpha 6 integrin+CD133+ epidermal population sort 3356

city: New York

first: Denise

last: Gay

address: 550 1st avenue

institute: NYU langone

description:
Gene expression data from sort 3356 human fetal scalp alpha 6 integrin+CD133+ epidermal cells.
3356_ITGA6+CD133+

hyb_protocol: 5.5ug of labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Gene 1.0ST GeneChips (Affymetrix Inc., Santa Clara CA)

scan_protocol: Gene chips were scanned using a GeneChip 3000 7G scanner.

data_processing: CEL files were normalized with RMA in Partek Genomics Suite v6.6

source_name: epidermis from 13 week human fetal scalp

label_protocol: cRNA, amplified from 250ng total RNA, was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling

growth_protocol: 13 week human fetal scalp tissue was obtained from 1st trimester abortions in conformity with federal and state laws and following National Institute of Health Human Fetal Tissue Research Review Panel of 1988 guidelines. 13 week gestation was defined based upon observance of hair follicle placodes and buds but not external hair shafts.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Plus kit

treatment_protocol: Tissue was dispase-treated to isolate epidermis.Single epidermal cells, obtained by rapid trypsin treatment and mechanical dissociation, were sorted for expression of alpha-6 integrin and CD133 and RNA extracted for gene array analyses.

value: 13 weeks

value: fetal scalp epidermis

tag: tissue population


title: THP-1 exposed to S1

description: Gene expression data from THP-1 exposed to S1 (LPS+, nigericin -)

source_name: THP-1 exposed to S1 (LPS+, nigericin -)


title: human fetal alpha 6 integrin-CD133- epidermal population sort 3356

description:
Gene expression data from sort 3356 human fetal scalp alpha 6 integrin-CD133- epidermal cells.
3356_DN


title: THP-1 control

description: Gene expression data from THP-1 control (LPS-, nigericin -)

source_name: THP-1 control (LPS-, nigericin -)

value: control


title: human fetal alpha 6 integrin+CD133- epidermal population sort 3356

description:
Gene expression data from sort 3356 human fetal scalp alpha 6 integrin+CD133- epidermal cells.
3356_ITGA6+


title: Stroke Paxgene blood UCDSS 452

description: miRNA expression from human blood cells


title: human fetal alpha 6 integrin+CD133- epidermal population sort 3292

description:
Gene expression data from sort 3292 human fetal scalp alpha 6 integrin+CD133- epidermal cells.
3292_ITGA6+


title: human fetal alpha 6 integrin+CD133+ epidermal population sort 3292

description:
Gene expression data from sort 3292 human fetal scalp alpha 6 integrin+CD133+ epidermal cells.
3292_ITGA6+CD133+


title: human fetal alpha 6 integrin-CD133- epidermal population sort 3292

description:
Gene expression data from sort 3292 human fetal scalp alpha 6 integrin-CD133- epidermal cells.
3292_DN


title: Stroke Paxgene blood UCDSS 381

description: miRNA expression from human blood cells


title: Stroke Paxgene blood UCDSS 424

description: miRNA expression from human blood cells


title: SFA, 114_W7

value: 36 yrs


title: Urothelial bladder tumor 1

value: Female

value: Urothelial bladder tumor

value: Carcinoma


title: p31 Tumor rep 2

city: Boston

first: Svitlana

last: Tyekucheva

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were RMA normalized using Bioconductor package 'oligo' version 1.24.2.

source_name: prostate

label_protocol: WT-Ovation FFPE System V2 (NuGEN Inc; San Carlos, CA)

extract_protocol: Areas of high-density tumor were identified, and 0.6 mm punches were taken from both tumor and adjacent non-tumor prostatic tissue for RNA extraction. The cores were deparaffinized using 800 μL Citrisolv (Fisher Scientific, Pittsburgh, PA) at 60°C for 20 minutes followed by 1.2 mL Citrisolv:absolute alcohol (2:1) at room temperature for 10 minutes. Cores were subsequently washed with absolute alcohol, dried at 55°C, and incubated overnight at 45°C in 300 μL lysis buffer (10 mM NaCl, 500 mM Tris [pH 7.6], 20 mM EDTA, 1% sodium dodecyl sulfate) containing 1 mg/mL proteinase K (Ambion, Austin, TX).  RNA was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Ambion). Post tissue digestion, following the manufacturer’s protocol, samples were incubated in 10x DNase (Ambion) and column purified to elute RNA.

tag: block age

tag: tissue type

value: Tumor

tag: gleason score

tag: amount


title: p19 Tumor rep 2


title: Stroke Paxgene blood UCDSS 291

description: miRNA expression from human blood cells


title: Stroke Paxgene blood UCDSS 127

description: miRNA expression from human blood cells


title: p14 Tumor rep 2


title: p16 Normal rep

value: Normal


title: SFA, 109_W7

value: abdominal subcutaneous adipose tissue

value: male

value: 26 yrs


title: SFA, 112_W7

value: 34 yrs

value: SFA diet

value: week 7


title: PUFA, 111_W7

value: 33 yrs

value: PUFA diet


title: p16 Tumor rep 2


title: Stroke Paxgene blood UCDSS 099

description: miRNA expression from human blood cells

value: Ischemic Stroke

value: venous blood


title: p16 Normal


title: Control Paxgene blood VAL-99

description: miRNA expression from human blood cells

value: Control


title: p31 Normal rep 2


title: p19 Tumor rep


title: p19 Normal rep


title: PUFA, 104_W7

value: 22 yrs


title: PUFA, 106_W7

value: 35 yrs


title: Stroke Paxgene blood UCDSS 084

description: miRNA expression from human blood cells


title: p1 Tumor rep


title: p14 Tumor rep


title: PUFA, 103_W7

value: female

value: 31 yrs


title: PUFA, 102_W7

value: 28 yrs


title: Healthy blood donor N260

type: other

city: Homburg/Saar

first: Christian

middle: Clemens

last: Harz

state: Saarland

address: Kirrberger Strasse 100

department: Department of Human Genetics

institute: Saarland University

description: 163 peptides, representing TXNDC16, were spotted in duplicates to identify seroreaction of serum autoantibodies

hyb_protocol: Arrays were blocked o.N. at 4°C (Blocking solution: 50mM Tris, 150mM NaCl, pH 7.5, 5% dry milk powder). Arrays were then incubated with serum (1:1,000 diluted in blocking solution) o.N. at 4°C. Arrays were washed three times with TBS-T (50mM Tris, 150mM NaCl, pH 7.5, 0.05% Tween20) for 10 min at RT and then incubated with Cy5-conjugated AffiniPure Rabbit Anti-Human IgA + IgG + IgM (H + L) (Dianova) (1:1,000 diluted in blocking solution) for 2h at RT. After secondary antibody incubation, arrays were washed twice with TBS-T and twice with TBS for 10 min at RT.

scan_protocol: The arrays were then scanned at 20-µm resolution (PTM Voltages 40) with a PerkinElmer ScanArray Express, images of the peptide arrays were processed with ScanArray Express software and signal intensities quantified

data_processing:
Column Ch1 Mean was extracted from all raw data files. All values for empty and GRID spots were excluded, leaving 326 (163 in duplicates) data point for each sample. All spots were classified into three groups via their mean foreground intensity values (2 “strongly seropositive” if x >= quantile 0.95, 1 “weakly seropositive” if quantile 0.8 <= x < quantile 0.95 and 0 “seronegative” if x < quantile 0.8). For each peptide, both spot values were multiplied, resulting 4 - strongly seroreactive, 2 - moderatly seroreactive, 1 - weakly seroreactive, 0 - seronegative.
Please note that the non_normalized.txt contains  Ch1 Mean values for all samples (each sequence represented in duplicates) and the identifiers in the 'index' column corresponds to those in the 'index' column in raw gpr files; sample data table contains classification values (for each sequence) described above.

molecule: other

source_name: Normal control serum

label_protocol: No label was performed on the serum sample.

extract_protocol: Blood samples were centrifuged immediatly after withdrawal at 3,000 x g for 10 min and sera were subsequently stored at -20°C.

tag: subject status

value: healthy control

tag: age (yrs)

tag: molecule type

value: serum autoantibodies


title: SFA, 108_W7

value: abdominal subcutaneous adipose tissue

tag: gender

value: male

value: 24 yrs


title: p14 Normal rep

value: Normal


title: Control Paxgene blood VAL-51

description: miRNA expression from human blood cells


title: p1 Normal


title: Healthy blood donor N230


title: Healthy blood donor N250


title: PUFA, 107_W7

tag: age

value: 27 yrs

value: week 7


title: p31 Normal rep


title: Healthy blood donor N270


title: PUFA, 101_W7

value: PUFA diet


title: SFA, 163_W0

source_name: white adipose tissue, SFA, week 0

value: 21 yrs

value: SFA diet

value: week 0


title: Healthy blood donor N220


title: SFA, 162_W0

value: 22 yrs


title: Control Paxgene blood VAL-22

description: miRNA expression from human blood cells

value: Control

value: venous blood


title: Control Paxgene blood UCDSS 550

description: miRNA expression from human blood cells


title: Control Paxgene blood UofASS 036

description: miRNA expression from human blood cells


title: Control Paxgene blood VAL-49

description: miRNA expression from human blood cells


title: Healthy blood donor N42

value: female


title: Control Paxgene blood UCDSS 546

description: miRNA expression from human blood cells


title: Control Paxgene blood UCDSS 549

description: miRNA expression from human blood cells


title: p14 Tumor

value: Tumor


title: PUFA, 161_W0

source_name: white adipose tissue, PUFA, week 0

value: 29 yrs


title: PUFA, 159_W0

value: 30 yrs


title: Healthy blood donor N40

value: healthy control

value: serum autoantibodies


title: SFA, 158_W0

value: abdominal subcutaneous adipose tissue

value: male

value: 20 yrs


title: Healthy blood donor N39


title: p19 Tumor


title: p14 Normal

value: Normal


title: PUFA, 151_W0

value: 26 yrs

value: PUFA diet


title: p1 Tumor


title: Control Paxgene blood UCDSS 537

description: miRNA expression from human blood cells


title: p7 Tumor rep


title: Healthy blood donor N41


title: Healthy blood donor N50


title: SFA, 155_W0

value: SFA diet


title: Control Paxgene blood UCDSS 536

description: miRNA expression from human blood cells


title: Healthy blood donor N37


title: p19 Normal


title: Control Paxgene blood UCDSS 514

description: miRNA expression from human blood cells


title: Control Paxgene blood UCDSS 510

description: miRNA expression from human blood cells


title: SFA, 150_W0

value: 25 yrs

value: week 0


title: Control Paxgene blood UCDSS 431

description: miRNA expression from human blood cells

value: Control


title: Healthy blood donor N32


title: Healthy blood donor N34


title: p31 Tumor rep


title: p31 Tumor


title: p8 Normal


title: PUFA, 145_W0


title: Healthy blood donor N38


title: Control Paxgene blood UCDSS 350

description: miRNA expression from human blood cells

value: venous blood


title: Healthy blood donor N31


title: PUFA, 146_W0

value: female


title: p7 Tumor

value: Tumor


title: Healthy blood donor N36


title: Control Paxgene blood UCDSS 281

description: miRNA expression from human blood cells


title: SFA, 133_W0

value: 23 yrs


title: p8 Tumor rep


title: PUFA, 139_W0

value: 24 yrs


title: p16 Tumor


title: PUFA, 136_W0

value: 29 yrs


title: Control Paxgene blood UCDSS 272

description: miRNA expression from human blood cells


title: Healthy blood donor N9

value: healthy control

value: serum autoantibodies


title: SFA, 130_W0

value: abdominal subcutaneous adipose tissue

value: male

value: 30 yrs


title: Meningioma patient H1434

source_name: Meningioma patient serum

value: Meningioma patient

tag: tumor stage

value: WHO grade I


title: p16 Tumor rep


title: Control Paxgene blood UCDSS 222

description: miRNA expression from human blood cells


title: Control Paxgene blood UCDSS 216

description: miRNA expression from human blood cells


title: SFA, 138_W0

value: 31 yrs

tag: treatment

value: SFA diet


title: p31 Normal

value: Normal


title: SFA, 129_W0

tag: time

value: week 0


title: Healthy blood donor N20


title: Healthy blood donor N13


title: p7 Normal


title: Meningioma patient H1428

value: WHO grade II


title: Control Paxgene blood UCDSS 211

description: miRNA expression from human blood cells

value: Control

value: venous blood


title: Meningioma patient H1408

value: female


title: p8 Tumor

value: Tumor


title: Control Paxgene blood UCDSS 210

description: miRNA expression from human blood cells


title: Control Paxgene blood UCDSS 212

description: miRNA expression from human blood cells


title: Control Paxgene blood UCDSS 196

description: miRNA expression from human blood cells


title: SFA, 127_W0

value: 33 yrs

tag: individual identifier


title: Meningioma patient H1401

value: WHO grade II/III


title: SFA, 126_W0

tag: tissue

value: 27 yrs


title: Bronchial Epithelial Cells control biological 1701J

description:
Freshly isolated  Bronchial Epithelial Cells
Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011). The bronchial brushings generally comprised >90% epithelial cells and were placed into Trizol for mRNA analysis.

tag: disease state

tag: cell type

value: Fresh Bronchial Epithelial Cells


title: Meningioma patient H1410

value: serum autoantibodies


title: Meningioma patient H1395


title: Control Paxgene blood UCDSS 174

description: miRNA expression from human blood cells

tag: diagnosis


title: G765 rep 2

source_name: ovarian cancer

extract_protocol: RNA was extracted from paraffin scrolls using the RNeasy FFPE kit (Qiagen) with modification.  In brief, 1 ml of xylene was first added to a 25 μm paraffin scroll, vortexed vigorously for 10 sec and centrifuged at full speed for 2 min.  Supernatant was then removed and 1 ml of ethanol (100%) was added to the pellet, mixed by vortexing and centrifuged at full speed for 2 min.  Supernatant was removed and the tube was incubated at room temperature from 10 min with lid opened.  Subsequently, RNA was extracted using reagents provided in the RNeasy FFPE extraction kit according to the manufacturer’s instruction.  Finally, purified RNA was eluted from the RNeasy MinElute spin column using 30 μl RNase-free water.

tag: block age

value: serous carcinoma

tag: percent tumor

tag: percent necrosis


title: Meningioma patient H1359

value: Meningioma patient


title: SFA, 132_W0

value: abdominal subcutaneous adipose tissue


title: G901 rep

value: clear cell carcinoma


title: Control Paxgene blood UCDSS 189

description: miRNA expression from human blood cells


title: Meningioma patient H1343


title: G969 rep


title: G403 rep


title: PUFA, 116_W0

value: male

value: 22 yrs

value: PUFA diet


title: Meningioma patient H1334

value: WHO grade I


title: G653 rep


title: SFA, 121_W0

value: 28 yrs

value: SFA diet

value: week 0


title: PUFA, 118_W0

value: 26 yrs


title: SFA, 117_W0


title: G678 rep


title: G776 rep