title: Rheumatoid arthritis, synovial membrane patient EB_110 (U133A)

description:
see publication for details
EB_110

source_name: synovial membrane patient EB_110 (rheumatoid arthritis)

treatment_protocol: NSARD, prednisolone


title: Rheumatoid arthritis, synovial membrane patient EB_141 (U133A)

status: Public on Mar 05 2014

type: RNA

city: Eisenberg

first: Raimund

middle: W

last: Kinne

address: Klosterlausnitzer Str. 81

department: Department of Orthopedics

country: Germany

institute: Jena University Hospital

description:
see publication for details
EB_141

hyb_protocol: according to supplier instructions, Affymetrix

scan_protocol: by laser scanning (Hewlett Packard gene scanner)

data_processing:
background corrected signal intensities were determined using the MAS 5.0 software (Affymetrix)
MAS5.0 signal intensity, ABS_CALL: presence/absence call, DETECTION P-VALUE: significance of 0-hypothesis (not expressed)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: synovial membrane patient EB_141 (rheumatoid arthritis)

extract_protocol: according RNeasy Kit, Qiagen

treatment_protocol: NSAID, prednisolone, Tilidin

tag: gender

value: female

tag: age

tag: clinical status

value: rheumatoid arthritis


title: genomic DNA from HIV/TB co-infected patient 11

type: genomic

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

country: USA

institute: The Wistar Institute

description:
HIV/TB co-infection
FAA0ZVHT-14_02-Feb-2010

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: Illumina's GenomeStudioV2010.1 was used to export Beta values, detection p-values and signals.  Raw data were quantile normalized.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMCs using the modified protocol of Sigma Aldrich Tri-reagent

value: Male

tag: sample type

value: PBMC

tag: disease state

value: HIV/TB


title: genomic DNA from HIV/TB co-infected patient 6

description:
HIV/TB co-infection
BAA0ZC4J-13_07-Dec-2009


title: genomic DNA from HIV/TB co-infected patient 8

description:
HIV/TB co-infection
CAA0ZN6L-12_13-Jan-2010


title: Rheumatoid arthritis, synovial membrane patient EB_124 (U133A)

description:
see publication for details
EB_124

source_name: synovial membrane patient EB_124 (rheumatoid arthritis)

label_protocol: according to supplier instructions, Affymetrix

treatment_protocol: COX-2 inhibitor, prednisolone, quensyl

value: male


title: genomic DNA from HIV/TB co-infected patient 12

description:
HIV/TB co-infection
GAA0S8NL-11_30-Sep-2008


title: genomic DNA from HIV/TB co-infected patient 2

description:
HIV/TB co-infection
AAA0RWJ0-14_02-Sep-2008

value: Female


title: genomic DNA from HIV/TB co-infected patient 4

description:
HIV/TB co-infection
AAA0ZSJX-10_26-Jan-2010


title: genomic DNA from HIV infected patient 19

description:
HIV
KAA0Q3QH-14_24-Apr-2008

value: HIV only


title: Analysis 2: European American - Biological replicate 7

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_3 sample in analysis 1, 3, 4, 6, 8

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray (G4858A-039494) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data was uploaded into Genespring version 11.5.1 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.

source_name: European American - Oropharyngeal squamous cell carcinoma - HPV Negative

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

extract_protocol: Total RNA was isolated from fresh frozen tumor samples using a miniaturized mortar and pestle system (CryoGrinder™, CryoCooler™, OPS diagnostics LLC) and TRIzol® Reagent (Ambion®, by Life Technologies).

tag: race

value: European American


title: Analysis 2: European American - Biological replicate 8

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_3 sample in analysis 1, 3, 4, 6, 8


title: genomic DNA from HIV/TB co-infected patient 5

description:
HIV/TB co-infection
BAA0YXVB-12_12-Nov-2009


title: Rheumatoid arthritis, synovial membrane patient EB_74 (U133A)

description:
see publication for details
EB_74

source_name: synovial membrane patient EB_74 (rheumatoid arthritis)

treatment_protocol: NSARD


title: Rheumatoid arthritis, synovial membrane patient EB_56 (U133A)

description:
see publication for details
EB_56

source_name: synovial membrane patient EB_56 (rheumatoid arthritis)

treatment_protocol: prednisolone, MTX


title: Rheumatoid arthritis, synovial membrane patient EB_108 (U133A)

description:
see publication for details
EB_108

source_name: synovial membrane patient EB_108 (rheumatoid arthritis)


title: Osteoarthritis, synovial membrane patient EB_54 (U133A)

description:
see publication for details
EB_54

source_name: synovial membrane patient EB_54 (osteoarthrisits)

value: osteoarthritis


title: genomic DNA from HIV infected patient 17

description:
HIV
JAA0W223-10_16-Apr-2009


title: genomic DNA from HIV/TB co-infected patient 7

description:
HIV/TB co-infection
BAA0ZXTF-11_08-Feb-2010


title: Analysis 2: European American - Biological replicate 6

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_3 sample in analysis 1, 3, 4, 6, 8


title: genomic DNA from HIV infected patient 16

description:
HIV
JAA0P0DQ-11_15-Feb-2008


title: genomic DNA from HIV/TB co-infected patient 3

description:
HIV/TB co-infection
AAA0Z4D1-15_25-Nov-2009


title: Rheumatoid arthritis, synovial membrane patient EB_40 (U133A)

description:
see publication for details
EB_40

source_name: synovial membrane patient EB_40 (rheumatoid arthritis)

treatment_protocol: NSARD, prednisolone, MTX


title: genomic DNA from HIV infected patient 15

description:
HIV
HAA0W3R9-13_21-Apr-2009


title: genomic DNA from HIV infected patient 14

description:
HIV
HAA0W3B8-14_20-Apr-2009


title: Rheumatoid arthritis, synovial membrane patient EB_35 (U133A)

description:
see publication for details
EB_35

source_name: synovial membrane patient EB_35 (rheumatoid arthritis)

treatment_protocol: NSARD, azulfidine, prednisolone, MTX


title: Analysis 2: European American - Biological replicate 5

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_1 sample in analysis 1, 3, 4, 6, 8


title: genomic DNA from HIV infected patient 11

description:
HIV
DAA0V9RP-16_25-Feb-2009


title: Rheumatoid arthritis, synovial membrane patient EB_27 (U133A)

description:
see publication for details
EB_27

source_name: synovial membrane patient EB_27 (rheumatoid arthritis)


title: Analysis 2: European American - Biological replicate 3

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_3 sample in analysis 1, 3, 4, 6, 8


title: genomic DNA from HIV infected patient 9

description:
HIV
CAA0W4LT-13_23-Apr-2009


title: Rheumatoid arthritis, synovial membrane patient EB_30 (U133A)

description:
see publication for details
EB_30

source_name: synovial membrane patient EB_30 (rheumatoid arthritis)


title: genomic DNA from HIV infected patient 12

description:
HIV
DAA0VD27-11_04-Mar-2009


title: Analysis 2: European American - Biological replicate 2

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_2 sample in analysis 1, 3, 4, 6, 8


title: genomic DNA from HIV infected patient 10

description:
HIV
DAA0PFCT-11_17-Jan-2008


title: genomic DNA from HIV infected patient 13

description:
HIV
FAA0W22D-13_16-Apr-2009


title: genomic DNA from HIV infected patient 7

description:
HIV
CAA0Q3CK-13_24-Apr-2008


title: Normal, synovial membrane patient J_12 (U133A)

description:
see publication for details
J_12

source_name: synovial membrane patient J_12 (normal controls)

value: normal control


title: Analysis 2: European American - Biological replicate 1

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_1 sample in analysis 1, 3, 4, 6, 8


title: Analysis 2: European American - Biological replicate 4

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_1 sample in analysis 1, 3, 4, 6, 8


title: Analysis 2: African American - Biological replicate 7

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_4 sample in analysis 1, 4, 6

source_name: African American - Oropharyngeal squamous cell carcinoma - HPV Negative

value: African American


title: genomic DNA from HIV infected patient 4

description:
HIV
BAA0W3BM-11_20-Apr-2009


title: Rheumatoid arthritis, synovial membrane patient EB_20 (U133A)

description:
see publication for details
EB_20

source_name: synovial membrane patient EB_20 (rheumatoid arthritis)

treatment_protocol: NSARD, azulfidine, prednisolone


title: Normal, synovial membrane patient J_7 (U133A)

description:
see publication for details
J_7

source_name: synovial membrane patient J_7 (normal controls)


title: genomic DNA from HIV infected patient 5

description:
HIV
BAA0W69B-10_29-Apr-2009


title: genomic DNA from HIV infected patient 3

description:
HIV
BAA0V9SR-15_25-Feb-2009


title: genomic DNA from HIV infected patient 2_2

description:
HIV
AAA0W22R-14_16-Apr-2009


title: genomic DNA from HIV infected patient 6

description:
HIV
BAA0WVPG-10_04-Jun-2009


title: genomic DNA from HIV infected patient 2_1

description:
HIV
AAA0W22R-11_16-Apr-2009


title: miR-2909 Transfected HeLa

city: Chandigarh

first: Deepak

last: Kaul

state: Chandigarh

address: Sec 12

department: Experimental Medicine & Biotechnology

country: India

institute: PGIMER

description: Gene Regulation by miR-2909

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 20 hr at 48°C on GeneChip HumanGene 1.1ST Array Strip. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Imaging Station.

data_processing:
The data was analyzed with Partek Express Affymetrix Edition using Affymetrix default analysis settings and global scaling as normalization method.
Signal intensity data are not available for this sample.
Ratio and fold-changes (Control/miR-2909 Treatment)

label: Biotin

source_name: HeLa Cell line_miR-2909_transfected

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

growth_protocol: Cells were grown in RPMI-1640 at 37°C, 5% CO2 invitro culture.

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

treatment_protocol: Cells were transfected at 80% confluency with miR-2909 expression vector and then incubated for 48 hrs at 37°C, 5% CO2.

tag: cell line

tag: tissue

value: cervix


title: genomic DNA from HIV infected patient 8

description:
HIV
CAA0W4LJ-15_23-Apr-2009


title: Analysis 2: African American - Biological replicate 6

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_3 sample in analysis 1, 4, 6


title: Analysis 2: African American - Biological replicate 8

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_1 sample in analysis 1, 4, 6


title: Analysis 2: African American - Biological replicate 5

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_3 sample in analysis 1, 4, 6


title: Normal, synovial membrane patient J_2 (U133A)

description:
see publication for details
J_2

source_name: synovial membrane patient J_2 (normal controls)


title: Control Transfected HeLa

description: control vector

source_name: HeLa Cell line_control_transfected


title: Normal, synovial membrane patient NST_1 (U133A)

description:
see publication for details
NST_1

source_name: synovial membrane patient NST_1 (normal controls)


title: Naive_rep3

city: London

first: Simone

last: Di Giovanni

address: DuCane Road W12 ONN UK

department: Medicine

country: United Kingdom

institute: Imperial College

description: 18,180 genes analyzed from '2007-02-27 MM8 CpG Island Promoter 385K RefSeq'

hyb_protocol: corresponding IP (experimental) and Input (control) samples were co-hybridized to a 385K array using the approproate protocol, according to the NimbleGen Guide. The proximal regions of gene promoters and additional CpG islands  were covered by close-set 50 base oligonucleotides (approx. -1,500 to + 800 bp around TSS)

scan_protocol: The two-color (IP-Cy5/Input-Cy3) arrays were scanned apllying the Nimblescan 2.4 software (used by NimbleGen, not supported anymore)

data_processing:
raw data was extracted from Nimblescan files and computed to scaled and centered log2-Cy5/Cy3 values for each oligonucleotide probe, coverted into graphic data set (.gff files with SignalMap software).
All steps from labelling to data processing  have been performed as a service of NimbleGen, according to NimbleGen Arrays User’s Guide for Epigenetic Arrays.
Scaled log2-values IP/Input ratios, Kolmogorov-Smirnov test to yield log10 p-values (or peaks) for significant methylaton for each promoter region. Peaks analyzed for 18,180 annotated genes (NCBI Gene ID) for each condition

organism: Mus musculus

source_name: me5-C MeDIP DNA from WT DRG_Naive [Cy5 Test]

label_protocol: 1 µg of whole-genome.amplified MeDIP DNA (IP) and genomic input DNA (Input) were labeled with Cy5 or Cy3 nonamers, respectively (via Klenow Fragment)

extract_protocol: From two mice per condition (1, 3, or 7 days following either sciatic nerve axotomy (SNA) or dorsal column axotomy (DCA), or naive), all (lumbar) L4-6 DRG were extracted (kept in ice-cold HBSS buffer), pooled, washed, qick-frozen in liquid nitrogen, crushed, and lysed in MeDIP lysis buffer (10 mM Tris/HCl, pH 8.0, 100 mM NaCl, 25 mM EDTA,  0.5 % SDS, 0.2 mg/ml Proteinase K). Genomic DNA was sonicated to an average fragment size of 700 bp (100 to 2,000 bp range), purified, quality-checked and quantified (peqlab NanoDrop ND-1000; agarose gel). All IP and Input samples were whole-genome-amplified (Sgma_Aldrich WGA2 kit) and shipped to Roche/NimbleGen for further processing

tag: genotype

value: wildtype

tag: strain

value: 2 to 3 months

value: all (lumbar) L4-6 DRG

tag: injury

value: no injury

tag: group

tag: medip antibody

value: 5-methyl-cytosine (IP)

source_name: Input DNA from WT DRG_Naive [Cy3 Input]

value: Sciatic nerve axotomy (SNA)

value: real injury

value: none  (input)


title: DCA 7days sham_rep2

source_name: me5-C MeDIP DNA from WT DRG_DCA 7D [Cy5 Test]

value: Dorsal column axotomy (DCA)

value: sham

source_name: Input DNA from WT DRG_DCA 7D [Cy3 Input]


title: genomic DNA from HIV infected patient 1

description:
HIV
AAA0VKQN-12_18-Mar-2009

source_name: PBMC

value: Female

value: PBMC


title: Analysis 2: African American - Biological replicate 3

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_3 sample in analysis 1, 4, 6


title: Normal, synovial membrane patient J_6 (U133A)

description:
see publication for details
J_6

source_name: synovial membrane patient J_6 (normal controls)

value: male


title: Analysis 1: HPV Negative - Biological replicate 16

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_3 sample in analysis 2, 3, 4, 6, 8

source_name: Oropharyngeal squamous cell carcinoma - HPV Negative

value: European American


title: Analysis 2: African American - Biological replicate 2

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_2 sample in analysis 1, 4, 6

value: Male


title: Analysis 2: African American - Biological replicate 1

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_4 sample in analysis 1, 4, 6

value: African American


title: Analysis 1: HPV Negative - Biological replicate 12

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_3 sample in analysis 2, 4, 6


title: HCT116 siCARLo-5 -1

city: Columbus

first: Taewan

last: Kim

state: OH

institute: The Ohio State University

description:
raw data file: HCT116 siCARLo-5.txt
nCounter Virtual Cell Cycle Gene Set

hyb_protocol: Hybridization reactions were performed according to manufacturer’s instructions with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h.

scan_protocol: A high density scan (600 fields of view) was performed

data_processing: The analysis of raw data was performed with nSlover Analysis Software provided by Nanostring Technologies.

source_name: Colorectal cancer-derived HCT116 cell line

growth_protocol: Cells were grown in 37 degree humidified incubator with 5% CO2.

extract_protocol: Total RNA samples were prepared usin TRIZOL (Invitrogen) in accordance with manufacturer's instruction

treatment_protocol: Cells were transfected with siRNA (Final concentration: 50nM for HCT116 and 100nM for PC3) by using Lipofectamine RNAiMAX from Invitrogen as the instruction of manufacturer

tag: treatment

value: siRNA targeting CARLo-5


title: HCT116 siCARLo-5 -2

value: Colorectal cancer-derived HCT116 cell line


title: HCT116 siCTRL-3

description:
raw data file: HCT116 siCTRL.txt
nCounter Virtual Cell Cycle Gene Set

hyb_protocol: Hybridization reactions were performed according to manufacturer's instructions with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h.

scan_protocol: A high-density scan (600 fields of view) was performed.

extract_protocol: Total RNA samples were prepared using TRIZOL (Invitrogen) in accordance with manufacturer's instruction

treatment_protocol: Cells were transfected with siRNA (Final concentration: 50nM for HCT116 and 100nM for PC3) by using Lipofectamine RNAiMAX from Invitrogen as the instruction of manufacturer.

value: control siRNA


title: Analysis 1: HPV Negative - Biological replicate 14

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_1 sample in analysis 2, 4, 6


title: Analysis 2: African American - Biological replicate 4

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_4 sample in analysis 1, 4, 6


title: Analysis 1: HPV Negative - Biological replicate 15

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_3 sample in analysis 2, 3, 4, 6, 8


title: Normal, synovial membrane patient J_19 (U133A)

description:
see publication for details
J_19

source_name: synovial membrane patient J_19 (normal controls)

value: normal control


title: Naive_rep2

value: wildtype

value: 2 to 3 months

value: all (lumbar) L4-6 DRG

value: no injury


title: Analysis 1: HPV Negative - Biological replicate 11

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_3 sample in analysis 2, 3, 4, 6, 8


title: Naive_rep1

value: 5-methyl-cytosine (IP)

value: Sciatic nerve axotomy (SNA)

value: real injury

value: none  (input)


title: HCT116 siCARLo-5 -3


title: HCT116 siCTRL-2


title: DCA 7days injury_rep3

value: Dorsal column axotomy (DCA)


title: Normal, synovial membrane patient EB_228 (U133A)

description:
see publication for details
EB_228

source_name: synovial membrane patient EB_228 (normal controls)

value: male


title: DCA 7days sham_rep1

value: sham


title: Normal, synovial membrane patient EB_188 (U133A)

description:
see publication for details
EB_188

source_name: synovial membrane patient EB_188 (normal controls)

value: female


title: Normal, synovial membrane patient EB_184 (U133A)

description:
see publication for details
EB_184

source_name: synovial membrane patient EB_184 (normal controls)


title: Analysis 1: HPV Negative - Biological replicate 10

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_3 sample in analysis 2, 4, 6

value: Female

value: African American


title: HCT116 siCTRL-1

value: Colorectal cancer-derived HCT116 cell line


title: Analysis 1: HPV Negative - Biological replicate 13

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_4 sample in analysis 2, 4, 6

value: Male


title: Analysis 1: HPV Negative - Biological replicate 9

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_1 sample in analysis 2, 3, 4, 6, 8

value: European American


title: DCA 7days injury_rep2

value: wildtype


title: DCA 7days injury_rep1

value: 2 to 3 months


title: Analysis 1: HPV Negative - Biological replicate 7

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_3 sample in analysis 2, 4, 6


title: Mouse k401_5, AIP_wt

city: Helsinki

first: Miika

last: Mehine

address: P.O. Box 63 (Haartmaninkatu 8)

country: Finland

institute: University of Helsinki

description:
k401_5
Expression data from Mouse k401_5, AIP_wt

hyb_protocol: According to the standard Affymetrix protocol

data_processing:
All samples were quantile-normalized by the RMA method (Robust Multichip Average) using re-mapped gene annotations from Brainarray Custom CDF files (MoEx10stv1, Version 14.1.0, http://brainarray.mbni.med.umich.edu/Brainarray/default.asp)
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: Mouse k401_5, AIP_wt

growth_protocol: Cells were cultured in 95% air, 5% CO2 at 37 °C and grown in high glucose DMEM (4.5 g/l glucose) supplemented with glutamine, 10% FBS and antibiotics. Cells were collected at second passage (p2).

extract_protocol: RNA was extracted with RNeasy Mini Kit (Qiagen) and purified with RNeasy MinElute TM clean up kit.

tag: cell type

value: embryonic fibroblast cells

tag: genotype/variation

value: AIP_wild type


title: Analysis 1: HPV Negative - Biological replicate 8

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_4 sample in analysis 2, 4, 6


title: DCA 3days sham_rep1

description: 18,180 genes analyzed from '2007-02-27 MM8 CpG Island Promoter 385K RefSeq'

source_name: me5-C MeDIP DNA from WT DRG_DCA 3D [Cy5 Test]

value: all (lumbar) L4-6 DRG

value: 5-methyl-cytosine (IP)

source_name: Input DNA from WT DRG_DCA 3D [Cy3 Input]


title: DCA 3days sham_rep2

value: Sciatic nerve axotomy (SNA)

value: real injury


title: Mouse k370_5, AIP_wt

description:
k370_5
Expression data from Mouse k370_5, AIP_wt

scan_protocol: According to the standard Affymetrix protocol

source_name: Mouse k370_5, AIP_wt


title: Mouse k564_1, AIP_wt

description:
k564_1
Expression data from Mouse k564_1, AIP_wt

source_name: Mouse k564_1, AIP_wt

label_protocol: According to the standard Affymetrix protocol


title: Dog 3 sample B1 PRP-SVF-6h,37 degrees

city: Lexington

first: Donald

last: Cohen

state: KY

address: 800 Rose Street

department: Microbiology, Immunology and Molecular Genetics

institute: Univ. of Kentucky

description: SAMPLE 9

hyb_protocol: Samples were hybridized overnight in a Affymetrix GeneChip Hybridization Oven 640 according to manufacturer's instructions

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner

data_processing: Data were analyzed using Partek Genomic Suite using Affymetrix default analysis settings and global scaling as normalization method.

organism: Canis lupus familiaris

source_name: visceral adipose

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: Visceral adipose tissue was isolated and stromal vascular fractions isolated by 3 different companies as indicated

extract_protocol: Total RNA was extracted from SVF using RNeasy Mini Kits from Qiagen according to the manufacturer's instructions.

treatment_protocol:
Samples 1 - 3 are adipose tissue that was digested by 3 individual companies using their own proprietary methods to prepare stromal vascular fraction.  Each sample was cryopreserved for one month and then thawed by this lab to isolate total RNA for microarray analysis.
Samples 4 - 11 are adipose tissues all digested by one company using their proprietary method for preparing stromal vascular fraction.  Samples were then treated by the same company with proprietary activated platelet-rich plasma (PRP) as indicated and then transported to this lab for incubation for 6 hours as indicated and then subsequent isolation of total RNA.

tag: dog

value: 10 year old neutered male German Shepard mix

value: adipose stromal vascular fraction (SVF)

value: photo-activated platelet-rich plasma (PRP), 6h,37 degrees


title: Normal, synovial membrane patient EB_125 (U133A)

description:
see publication for details
EB_125

source_name: synovial membrane patient EB_125 (normal controls)

tag: gender

value: male

value: normal control


title: Rheumatoid arthritis, synovial membrane patient EB_41 (U133A)

description:
see publication for details
EB_41

source_name: synovial membrane patient EB_41 (rheumatoid arthritis)

value: female

tag: age

value: rheumatoid arthritis


title: Mouse k431_6, AIP_wt

description:
k431_6
Expression data from Mouse k431_6, AIP_wt

source_name: Mouse k431_6, AIP_wt


title: DCA 3days injury_rep2

value: Dorsal column axotomy (DCA)

value: none  (input)


title: DCA 3days injury_rep3

value: wildtype


title: Analysis 1: HPV Negative - Biological replicate 5

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_1 sample in analysis 2, 3, 4, 6, 8

value: Male

value: European American


title: Analysis 1: HPV Negative - Biological replicate 6

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_2_2 sample in analysis 2, 4, 6

value: African American


title: Dog 3 sample A2 SVF-no incubation

description: SAMPLE 10

value: no incubation


title: Dog 3 sample B2 PRP-SVF-6h,37 degrees

description: SAMPLE 11


title: genomic DNA from HIV/TB co-infected patient 1

description:
HIV/TB co-infection
AAA0KHPN-10_14-Jun-2007

source_name: PBMC

value: Female

value: PBMC

value: HIV/TB


title: DCA 3days injury_rep1

value: 2 to 3 months

value: all (lumbar) L4-6 DRG

value: real injury

value: 5-methyl-cytosine (IP)

value: Sciatic nerve axotomy (SNA)


title: Mouse k367_2, AIP_wt

description:
k367_2
Expression data from Mouse k367_2, AIP_wt

source_name: Mouse k367_2, AIP_wt

value: embryonic fibroblast cells

value: AIP_wild type


title: Mouse k358_6, replicate 1, AIP_KO

description:
k358_6_1
Expression data from Mouse k358_6, AIP_KO

source_name: Mouse k358_6, AIP_KO


title: Dog 2 sample B2 PRP-SVF-6h,37 degrees

description: SAMPLE 7

value: 10 year old neutered male German Shepard mix

value: adipose stromal vascular fraction (SVF)

value: photo-activated platelet-rich plasma (PRP), 6h,37 degrees


title: Dog 3 sample A1 SVF-no incubation

description: SAMPLE 8


title: Mouse k358_2, AIP_wt

description:
k358_2
Expression data from Mouse k358_2, AIP_wt

source_name: Mouse k358_2, AIP_wt


title: Mouse k358_6, replicate 3, AIP_KO

description:
k358_6_3
Expression data from Mouse k358_6, AIP_KO


title: Mouse k358_6, replicate 2, AIP_KO

description:
k358_6_2
Expression data from Mouse k358_6, AIP_KO


title: genomic DNA from HIV infected patient 18

description:
HIV
KAA0PBTZ-17_06-Mar-2008

value: HIV only


title: Analysis 1: HPV Negative - Biological replicate 2

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_2 sample in analysis 2, 3, 4, 6, 8

source_name: Oropharyngeal squamous cell carcinoma - HPV Negative

value: European American


title: Analysis 1: HPV Negative - Biological replicate 3

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_3 sample in analysis 2, 3, 4, 6, 8

value: Male


title: DCA 1day sham_rep2

source_name: me5-C MeDIP DNA from WT DRG_DCA 1D [Cy5 Test]

value: wildtype

value: Dorsal column axotomy (DCA)

value: sham

source_name: Input DNA from WT DRG_DCA 1D [Cy3 Input]

value: none  (input)


title: DCA 1day sham_rep1

value: 2 to 3 months


title: Analysis 1: HPV Negative - Biological replicate 4

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_4 sample in analysis 2, 4, 6

value: Female

value: African American


title: DCA 1day injury_rep3

value: all (lumbar) L4-6 DRG

value: real injury

value: 5-methyl-cytosine (IP)


title: Dog 2 sample A2 SVF-no incubation

description: SAMPLE 6

value: no incubation


title: DCA 1day injury_rep2

value: Sciatic nerve axotomy (SNA)


title: DCA 1day injury_rep1


title: Mouse k349_8, replicate 2, AIP_KO

description:
k349_8_2
Expression data from Mouse k349_8, AIP_KO

source_name: Mouse k349_8, AIP_KO

value: embryonic fibroblast cells


title: Dog 2 sample B1 PRP-SVF-6h,37 degrees

description: SAMPLE 5

value: 10 year old neutered male German Shepard mix

value: adipose stromal vascular fraction (SVF)

value: photo-activated platelet-rich plasma (PRP), 6h,37 degrees


title: Mouse k349_8, replicate 3, AIP_KO

description:
k349_8_3
Expression data from Mouse k349_8, AIP_KO


title: Mouse k349_5, replicate 3, AIP_KO

description:
k349_5_3
Expression data from Mouse k349_5, AIP_KO

source_name: Mouse k349_5, AIP_KO


title: SNA 7days sham_rep2

description: 18,180 genes analyzed from '2007-02-27 MM8 CpG Island Promoter 385K RefSeq'

source_name: me5-C MeDIP DNA from WT DRG_SNA 7D [Cy5 Test]

source_name: Input DNA from WT DRG_SNA 7D [Cy3 Input]


title: Dog 2 sample A1 SVF-no incubation

description: SAMPLE 4


title: Company B - Thawed SVF - untreated

description: SAMPLE 2

value: 6 year old neutered male Labrador

value: untreated


title: Company C - Thawed SVF - untreated

description: SAMPLE 3


title: Company A - Thawed SVF - untreated

description: SAMPLE 1


title: Analysis 1: HPV Inactive - Biological replicate 7

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_2 sample in analysis 4

source_name: Oropharyngeal squamous cell carcinoma - HPV Inactive

value: Male


title: SNA 7days sham_rep1

value: wildtype

value: sham


title: Analysis 1: HPV Inactive - Biological replicate 8

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_4 sample in analysis 3, 4, 7

value: European American


title: Analysis 1: HPV Inactive - Biological replicate 5

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_1 sample in analysis 4

value: Female


title: Analysis 1: HPV Negative - Biological replicate 1

description: re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_1 sample in analysis 2, 3, 4, 6, 8


title: Analysis 1: HPV Inactive - Biological replicate 4

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_2 sample in analysis 4

value: African American


title: Mouse k349_5, replicate 1, AIP_KO

description:
k349_5_1
Expression data from Mouse k349_5, AIP_KO


title: Analysis 1: HPV Inactive - Biological replicate 6

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_1_2 sample in analysis 4


title: Mouse k349_8, replicate 1, AIP_KO

description:
k349_8_1
Expression data from Mouse k349_8, AIP_KO


title: Mouse k349_4, AIP_wt

description:
k349_4
Expression data from Mouse k349_4, AIP_wt

source_name: Mouse k349_4, AIP_wt

value: AIP_wild type


title: Analysis 1: HPV Inactive - Biological replicate 3

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_1 sample in analysis 3, 4, 7


title: SNA 7days injury_rep3

value: 2 to 3 months

value: all (lumbar) L4-6 DRG

value: real injury

value: none  (input)


title: SNA 7days injury_rep2

value: Sciatic nerve axotomy (SNA)

value: 5-methyl-cytosine (IP)


title: Mouse K728_8, replicate 3, AIP_KO

description:
K728_8_3
Expression data from Mouse K728_8, AIP_KO

source_name: Mouse K728_8, AIP_KO

value: embryonic fibroblast cells


title: SNA 7days injury_rep1


title: Analysis 1: HPV Inactive - Biological replicate 1

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_2 sample in analysis 3, 4, 7


title: SNA 3days sham_rep2

source_name: me5-C MeDIP DNA from WT DRG_SNA 3D [Cy5 Test]

source_name: Input DNA from WT DRG_SNA 3D [Cy3 Input]


title: Mouse K728_6, replicate 3, AIP_KO

description:
K728_6_3
Expression data from Mouse K728_6, AIP_KO

source_name: Mouse K728_6, AIP_KO


title: Analysis 1: HPV Active - Biological replicate 12

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_3 sample in analysis 3, 5

source_name: Oropharyngeal squamous cell carcinoma - HPV Active


title: Mouse k349_5, replicate 2, AIP_KO

description:
k349_5_2
Expression data from Mouse k349_5, AIP_KO


title: Mouse K728_8, replicate 1, AIP_KO

description:
K728_8_1
Expression data from Mouse K728_8, AIP_KO


title: Mouse K728_8, replicate 2, AIP_KO

description:
K728_8_2
Expression data from Mouse K728_8, AIP_KO


title: Analysis 1: HPV Active - Biological replicate 11

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_1 sample in analysis 3, 5


title: Analysis 1: HPV Active - Biological replicate 10

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_3 sample in analysis 3, 5


title: SNA 3days injury_rep3

description: 18,180 genes analyzed from '2007-02-27 MM8 CpG Island Promoter 385K RefSeq'


title: SNA 3days injury_rep1


title: SNA 3days sham_rep1


title: SNA 3days injury_rep2


title: Mouse K680_6, replicate 2, AIP_KO

description:
K680_6_2
Expression data from Mouse K680_6, AIP_KO

source_name: Mouse K680_6, AIP_KO


title: Analysis 1: HPV Active - Biological replicate 8

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_4 sample in analysis 3, 5


title: Mouse K728_6, replicate 2, AIP_KO

description:
K728_6_2
Expression data from Mouse K728_6, AIP_KO


title: SNA 1day sham_rep2

source_name: me5-C MeDIP DNA from WT DRG_SNA 1D [Cy5 Test]

source_name: Input DNA from WT DRG_SNA 1D [Cy3 Input]


title: SNA 1day sham_rep1


title: Analysis 1: HPV Active - Biological replicate 9

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_1 sample in analysis 5


title: SNA 1day injury_rep3


title: Mouse K642_3, AIP_wt

description:
K642_3
Expression data from Mouse K642_3, AIP_wt

source_name: Mouse K642_3, AIP_wt


title: SNA 1day injury_rep1


title: SNA 1day injury_rep2


title: Mouse K680_6, replicate 3, AIP_KO

description:
K680_6_3
Expression data from Mouse K680_6, AIP_KO


title: Analysis 1: HPV Active - Biological replicate 7

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_3 sample in analysis 3, 5


title: Mouse K680_2, AIP_wt

description:
K680_2
Expression data from Mouse K680_2, AIP_wt

source_name: Mouse K680_2, AIP_wt


title: Analysis 1: HPV Active - Biological replicate 3

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_4 sample in analysis 3, 5


title: Mouse K680_6, replicate 1, AIP_KO

description:
K680_6_1
Expression data from Mouse K680_6, AIP_KO


title: Mouse K728_6, replicate 1, AIP_KO

description:
K728_6_1
Expression data from Mouse K728_6, AIP_KO


title: Mouse K642_4, replicate 2, AIP_KO

description:
K642_4_2
Expression data from Mouse K642_4, AIP_KO

source_name: Mouse K642_4, AIP_KO


title: Mouse K642_4, replicate 3, AIP_KO

description:
K642_4_3
Expression data from Mouse K642_4, AIP_KO


title: Analysis 1: HPV Active - Biological replicate 4

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_1 sample in analysis 3, 5


title: Analysis 1: HPV Active - Biological replicate 5

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_4 sample in analysis 3, 5


title: Analysis 1: HPV Active - Biological replicate 6

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_2 sample in analysis 3, 5


title: Mouse K642_4, replicate 1, AIP_KO

description:
K642_4_1
Expression data from Mouse K642_4, AIP_KO


title: Analysis 1: HPV Active - Biological replicate 1

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_4 sample in analysis 3, 5


title: 545060_A12_I320_circadien_B73_CRS_B73_0_cc12h

status: Public on Mar 04 2014

city: Montpellier

first: Cecilio

middle: Frois

last: Caldeira

address: 2 place Viala

department: Herault

country: France

institute: INRA - Institut National de la Recherche Agronomique

description: This sample of leaf elongation zone was collected from maize plants 12h after lights on. It is the second of three biological replicates used in this experiment, each from separate plants.

hyb_protocol: Hybridization was performed using Nimblegen Hybridization system  following the standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed with scanner MS200 Roche-NimbleGen with autogain mode, following the 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)and quantile normalization (Bolstad et al. Bioinformatics 19(2):185) as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Zea mays subsp. mays

source_name: maize_B73_circadian cycle_12h_light

label_protocol: Labeling was performed using One-Color DNA Labeling 5223555001 kit, Roche NimbleGen Inc. following the standard operating protocol. See www.nimblegen.com.

growth_protocol:
Well watered plants of the maize line B73 were previously grown (entrainement period) with 12h of photoperiod and with high day/night variations of evaporative demand in controlled conditions (day: 28°C, vapour pressure deficit of 3kPa and light 600µmol m-2 s-1; night: 20°C, vapour pressure deficit of 0.8kPa and darkness).
Leaf samples were collected at predawn (1h before lights on) and 12 and 24 hours in continuous light after light switched on.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with NanoDrop.

value: standard maize line B73

tag: phenotype

value: sampled after  12h in continuous light

value: leaf elongation zone


title: Analysis 1: HPV Active - Biological replicate 2

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_2 sample in analysis 3, 5

value: Male


title: 545060_A01_I321_circadien_B73_CRS_B73_0_cc12h

description: This sample of leaf elongation zone was collected from maize plants 12h after lights on. It is the third of three biological replicates used in this experiment, each from separate plants.


title: T cells cultured with medium

city: Boston

first: Francisco

last: Quintana

state: MA

address: 77 Ave Louis Pasteur

department: Center for Neurological Diseases

institute: Harvard Medical Institute

description: Control treated T cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: (Affymatrix)Array scanning was performed according to the manufacture's instructions.

data_processing:
Data were processed using GeneSpring 11.5 guided work flow. ExonRAM16 - summarization algorithm. Gene level expression were summarize after quantile normalization.
MoEx-1_0-st-v1.r.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Wild Type Naïve CD4 T cells, 8 weeks old

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

growth_protocol: Mouse Naïve CD4+ T cells

extract_protocol: Purified RNA was sent to Expression Analysis (http://www.expressionanalysis.com/) for preparation and hybridization.

treatment_protocol: T cells were activated with IL-21 or IL-6 + TGFb1

value: Naïve CD4+ T cells

value: Wild type

value: Vehicle

value: 8 weeks old


title: 545060_A07_I318_circadien_B73_CRS_B73_0_cc24h

description: This sample of leaf elongation zone was collected from maize plants 24h after lights on. It is the third of three biological replicates used in this experiment, each from separate plants.

source_name: maize_B73_circadian cycle_24h_light

value: sampled after  24h in continuous light


title: 545060_A05_I316_circadien_B73_CRS_B73_0_cc24h

description: This sample of leaf elongation zone was collected from maize plants 24h after lights on. It is the first of three biological replicates used in this experiment, each from separate plants.


title: 544647_A02_I310_circadien_B73_CRS_B73_0_nuit

description: This sample of leaf elongation zone was collected from maize plants during the predawn. It is the second of three biological replicates used in this experiment, each from separate plants.

source_name: maize_B73_circadian cycle_predawn

value: sampled at predawn


title: 545057_A09_I311_circadien_B73_CRS_B73_0_nuit

description: This sample of leaf elongation zone was collected from maize plants during the predawn. It is the third of three biological replicates used in this experiment, each from separate plants.


title: T cells cultured with IL-6 and TGFb1

description: IL-6 + TGFb1 treated T cells

value: IL-6 + TGFb1


title: dsRed2 EpiSCs plus CHI 48h replicate 3

city: Edinburgh

first: Anestis

last: Tsakiridis

address: 5 Little France Drive

institute: MRC Centre for Regenerative Medicine

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol (performed by the Wellcome Trust Clinical Research Facility, Edinburgh)

scan_protocol: Standard Illumina scanning protocol (performed by the Wellcome Trust Clinical Research Facility, Edinburgh)

data_processing: Background subtraction, variance stabilising transformation (VST) and robust spline normalisation (RSN) with lumi package in R.

label_protocol: Labeling and amplification were performed using the Illumina® TotalPrep™ RNA Amplification Kit (Life Technologies) according to the manufacturer's instructions

growth_protocol: Cells were maintained in standard EpiSC medium supplemented with 20 ng/ml Activin A and 10 ng/ml Bfgf

extract_protocol: RNA was isolated using the Rneasy minikit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Untreated EpiSC or EpiSC treated with 3 uM CHIRON for 48 hrs

value: dsRed2 EpiSCs

value: male

value: 129 background


title: dsRed2 EpiSCs plus CHI 48h replicate 1

description: replicate 1


title: MDA-MB-231-SA

city: Ibbenbüren

first: Dirk

last: Kemming

address: Roggenkampstr.

institute: ELA

description: Gene expression of MDA-MB-231-SA treated with 5-Aza-2'-deoxycytidine  vs untreated

hyb_protocol: Following fragmentation, 825 ng of each cRNA were hybridized for 17 hr at 65C on Agilent 4x44k Whole Human Genome Array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Agilent Technologies Scanner G2505B; Agilent Scanner protocol GE1-v5_95_Feb07; Scan resolution 5 µm; XDR Hi 100% XDR Lo 10%

data_processing: Data extraction was done using Agilent Feature Extraction Software; raw Data have been median scaled; replicate spots have been averaged

label_protocol: Cy3 and Cy5 labeled cRNA were prepared according to the standard Agilent protocol from 500ng total RNA.

growth_protocol: The different MDA-MB-231 cell lines were grown in DMEM medium  supplemented with 10% FBS, 2 mM Glutamine . MCF 10A cells were grown in DMEM/Ham's F-12  with 5% FBS, 10 μg/ml Insulin, 5 μg/ml Hydrocortisone, 20 ng/ml EGF, 100 ng/ml Cholera toxin and 2 mM L-Glutamine. All cells were maintained in a humidified incubator at 37°C and 10% CO2. All cells were tested free of mycoplasma.

extract_protocol: Total RNA of the cells was isolated using RNAeasy kit (Qiagen, Hilden Germany)

treatment_protocol: Cells were seeded at 10% (MDA-MB-231 and subtypes) or 20% (MCF 10A) confluence. 5-Aza-2'-deoxycytidine was dissolved in sterile water. After 4 hours of plating the cells were cultured in absence or presence of 1 µM 5-Aza-CdR, and the medium was changed daily until the cells reached a confluence of 90-100%.

source_name: MDA-MB-231-SA untreated

value: untreated


title: T cells cultured with IL-21

description: IL-21 treated T cells


title: sorted dsRed2 negative EpiSCs replicate 2

description: replicate 2


title: 545060_A03_I319_circadien_B73_CRS_B73_0_cc12h

description: This sample of leaf elongation zone was collected from maize plants 12h after lights on. It is the first of three biological replicates used in this experiment, each from separate plants.


title: MDA-MB-231-WT

description: Gene expression of MDA-MB-231-WT treated with 5-Aza-2'-deoxycytidine  vs untreated

source_name: MDA-MB-231-WT untreated


title: sorted dsRed2 positive EpiSCs replicate 3

description: replicate 3


title: dsRed2 EpiSCs plus CHI 48h replicate 2

description: replicate 2


title: sorted dsRed2 negative EpiSCs replicate 1

description: replicate 1


title: sorted dsRed2 positive EpiSCs replicate 2

description: replicate 2


title: MCF_10A

description: Gene expression of MCF_10A treated with 5-Aza-2'-deoxycytidine vs untreated

value: MCF 10A

source_name: MCF 10A untreated


title: MDA-MB-231-BR

description: Gene expression of MDA-MB-231-BR treated with 5-Aza-2'-deoxycytidine  vs untreated

source_name: MDA-MB-231-BR untreated


title: sorted dsRed2 positive EpiSCs replicate 1

description: replicate 1


title: sorted dsRed2 negative EpiSCs replicate 3

description: replicate 3


title: PT 24 TO1

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Arrays were imaged using a Affymetrix GeneChip scanner 3000

data_processing: Partek Genomic Suite was used for RMA and for unsupervised hierarchical clustering of total gene expression and all pathway and gene set analysis.

source_name: tumor, day1, before treatment

label_protocol: Standard Affymetrix Protocol

extract_protocol: Total RNAs were extracted from patient biopsies (tumor or ascites) using TRIzol reagent

treatment_protocol: Treatment consisted of the DNA-hypomethylating agent decitabine (Eisai, Tokyo, Japan) at 10mg/m2 given intravenously (iv) daily for 5 days, and carboplatin (Bristol Meyers Squibb, Princeton, NJ) administered iv on day 8 for an area under the curve (AUC) of 5. Each cycle was 4 weeks and treatment continued until disease progression (PD) or intolerable toxicity.

tag: ecog ps

tag: histological subtype

value: serous

tag: platinum-sensitivity (refractory or resistant)

value: resistant

tag: measurable disease (check if it's measurable)

value: measurable

tag: tissue state

value: ovarian cancer tissue before treatment


title: PT 29 AO1

source_name: ascites, day1, before treatment

value: mixed epithelial

value: ascites from ovarian cancer patient before treatment


title: PT 30 TO1


title: PT 26 TO2

source_name: tumor, day8, after treatment

tag: platinum-sensitivity (refractory or resistant):

tag: measurable disease (check if it's measurable):

value: ovarian cancer tissue after treatment


title: PT 29 AO2

source_name: ascites, day8, after treatment

value: ascites from ovarian cancer patient after treatment


title: PT 30 TO2


title: PT 27 TO1


title: PT 24 TO2


title: PT 28 AO2


title: PT 23 AO2


title: PT 26 TO1


title: PT 20 TO1


title: PT 28 AO1

value: refractory


title: PT 22 AO2


title: PT 22 AO1


title: PT 20 TO2


title: PT 15 TO2


title: PT 19 TO2


title: PT 17 TO1


title: PT 19 TO1


title: PT 17 TO2


title: Analysis 1: HPV Inactive - Biological replicate 2

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_4 sample in analysis 3, 4, 7

source_name: Oropharyngeal squamous cell carcinoma - HPV Inactive

value: Female

tag: race

value: European American


title: PT 15 TO1


title: PT 16 TO2


title: PT 16 TO1


title: 544647_A11_I309_circadien_B73_CRS_B73_0_nuit

description: This sample of leaf elongation zone was collected from maize plants during the predawn. It is the first of three biological replicates used in this experiment, each from separate plants.

tag: genotype

value: standard maize line B73

value: sampled at predawn

tag: tissue

value: leaf elongation zone


title: Airway sample from field cancerization case 23 [GFS_IW00529]

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Gene expression of airway sample from field cancerization case 23

hyb_protocol: 2.5 ug of fragmented and labeled cDNA, was generated using the Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, were hybridized onto Human Gene 1.0 ST arrays according to the manufacturer’s instructions (Affymetrix). Hybridization cocktails containing samples, control oligonucleotide and eukaryotic hybridization controls in addition to hybridization mixes, DMSO and nuclease-free water were heat denatured at 99oC for 5 minutes, cooled to 45oC for 5 minutes, and finally centrifuged at maximum speed for 1 minute.   After injecting 80 uL of the hybridization cocktails, arrays were incubated for 17 hours in a hybridization oven set to a temperature of 45oC with 60 rpm rotation.   Arrays were washed, stained and processed using Affymetrix GeneChip Fluidics Station 450 systems.

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip Scanner 3000 7G for subsequent generation of raw data (*CEL files)

data_processing: Raw expression data (.CEL files) were quantified using the RMA background correction, quantile normalization and RmaPlm (Probe-Level Models using RMA) summarization methods using original scale. A log base 2 transformation was then applied. All processes were conducted using the aroma.affymetrix package in R.

source_name: NSCLC patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Affymetrix).

extract_protocol: Total RNA was isolated using the miRNAeasy kit (Qiagen) acording to the manufacturer's instructions.

value: airway

tag: sample collection

value: airway brushing

tag: airway distance from tumor (1, closest; 5, farthest)


title: Airway sample from field cancerization case 23 [GFS_IW00531]


title: Airway sample from field cancerization case 23 [GFS_IW00530]


title: CD34+ cells, SLPI shRNA 2

city: Hannover

first: Siarhei

last: Kandabarau

address: Carl-Neuberg-Str 1

institute: Hannover Medical School

description: SAMPLE 4

hyb_protocol: After chemical fragmentation of the biotin-labeled cRNA targets, they were hybridized to Affymetrix Human Exome microarrays using the Fluidics Station 450

scan_protocol: Microarrays were scanned using the Affymetrix Genechip Scanner 3000 with Genechip Operating Software 1.4 (Affymetrix, Santa Clara, CA).

data_processing: CEL files were analyzed within Expression Console using gene-level RMA-Sketch default settings

source_name: CD34+ cells_SLPI shRNA

label_protocol: The Genechip WT cDNA Synthesis and Amplification Kit was used to make double-stranded cDNA from total RNA, which was then labeled with biotin (Genechip WT Terminal Labeling Kit).

growth_protocol: Cells were cultured in Ex-vivo medium supplemented with 10 % HSA, 20 ng/ml IL-3, 20 ng/ml IL-6, 20 ng/ml TPO, 50 ng/ml SCF and 50 ng/ml Flt-3L.

extract_protocol: Extraction of total RNA was performed using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: After 3 days of the transductions, RFP+ cells were sorted, serum starved for 24 hours and treated with G-CSF 10 ng/ml for 18 hours. Total RNA of sorted cells was isolated and used for Affymetrix Exome arrays.

value: bone marrow of healthy individuals

tag: cell type

value: CD34+ hematopoietic cells

tag: transduced with

value: lenitvirus-based RFP-expressed shRNA constructs targeting SLPI mRNA

tag: cell subtype

value: sorted RFP+ cells


title: Airway sample from field cancerization case 23 [GFS_IW00528]


title: Airway sample from field cancerization case 22 [GFS_IW00522]

description: Gene expression of airway sample from field cancerization case 22

source_name: Lung cancer patient


title: NSCLC specimen from field cancerization case 23 [GFS_IW00526]

description: Gene expression of NSCLC specimen from field cancerization case 23

value: NSCLC

value: Lung tumor brushing


title: NSCLC tissue from field cancerization case 23 [GFS_IW00524]

description: Gene expression of NSCLC tissue from field cancerization case 23

value: Tumor tissue in RNAlater


title: CD34+ cells, SLPI shRNA 1

description: SAMPLE 3


title: Airway sample from field cancerization case 22 [GFS_IW00520]


title: Airway sample from field cancerization case 22 [GFS_IW00519]


title: CD34+ cells, ctrl shRNA 2

description: SAMPLE 2

source_name: CD34+ cells_ctrl shRNA

value: scrambled ctrl shRNA


title: Normal lung tissue from field cancerization case 23 [GFS_IW00525]

description: Gene expression of normal lung tissue from field cancerization case 23

value: Normal lung

value: Normal lung tissue in RNAlater


title: Airway sample from field cancerization case 22 [GFS_IW00521]


title: Normal lung specimen from field cancerization case 23 [GFS_IW00527]

description: Gene expression of normal lung specimen from field cancerization case 23

value: Normal lung tissue brushing


title: Airway sample from field cancerization case 21 [GFS_IW00510]

description: Gene expression of airway sample from field cancerization case 21


title: Lung carcinoid specimen from field cancerization case 22 [GFS_IW00516]

description: Gene expression of lung carcinoid specimen from field cancerization case 22

value: Lung carcinoid tumor


title: Normal lung tissue from field cancerization case 22 [GFS_IW00513]

description: Gene expression of normal lung tissue from field cancerization case 22

value: Frozen normal lung tissue


title: Airway sample from field cancerization case 21 [GFS_IW00511]


title: Normal lung tissue from field cancerization case 23 [GFS_IW00523]


title: CD34+ cells, ctrl shRNA 1

description: SAMPLE 1


title: Normal lung specimen from field cancerization case 22 [GFS_IW00517]

description: Gene expression of normal lung specimen from field cancerization case 22


title: Airway sample from field cancerization case 23 [GFS_IW00532]


title: Airway sample from field cancerization case 22 [GFS_IW00518]


title: 545060_A09_I317_circadien_B73_CRS_B73_0_cc24h

description: This sample of leaf elongation zone was collected from maize plants 24h after lights on. It is the second of three biological replicates used in this experiment, each from separate plants.

value: standard maize line B73

value: sampled after  24h in continuous light


title: Lung carcinoid tissue from field cancerization case 22 [GFS_IW00514]

description: Gene expression of lung carcinoid tissue from field cancerization case 22


title: Normal lung specimen from field cancerization case 21 [GFS_IW00506]

description: Gene expression of normal lung specimen from field cancerization case 21


title: Airway sample from field cancerization case 21 [GFS_IW00509]

value: airway


title: Airway sample from field cancerization case 21 [GFS_IW00508]

value: airway brushing


title: Lung carcinoid specimen from field cancerization case 21 [GFS_IW00505]

description: Gene expression of lung carcinoid specimen from field cancerization case 21


title: Normal lung tissue from field cancerization case 21 [GFS_IW00502]

description: Gene expression of normal lung tissue from field cancerization case 21


title: Lung carcinoid tissue from field cancerization case 21 [GFS_IW00503]

description: Gene expression of lung carcinoid tissue from field cancerization case 21


title: Normal lung tissue from field cancerization case 21 [GFS_IW00504]


title: Lung carcinoid tissue from field cancerization case 21 [GFS_IW00501]

value: Frozen lung tumor tissue


title: Airway sample from field cancerization case 20 [GFS_IW00499]

description: Gene expression of airway sample from field cancerization case 20


title: Airway sample from field cancerization case 21 [GFS_IW00507]


title: Airway sample from field cancerization case 20 [GFS_IW00500]


title: Airway sample from field cancerization case 20 [GFS_IW00496]


title: Airway sample from field cancerization case 20 [GFS_IW00498]


title: PT 27 TO2

tag: age

value: serous

value: ovarian cancer tissue after treatment


title: Normal lung tissue from field cancerization case 20 [GFS_IW00491]

description: Gene expression of normal lung tissue from field cancerization case 20


title: NSCLC specimen from field cancerization case 20 [GFS_IW00494]

description: Gene expression of NSCLC specimen from field cancerization case 20


title: NSCLC tissue from field cancerization case 20 [GFS_IW00492]

description: Gene expression of NSCLC tissue from field cancerization case 20


title: Airway sample from field cancerization case 19 [GFS_IW00488]

description: Gene expression of airway sample from field cancerization case 19


title: Airway sample from field cancerization case 19 [GFS_IW00489]


title: NSCLC tissue from field cancerization case 20 [GFS_IW00490]


title: Airway sample from field cancerization case 20 [GFS_IW00497]


title: Normal lung tissue from field cancerization case 20 [GFS_IW00493]


title: Normal lung tissue from field cancerization case 22 [GFS_IW00515]


title: Airway sample from field cancerization case 19 [GFS_IW00485]


title: Normal lung specimen from field cancerization case 20 [GFS_IW00495]

description: Gene expression of normal lung specimen from field cancerization case 20


title: Airway sample from field cancerization case 19 [GFS_IW00486]


title: Normal lung specimen from field cancerization case 19 [GFS_IW00484]

description: Gene expression of normal lung specimen from field cancerization case 19


title: Airway sample from field cancerization case 19 [GFS_IW00487]


title: PT 23 AO1

value: refractory

value: measurable

value: ascites from ovarian cancer patient before treatment


title: NSCLC specimen from field cancerization case 19 [GFS_IW00483]

description: Gene expression of NSCLC specimen from field cancerization case 19

value: NSCLC

value: Lung tumor brushing


title: Normal lung tissue from field cancerization case 19 [GFS_IW00482]

description: Gene expression of normal lung tissue from field cancerization case 19

value: Normal lung


title: Normal lung tissue from field cancerization case 19 [GFS_IW00480]


title: Airway sample from field cancerization case 18 [GFS_IW00478]

description: Gene expression of airway sample from field cancerization case 18


title: NSCLC tissue from field cancerization case 19 [GFS_IW00479]

description: Gene expression of NSCLC tissue from field cancerization case 19


title: Airway sample from field cancerization case 18 [GFS_IW00477]


title: Airway sample from field cancerization case 18 [GFS_IW00476]


title: NSCLC tissue from field cancerization case 18 [GFS_IW00473]

description: Gene expression of NSCLC tissue from field cancerization case 18

value: Tumor tissue in RNAlater


title: Normal lung specimen from field cancerization case 18 [GFS_IW00475]

description: Gene expression of normal lung specimen from field cancerization case 18

value: Normal lung tissue brushing


title: NSCLC tissue from field cancerization case 19 [GFS_IW00481]


title: Airway sample from field cancerization case 17 [GFS_IW00471]

description: Gene expression of airway sample from field cancerization case 17


title: Airway sample from field cancerization case 17 [GFS_IW00472]


title: Normal lung tissue from field cancerization case 17 [GFS_IW00465]

description: Gene expression of normal lung tissue from field cancerization case 17


title: Normal lung specimen from field cancerization case 17 [GFS_IW00469]

description: Gene expression of normal lung specimen from field cancerization case 17


title: Normal lung tissue from field cancerization case 18 [GFS_IW00474]

description: Gene expression of normal lung tissue from field cancerization case 18

value: Normal lung tissue in RNAlater


title: NSCLC specimen from field cancerization case 17 [GFS_IW00468]

description: Gene expression of NSCLC specimen from field cancerization case 17


title: NSCLC specimen from field cancerization case 16 [GFS_IW00458]

description: Gene expression of NSCLC specimen from field cancerization case 16


title: NSCLC tissue from field cancerization case 17 [GFS_IW00464]

description: Gene expression of NSCLC tissue from field cancerization case 17


title: Normal lung specimen from field cancerization case 16 [GFS_IW00459]

description: Gene expression of normal lung specimen from field cancerization case 16


title: NSCLC tissue from field cancerization case 16 [GFS_IW00456]

description: Gene expression of NSCLC tissue from field cancerization case 16


title: Airway sample from field cancerization case 17 [GFS_IW00470]


title: NSCLC tissue from field cancerization case 17 [GFS_IW00466]


title: Airway sample from field cancerization case 16 [GFS_IW00460]

description: Gene expression of airway sample from field cancerization case 16


title: Normal lung tissue from field cancerization case 16 [GFS_IW00457]

description: Gene expression of normal lung tissue from field cancerization case 16


title: Normal lung tissue from field cancerization case 17 [GFS_IW00467]


title: Airway sample from field cancerization case 16 [GFS_IW00461]


title: Airway sample from field cancerization case 16 [GFS_IW00463]


title: NSCLC tissue from field cancerization case 16 [GFS_IW00454]


title: Airway sample from field cancerization case 16 [GFS_IW00462]


title: Airway sample from field cancerization case 15 [GFS_IW00452]

description: Gene expression of airway sample from field cancerization case 15


title: Airway sample from field cancerization case 14 [GFS_IW00443]

description: Gene expression of airway sample from field cancerization case 14


title: NSCLC tissue from field cancerization case 15 [GFS_IW00444]

description: Gene expression of NSCLC tissue from field cancerization case 15


title: Normal lung tissue from field cancerization case 15 [GFS_IW00445]

description: Gene expression of normal lung tissue from field cancerization case 15

value: Frozen normal lung tissue


title: Normal lung tissue from field cancerization case 16 [GFS_IW00455]


title: NSCLC tissue from field cancerization case 15 [GFS_IW00447]


title: Airway sample from field cancerization case 15 [GFS_IW00451]


title: Normal lung specimen from field cancerization case 15 [GFS_IW00449]

description: Gene expression of normal lung specimen from field cancerization case 15


title: Airway sample from field cancerization case 15 [GFS_IW00450]


title: NSCLC specimen from field cancerization case 15 [GFS_IW00448]

description: Gene expression of NSCLC specimen from field cancerization case 15


title: Airway sample from field cancerization case 15 [GFS_IW00453]


title: Airway sample from field cancerization case 14 [GFS_IW00442]


title: Lung carcinoid tissue from field cancerization case 22 [GFS_IW00512]

description: Gene expression of lung carcinoid tissue from field cancerization case 22

value: Lung carcinoid tumor


title: Normal lung tissue from field cancerization case 14 [GFS_IW00439]

description: Gene expression of normal lung tissue from field cancerization case 14


title: Airway sample from field cancerization case 13 [GFS_IW00435]

description: Gene expression of airway sample from field cancerization case 13


title: Normal lung tissue from field cancerization case 15 [GFS_IW00446]


title: NSCLC tissue from field cancerization case 14 [GFS_IW00438]

description: Gene expression of NSCLC tissue from field cancerization case 14


title: NSCLC tissue from field cancerization case 14 [GFS_IW00436]


title: Normal lung tissue from field cancerization case 14 [GFS_IW00437]


title: Airway sample from field cancerization case 13 [GFS_IW00432]


title: Airway sample from field cancerization case 13 [GFS_IW00433]


title: Normal lung tissue from field cancerization case 13 [GFS_IW00427]

description: Gene expression of normal lung tissue from field cancerization case 13


title: Airway sample from field cancerization case 14 [GFS_IW00441]


title: Normal lung specimen from field cancerization case 13 [GFS_IW00431]

description: Gene expression of normal lung specimen from field cancerization case 13


title: No addition rep 2

type: mixed

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: Samples were hybridized on the arrays for 16 h.

scan_protocol: Scanning of the arrays was performed using the Axon 4000B GenePix Scanner, data extraction software was GenePix Pro 6, both from Molecular Devices (Sunnyvale, USA).

data_processing: Array data were processed using R and Bioconductor.  Following Quantile normalization, differential expression was identified using Bayesian adjusted t-statistics with false discovery rate correction for multiple testing.

organism: Pseudomonas aeruginosa PAO1

source_name: No addition , Total extract

label_protocol: For each array, 10 ug of RNA was reverse transcribed and directly labelled with Cy5-dCTP and 2 ug of genomic DNA was directly labelled with Cy3-dCTP.

growth_protocol: Cells were grown for 8hr at 37°C in 25 ml LB broth and 250 ml flasks with shaking at 200 r.p.m.

extract_protocol:
RNA was extracted from each culture after 8 h incubation (late exponential / early stationary phase of growth). Cells were treated with RNAprotect Bacteria Reagent (Qiagen), and total RNA extraction was performed with the RNeasy Midi Kit (Qiagen) as per the manufacturer’s instructions.
gDNA reference

treatment_protocol: There were four treatments: (a) no addition; (b) 3-oxo- C12-HSL; (c) C4-HSL; and (d) both 3-oxo-C12-HSL and C4-HSL.  Each treatment had 2 replicates.

tag: genotype/variation

value: double QS synthase mutant lasI/rhlI

tag: treatment

value: No addition

source_name: genomic DNA reference, Total extract

tag: sample type

value: gDNA reference


title: Airway sample from field cancerization case 14 [GFS_IW00440]

value: airway

value: airway brushing


title: NSCLC specimen from field cancerization case 13 [GFS_IW00430]

description: Gene expression of NSCLC specimen from field cancerization case 13


title: NSCLC tissue from field cancerization case 13 [GFS_IW00428]

description: Gene expression of NSCLC tissue from field cancerization case 13


title: Normal lung tissue from field cancerization case 13 [GFS_IW00429]


title: Airway sample from field cancerization case 12 [GFS_IW00425]

description: Gene expression of airway sample from field cancerization case 12


title: NSCLC tissue from field cancerization case 13 [GFS_IW00426]

value: Frozen lung tumor tissue


title: C4-HSL treatment rep 2

source_name: C4-HSL treatment , Total extract

value: C4-HSL included at 15uM


title: Airway sample from field cancerization case 12 [GFS_IW00424]


title: Airway sample from field cancerization case 13 [GFS_IW00434]


title: C4-HSL treatment rep 1


title: Airway sample from field cancerization case 12 [GFS_IW00423]


title: No addition rep 1


title: C12-HSL and C4-HSL treatment rep 1

source_name: C12-HSL and C4-HSL treatment , Total extract

value: C12-HSL and C4-HSL included at 15uM each


title: C12-HSL and C4-HSL treatment rep 2


title: C12-HSL treatment rep 2

source_name: C12-HSL treatment , Total extract

value: C12-HSL included at 15uM


title: C12-HSL treatment rep 1


title: Normal lung specimen from field cancerization case 12 [GFS_IW00420]

description: Gene expression of normal lung specimen from field cancerization case 12


title: NSCLC specimen from field cancerization case 12 [GFS_IW00419]

description: Gene expression of NSCLC specimen from field cancerization case 12

value: NSCLC


title: Normal lung tissue from field cancerization case 12 [GFS_IW00418]

description: Gene expression of normal lung tissue from field cancerization case 12


title: Airway sample from field cancerization case 12 [GFS_IW00422]


title: NSCLC tissue from field cancerization case 12 [GFS_IW00415]

description: Gene expression of NSCLC tissue from field cancerization case 12


title: White adipose tissue sample 210

city: Cleveland

first: James

last: Hester

state: Ohio

address: 9500 Euclid Avenue

department: Genomic Medicine

institute: Cleveland Clinic

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in Beadstudio

source_name: Mouse WAT

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: White adipose tissue

tag: Sex

value: M

tag: cage

tag: maternal diet

value: LF

tag: diet

tag: weight (g) 3 weeks

tag: weight (g) weaning

tag: glucose (mg/dl)

tag: length (mm)

tag: bmi

tag: genetic background


title: NSCLC tissue from field cancerization case 12 [GFS_IW00417]

tag: tissue

tag: sample collection

value: Tumor tissue in RNAlater


title: White adipose tissue sample 211


title: White adipose tissue sample 227

value: HF


title: White adipose tissue sample 208


title: Airway sample from field cancerization case 11 [GFS_IW00414]

description: Gene expression of airway sample from field cancerization case 11

tag: airway distance from tumor (1, closest; 5, farthest)


title: Airway sample from field cancerization case 11 [GFS_IW00413]


title: White adipose tissue sample 201


title: White adipose tissue sample 209


title: Normal lung tissue from field cancerization case 12 [GFS_IW00416]

value: Normal lung

value: Frozen normal lung tissue


title: Normal lung specimen from field cancerization case 11 [GFS_IW00412]

description: Gene expression of normal lung specimen from field cancerization case 11

value: Normal lung tissue brushing


title: NSCLC tissue from field cancerization case 11 [GFS_IW00407]

description: Gene expression of NSCLC tissue from field cancerization case 11


title: White adipose tissue sample 200


title: White adipose tissue sample 182


title: Airway sample from field cancerization case 10 [GFS_IW00403]

description: Gene expression of airway sample from field cancerization case 10


title: Normal lung tissue from field cancerization case 11 [GFS_IW00410]

description: Gene expression of normal lung tissue from field cancerization case 11

value: Normal lung tissue in RNAlater


title: Normal lung tissue from field cancerization case 11 [GFS_IW00408]


title: Normal lung specimen from field cancerization case 10 [GFS_IW00401]

description: Gene expression of normal lung specimen from field cancerization case 10


title: White adipose tissue sample 207


title: Airway sample from field cancerization case 10 [GFS_IW00402]


title: Airway sample from field cancerization case 10 [GFS_IW00406]


title: Airway sample from field cancerization case 10 [GFS_IW00404]


title: White adipose tissue sample 172


title: White adipose tissue sample 181


title: White adipose tissue sample 183


title: Airway sample from field cancerization case 10 [GFS_IW00405]


title: NSCLC specimen from field cancerization case 11 [GFS_IW00411]

description: Gene expression of NSCLC specimen from field cancerization case 11

value: Lung tumor brushing


title: White adipose tissue sample 173


title: NSCLC tissue from field cancerization case 11 [GFS_IW00409]


title: White adipose tissue sample 127


title: White adipose tissue sample 133


title: NSCLC specimen from field cancerization case 10 [GFS_IW00400]

description: Gene expression of NSCLC specimen from field cancerization case 10


title: White adipose tissue sample 177


title: White adipose tissue sample 123


title: White adipose tissue sample 199


title: White adipose tissue sample 128


title: White adipose tissue sample 174


title: White adipose tissue sample 122


title: Normal lung tissue from field cancerization case 10 [GFS_IW00399]

description: Gene expression of normal lung tissue from field cancerization case 10


title: White adipose tissue sample 124


title: Airway sample from field cancerization case 12 [GFS_IW00421]

value: airway


title: White adipose tissue sample 228


title: White adipose tissue sample 134


title: Airway sample from field cancerization case 9 [GFS_IW00392]

description: Gene expression of airway sample from field cancerization case 9

value: airway brushing


title: White adipose tissue sample 102


title: NSCLC tissue from field cancerization case 10 [GFS_IW00396]

description: Gene expression of NSCLC tissue from field cancerization case 10

value: Frozen lung tumor tissue


title: Normal lung tissue from field cancerization case 10 [GFS_IW00397]


title: White adipose tissue sample 109


title: White adipose tissue sample 108


title: Airway sample from field cancerization case 9 [GFS_IW00395]


title: Airway sample from field cancerization case 9 [GFS_IW00393]


title: White adipose tissue sample 101


title: NSCLC tissue from field cancerization case 10 [GFS_IW00398]


title: Airway sample from field cancerization case 9 [GFS_IW00391]


title: White adipose tissue sample 100


title: Airway sample from field cancerization case 9 [GFS_IW00394]


title: White adipose tissue sample 126


title: White adipose tissue sample 99


title: White adipose tissue sample 97


title: NSCLC specimen from field cancerization case 9 [GFS_IW00389]

description: Gene expression of NSCLC specimen from field cancerization case 9


title: Normal lung specimen from field cancerization case 9 [GFS_IW00390]

description: Gene expression of normal lung specimen from field cancerization case 9


title: White adipose tissue sample 52


title: Normal lung tissue from field cancerization case 9 [GFS_IW00388]

description: Gene expression of normal lung tissue from field cancerization case 9


title: White adipose tissue sample 54


title: Airway sample from field cancerization case 8 [GFS_IW00384]

description: Gene expression of airway sample from field cancerization case 8


title: Airway sample from field cancerization case 8 [GFS_IW00383]


title: NSCLC tissue from field cancerization case 9 [GFS_IW00387]

description: Gene expression of NSCLC tissue from field cancerization case 9


title: White adipose tissue sample 55


title: NSCLC specimen from field cancerization case 8 [GFS_IW00378]

description: Gene expression of NSCLC specimen from field cancerization case 8


title: White adipose tissue sample 15


title: NSCLC tissue from field cancerization case 9 [GFS_IW00385]


title: White adipose tissue sample 14


title: Airway sample from field cancerization case 8 [GFS_IW00381]


title: White adipose tissue sample 23


title: Pancreas sample 227

source_name: Mouse Pancreas

value: pancreas


title: Normal lung tissue from field cancerization case 9 [GFS_IW00386]


title: Normal lung specimen from field cancerization case 8 [GFS_IW00379]

description: Gene expression of normal lung specimen from field cancerization case 8


title: Airway sample from field cancerization case 8 [GFS_IW00382]


title: Airway sample from field cancerization case 8 [GFS_IW00380]


title: Normal lung tissue from field cancerization case 8 [GFS_IW00377]

description: Gene expression of normal lung tissue from field cancerization case 8


title: White adipose tissue sample 13


title: White adipose tissue sample 24


title: Pancreas sample 228


title: Pancreas sample 210


title: Normal lung tissue from field cancerization case 8 [GFS_IW00375]


title: NSCLC tissue from field cancerization case 8 [GFS_IW00374]

description: Gene expression of NSCLC tissue from field cancerization case 8


title: Pancreas sample 209


title: Pancreas sample 211


title: Pancreas sample 208


title: NSCLC tissue from field cancerization case 8 [GFS_IW00376]


title: Airway sample from field cancerization case 7 [GFS_IW00373]

description: Gene expression of airway sample from field cancerization case 7


title: Airway sample from field cancerization case 7 [GFS_IW00371]


title: Pancreas sample 207


title: Pancreas sample 200


title: Pancreas sample 201


title: Normal lung specimen from field cancerization case 7 [GFS_IW00370]

description: Gene expression of normal lung specimen from field cancerization case 7


title: Pancreas sample 199


title: Airway sample from field cancerization case 7 [GFS_IW00372]


title: Pancreas sample 183


title: NSCLC tissue from field cancerization case 7 [GFS_IW00367]

description: Gene expression of NSCLC tissue from field cancerization case 7


title: Normal lung tissue from field cancerization case 7 [GFS_IW00368]

description: Gene expression of normal lung tissue from field cancerization case 7


title: Pancreas sample 182


title: Pancreas sample 181


title: Airway sample from field cancerization case 6 [GFS_IW00364]

description: Gene expression of airway sample from field cancerization case 6


title: Pancreas sample 177


title: Normal lung tissue from field cancerization case 7 [GFS_IW00366]


title: Pancreas sample 174


title: Pancreas sample 173


title: NSCLC specimen from field cancerization case 7 [GFS_IW00369]

description: Gene expression of NSCLC specimen from field cancerization case 7


title: Airway sample from field cancerization case 6 [GFS_IW00360]


title: Pancreas sample 134


title: Airway sample from field cancerization case 6 [GFS_IW00363]


title: Airway sample from field cancerization case 6 [GFS_IW00362]


title: NSCLC specimen from field cancerization case 6 [GFS_IW00359]

description: Gene expression of NSCLC specimen from field cancerization case 6


title: NSCLC tissue from field cancerization case 7 [GFS_IW00365]


title: Pancreas sample 133


title: Pancreas sample 124


title: Pancreas sample 123


title: NSCLC tissue from field cancerization case 6 [GFS_IW00358]

description: Gene expression of NSCLC tissue from field cancerization case 6


title: Pancreas sample 126


title: Normal lung tissue from field cancerization case 6 [GFS_IW00356]

description: Gene expression of normal lung tissue from field cancerization case 6


title: Pancreas sample 172


title: Pancreas sample 108


title: Normal lung tissue from field cancerization case 6 [GFS_IW00357]


title: Pancreas sample 102


title: Airway sample from field cancerization case 6 [GFS_IW00361]


title: Airway sample from field cancerization case 5 [GFS_IW00352]

description: Gene expression of airway sample from field cancerization case 5


title: Airway sample from field cancerization case 5 [GFS_IW00354]


title: Pancreas sample 122


title: Pancreas sample 109


title: Pancreas sample 127


title: NSCLC tissue from field cancerization case 6 [GFS_IW00355]


title: Lung carcinoid specimen from field cancerization case 5 [GFS_IW00349]

description: Gene expression of lung carcinoid specimen from field cancerization case 5

value: Lung carcinoid tumor


title: Pancreas sample 97


title: Pancreas sample 99


title: Airway sample from field cancerization case 5 [GFS_IW00351]


title: Airway sample from field cancerization case 5 [GFS_IW00353]


title: Airway sample from field cancerization case 5 [GFS_IW00350]


title: Normal lung tissue from field cancerization case 5 [GFS_IW00348]

description: Gene expression of normal lung tissue from field cancerization case 5


title: Pancreas sample 55


title: Pancreas sample 100


title: Lung carcinoid tissue from field cancerization case 5 [GFS_IW00347]

description: Gene expression of lung carcinoid tissue from field cancerization case 5


title: Pancreas sample 101


title: Normal lung tissue from field cancerization case 5 [GFS_IW00346]


title: Pancreas sample 54


title: Pancreas sample 24


title: Airway sample from field cancerization case 4 [GFS_IW00344]

description: Gene expression of airway sample from field cancerization case 4


title: Airway sample from field cancerization case 4 [GFS_IW00342]


title: Airway sample from field cancerization case 4 [GFS_IW00343]


title: Normal lung specimen from field cancerization case 4 [GFS_IW00341]

description: Gene expression of normal lung specimen from field cancerization case 4


title: Lung carcinoid tissue from field cancerization case 5 [GFS_IW00345]


title: Pancreas sample 52


title: Pancreas sample 23


title: Pancreas sample 15


title: Pancreas sample 14


title: NSCLC specimen from field cancerization case 4 [GFS_IW00340]

description: Gene expression of NSCLC specimen from field cancerization case 4


title: Muscle sample 228

source_name: Mouse skeletal muscle

value: skeletal muscle


title: Muscle sample 227


title: Pancreas sample 13


title: Normal lung tissue from field cancerization case 4 [GFS_IW00339]

description: Gene expression of normal lung tissue from field cancerization case 4


title: Muscle sample 210


title: Muscle sample 211


title: Normal lung tissue from field cancerization case 4 [GFS_IW00337]


title: NSCLC tissue from field cancerization case 4 [GFS_IW00338]

description: Gene expression of NSCLC tissue from field cancerization case 4

value: NSCLC


title: Airway sample from field cancerization case 3 [GFS_IW00333]

description: Gene expression of airway sample from field cancerization case 3


title: Muscle sample 208


title: Airway sample from field cancerization case 3 [GFS_IW00335]


title: Muscle sample 209


title: Muscle sample 207


title: Airway sample from field cancerization case 3 [GFS_IW00334]


title: Normal lung specimen from field cancerization case 3 [GFS_IW00332]

description: Gene expression of normal lung specimen from field cancerization case 3


title: NSCLC tissue from field cancerization case 4 [GFS_IW00336]


title: NSCLC specimen from field cancerization case 3 [GFS_IW00331]

description: Gene expression of NSCLC specimen from field cancerization case 3


title: Muscle sample 199


title: Muscle sample 174


title: Muscle sample 183


title: NSCLC tissue from field cancerization case 3 [GFS_IW00329]

description: Gene expression of NSCLC tissue from field cancerization case 3


title: Muscle sample 181


title: Airway sample from field cancerization case 2 [GFS_IW00325]

description: Gene expression of airway sample from field cancerization case 2


title: Airway sample from field cancerization case 2 [GFS_IW00324]


title: Normal lung tissue from field cancerization case 3 [GFS_IW00330]

description: Gene expression of normal lung tissue from field cancerization case 3


title: Muscle sample 172


title: Airway sample from field cancerization case 2 [GFS_IW00322]


title: Airway sample from field cancerization case 2 [GFS_IW00326]


title: NSCLC tissue from field cancerization case 3 [GFS_IW00327]


title: Muscle sample 200


title: Muscle sample 177


title: Muscle sample 133


title: Airway sample from field cancerization case 2 [GFS_IW00323]


title: Normal lung tissue from field cancerization case 3 [GFS_IW00328]


title: Muscle sample 134


title: Muscle sample 128


title: NSCLC specimen from field cancerization case 2 [GFS_IW00320]

description: Gene expression of NSCLC specimen from field cancerization case 2


title: Normal lung specimen from field cancerization case 2 [GFS_IW00321]

description: Gene expression of normal lung specimen from field cancerization case 2


title: Muscle sample 126


title: NSCLC tissue from field cancerization case 2 [GFS_IW00318]

description: Gene expression of NSCLC tissue from field cancerization case 2


title: Normal lung tissue from field cancerization case 2 [GFS_IW00319]

description: Gene expression of normal lung tissue from field cancerization case 2


title: Muscle sample 122


title: Normal lung tissue from field cancerization case 2 [GFS_IW00317]


title: Muscle sample 124


title: Muscle sample 123


title: Muscle sample 127


title: Muscle sample 109


title: Muscle sample 102


title: Muscle sample 173


title: Airway sample from field cancerization case 1 [GFS_IW00314]

description: Gene expression of airway sample from field cancerization case 1


title: NSCLC tissue from field cancerization case 2 [GFS_IW00316]


title: Muscle sample 100


title: Muscle sample 101


title: Muscle sample 108


title: Airway sample from field cancerization case 1 [GFS_IW00315]


title: Normal lung specimen from field cancerization case 1 [GFS_IW00312]

description: Gene expression of normal lung specimen from field cancerization case 1


title: NSCLC specimen from field cancerization case 1 [GFS_IW00311]

description: Gene expression of NSCLC specimen from field cancerization case 1


title: Airway sample from field cancerization case 1 [GFS_IW00313]


title: Pancreas sample 128


title: NSCLC tissue from field cancerization case 1 [GFS_IW00309]

description: Gene expression of NSCLC tissue from field cancerization case 1


title: Muscle sample 97


title: Muscle sample 99


title: Normal lung tissue from field cancerization case 1 [GFS_IW00310]

description: Gene expression of normal lung tissue from field cancerization case 1


title: Muscle sample 55


title: Normal lung tissue from field cancerization case 1 [GFS_IW00308]


title: Muscle sample 52


title: Muscle sample 54


title: Muscle sample 15


title: pre-release1_Male_SS.2_rep9

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

hyb_protocol: Samples and reference were combined, fragmented, then hybridized to randomized-order cGRASP 4x44k salmonid arrays (Agilent eArray AMADID: 025055) as per manufacturers’ instructions with the added stabilization solution step to prevent ozone-related problems (Agilent). Slides were kept in the dark in a low ozone atmosphere until scanned.

scan_protocol: All slides were scanned on a Perkin Elmer ScanArray® Express at 5 µm at constant PMT settings optimized to have the median signal of ~1-2% of all array spots saturated scanned on a ScanArray Express (Perkin Elmer) PMTs: Cy3:75; Cy5:70).

data_processing: Images were quantified in Imagene 8.0 (Biodiscovery) using an eArray GAL file (Design ID: 024389; Agilent). Poor and control spots were flagged for downstream filtering, and the median background intensity was subtracted from the median signal value for each probe. Samples were loaded into GeneSpring 11.5.1 (Agilent). Negative raw values were set at 1.0, each array was normalized by an intensity-dependent Lowess, and a baseline to median transformation of normalized expression values was performed per gene. Control spots, and any probes not passing the following were removed: raw values ≥ 500 in both channels, and no poor quality flags in at least 65% of the samples in any one condition. Probes passing quality control thresholds were analyzed for differential expression among resident or migratory conditions (not including pre-release samples) by one-way ANOVA and pairwise Tukey’s HSD tests of each resident condition against the migratory condition (Benjamini-Hochberg corrected p <= 0.01). Additionally, pairwise fold change filters were conducted between each resident condition and the migratory condition. Differential genes between resident and migrating salmon were analyzed for expression differences between individuals in the pre-release group that displayed phenotypic differences characteristic of smolting or residing (smolt scale: 1, 2 or 3). The smolt scale conditions in the pre-release groups were contrasted against each other with a fold change filter to find genes that may provide predictive markers for migration or resident gene expression programs.

organism: Oncorhynchus mykiss

label_protocol: cDNA synthesis and cRNA amplification was performed on 200ng input total RNA using the Low Input Quick Amp system (Agilent Technologies; v6.5) with Cy5- or Cy3-CTP (Perkin Elmer). A reference pool was generated by synthesizing Cy3-labeled cRNA from one male and one female from each of the six conditions (except two males and two females were synthesized for the smolt trap condition). Equimolar concentrations of each synthesized Cy3-cRNA sample (n = 14) was pooled to create a common reference used to hybridize to each array alongside sample Cy5-cRNA. All cRNA samples were quality checked for specific activity as per manufacturers’ protocol (Agilent) and kept at -80 °C in the dark until hybridization.

growth_protocol: Adult hatchery-origin winter steelhead returning to Abernathy FTC were captured and spawned in March, 2011.  Juveniles were raised on well water in circular tanks in a hatchery building until September 2011, then transferred to an outdoor raceway fed by unfiltered water from Abernathy Creek.

extract_protocol: Samples were randomized and total RNA was extracted from gill samples using Trizol (Invitrogen) by physical disruption with a MixerMill (Retsch). Samples were then purified through RNeasy columns with the optional on-column DNase digestion to remove any genomic DNA (QIAGEN). Total RNA was quantified and quality checked by spectrophotometry (NanoDrop-1000) and 1% agarose gel electrophoresis, then stored at -80 °C.

treatment_protocol: The samples for the present study were derived from fish either prior to release from hatchery (13 days prior to each of two releases), or after release from hatchery sampled near the hatchery or on the way to the ocean (while still in freshwater). Non-migrants were captured eight days following each release by electrofishing. Migrants were captured eight days following the second release only from a rotary trap in a weir located at the mouth of Abernathy Creek. A final sample, 48 days post second release was obtained by electrofishing near the hatchery for a last group of non-migrants. All fish were euthanized by a sharp blow to the head, weighed, measured, and photographed.  Each fish was assigned a smolt scale rating of 1-3 based on color, parr marks and body shape, with 1 being a typical parr, 3 being a typical smolt, and 2 being intermediate or having characteristics of both (or if not all members of the sampling crew agreed on the rating). Fish were dissected rapidly on site, and gills, brain, muscle and kidney were preserved in RNAlater (QIAGEN). Tissues in RNAlater were stored overnight at 4°C, then transferred to -20°C.

tag: sampling location

value: Male

value: gill

source_name: pool of samples from all experimental conditions, containing equimolar sample(s) per condition

value: reference pool


title: NSCLC tissue from field cancerization case 1 [GFS_IW00307]


title: smolt_trap2_Female_SS.3_rep6

value: Female


title: Muscle sample 23

value: M

value: LF

value: HF


title: Muscle sample 24


title: Muscle sample 14


title: pre-release2_Male_SS.3_rep7


title: Liver sample 227

source_name: Mouse Liver

value: liver


title: Muscle sample 13


title: Liver sample 211


title: pre-release1_Female_SS.1_rep4


title: Liver sample 228


title: pre-release1_Male_SS.2_rep10


title: pre-release2_Male_SS.3_rep8


title: Liver sample 210


title: in_creek3_Female_SS.1_rep2


title: pre-release2_Male_SS.2_rep9


title: in_creek1_Female_SS.1_rep3


title: Liver sample 207


title: in_creek3_Female_SS.1_rep1


title: in_creek1_Male_SS.1_rep6


title: Liver sample 209


title: in_creek3_Female_SS.1_rep3


title: smolt_trap2_Male_SS.3_rep11


title: Liver sample 200


title: Liver sample 183


title: Liver sample 201


title: Muscle sample 201


title: in_creek2_Female_SS.1_rep3


title: pre-release1_Male_SS.2_rep8


title: Liver sample 182


title: pre-release1_Female_SS.1_rep2


title: Liver sample 181


title: Liver sample 174


title: pre-release2_Female_SS.2_rep4


title: Liver sample 199


title: Liver sample 173


title: Liver sample 177


title: in_creek3_Male_SS.1_rep6


title: in_creek1_Female_SS.1_rep1


title: in_creek2_Female_SS.1_rep2


title: pre-release1_Female_SS.2_rep3


title: Liver sample 127


title: smolt_trap2_Female_SS.3_rep5


title: Liver sample 126


title: Liver sample 134


title: smolt_trap2_Male_SS.3_rep10


title: Liver sample 172


title: Liver sample 124


title: in_creek3_Male_SS.1_rep5


title: Liver sample 123


title: pre-release1_Male_SS.3_rep7


title: Liver sample 122


title: in_creek1_Male_SS.1_rep5


title: Muscle sample 182


title: Liver sample 109


title: in_creek2_Male_SS.1_rep6


title: Liver sample 101


title: smolt_trap2_Male_SS.3_rep8


title: smolt_trap2_Male_SS.3_rep9


title: smolt_trap2_Female_SS.3_rep4


title: Liver sample 55


title: in_creek2_Male_SS.1_rep5


title: Liver sample 102


title: Liver sample 97


title: Liver sample 100


title: pre-release2_Male_SS.2_rep6


title: Liver sample 108


title: Liver sample 13


title: pre-release2_Female_SS.2_rep2


title: in_creek1_Male_SS.1_rep4


title: pre-release2_Female_SS.3_rep3


title: Liver sample 52


title: Liver sample 99


title: in_creek3_Male_SS.1_rep4


title: Liver sample 54


title: in_creek2_Female_SS.1_rep1


title: smolt_trap2_Female_SS.3_rep2


title: in_creek2_Male_SS.1_rep4


title: Liver sample 14


title: pre-release1_Male_SS.3_rep6


title: Liver sample 23


title: pre-release2_Male_SS.2_rep5


title: pre-release1_Male_SS.2_rep5


title: Heart sample 227

source_name: Mouse Heart

value: heart


title: Liver sample 15


title: smolt_trap2_Female_SS.3_rep3


title: total_IPF_IPFECM_5

city: Minneaplois

first: Matthew

last: Parker

state: MINNESOTA

address: 420 Delaware St. SE

department: Department of Medicine

institute: University of Minnesota

description: SAMPLE 40

scan_protocol: Standard Illumina scanning protocol (illumina iScan)

data_processing: The data was normalized using the robust spline normalization (RSN) and log2 transformed in the statistical R package (v.2.15.3).

source_name: IPF lung fibroblast_IPF-ECM

label_protocol: Illumina Total Pre-96 RNA Amp. Kit

extract_protocol: Cells were treated with cycloheximide to immobilize ribosomes on RNA. Total RNA was isolated using Tri Reagent. Polysome-associated RNA was obtained by centrifuging samples on sucrose gradient, fractionating, and isolating using Tri Reagent.

tag: cell type

value: IPF lung fibroblast

tag: ecm type

value: IPF

tag: cell line

value: IPF 5

tag: batch

tag: molecule subtype

value: total RNA


title: Heart sample 209

tag: Sex

tag: cage

tag: maternal diet


title: smolt_trap2_Female_SS.3_rep1

tag: sample type


title: heavy_IPF_IPFECM_5

description: SAMPLE 39

value: polysome-associated RNA


title: Heart sample 208

tag: diet

tag: weight (g) 3 weeks

tag: weight (g) weaning

tag: glucose (mg/dl)


title: Heart sample 228

tag: tissue

tag: length (mm)

tag: bmi

tag: genetic background


title: Heart sample 211


title: Heart sample 207


title: Heart sample 201


title: pre-release2_Female_SS.2_rep1

tag: sampling location


title: Heart sample 210


title: smolt_trap2_Male_SS.3_rep7


title: Heart sample 199


title: heavy_IPF_controlECM_5

description: SAMPLE 37

source_name: IPF lung fibroblast_control-ECM

tag: cell type

tag: ecm type

value: control


title: Heart sample 200


title: total_IPF_controlECM_5

description: SAMPLE 38

tag: cell line

tag: batch


title: total_IPF_IPFECM_4

description: SAMPLE 36

value: IPF 4

tag: molecule subtype


title: Heart sample 177

tag: Sex

tag: cage


title: Heart sample 181

tag: maternal diet


title: heavy_IPF_IPFECM_4

description: SAMPLE 35


title: Heart sample 183

tag: diet


title: pre-release1_Female_SS.2_rep1

tag: sample type


title: Heart sample 182

tag: weight (g) 3 weeks

tag: weight (g) weaning


title: Heart sample 173

tag: tissue

tag: glucose (mg/dl)


title: heavy_IPF_controlECM_4

description: SAMPLE 33


title: Heart sample 174

tag: length (mm)

tag: bmi


title: Heart sample 172

tag: genetic background


title: total_IPF_controlECM_3

description: SAMPLE 30

tag: cell type

value: IPF 3


title: Heart sample 133


title: Heart sample 128


title: Heart sample 134


title: total_IPF_controlECM_4

description: SAMPLE 34

tag: ecm type


title: Heart sample 126


title: heavy_IPF_controlECM_3

description: SAMPLE 29

tag: cell line


title: total_IPF_IPFECM_2

description: SAMPLE 28

value: IPF 2

tag: batch


title: total_IPF_controlECM_2

description: SAMPLE 26

tag: molecule subtype


title: Heart sample 124

tag: Sex


title: Heart sample 123

tag: cage


title: heavy_IPF_IPFECM_3

description: SAMPLE 31


title: heavy_IPF_IPFECM_2

description: SAMPLE 27


title: heavy_IPF_controlECM_2

description: SAMPLE 25


title: Heart sample 108

tag: maternal diet


title: total_IPF_controlECM_1

description: SAMPLE 22

value: IPF 1


title: heavy_IPF_IPFECM_1

description: SAMPLE 23


title: heavy_IPF_controlECM_1

description: SAMPLE 21


title: Heart sample 127

tag: diet


title: Heart sample 109


title: Heart sample 122


title: heavy_control_IPFECM_5

description: SAMPLE 19

source_name: control lung fibroblast_IPF-ECM

value: control lung fibroblast

value: control 5


title: Heart sample 102

value: M


title: total_IPF_IPFECM_1

description: SAMPLE 24


title: heavy_control_controlECM_5

description: SAMPLE 17

source_name: control lung fibroblast_control-ECM


title: heavy_control_IPFECM_4

description: SAMPLE 15

value: control 4


title: Heart sample 100

value: LF


title: Heart sample 101


title: total_control_IPFECM_5

description: SAMPLE 20


title: Heart sample 97

value: HF


title: Heart sample 99

value: heart


title: Heart sample 54