title: G1-R1

description: Control

source_name: Control

value: Control


title: G1-R2

status: Public on Sep 28 2017

type: RNA

city: Toledo

first: Gerardo

last: Avila Martín

address: Finca La Peraleda s/n

department: Research Unit

country: Spain

institute: National Paraplejic Hospital

description: Control

hyb_protocol: Standard affymetrix hybridization protocol for FS450

scan_protocol: Standard affymetrix scan protocol for GS 3000

data_processing: Affymetrix Expression Console used to calculate RMA.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Standard affymetrix protrocol to apmplify and generate biotinilated complementary RNA

extract_protocol: Trizol

treatment_protocol: injection of HOA associated with albumine (commercial name 'minerval').

tag: tissue

value: spinal cord

tag: strain

value: Wistar

tag: group


title: G5-R25

description: Moderate contusion + A-HOA 7 days

source_name: Moderate contusion + A-HOA 7 days

value: Moderate contusion + A-HOA 7 days


title: G5-R22

description: Moderate contusion + A-HOA 7 days


title: G5-R7

description: Moderate contusion + A-HOA 7 days


title: M1.2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

hyb_protocol: Refer to the NanoString nCounter Assay System Manual.

data_processing: The raw data were normalized using 6 housekeeping genes (Actb, Gapdh, Hprt, Ldha, Ms4a1 and Tbp).  nSolver Analysis Software was used for normalization and we followed their internal protocol with geometric mean as normalization factor.

organism: Mus musculus

source_name: Spleen

extract_protocol: Buffer RLT

tag: age

value: 6 Weeks Old

tag: Sex

value: Female

tag: genotype

value: WT

value: spleen

tag: cell type

value: CD4+ T cells


title: G1-R5

description: Control


title: G4-R8

description: Moderate contusion

source_name: Moderate contusion

value: Moderate contusion


title: M1.1

scan_protocol: Refer to the NanoString nCounter Assay System Manual.


title: G4-R16

description: Moderate contusion


title: G1-R

description: Control


title: G4-R18

description: Moderate contusion


title: GBS-1_12h_LBH589

status: Public on Sep 27 2017

city: Kagoshima

first: Yoshinobu

last: Saito

address: 8-35-1, Sakuragaoka

country: Japan

institute: Kagoshima University

description: Gene expression 12 hours after LBH589 treatment

hyb_protocol: 0.6ug of Cy-3 labelled cRNA was fragmented at 60℃ for 30 minutes in a reaction volume of 25 ul containing 1× Agilent fragmentation buffer and 2×Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8×60K Microarray Ver2.0 (Agilent) for 17 hours at 65℃ 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℃ GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8×60k array slides (Scan Area 61×21.6mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with feature Extraction software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and satially detrended Processed Signal intensities.

organism: Homo sapiens

source_name: cell line_12h_LBH589

label_protocol: Cyanine-3 (Cy-3) labeled cRNA was prepared from 0.1 ug Total RNA using the Low Imput Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by Rneasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop NS-2000 spectrophotometer.

extract_protocol: RNA was prepared using the High Pure RNA Isolation Kit (Roche, Basel, Switzerland) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop ND-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: GBS-1 was kindly provided by Kobe University. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/mL) and Streptomycin (100 μg/mL)  in a humidified incubator with 5 % CO2 at 37℃ .

tag: cell line

tag: tumor

value: undifferentiated pleomorphic saracoma


title: from_Surgical resection_non-tumoral brain epilepsy_TuBa 2901-NB

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

country: Switzerland

institute: CHUV / BCF / SIB

description:
TuBa 2901-NB
Normal brain I  (BNT104)

hyb_protocol: Affymetrix hybridisation protocol

scan_protocol: GeneChip Operating Software instructions using GeneChip Scanner 3000 High-Resolution Scanning Patch

data_processing: RMA: background substruction, quantile normalization and median polish summarization

source_name: tissue

label_protocol: Affymetrix Small sample target labelling assay (double amplification) with ENZO kit, start with 100ng

extract_protocol: Qiagen Rneasy Lipid Tissue mini kit protocol

tag: disease

value: non-tumor brain


title: GBS-1_24h_LBH589

description: Gene expression 24 hours after LBH589 treatment

source_name: cell line_24h_LBH589


title: Surgical resection GBM_TuBa 2683

description:
TuBa 2683
Tuba 2683

value: Glioblastoma


title: GBS-1_0h_LBH589

description: Gene expression without LBH589 treatment

source_name: cell line_0h_LBH589


title: Surgical resection GBM_TuBa 2540

description:
TuBa 2540
TuBa 2540


title: Surgical resection GBM_TuBa 2669

description:
TuBa 2669
TuBa 2669


title: adherent GBM derived cell line_LN-2669_replicate 2

description:
LN-2669, replicate 2
LN 2669_2


title: GBM derived Sphere line_passaged_intra-cerebrally_in_nude mouse_N-2540GS

description:
N-2540GS
N-2540 CD


title: adherent GBM derived cell line_LN-2669_replicate 1

description:
LN-2669, replicate 1
LN 2669_1


title: adherent GBM derived cell line_LN-2207_replicate 2

description:
LN-2207, replicate 2
LN 2207_2


title: adherent GBM derived cell line_LN-2207_replicate 1

description:
LN-2207, replicate 1
LN 2207_1


title: adherent GBM derived cell line_LN-2207_replicate 3

description:
LN-2207, replicate 3
LN 2207_3


title: GBM derived Sphere line_LN-2669GS_replicate 3

description:
LN-2669GS, replicate 3
CD 2669_3


title: GBM derived Sphere line_passaged_intra-cerebrally_in_nude mouse_N-2669GS

description:
N-2669GS
N-2669 CD


title: GBM derived Sphere line_LN-2683GS_replicate 1

description:
LN-2683GS, replicate 1
CD 2683_1


title: from_Surgical resection_non-tumoral brain epilepsy_TuBa 1780-NB

description:
TuBa 1780-NB
Normal brain II  (TuBa 1780)


title: Surgical resection GBM_TuBa 2207

description:
TuBa 2207
TuBa 2207


title: GBM derived Sphere line_LN-2683GS_replicate 2

description:
LN-2683GS, replicate 2
CD 2683_2


title: GBM derived Sphere line_LN-2683GS_replicate 3

description:
LN-2683GS, replicate 3
CD 2683_3


title: adherent GBM derived cell line_LN-2669_replicate 3

description:
LN-2669, replicate 3
LN 2669_3


title: GBM derived Sphere line_LN-2669GS_replicate 1

description:
LN-2669GS, replicate 1
CD 2669_1


title: T-ALL1 GSI treated cells rep1

first: Eric

middle: A

last: Severson

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

description: SAMPLE 3

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays.

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner.

data_processing: Data was processed using R with the 'affy' package (v1.50.0) using RMA normalization

label: Biotin

source_name: T-ALL patient derived cell line_GSI

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7-10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: TALL1 cells were cultured in RPMI1640 medium supplemented with 10% FBS and 1x penicillin and streptomycin.

extract_protocol: Total RNA extraction was performed using Trizol reagent (Life Technologies) and RNAeasy kit (Qiagen).

treatment_protocol: Cells were treated with vehicle (DMSO) for 1 day, GSI (compound E 1μM) for 1 day, or NOTCH3 NRR antibodies (A4) for 72hrs.

value: T-Acute Lymphoblastic Leukemia (T-ALL) patient derived cell line

tag: treated with

value: GSI (compound E 1μM) for 1 day


title: SK-MEL-3 GSE Triplicate3

city: Tallahassee

first: Elizabeth

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

description:
Malignant melanoma (P13) hypotetraploid to hypertetraploid with abnormalities including dicentrics, pulverizations, secondary constrictions and minutes
Gene expression data from SK-MEL-3 cells grown under variable experimental treatment

hyb_protocol: Hybrization was conducted according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, ThermoFisher Scientific)

data_processing: The data was processed using Affymetrix expression console and evaluated by Affymetrix transcription console software (Affymetrix, ThermoFisher Scientific). RMA algorithm.

source_name: SK-MEL-3 GSE

label_protocol: cDNA was labeled using according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

growth_protocol: SK-MEL-3, [ATCC HTB-69] cells were cultured in 175 cm2 flasks containing ATCCs-formulated McCoy's 5a Medium Modified , [ATCC Catalog No. 30-2007] supplemented with fetal bovine serum [ 10%,] and [100 U/ml penicillin G sodium/100 μg/ml streptomycin sulfate]. Cells were grown at 37°C with 95% air and 5% CO2 and sub-cultured every three to five days.

extract_protocol: After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. Total RNA was isolated/ purified using the Aurum total RNA mini kit (Bio-rad) quality was assessed and concentration was equalized to 82ng/ul in nuclease free water.

treatment_protocol: Trichostatin A was prepared in DMSO ( 2 mg/ml), then diluted in HBSS and added to cell culture media to a final working concentration of 1uM (sublethal concentration). Grape Seed extract [Vitis Vinifera ] was prepared in absolute ethanol ( 50mg/ml ) then diluted in HBSS and added to cell culture media to a final working concentration of 120 ug/ml. Both conditions were evaluted vs control in SK-MEL-3 cells.

tag: treatment

value: Grape Seed Extract


title: GBM derived Sphere line_LN-2540GS_replicate 1

description:
LN-2540GS, replicate 1
CD 2540_1


title: GBM derived Sphere line_LN-2669GS_replicate 2

description:
LN-2669GS, replicate 2
CD 2669_2


title: GBM derived Sphere line_LN-2540GS_replicate 3

description:
LN-2540GS, replicate 3
CD 2540_3


title: GBM derived Sphere line_LN-2207GS_replicate 3

description:
LN-2207GS, replicate 3
CD 2207_3


title: SK-MEL-3 TSA Replicate1

source_name: SK-MEL-3 TSA

value: Trichostatin A


title: T-ALL1 A4 treated cells rep1

description: SAMPLE 5

source_name: T-ALL patient derived cell line_A4

value: NOTCH3 NRR antibodies (A4) for 72hrs


title: GBM derived Sphere line_LN-2540GS_replicate 2

description:
LN-2540GS, replicate 2
CD 2540_2


title: SK-MEL-3 GSE Triplicate1


title: GBM derived Sphere line_LN-2207GS_replicate 2

description:
LN-2207GS, replicate 2
CD 2207_2


title: T-ALL1 A4 treated cells rep2

description: SAMPLE 6


title: LINC-PINT_overexpression_rep3

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

hyb_protocol: Samples were hybridized to GeneChip HuGene-2_0 ST Arrays (Affymetrix) and scanned at the CIMA Genomic Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Both background correction and normalization were done using RMA algorithm of Bioconductor platform

source_name: HCT116 cell line

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated from 1million cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. All samples were treated with DNAse (Quiagen) to remove trace amounts of genomic DNA.

value: colon adenocarcinoma


title: control_rep2


title: control_rep3


title: SK-MEL-3 TSA Replicate2


title: GBM derived Sphere line_LN-2207GS_replicate 1

description:
LN-2207GS, replicate 1
CD 2207_1


title: LINC-PINT_overexpression_rep1


title: LINC-PINT_overexpression_rep2


title: T-ALL1 GSI treated cells rep2

description: SAMPLE 4


title: SK-MEL-3 GSE Triplicate2


title: 8_Human LAM_shSRPK2_DMSO [splice isoform ananlysis]

city: New York

first: John

last: Blenis

state: NY

address: 413 East 69th Street

department: Meyer Cancer Center and Department of Pharmacology

institute: Weill Cornell Medicine

description:
8_1998N
Splice isoform analysis; RMA expression value derived from Expression Console software

hyb_protocol: Following fragmentation, 5.5 μg of cDNA were hybridized for 16 hr at 45 celsius on Human Transcriptome 2.0 Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2 at the Partners Healthcare Microarray Core Facility, Harvard Medical School.

data_processing:
Raw data were processed by Affymetrix Expression Console Software 1.4.1. using Analysis algorithm RMA to generate CHP files for gene expression and splice isoform analyses.
affymetrix-algorithm-name = sst-rma-alt-splice : sst-dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: human LAM_shSRPK2_DMSO

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using amplification kit GeneChip WT Plus, Lot # 4215353, followed by labeling 5.5 μg cDNA using Affymetrix GeneChip WT Terminal Labeling (part of WT Plus kit).

growth_protocol: Lymphangioleiomyomatosis (LAM 621-101) cells were cultured on petri-dish.

extract_protocol: Total RNA was isolated from cells cultured on 60 mm petri-dish using RNeasy Mini Kit (Qiagen) and treated with DNase I (Qiagen) according to the manufacturer’s instructions. All samples passed RIN scores and 260/280 ratios from QC.

treatment_protocol: Cells stably expressing shRNA targeting GFP (pLKO-puro-shGFP) or SRPK2 (pLKO-puro-shSRPK2) were treated with DMSO (vehicle control) or 100 nM rapamycin (dissolved in DMSO, Sigma) for 24 hr.

value: female

value: Lymphangioleiomyomatosis cell line

tag: genotype/variation

value: stably expressing shRNA targeting SRPK2 (pLKO-puro-shSRPK2)

value: DMSO (vehicle control) for 24hrs


title: SK-MEL-3 Control Triplicate3

source_name: SK-MEL-3 Control

value: control


title: T-ALL1 DMSO treated cells rep2

description: SAMPLE 2

source_name: T-ALL patient derived cell line_DMSO

value: vehicle (DMSO) for 1 day


title: 1_Human LAM_shGFP_DMSO [splice isoform ananlysis]

description:
1_1998A
Splice isoform analysis; RMA expression value derived from Expression Console software

source_name: human LAM_shGFP_DMSO

value: stably expressing shRNA targeting GFP (pLKO-puro-shGFP)


title: SK-MEL-3 TSA Replicate2 [miRNA]

description:
Malignant melanoma (P13) hypotetraploid to hypertetraploid with abnormalities including dicentrics, pulverizations, secondary constrictions and minutes
miRNA expression data from SK-MEL-3 cells grown under variable experimental treatment

hyb_protocol: Hybrization was conducted according to manufacturer's instructions as per the Genechip miRNA 4.1 human array / FlashTag™ Biotin HSR RNA kit (Affymetrix, ThermoFisher Scientific).

label_protocol: Briefly, after RNA purification, samples were labeled with a POLY A tail, and ligated using a flash tag ligation mix from the FlashTag™ Biotin HSR RNA kit (Affymetrix). Subsequently, biotin labeled RNA was detected using streptavidin – EP and hybridized on to a Genechip miRNA 4.1 human array, prior to fluidics and imaging by the Gene Atlas.

extract_protocol: After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. miRNA was isolated using the quiazol reagent and miRNeasy Mini Kit (Qiagen, Germantown, MD), quality was assessed and concentration was equalized to 50ng/ul in nuclease free water.


title: T-ALL1 DMSO treated cells rep1

description: SAMPLE 1


title: control_rep1


title: SK-MEL-3 GSE Triplicate2 [miRNA]


title: SK-MEL-3 GSE Triplicate3 [miRNA]


title: SK-MEL-3 TSA Replicate1 [miRNA]


title: SK-MEL-3 Control Triplicate2


title: SK-MEL-3 Control Triplicate1


title: 22Rv1 3 µM Enzalutamide 6 h rep 1

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

description: Sample 21

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Background subtraction, normalization and gene expression index calculation were performed using Rosetta Resolver software

source_name: 22Rv1 3 uM Enzalutamide 6 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (using Affymetrix 3IVT Plus amplification kit).

growth_protocol: RPMI media + 10% Charcoal Stripped Fetal Bovine Serum

extract_protocol: Qiazol extraction of total RNA followed by Qiagen Rneasy purification was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with either A-485 or enzalutamide for 30 minutes and then further treated with either DHT or ethanol for 6 h.


title: 7_Human LAM_shSRPK2_DMSO [splice isoform ananlysis]

description:
7_1998M
Splice isoform analysis; RMA expression value derived from Expression Console software


title: 22Rv1 0.3 µM Enzalutamide 6 h rep 2

description: Sample 20

source_name: 22Rv1 0.3 uM Enzalutamide 6 h


title: H1 at D10, chip HG-U133A, biological rep2

city: New Haven

first: Natalia

last: Ivanova

state: CT

address: 10 Amistad Street, Room 220

department: Genetics

institute: Yale University

description:
H1_d10_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 10)

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hours at 45°C on the Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G with AutoLoader Carousel.

data_processing: Expression data were extracted using the MAS5.0 software package (Affymetrix). Data analyses were performed in MatLab R2010b (The MathWorks Inc.). Data were normalized using cubic spline normalization algorithm with H1 d0 array used as a reference sample.

source_name: H1 human embryonic stem cells, day 10 of retinoic acid differentiation

label_protocol: 1 μg of total RNA was converted into biotinylated cRNA using the Illumina TotalPrep RNA Amplification Kit (Ambion) following the manufacturer's instructions.

growth_protocol: All hESC lines were maintained in mTeSR media on Matrigel-coated plates and passaged every 5-6 days. H1 hESCs were differentiated in the presence of 5μM retinoic acid.

extract_protocol: Total RNA was isolated using Trizol, treated with DNAseI to eliminate genomic DNA, and subjected to 1:1 phenol:chloriform extraction, with precipitation and dilution of RNA in water.

value: human embryonic stem cells

tag: agent

value: retinoic acid

tag: time

value: day 10

tag: status

value: differentiating in retinoic acid for 10 days


title: 2_Human LAM_shGFP_DMSO [splice isoform ananlysis]

description:
2_1998H
Splice isoform analysis; RMA expression value derived from Expression Console software


title: H1 at D9, chip HG-U133A, biological rep2

description:
H1_d9_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 9)

source_name: H1 human embryonic stem cells, day 9 of retinoic acid differentiation

value: day 9

value: differentiating in retinoic acid for 9 days


title: 22Rv1 3 µM Enzalutamide 6 h rep 2

description: Sample 22


title: SK-MEL-3 GSE Triplicate1 [miRNA]

value: Grape Seed Extract


title: 3_Human LAM_shGFP_DMSO [splice isoform ananlysis]

description:
3_1998I
Splice isoform analysis; RMA expression value derived from Expression Console software


title: 6_Human LAM_shGFP_rapamycin [splice isoform ananlysis]

description:
6_1998L
Splice isoform analysis; RMA expression value derived from Expression Console software

source_name: human LAM_shGFP_rapamycin

value: 100 nM rapamycin for 24 hr


title: 22Rv1 0.3 µM Enzalutamide 6 h rep 1

description: Sample 19


title: 9_Human LAM_shSRPK2_DMSO [splice isoform ananlysis]

description:
9_1998O
Splice isoform analysis; RMA expression value derived from Expression Console software


title: H1 at D8, chip HG-U133A, biological rep2

description:
H1_d8_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 8)

source_name: H1 human embryonic stem cells, day 8 of retinoic acid differentiation

value: day 8

value: differentiating in retinoic acid for 8 days


title: H1 at D9, chip HG-U133A, biological rep1

description:
H1_d9_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 9)


title: H1 at D10, chip HG-U133A, biological rep1

description:
H1_d10_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 10)


title: 4_Human LAM_shGFP_rapamycin [splice isoform ananlysis]

description:
4_1998J
Splice isoform analysis; RMA expression value derived from Expression Console software

value: female


title: H1 at D8, chip HG-U133A, biological rep1

description:
H1_d8_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 8)


title: SK-MEL-3 Control Triplicate3 [miRNA]


title: H1 at D7, chip HG-U133A, biological rep1

description:
H1_d7_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 7)

source_name: H1 human embryonic stem cells, day 7 of retinoic acid differentiation

value: day 7

value: differentiating in retinoic acid for 7 days


title: H1 at D7, chip HG-U133A, biological rep2

description:
H1_d7_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 7)


title: SK-MEL-3 Control Triplicate1 [miRNA]


title: SK-MEL-3 Control Triplicate2 [miRNA]


title: 5_Human LAM_shGFP_rapamycin [splice isoform ananlysis]

description:
5_1998K
Splice isoform analysis; RMA expression value derived from Expression Console software

value: Lymphangioleiomyomatosis cell line


title: H1 at D6, chip HG-U133A, biological rep1

description:
H1_d6_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 6)

source_name: H1 human embryonic stem cells, day 6 of retinoic acid differentiation

value: day 6

value: differentiating in retinoic acid for 6 days


title: H1 at D5, chip HG-U133A, biological rep2

description:
H1_d5_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 5)

source_name: H1 human embryonic stem cells, day 5 of retinoic acid differentiation

value: day 5

value: differentiating in retinoic acid for 5 days


title: H1 at D4, chip HG-U133A, biological rep2

description:
H1_d4_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 4)

source_name: H1 human embryonic stem cells, day 4 of retinoic acid differentiation

value: human embryonic stem cells

value: retinoic acid

value: day 4

value: differentiating in retinoic acid for 4 days


title: H1 at D6, chip HG-U133A, biological rep2

description:
H1_d6_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 6)


title: Day 12 cells from donor 2

first: Liang

last: Shan

address: 300 Cedar Street

department: Immunobiology

hyb_protocol: cRNA were prepared according to the standard Affymetrix protocol and was hybridized to GeneChip PrimeView Human Gene Expression Array (Affymetrix, Germany)

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

data_processing: Spotfire DecisionSite for Functional Genomics, log2 of intensity levels and performed RMA normalization.

source_name: Day 12 cells from donor 2

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

growth_protocol: Human primary cells were cultured in RPMI1640 medium (Gibco) containing 10% fetal bovine serum at 37°c, 5% CO2.

extract_protocol: Total RNA was extracted using Qiagen RNAeasy Mini kit

treatment_protocol: Resting CD4+ T cells were isolated from healthy donors or patients with CD4+ Isolation Kit II followed by negative depletion using CD25, CD69 and HLA-DR microbeads (Miltenyi). Activated CD4+ T cells were generated by co-stimulation of resting CD4+ T cells with CD3 and CD28 antibodies with the presence of IL-2 (100U/ml) for 3 days. To obtain day 6, 9 ,12 CD4+ T cells, activated CD4+ T cells were cultured in basal medium after removal of antibodies and cytokine for additional days.

value: CD4+ T

value: Healthy donor blood


title: Day 12 cells from donor 1

source_name: Day 12 cells from donor 1


title: H1 at D2, chip HG-U133A, biological rep1

description:
H1_d2_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 2)

source_name: H1 human embryonic stem cells, day 2 of retinoic acid differentiation

value: day 2

value: differentiating in retinoic acid for 2 days


title: H1 at D3, chip HG-U133A, biological rep2

description:
H1_d3_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 3)

source_name: H1 human embryonic stem cells, day 3 of retinoic acid differentiation

value: day 3

value: differentiating in retinoic acid for 3 days


title: H1 at D3, chip HG-U133A, biological rep1

description:
H1_d3_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 3)


title: H1 at D5, chip HG-U133A, biological rep1

description:
H1_d5_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 5)


title: Resting cells from donor 2

source_name: Resting cells from donor 2


title: Day 9 cells from donor 3

source_name: Day 9 cells from donor 3


title: Day 12 cells from donor 3

source_name: Day 12 cells from donor 3


title: H1 at D1, chip HG-U133A, biological rep1

description:
H1_d1_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 1)

source_name: H1 human embryonic stem cells, day 1 of retinoic acid differentiation

value: day 1

value: differentiating in retinoic acid for 1 day


title: Resting cells from donor 3

source_name: Resting cells from donor 3


title: H1 at D1, chip HG-U133A, biological rep2

description:
H1_d1_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 1)


title: H1 at D0, chip HG-U133A, biological rep1

description:
H1_d0_A-1
Gene expression data from undifferentatied H1 hESCs (day 0)

source_name: H1 human embryonic stem cells, day 0 of retinoic acid differentiation

value: control

value: day 0

value: undifferentiated


title: H1 at D2, chip HG-U133A, biological rep2

description:
H1_d2_A-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 2)


title: Day 6 cells from donor 3

source_name: Day 6 cells from donor 3


title: Day 9 cells from donor 1

source_name: Day 9 cells from donor 1


title: Resting cells from donor 1

source_name: Resting cells from donor 1


title: H1 at D0, chip HG-U133A, biological rep2

description:
H1_d0_A-2
Gene expression data from undifferentatied H1 hESCs (day 0)


title: Day 6 cells from donor 1

source_name: Day 6 cells from donor 1


title: H1 at D4, chip HG-U133A, biological rep1

description:
H1_d4_A-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 4)


title: Day 9 cells from donor 2

source_name: Day 9 cells from donor 2


title: H9, chip HG-U133A, biological rep2

description:
H9_A-2
Gene expression data from undifferentiated H9 hESCs

source_name: H9 human embryonic stem cells, undifferentiated


title: Day 6 cells from donor 2

source_name: Day 6 cells from donor 2


title: Day 3 cells from donor 3

source_name: Day 3 cells from donor 3


title: Day 3 cells from donor 2

source_name: Day 3 cells from donor 2


title: H9, chip HG-U133A, biological rep1

description:
H9_A-1
Gene expression data from undifferentiated H9 hESCs


title: H1 at D9, chip HG-U133B, biological rep2

description:
H1_d9_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 9)

source_name: H1 human embryonic stem cells, day 9 of retinoic acid differentiation

value: day 9

value: differentiating in retinoic acid for 9 days


title: H1 at D10, chip HG-U133B, biological rep1

description:
H1_d10_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 10)

source_name: H1 human embryonic stem cells, day 10 of retinoic acid differentiation

value: human embryonic stem cells

value: day 10

value: differentiating in retinoic acid for 10 days


title: Day 3 cells from donor 1

source_name: Day 3 cells from donor 1


title: HUES8, chip HG-U133A, biological rep1

description:
HUES8_A-1
Gene expression data from undifferentiated HUES8 hESCs

source_name: HUES8 human embryonic stem cells, undifferentiated


title: H1 at D10, chip HG-U133B, biological rep2

description:
H1_d10_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 10)

value: retinoic acid


title: H1 at D9, chip HG-U133B, biological rep1

description:
H1_d9_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 9)


title: H1 at D8, chip HG-U133B, biological rep1

description:
H1_d8_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 8)

source_name: H1 human embryonic stem cells, day 8 of retinoic acid differentiation

value: day 8

value: differentiating in retinoic acid for 8 days


title: H1 at D6, chip HG-U133B, biological rep2

description:
H1_d6_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 6)

source_name: H1 human embryonic stem cells, day 6 of retinoic acid differentiation

value: day 6

value: differentiating in retinoic acid for 6 days


title: H1 at D5, chip HG-U133B, biological rep2

description:
H1_d5_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 5)

source_name: H1 human embryonic stem cells, day 5 of retinoic acid differentiation

value: day 5

value: differentiating in retinoic acid for 5 days


title: H1 at D4, chip HG-U133B, biological rep1

description:
H1_d4_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 4)

source_name: H1 human embryonic stem cells, day 4 of retinoic acid differentiation

value: day 4

value: differentiating in retinoic acid for 4 days


title: H1 at D6, chip HG-U133B, biological rep1

description:
H1_d6_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 6)


title: H1 at D8, chip HG-U133B, biological rep2

description:
H1_d8_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 8)


title: H1 at D5, chip HG-U133B, biological rep1

description:
H1_d5_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 5)


title: H1 at D4, chip HG-U133B, biological rep2

description:
H1_d4_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 4)


title: D1

city: Galveston

first: Fengliang

last: Liu

state: Texas

address: 301 University Blvd

department: Microbiology and Immunlogy

institute: The University of Texas Medical Branch

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Human_ALVAC_24h_donor 1

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

growth_protocol: Monocytes were isolated from health PBMCs with EasySep™ Human CD14 Positive Selection Kit II according to the manufacture's protocol. Then isolated monocytes were induced to differentiate to dendritic cells under the treatment of human recombinant IL-4 and GM-CSF for 5 days.

extract_protocol: RNA was extracted with Quick-RNA™ MicroPrep Kit following the manufacture's protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Monocyte-derived dendritic cells were infected with ALVAC or Ad5 empty viral vectors (MOI=3) for 24 hours.

value: monocyte-derived dendritic cells

tag: source

value: Human PBMCs


title: H1 at D2, chip HG-U133B, biological rep1

description:
H1_d2_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 2)

source_name: H1 human embryonic stem cells, day 2 of retinoic acid differentiation

value: day 2

value: differentiating in retinoic acid for 2 days


title: H1 at D7, chip HG-U133B, biological rep2

description:
H1_d7_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 7)

source_name: H1 human embryonic stem cells, day 7 of retinoic acid differentiation

value: day 7

value: differentiating in retinoic acid for 7 days


title: H1 at D2, chip HG-U133B, biological rep2

description:
H1_d2_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 2)

value: human embryonic stem cells


title: H1 at D3, chip HG-U133B, biological rep1

description:
H1_d3_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 3)

source_name: H1 human embryonic stem cells, day 3 of retinoic acid differentiation

value: day 3

value: differentiating in retinoic acid for 3 days


title: H1 at D3, chip HG-U133B, biological rep2

description:
H1_d3_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 3)

value: retinoic acid


title: D4

description: replicate 1

source_name: Human_Ad5_24h_donor 1


title: D5

description: replicate 2

source_name: Human_Ad5_24h_donor 2


title: H1 at D0, chip HG-U133B, biological rep2

description:
H1_d0_B-2
Gene expression data from undifferentatied H1 hESCs (day 0)

source_name: H1 human embryonic stem cells, day 0 of retinoic acid differentiation

value: control

value: day 0

value: undifferentiated


title: D3

description: replicate 3

source_name: Human_ALVAC_24h_donor 3


title: H1 at D7, chip HG-U133B, biological rep1

description:
H1_d7_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 7)


title: D2

description: replicate 2

source_name: Human_ALVAC_24h_donor 2


title: T_H012 lncRNA

city: Zhengzhou

first: Jianjun

last: Gu

address: No.7 Weiwulu

country: China

institute: Henan Provincial People's Hospital

hyb_protocol: The pre-hybridization of HOA v7 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The Matrix value is normalized intensities. The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: tissue

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

tag: sample type

value: tissue


title: H1 at D1, chip HG-U133B, biological rep2

description:
H1_d1_B-2
Gene expression data from H1 hESCs differentiating in retinoic acid (day 1)

source_name: H1 human embryonic stem cells, day 1 of retinoic acid differentiation

value: day 1

value: differentiating in retinoic acid for 1 day


title: H9, chip HG-U133B, biological rep1

description:
H9_B-1
Gene expression data from undifferentiated H9 hESCs

source_name: H9 human embryonic stem cells, undifferentiated


title: H1 at D1, chip HG-U133B, biological rep1

description:
H1_d1_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 1)


title: T_H010 lncRNA


title: G1_control

type: genomic

city: Linköping

first: Jyotirmoy

last: Das

address: Sandbäcksgatan 7

department: Medical Microbiology

country: Sweden

institute: Linkoping University

description:
LM7_4556D0.v1_2R06C01
Array B
200078650092_R06C01

hyb_protocol: DNA samples were bisulphite converted, amplified, fragmented and hybridized to an Illumina Infinium Human Methylation 450K Bead Chip and scanned

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

data_processing: GenomeStudio 2011.1 from Illumina Inc.  Average Beta values are available in the processed data files on the series record. CEP_C1.7 is a HapMap CEPH sample C1 from CEPH family #1362. It is used as quality control of other samples and thus placed with every Sentrix_ID.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA was isolated from NK cells

label_protocol: Standard Illumina Protocol

extract_protocol: 8 Sample DNAs were isolated from NK cells and the aPBMCs using QiAmp DNA isolation kit following the instructions

treatment_protocol: 70ml blood were collected in heparinized tubes 2 weeks prior to BCG vaccination and 3weeks, 3 months, and 8 months after the vaccination from 8 healthy individuals. The subjects were all non-smoking, PPD-negative, Swedish-born Caucasians (20-35 years, mean age 24 years) with normal BMI and no history of BCG vaccination.

tag: patient id

tag: tissue

value: blood

tag: gender

value: NK

value: Male

value: 2weeks before vaccination


title: G7_control

description:
LM7_1421D0.v1_2R04C01
Array B
200078650092_R04C01


title: T_H008 lncRNA


title: G6_control

description:
LM7_4516D0.v1_2R01C02
Array B
200078650092_R01C02

value: Female


title: H9, chip HG-U133B, biological rep2

description:
H9_B-2
Gene expression data from undifferentiated H9 hESCs


title: T_H011 lncRNA


title: T_H005 lncRNA


title: T_H009 lncRNA


title: D6

description: replicate 3

source_name: Human_Ad5_24h_donor 3

value: monocyte-derived dendritic cells

value: Human PBMCs


title: G6_3w

description:
LM7_4516W3.v1_2R03C01
Array B
200078650092_R03C01

value: 3weeks after vaccination


title: G8_3w

description:
LM7_9182W3.v1_2R05C01
Array B
200078650092_R05C01


title: HUES8, chip HG-U133B, biological rep2

description:
HUES8_B-2
Gene expression data from undifferentiated HUES8 hESCs

source_name: HUES8 human embryonic stem cells, undifferentiated

value: human embryonic stem cells


title: G3_control

description:
LM7_0870D0.v1_1R03C01
Array A
200078650186_R03C01


title: G4_3w

description:
LM7_5667W3.v1_1R02C02
Array A
200078650186_R02C02


title: T_H006 lncRNA


title: C_H002 lncRNA


title: A_Control_rep5

city: CHERAS

first: NORALISA

last: ABDUL KARIM

state: KUALA LUMPUR

address: JALAN YAACOB LATIFF

department: CELL THERAPY CENTRE

country: Malaysia

institute: UKM MEDICAL CENTRE

description: Nematodes at normal development and aging

hyb_protocol: The biotin-labeled amplified RNA (aRNA) was then fragmented before being hybridized onto the genome array. The hybridization controls was used to monitor the hybridization quality, which composed of a mixture of biotinylated and fragmented cRNA of bioB, bioC, bioD and cre prepared in staggered concentrations (1.5, 5, 25, and 100 pM respectively). Using Affymetrix Genechip C. elegans Genome Array, 22 625 transcripts were screened for changes in expression patterns and levels. After 17 hours of hybridization, washing and scanning of the arrays was carried out using GeneChip Hybridization, Wash and Stain Kit (Affymetrix) in GeneChip Fluidics 450 system.

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method in Expression Console software (Affymetrix).

organism: Caenorhabditis elegans

source_name: Control

label_protocol: Purified total RNA was amplified and labeled with biotinylated nucleotide analog using Affymetrix GeneChip 3’ IVT Express Kit according to the manufacturer’s protocol.

growth_protocol: The wild type C. elegans strain (N2) were grown at 20°C on nematode growth medium (NGM), with E. coli OP50 as food source

extract_protocol: Total RNA from each group was extracted using TRIzol reagent following manufacturer’s instruction (Invitrogen, USA), purified using RNeasy Mini Kit (Qiagen, USA)

treatment_protocol: No specific treatment prior to extraction

tag: strain

value: Wild type (N2)


title: G8_control

description:
LM7_9182D0.v1_2R02C01
Array B
200078650092_R02C01


title: HUES8, chip HG-U133B, biological rep1

description:
HUES8_B-1
Gene expression data from undifferentiated HUES8 hESCs


title: R5_control

description:
LM3_8331D0.v1_6R06C01
Array B
9769100138_R06C01

source_name: genomic DNA was isolated from aPBMC cells

value: aPBMC


title: B_H2O2_rep5

description: Nematodes after 2-hours induction with 0.3 mM H2O2 at L4 stage

source_name: H2O2 induction


title: C_H001 lncRNA


title: R6_control

description:
LM3_4516D0.v1_6R04C01
Array B
9769100138_R04C01


title: G3_3w

description:
LM7_0870W3.v1_1R05C02
Array A
200078650186_R05C02


title: G7_3w

description:
LM7_1421W3.v1_1R06C01
Array A
200078650186_R06C01


title: R3_3w

description:
LM3_0870W3.v1_6R04C02
Array B
9769100138_R04C02


title: G5_control

description:
LM7_8331D0.v1_1R04C02
Array A
200078650186_R04C02


title: G1_3w

description:
LM7_4556W3.v1_2R02C02
Array B
200078650092_R02C02


title: T_H007 lncRNA


title: G2_control

description:
LM7_9294D0.v1_1R04C01
Array A
200078650186_R04C01


title: R1_control

description:
LM3_4556D0.v1_6R05C01
Array B
9769100138_R05C01


title: G5_3w

description:
LM7_8331W3.v1_1R02C01
Array A
200078650186_R02C01


title: G2_3w

description:
LM7_9294W3.v1_1R03C02
Array A
200078650186_R03C02


title: R8_3w

description:
LM3_9182W3.v1_6R02C01
Array B
9769100138_R02C01


title: R4_control

description:
LM3_5667D0.v1_6R05C02
Array B
9769100138_R05C02


title: R4_3w

description:
LM3_5667W3.v1_6R01C02
Array B
9769100138_R01C02


title: R7_3w

description:
LM3_1421W3.v1_6R01C01
Array B
9769100138_R01C01


title: G4_control

description:
LM7_5667D0.v1_1R05C01
Array A
200078650186_R05C01


title: R2_control

description:
LM3_9294D0.v1_6R03C02
Array B
9769100138_R03C02


title: T_H004 lncRNA


title: R3_control

description:
LM3_0870D0.v1_2R06C02
Array A
9721367120_R06C02


title: C_H003 lncRNA


title: R7_control

description:
LM3_1421D0.v1_6R03C01
Array B
9769100138_R03C01


title: R8_control

description:
LM3_9182D0.v1_6R02C02
Array B
9769100138_R02C02


title: R5_3w

description:
LM3_8331W3.v1_2R02C02
Array A
9721367120_R02C02


title: R1_8m

description:
LM5_4556M8.v1_3R05C02
Array C
3999442037_R05C02

value: 8months after vaccination


title: R5_8m

description:
LM5_8331M8.v1_3R06C02
Array C
3999442037_R06C02


title: R2_8m

description:
LM5_9294M8.v1_3R02C02
Array C
3999442037_R02C02


title: R1_3w

description:
LM3_4556W3.v1_2R03C02
Array A
9721367120_R03C02


title: R8_8m

description:
LM5_9182M8.v1_3R05C01
Array C
3999442037_R05C01


title: R3_3m

description:
LM4_0870M3.v1_1R06C01
Array C
3999308001_R06C01

value: 3months after vaccination


title: R5_3m

description:
LM4_8331M3.v1_1R05C01
Array C
3999308001_R05C01


title: R7_8m

description:
LM5_1421M8.v1_3R01C02
Array C
3999442037_R01C02


title: R4_8m

description:
LM5_5667M8.v1_3R04C02
Array C
3999442037_R04C02


title: R2_3w

description:
LM3_9294W3.v1_2R04C02
Array A
9721367120_R04C02


title: R7_3m

description:
LM4_1421M3.v1_1R03C01
Array C
3999308001_R03C01


title: R3_8m

description:
LM5_0870M8.v1_3R03C02
Array C
3999442037_R03C02


title: R4_3m

description:
LM4_5667M3.v1_1R04C01
Array C
3999308001_R04C01


title: R6_8m

description:
LM5_4516M8.v1_3R06C01
Array C
3999442037_R06C01


title: R1_3m

description:
LM4_4556M3.v1_1R02C02
Array C
3999308001_R02C02


title: R6_3m

description:
LM4_4516M3.v1_1R02C01
Array C
3999308001_R02C01


title: HUES8, chip HG-U133A, biological rep2

description:
HUES8_A-2
Gene expression data from undifferentiated HUES8 hESCs

value: control

value: undifferentiated


title: R6_3w

description:
LM3_4516W3.v1_2R05C02
Array A
9721367120_R05C02


title: T_H012 mRNA

value: tissue


title: T_H007 mRNA


title: AIMP3f/f;cre-ERT2 mESCs_tamoxifen_4days_rep2

city: Goyang-si, Gyeonggi-do

first: Sun Mi

last: Kim

address: Ilsan-ro 323

country: South Korea

institute: National Cancer Center

description: Gene expression after 4 days  in tamoxifen-treated AIMP3f/f;cre-ERT2 mouse embryonic stem cells

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (60K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: AIMP3-depleted (tamoxifen-treated)

label_protocol: RNA was extracted from two replicates of control and two replicates of AIMP3-depleted for microarray analysis. RNA extracts from two replicates of control were pooled and labeled with Cy3. AIMP3-depleted samples were labeled with Cy5. Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Mouse embryonic stem cells were maintained in Dulbecco’s modified Eagle medium supplemented with 15% fetal bovine serum, 0.055 mM β-mertcaptoethanol , 2 mM L-glutamine, 0.1 mM nonessential amino acid and 5,000 units/ml of penicillin/streptomycin. Generally, cells were cultured on MEF feeder layers at 37℃ with 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Control cells and tamoxifen-treated cells were incubated with 100% ethanol and 2 μM Tamoxifen, respectively, in LIF-containing growth media for 4 days.

value: mouse embryonic stem cells

source_name: AIMP3-control (ethanol treated)


title: R2_3m

description:
LM4_9294M3.v1_1R01C02
Array C
3999308001_R01C02

value: blood


title: C_H003 mRNA


title: T_H005 mRNA


title: T_H010 mRNA


title: R8_3m

description:
LM4_9182M3.v1_1R01C01
Array C
3999308001_R01C01


title: AIMP3f/f;cre-ERT2 mESCs_tamoxifen_4days_rep1


title: Combination Treated Bone Marrow Derived Macrophages

city: Baltimore

first: Michael

middle: Jonathan

last: Topper

state: MD

address: 1650 Orleans St., Suite 530

department: Oncology

institute: Johns Hopkins University

description: 500nM Aza+ 100nM ITF-2357

hyb_protocol: Agilent Mouse GE 4x 44K v2 microarrays. 825 ng of each Cyanine-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure

scan_protocol: Microarrays were scanned using an Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 software.

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

source_name: primary BMDM_mock

label_protocol: Sample amplification and labeling procedures were carried out by using Quick RNA Amplification and Labeling Kit (Cat# 5190-0447, Agilent Technologies) with minor modifications. Briefly, 400 ng total RNA was reverse-transcribed into cDNA by MMLV-RT using oligo dT primers (Cat# RA300A-2, System Bioscience) that incorporate T7 promoter sequence. The cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-labeled CTP (Perkin Elmer). The labeled cRNA is purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.

extract_protocol: RNA was extracted and purified using using the RNeasy Mini kit (Qiagen) and processed for hybridization on an Mouse Gene Expression v2 4x44K Microarray chip.

treatment_protocol: Mice (6-8) week old were euthanized and hind legs were harvested under aseptic conditions. Femors and tibia were obtained and flushed with RPMI medium. Cells were then centrigued and treated with ACK buffer to lyse RBC’s. Cell pellets washed, resuspended in RPMI medium and plated in six well plates in 10% FBS RPMI media supplemented with M-CSF. Supplemented medium was changed every 2 days. Treatment with 500nM Aza was initated after 4 days of in vitro culture in the following manner: 5 days of 500nM Aza, media changed daily followed by either vehicle or 100nM ITF-2357 for a period of 2 days.

tag: age

value: 6-8 weeks

value: Primary Bone Marrow Derived Macrophages (BMDM)

value: Mock

source_name: primary BMDM_500nM Aza+ 100nM ITF-2357


title: C_H001 mRNA


title: T_H008 mRNA


title: T_H009 mRNA


title: CTRL WT6

status: Public on Sep 26 2017

first: Clemente

last: Britto

address: 300 Cedar St TAC S419

description: Gene expression at baseline in whole lung

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55C on Agilent V2 8X60K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.0 (Agilent) using default parameters.

source_name: Lung, PBS, 0h

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

growth_protocol: BPIFA1-/- and WT controls, age 8-12 weeks

extract_protocol: whole lung tissue homogenized with TriZol reagent, aqueous phase RNA extracted, purified using automated Qiacube protocol for mRNA isolation

treatment_protocol: 5micrograms of LPS diluted in 50 microliters of LPS, delivered intranasally (one dose), controls received PBS,

value: lung

tag: genotype

value: WT

tag: time (hours)


title: CTRL WT2


title: T_H011 mRNA


title: T_H006 mRNA


title: CTRL WT1


title: CTRL WT4


title: CTRL KO4

value: BPIFA1 KO


title: T_H004 mRNA


title: C_H002 mRNA


title: CTRL KO6


title: CTRL KO5


title: CTRL KO2


title: CTRL KO3


title: CTRL WT3


title: CTRL WT5


title: H1 at D0, chip HG-U133B, biological rep1

description:
H1_d0_B-1
Gene expression data from undifferentatied H1 hESCs (day 0)

source_name: H1 human embryonic stem cells, day 0 of retinoic acid differentiation

tag: cell type

tag: cell line

value: day 0


title: 24H KO6

description: Gene expression in whole lung 24 hours after LPS

source_name: Lung, LPS, 24h


title: 24H KO7


title: 24H WT5


title: 24H WT4


title: CTRL KO1


title: 24H KO1


title: 24H KO5


title: 24H WT1


title: 8H WT5

description: Gene expression in whole lung 8 hours after LPS

source_name: Lung, LPS, 8h


title: 8H WT3


title: 24H WT3


title: 8H WT1


title: 8H WT2


title: 24H KO2


title: 8H KO5


title: 8H KO7


title: 8H WT6


title: 8H KO6


title: 24H WT2


title: 8H KO2


title: 8H KO1


title: Liver, BCMO Knockout, male, beta-carotene diet, replicate 3

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description:
BCMO KO_ M_ BC_ 3
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 4rpm rotation. After hybridization, slides were washed sequentially following Agilents' recommendations.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 9.5.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays in both channels were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

source_name: liver, BCMO knockout, male, beta-carotene diet

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis, split into two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent linear amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010). Cy-3 labelled samples were pooled on an equimolar basis and served as reference pool; this comprised all samples.

extract_protocol: Total RNA was isolated from liver tissue using TRIzol Reagent (Sigma-Aldrich) according to the manufacturer’s instruction. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with Experion automated electrophoresis system (BioRad).

treatment_protocol: The experimental setup has been described previously (van Helden et al., CMLS 2010 and van Helden et al., Carcinogenesis 2011). Twelve female and 12 male B6129SF1 (Bcmo1+/+) and 12 female and 12 male B6;129S-Bcmo1tm1dnp (Bcmo1-/-) mice (Hessel et al., JBC 2007) were used for the dietary intervention, which was conducted in accordance with the German animal protection laws by the guidelines of the local veterinary authorities. During the breeding and weaning periods of the mice, mothers were maintained on KLIBA 3430 chow containing 14,000 IU vitamin A/kg diet (Provima Kliba AG, Kaiseraugst, Switzerland). Five-week-old female and male Bcmo1+/+ and Bcmo1-/- mice were caged in groups containing two to four siblings per group and were maintained under environmentally controlled conditions (temperature 24 C, 12 h/12 h light/dark cycle). Mice had ad libitum access to feed and water. Basic feed consisted of the pelletized diet D12450B (Research Diets Inc, USA) with a fat content of 10%. The diet was modified to contain 1,500 IU vitamin A/kg of diet, which is a vitamin A-sufficient diet, and the control diet (control) was supplemented with water-soluble vehicle beadlets (DSM Nutritional Products Ltd., Basel, Switzerland) containing L-alpha-tocopherol and ascorbyl palmitate as stabilizers, as well as carriers such as gelatin, corn oil, sucrose and starch. The BC diet (BC) was supplemented with identical water-soluble beadlets containing BC (DSM Nutritional Products Ltd., Basel, Switzerland) to generate 150 mg BC/kg diet. Beadlets were added by the manufacturer before low temperature pelletting. Feed pellets were color marked and stored at 4 C in the dark. After 14 weeks of dietary intervention, male and female mice were anesthesised using isoflurane and ketamin and killed. After sacrifice, liver was immediately dissected and snap frozen in liquid nitrogen and stored at -80C.

tag: Sex

value: male

value: adult

value: beta-carotene diet

value: liver

source_name: liver, reference pool

value: pooled B6129SF1 and B6;129S-Bcmo1-/-

value: pooled male and female

value: reference


title: Liver, BCMO Knockout, male, beta-carotene diet, replicate 6

description:
BCMO KO_ M_ BC_ 6
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

tag: treatment


title: Liver, BCMO Knockout, male, control diet, replicate 5

description:
BCMO KO_ M_ Con_ 5
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: liver, BCMO knockout, male, control diet

value: control diet


title: Liver, BCMO Knockout, male, beta-carotene diet, replicate 2

description:
BCMO KO_ M_ BC_ 2
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, male, beta-carotene diet, replicate 5

description:
BCMO KO_ M_ BC_ 5
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, male, beta-carotene diet, replicate 4

description:
BCMO KO_ M_ BC_ 4
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, male, control diet, replicate 6

description:
BCMO KO_ M_ Con_ 6
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, male, beta-carotene diet, replicate 1

description:
BCMO KO_ M_ BC_ 1
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, male, control diet, replicate 1

description:
BCMO KO_ M_ Con_ 1
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, male, control diet, replicate 2

description:
BCMO KO_ M_ Con_ 2
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, male, beta-carotene diet, replicate 5

description:
WT_ M_ BC_ 5
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: liver, wildtype, male, beta-carotene diet


title: Liver, Wildtype, male, beta-carotene diet, replicate 6

description:
WT_ M_ BC_ 6
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, male, beta-carotene diet, replicate 4

description:
WT_ M_ BC_ 4
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, male, beta-carotene diet, replicate 2

description:
WT_ M_ BC_ 2
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: human iPS cell 2

city: Isehara

first: Akihide

last: Kamiya

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University

description: Gene expression after 6hr in 0Gy-irradiated human blood

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the Agilent instructions. After hybridization, microarrays were washed and dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software according to the Agilent instructions.

source_name: human iPS cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA according to the Agilent instructions.

growth_protocol: human iPS cells were culture with activin, fibroblast growth factor, and hepatocyte growth factor.

extract_protocol: RNA was extracted using RNeasy Micro Kit (Qiagen; Venlo, The Netherlands).

treatment_protocol: CD13+CD133+ cells derived from human iPS cell culture were sorted using flowcytometry. CD13+CD133+ cells were cultured and CD13- and CD13+ cells were purified.

tag: Stage

value: human iPS cell culture

value: human iPS cell


title: Liver, Wildtype, male, beta-carotene diet, replicate 1

description:
WT_ M_ BC_ 1
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, male, beta-carotene diet, replicate 3

description:
WT_ M_ BC_ 3
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: CD13+CD13+ cultured progenitor 2

value: CD13+CD13+ cultured progenitor


title: human iPS cell 1


title: CD13-CD13- cultured progenitor 2

value: CD13-CD13- cultured progenitor


title: Liver, Wildtype, male, control diet, replicate 3

description:
WT_ M_ Con_ 3
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: liver, wildtype, male, control diet


title: Liver, Wildtype, male, control diet, replicate 6

description:
WT_ M_ Con_ 6
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: CD13-CD13- cultured progenitor 1


title: CD13+CD13+ cultured progenitor 1


title: Liver, BCMO Knockout, male, control diet, replicate 4

description:
BCMO KO_ M_ Con_ 4
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, male, control diet, replicate 5

description:
WT_ M_ Con_ 5
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, beta-carotene diet, replicate 6

description:
BCMO KO_ F_ BC_ 6
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: liver, BCMO knockout, female, beta-carotene diet

value: female


title: Liver, Wildtype, male, control diet, replicate 4

description:
WT_ M_ Con_ 4
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, male, control diet, replicate 1

description:
WT_ M_ Con_ 1
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, male, control diet, replicate 2

description:
WT_ M_ Con_ 2
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, beta-carotene diet, replicate 4

description:
BCMO KO_ F_ BC_ 4
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: CD13+CD133+ HPCs 1

value: CD13+CD133+ HPCs


title: CD13+CD133+ HPCs 2


title: 8H WT4

description: Gene expression in whole lung 8 hours after LPS

value: lung

value: WT


title: Liver, BCMO Knockout, Female, beta-carotene diet, replicate 1

description:
BCMO KO_ F_ BC_ 1
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, male, control diet, replicate 3

description:
BCMO KO_ M_ Con_ 3
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, beta-carotene diet, replicate 5

description:
BCMO KO_ F_ BC_ 5
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, beta-carotene diet, replicate 3

description:
BCMO KO_ F_ BC_ 3
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, beta-carotene diet, replicate 2

description:
BCMO KO_ F_ BC_ 2
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, control diet, replicate 4

description:
BCMO KO_ F_ Con_ 4
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: liver, BCMO knockout, female, control diet


title: Liver, Wildtype, Female, beta-carotene diet, replicate 6

description:
WT_ F_ BC_ 6
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: liver, wildtype, female, beta-carotene diet


title: Liver, BCMO Knockout, Female, control diet, replicate 6

description:
BCMO KO_ F_ Con_ 6
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, control diet, replicate 1

description:
BCMO KO_ F_ Con_ 1
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, Female, beta-carotene diet, replicate 5

description:
WT_ F_ BC_ 5
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, control diet, replicate 3

description:
BCMO KO_ F_ Con_ 3
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, control diet, replicate 5

description:
BCMO KO_ F_ Con_ 5
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, BCMO Knockout, Female, control diet, replicate 2

description:
BCMO KO_ F_ Con_ 2
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, Female, beta-carotene diet, replicate 2

description:
WT_ F_ BC_ 2
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, Female, control diet, replicate 6

description:
WT_ F_ Con_ 6
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: liver, wildtype, female, control diet


title: Liver, Wildtype, Female, control diet, replicate 5

description:
WT_ F_ Con_ 5
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, Female, control diet, replicate 4

description:
WT_ F_ Con_ 4
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, Female, beta-carotene diet, replicate 1

description:
WT_ F_ BC_ 1
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Lung, BCMO Knockout, Male, beta-carotene diet, replicate 3

description: Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

source_name: lung, BCMO knockout, male, beta-carotene diet

extract_protocol: Total RNA was isolated from left lung lobes using TRIzol Reagent (Sigma-Aldrich) according to the manufacturer’s instruction. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with Experion automated electrophoresis system (BioRad).

treatment_protocol: The experimental setup has been described previously (van Helden et al., CMLS 2010 and van Helden et al., Carcinogenesis 2011). Twelve female and 12 male B6129SF1 (Bcmo1+/+) and 12 female and 12 male B6;129S-Bcmo1tm1dnp (Bcmo1-/-) mice (Hessel et al., JBC 2007) were used for the dietary intervention, which was conducted in accordance with the German animal protection laws by the guidelines of the local veterinary authorities. During the breeding and weaning periods of the mice, mothers were maintained on KLIBA 3430 chow containing 14,000 IU vitamin A/kg diet (Provima Kliba AG, Kaiseraugst, Switzerland). Five-week-old female and male Bcmo1+/+ and Bcmo1-/- mice were caged in groups containing two to four siblings per group and were maintained under environmentally controlled conditions (temperature 24 C, 12 h/12 h light/dark cycle). Mice had ad libitum access to feed and water. Basic feed consisted of the pelletized diet D12450B (Research Diets Inc, USA) with a fat content of 10%. The diet was modified to contain 1,500 IU vitamin A/kg of diet, which is a vitamin A-sufficient diet, and the control diet (control) was supplemented with water-soluble vehicle beadlets (DSM Nutritional Products Ltd., Basel, Switzerland) containing L-alpha-tocopherol and ascorbyl palmitate as stabilizers, as well as carriers such as gelatin, corn oil, sucrose and starch. The BC diet (BC) was supplemented with identical water-soluble beadlets containing BC (DSM Nutritional Products Ltd., Basel, Switzerland) to generate 150 mg BC/kg diet. Beadlets were added by the manufacturer before low temperature pelletting. Feed pellets were color marked and stored at 4 C in the dark. After 14 weeks of dietary intervention, male and female mice were anesthesised using isoflurane and ketamin and killed. After sacrifice, lungs were immediately dissected and snap frozen in liquid nitrogen and stored at -80C.

value: lung, left lobe

source_name: lung, reference pool


title: Liver, Wildtype, Female, beta-carotene diet, replicate 4

description:
WT_ F_ BC_ 4
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Liver, Wildtype, Female, beta-carotene diet, replicate 3

description:
WT_ F_ BC_ 3
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Lung, BCMO Knockout, Male, beta-carotene diet, replicate 5

value: male


title: Lung, BCMO Knockout, Male, control diet, replicate 4

source_name: lung, BCMO knockout, male, control diet

value: adult


title: Liver, Wildtype, Female, control diet, replicate 1

description:
WT_ F_ Con_ 1
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: Lung, BCMO Knockout, Male, control diet, replicate 6


title: Lung, BCMO Knockout, Male, beta-carotene diet, replicate 4

value: beta-carotene diet


title: Lung, BCMO Knockout, Male, control diet, replicate 3


title: Lung, BCMO Knockout, Male, beta-carotene diet, replicate 6


title: Liver, Wildtype, Female, control diet, replicate 3

description:
WT_ F_ Con_ 3
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: liver


title: Lung, Wildtype, Male, beta-carotene diet, replicate 6

source_name: lung, wildtype, male, beta-carotene diet

value: pooled B6129SF1 and B6;129S-Bcmo1-/-


title: Liver, Wildtype, Female, control diet, replicate 2

description:
WT_ F_ Con_ 2
Cy3 samples were pooled on an equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

value: pooled male and female


title: Lung, BCMO Knockout, Male, beta-carotene diet, replicate 2

value: reference


title: Lung, BCMO Knockout, Male, control diet, replicate 2

value: control diet


title: Lung, Wildtype, Male, beta-carotene diet, replicate 4


title: Lung, BCMO Knockout, Male, control diet, replicate 5


title: Lung, Wildtype, Male, beta-carotene diet, replicate 2


title: Lung, BCMO Knockout, Male, beta-carotene diet, replicate 1


title: Lung, Wildtype, Male, beta-carotene diet, replicate 3


title: Lung, BCMO Knockout, Male, control diet, replicate 1


title: Lung, Wildtype, Male, beta-carotene diet, replicate 1


title: Lung, Wildtype, Male, control diet, replicate 6

source_name: lung, wildtype, male, control diet


title: Lung, Wildtype, Male, beta-carotene diet, replicate 5


title: Lung, Wildtype, Male, control diet, replicate 5


title: DO mouse on HP Diet, Sample 597 replicate on plate 4 DO2.597.plate4

city: Ithaca

first: Praveen

last: Sethupathy

address: Cornell University

institute: Cornell University

description: Gene expression in homogenized liver of DO mouse

hyb_protocol: Done according to Affymetrix MoGene 2.1 ST Array Protocol

data_processing: Probes containing known SNPs from the founder strains were masked. Affymetrix Expression Console was used for QC and identifying low quality samples, which were removed. Several samplers were run in duplicate on at least 2 plates. Control, reporter, and normalizing probes were removed.

source_name: Adult mouse liver

growth_protocol: 4-week old DO mice were put on AIN-76 diet for 2 weeks. Then one of each sibling pair was put on either HFCA or HP diet for 18 weeks.

extract_protocol: RNA was harvested using Norgen Total RNA Purification Kit (Cat# 24300).

treatment_protocol: Livers were removed, flash frozen in liquid nitrogen, and homogenized.

tag: sibling pair


title: DO mouse on HP Diet DO2.823

scan_protocol: Done according to Affymetrix MoGene 2.1 ST Array Protocol


title: DO mouse on HFCA Diet, Sample 739 replicate on plate 2 DO2.739.plate2

label_protocol: Done according to Affymetrix MoGene 2.1 ST Array Protocol


title: DO mouse on HP Diet DO2.821


title: DO mouse on HP Diet DO2.549


title: blank on plate 2 blank.plate2

type: other

description: Blanks used as control

molecule: other

organism: unidentified

source_name: No Sample


title: DO mouse on HP Diet DO2.810


title: blank on plate 3 blank.plate3

description: Blanks used as control


title: DO mouse on HFCA Diet, Sample 739 replicate on plate 3 DO2.739.plate3


title: DO mouse on HP Diet DO2.566


title: Lung, BCMO Knockout, Female, beta-carotene diet, replicate 6

source_name: lung, BCMO knockout, female, beta-carotene diet


title: Lung, BCMO Knockout, Female, beta-carotene diet, replicate 5


title: Lung, BCMO Knockout, Female, beta-carotene diet, replicate 3


title: Lung, Wildtype, Male, control diet, replicate 2


title: Lung, Wildtype, Male, control diet, replicate 4


title: Lung, BCMO Knockout, Female, control diet, replicate 5

source_name: lung, BCMO knockout, female, control diet


title: Lung, BCMO Knockout, Female, control diet, replicate 6


title: Lung, BCMO Knockout, Female, beta-carotene diet, replicate 2


title: Lung, BCMO Knockout, Female, beta-carotene diet, replicate 4


title: Lung, BCMO Knockout, Female, control diet, replicate 4


title: Lung, Wildtype, Male, control diet, replicate 1


title: Lung, BCMO Knockout, Female, control diet, replicate 3


title: Lung, BCMO Knockout, Female, beta-carotene diet, replicate 1


title: Lung, BCMO Knockout, Female, control diet, replicate 1


title: Lung, BCMO Knockout, Female, control diet, replicate 2


title: DO mouse on HP Diet DO2.517


title: Lung, Wildtype, Male, control diet, replicate 3


title: Lung, Wildtype, Female, beta-carotene diet, replicate 5

source_name: lung, wildtype, female, beta-carotene diet


title: DO mouse on HP Diet, Sample 528 replicate on plate 4 DO2.528.plate4


title: DO mouse on HFCA Diet, Sample 475 replicate on plate 3 DO2.475.plate3


title: DO mouse on HFCA Diet, Sample 471 replicate on plate 4 DO2.471.plate4


title: DO mouse on HFCA Diet, Sample 498 replicate on plate 3 DO2.498.plate3


title: DO mouse on HFCA Diet, Sample 467 replicate on plate 3 DO2.467.plate3


title: Lung, Wildtype, Female, beta-carotene diet, replicate 4


title: DO mouse on HFCA Diet, Sample 441 replicate on plate 4 DO2.441.plate4


title: DO mouse on HFCA Diet, Sample 451 replicate on plate 4 DO2.451.plate4


title: DO mouse on HFCA Diet, Sample 441 replicate on plate 3 DO2.441.plate3


title: DO mouse on HFCA Diet, Sample 434 replicate on plate 3 DO2.434.plate3


title: Lung, Wildtype, Female, beta-carotene diet, replicate 2


title: Lung, Wildtype, Female, beta-carotene diet, replicate 3


title: Lung, Wildtype, Female, control diet, replicate 4

source_name: lung, wildtype, female, control diet


title: DO mouse on HFCA Diet, Sample 403 replicate on plate 4 DO2.403.plate4


title: Lung, Wildtype, Female, control diet, replicate 5


title: Lung, Wildtype, Female, beta-carotene diet, replicate 1


title: Lung, Wildtype, Female, control diet, replicate 1


title: Lung, Wildtype, Female, control diet, replicate 2


title: DO mouse on HFCA Diet, Sample 462 replicate on plate 3 DO2.462.plate3


title: Lung, Wildtype, Female, control diet, replicate 3


title: DO mouse on HP Diet DO2.846


title: DO mouse on HP Diet DO2.843


title: DO mouse on HP Diet DO2.844


title: D10LacZ1

city: Birmingham

first: Yang

last: Zhou

state: AL

address: 1825 University Blvd

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

description: Gene expression of day 10-control CFs infected with LacZ

hyb_protocol: Standard Agilent Protocol

scan_protocol: Standard Agilent Protocol

data_processing: Data were processed using the limma package from Bioconductor (Ritchie et al., 2015). Raw data were first background corrected and normalized using ‘normexp’ and ‘quantile’ methods, respectively.

source_name: intermediate control_D10, #1

label_protocol: Standard Agilent Protocol

growth_protocol: Mouse neonatal CMs and CFs were isolated as described in (Wang et al., Circ. Res.  2015) from P1.5 pups. iCMs were generated by infecting CFs with retroviruses expressing a polycistronic Mef2c, Gata4 and Tbx5 transgene (Wang et al., J. Vis. Exp. 2015). CF-derived iPSCs were generated by transduction of Oct4, Sox2, Klf4 an cMyc as described in (Takahashi et al., Nat Protoc 2007 ) and were subsequently differentiated into CMs by cardiac differentiation methods as described in (Kattman et al., Cell Stem Cell 2011). Both contractile iCMs and iPSC derived CMs were cultured in Stem Pro 34 medium supplemented with GlutaMAX (10 µl/ml), Ascorbic Acid (50 µg/mL) and VEGF (5 ng/ml), bFGF (10 ng/ml) and FGF10 (25 ng/ml).

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen) and purified using RNeasy mini kit (QIAGEN) according to the manufacturer’s instruction.

treatment_protocol: Cells were lysed using TRIzol.

value: D10 CFs infected with LacZ

value: aMHC-GFP


title: D10LacZ2

source_name: intermediate control_D10, #2


title: DO mouse on HP Diet DO2.841


title: DO mouse on HP Diet DO2.839


title: DO mouse on HP Diet DO2.842


title: DO mouse on HP Diet DO2.840


title: D14LacZ2

description: Gene expression of day 14-control CFs infected with LacZ

source_name: intermediate control_D14, #2

value: D14 CFs infected with LacZ


title: DO mouse on HP Diet DO2.838


title: D5LacZ2

description: Gene expression of day 5-control CFs infected with LacZ

source_name: intermediate control_D5, #2

value: D5 CFs infected with LacZ


title: D7LacZ1

description: Gene expression of day 7-control CFs infected with LacZ

source_name: intermediate control_D7, #1

value: D7 CFs infected with LacZ


title: D7LacZ2

source_name: intermediate control_D7, #2


title: D3LacZ2

description: Gene expression of day 3-control CFs infected with LacZ

source_name: intermediate control_D3, #2

value: D3 CFs infected with LacZ


title: D5LacZ1

source_name: intermediate control_D5, #1


title: D14iCM2

description: Gene expression of day 14-iCMs directly reprogrammed from CFs

source_name: intermediate iCMs_D14, #2

value: D14 CFs infected with MGT


title: D14LacZ1

source_name: intermediate control_D14, #1


title: DO mouse on HP Diet DO2.835


title: DO mouse on HP Diet DO2.837


title: D14iCM1

source_name: intermediate iCMs_D14, #1


title: D7iCM2

description: Gene expression of day 7-iCMs directly reprogrammed from CFs

source_name: intermediate iCMs_D7, #2

value: D7 CFs infected with MGT


title: D3LacZ1

source_name: intermediate control_D3, #1


title: DO mouse on HP Diet DO2.834

source_name: Adult mouse liver


title: D7iCM1

source_name: intermediate iCMs_D7, #1


title: D10iCM2

description: Gene expression of day 10-iCMs directly reprogrammed from CFs

source_name: intermediate iCMs_D10, #2

value: D10 CFs infected with MGT


title: D10iCM1

source_name: intermediate iCMs_D10, #1


title: DO mouse on HP Diet DO2.831


title: DO mouse on HP Diet DO2.836


title: DO mouse on HP Diet DO2.830


title: DO mouse on HP Diet DO2.833


title: D5iCM1

description: Gene expression of day 5-iCMs directly reprogrammed from CFs

source_name: intermediate iCMs_D5, #1

value: D5 CFs infected with MGT


title: DO mouse on HP Diet DO2.828


title: D5iCM2

source_name: intermediate iCMs_D5, #2


title: DO mouse on HP Diet DO2.827


title: DO mouse on HP Diet DO2.829


title: D3iCM2

description: Gene expression of day 3-iCMs directly reprogrammed from CFs

source_name: intermediate iCMs_D3, #2

value: D3 CFs infected with MGT


title: DO mouse on HP Diet DO2.824


title: D0CF2

description: Gene expression of day 0-CFs for iCM reprogramming

source_name: Initial cardiac fibroblasts_D0, #2

value: D0 CFs for iCM reprogramming


title: iPSC2CMLT1

description: Gene expression of long-term cultured cardiomyocytes differentiated from CF-derived iPSC

value: long-term cultured Cardiomyocytes differentiated from iPSC


title: DO mouse on HP Diet DO2.822


title: iPSC2CMLT2


title: DO mouse on HP Diet DO2.825


title: D3iCM1

source_name: intermediate iCMs_D3, #1


title: iPSC1CM2

description: Gene expression of cardiomyocytes differentiated from CF-derived iPSC

value: Cardiomyocytes differentiated from iPSC


title: DO mouse on HP Diet DO2.826


title: DO mouse on HP Diet DO2.817


title: D0CF1

source_name: Initial cardiac fibroblasts_D0, #1


title: iPSC2CM2


title: DO mouse on HP Diet DO2.819


title: iPSC1CM1


title: DO mouse on HP Diet DO2.809


title: DO mouse on HP Diet DO2.812


title: DO mouse on HP Diet DO2.814


title: DO mouse on HP Diet DO2.815


title: DO mouse on HP Diet DO2.808


title: DO mouse on HP Diet DO2.807


title: DO mouse on HP Diet DO2.818


title: iCM1

description: Gene expression of 4 week-iCMs directly reprogrammed from CFs

source_name: Induced cardiomyocytes (iCMs)_4 weeks derived from neoCFs, #1

value: 4 week iCMs derived from CFs


title: DO mouse on HP Diet DO2.805


title: neoCF2

description: Gene expression of primary isolated cardiac fibroblasts

source_name: Neonatal cardiac fibroblasts freshly isolated from P1.5 pups, #2

value: Neonatal cardiac fibroblasts


title: neoCF1

source_name: Neonatal cardiac fibroblasts freshly isolated from P1.5 pups, #1


title: iCM2

source_name: Induced cardiomyocytes (iCMs)_4 weeks derived from neoCFs, #2


title: DO mouse on HP Diet DO2.804


title: DO mouse on HP Diet DO2.801


title: DO mouse on HP Diet DO2.813


title: neoCM2

description: Gene expression of primary isolated cardiomyocytes

source_name: Neonatal cardiomyocytes freshly isolated from P1.5 pups, # 2

value: Neonatal cardiomyocytes


title: DO mouse on HP Diet DO2.803

description: Gene expression in homogenized liver of DO mouse


title: DO mouse on HFCA Diet DO2.740


title: DO mouse on HFCA Diet DO2.741


title: DO mouse on HFCA Diet DO2.744


title: DO mouse on HFCA Diet DO2.743


title: DO mouse on HFCA Diet DO2.737


title: DO mouse on HFCA Diet DO2.788


title: DO mouse on HFCA Diet, Sample 739 replicate on plate 4 DO2.739


title: DO mouse on HP Diet DO2.802


title: neoCM1

source_name: Neonatal cardiomyocytes freshly isolated from P1.5 pups, # 1


title: DO mouse on HFCA Diet DO2.745


title: DO mouse on HFCA Diet DO2.736


title: DO mouse on HFCA Diet DO2.730


title: DO mouse on HFCA Diet DO2.742


title: DO mouse on HFCA Diet DO2.723


title: DO mouse on HFCA Diet DO2.720


title: DO mouse on HFCA Diet DO2.731


title: DO mouse on HFCA Diet DO2.729


title: DO mouse on HFCA Diet DO2.734


title: DO mouse on HFCA Diet DO2.724


title: DO mouse on HFCA Diet DO2.727


title: DO mouse on HFCA Diet DO2.726


title: DO mouse on HFCA Diet DO2.722


title: DO mouse on HFCA Diet DO2.725


title: iPSC2CM1


title: DO mouse on HFCA Diet DO2.716


title: DO mouse on HFCA Diet DO2.735


title: DO mouse on HFCA Diet DO2.721


title: DO mouse on HFCA Diet DO2.718


title: DO mouse on HFCA Diet DO2.713


title: DO mouse on HFCA Diet DO2.719


title: DO mouse on HFCA Diet DO2.733


title: DO mouse on HFCA Diet DO2.717


title: DO mouse on HFCA Diet DO2.715


title: DO mouse on HFCA Diet DO2.710


title: DO mouse on HFCA Diet DO2.704


title: DO mouse on HFCA Diet DO2.712


title: DO mouse on HFCA Diet DO2.711


title: DO mouse on HFCA Diet DO2.703


title: DO mouse on HFCA Diet DO2.709


title: DO mouse on HFCA Diet DO2.707


title: DO mouse on HP Diet DO2.596


title: DO mouse on HP Diet DO2.599


title: DO mouse on HFCA Diet DO2.706


title: DO mouse on HP Diet DO2.589


title: DO mouse on HFCA Diet DO2.705


title: DO mouse on HFCA Diet DO2.701


title: DO mouse on HP Diet DO2.598


title: DO mouse on HP Diet DO2.587


title: DO mouse on HFCA Diet DO2.702


title: DO mouse on HP Diet DO2.590


title: DO mouse on HP Diet DO2.594


title: DO mouse on HP Diet DO2.586


title: DO mouse on HP Diet DO2.593


title: DO mouse on HP Diet, Sample 597 replicate on plate 3 DO2.597


title: DO mouse on HP Diet DO2.588


title: DO mouse on HP Diet DO2.592


title: DO mouse on HP Diet DO2.581


title: DO mouse on HP Diet DO2.591


title: DO mouse on HP Diet DO2.575


title: DO mouse on HP Diet DO2.576


title: DO mouse on HP Diet DO2.585


title: DO mouse on HP Diet DO2.583


title: DO mouse on HP Diet DO2.816


title: DO mouse on HP Diet DO2.571


title: DO mouse on HP Diet DO2.572


title: DO mouse on HP Diet DO2.582


title: DO mouse on HP Diet DO2.584


title: DO mouse on HP Diet DO2.579


title: DO mouse on HP Diet DO2.580


title: DO mouse on HP Diet DO2.578


title: DO mouse on HP Diet DO2.564


title: DO mouse on HP Diet DO2.577


title: DO mouse on HP Diet DO2.569


title: DO mouse on HP Diet DO2.567


title: DO mouse on HP Diet DO2.558


title: DO mouse on HFCA Diet DO2.714


title: DO mouse on HP Diet DO2.573


title: DO mouse on HP Diet DO2.562


title: DO mouse on HP Diet DO2.568


title: DO mouse on HP Diet DO2.570


title: DO mouse on HP Diet DO2.561


title: DO mouse on HP Diet DO2.557


title: DO mouse on HP Diet DO2.553


title: DO mouse on HP Diet DO2.559


title: DO mouse on HP Diet DO2.555


title: DO mouse on HP Diet DO2.556


title: DO mouse on HP Diet DO2.551


title: DO mouse on HP Diet DO2.560


title: DO mouse on HP Diet DO2.550


title: DO mouse on HP Diet DO2.546


title: DO mouse on HP Diet DO2.541


title: DO mouse on HP Diet DO2.547


title: DO mouse on HP Diet DO2.540


title: DO mouse on HP Diet DO2.548


title: DO mouse on HP Diet DO2.542


title: DO mouse on HP Diet DO2.543


title: DO mouse on HP Diet DO2.536


title: DO mouse on HP Diet DO2.537


title: DO mouse on HP Diet DO2.534


title: DO mouse on HP Diet DO2.531


title: DO mouse on HP Diet DO2.532


title: DO mouse on HP Diet DO2.544


title: DO mouse on HP Diet DO2.563


title: DO mouse on HP Diet DO2.530


title: DO mouse on HP Diet DO2.535


title: DO mouse on HP Diet, Sample 528 replicate on plate 3 DO2.528


title: DO mouse on HP Diet DO2.545


title: DO mouse on HP Diet DO2.524


title: DO mouse on HP Diet DO2.539


title: DO mouse on HP Diet DO2.533


title: DO mouse on HP Diet DO2.529


title: DO mouse on HP Diet DO2.522


title: DO mouse on HP Diet DO2.523


title: DO mouse on HP Diet DO2.521


title: DO mouse on HP Diet DO2.527


title: DO mouse on HP Diet DO2.514


title: DO mouse on HP Diet DO2.516


title: DO mouse on HP Diet DO2.518


title: DO mouse on HP Diet DO2.513


title: DO mouse on HP Diet DO2.512


title: DO mouse on HP Diet DO2.510


title: DO mouse on HP Diet DO2.509


title: DO mouse on HP Diet DO2.507


title: DO mouse on HP Diet DO2.506


title: DO mouse on HP Diet DO2.505


title: DO mouse on HP Diet DO2.501


title: DO mouse on HP Diet DO2.503


title: DO mouse on HP Diet DO2.511


title: DO mouse on HFCA Diet, Sample 498 replicate on plate 2 DO2.498


title: DO mouse on HFCA Diet DO2.499


title: DO mouse on HP Diet DO2.504


title: DO mouse on HFCA Diet DO2.497


title: DO mouse on HP Diet DO2.508


title: DO mouse on HFCA Diet DO2.495


title: DO mouse on HFCA Diet DO2.494


title: DO mouse on HFCA Diet DO2.493


title: DO mouse on HFCA Diet DO2.496


title: DO mouse on HP Diet DO2.525


title: DO mouse on HFCA Diet DO2.490


title: DO mouse on HFCA Diet DO2.488


title: DO mouse on HFCA Diet DO2.492


title: DO mouse on HFCA Diet DO2.491


title: DO mouse on HFCA Diet DO2.486


title: DO mouse on HFCA Diet DO2.487


title: DO mouse on HFCA Diet DO2.482


title: DO mouse on HFCA Diet DO2.481


title: DO mouse on HFCA Diet DO2.483


title: DO mouse on HFCA Diet DO2.485


title: DO mouse on HFCA Diet DO2.489


title: DO mouse on HFCA Diet DO2.480


title: DO mouse on HFCA Diet DO2.484


title: genomic DNA_melanocytes3

city: São Paulo

first: Ana

last: Krepischi

state: São Paulo

address: Rua do Matão, 277

country: Brazil

institute: University of São Paulo

description:
melanocytes DNA from health individual 3
melan.3

hyb_protocol: Bisulphite converted DNA (EZ DNA methylation kit; Zymo Research) was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: Only experiments exhibiting call rate >0.98 of probes with detection p-value ≤0.01 were considered for data analysis. Microarray data were extracted using the GenomeStudio software (v.2011.1) with the methylation module (v.1.9.0) (Illumina). DNA methylation level of each CpG was obtained in β values (β= intensity of the methylated allele (M)/ intensity of the unmethylated allele (U) + intensity of the M + 100) ranging from 0 to 1, with 0 indicating unmethylated sites and 1, fully methylated sites. Background subtraction and normalization of data were performed using the Illumina default protocol with internal controls. CpG sites with detection p-value ≥0.01 as well as those mapped at X and Y chromosomes were excluded from further analysis.

source_name: melanocytes

extract_protocol: Genomic DNA was extracted from leukocytes using Gentra Puregene Blood Core Kit (Qiagen) or QIAmp DNA Blood Mini QIACUBE kit (Quiagen)

value: male

value: melanocytes


title: DO mouse on HFCA Diet DO2.479

source_name: Adult mouse liver


title: DO mouse on HFCA Diet DO2.478


title: DO mouse on HFCA Diet DO2.477


title: DO mouse on HFCA Diet DO2.476


title: genomic DNA_melanocytes1

description:
melanocytes DNA from health individual 1
melan.1


title: genomic DNA_chorionic villus2

description:
chorionic villus DNA from health individual 2
chorionic.v2

source_name: chorionic villus

value: female

value: chorionic villus


title: DO mouse on HFCA Diet, Sample 475 replicate on plate 2 DO2.475


title: genomic DNA_chorionic villus1

description:
chorionic villus DNA from health individual 1
chorionic.v1


title: genomic DNA_melanocytes2

description:
melanocytes DNA from health individual 2
melan.2


title: DO mouse on HFCA Diet DO2.474


title: DO mouse on HFCA Diet DO2.473


title: DO mouse on HFCA Diet DO2.472


title: genomic DNA_leukocytes 36

description:
leukocytes DNA from health individual 36
leuko.36

source_name: leukocytes

value: leukocytes


title: genomic DNA_leukocytes 33

description:
leukocytes DNA from health individual 33
leuko.33


title: genomic DNA_leukocytes 31

description:
leukocytes DNA from health individual 31
leuko.31


title: genomic DNA_leukocytes 30

description:
leukocytes DNA from health individual 30
leuko.30


title: genomic DNA_leukocytes 34

description:
leukocytes DNA from health individual 34
leuko.34


title: genomic DNA_leukocytes 26

description:
leukocytes DNA from health individual 26
leuko.26


title: genomic DNA_leukocytes 28

description:
leukocytes DNA from health individual 28
leuko.28


title: genomic DNA_leukocytes 25

description:
leukocytes DNA from health individual 25
leuko.25


title: genomic DNA_leukocytes 29

description:
leukocytes DNA from health individual 29
leuko.29


title: DO mouse on HFCA Diet, Sample 471 replicate on plate 3 DO2.471


title: DO mouse on HFCA Diet DO2.470


title: genomic DNA_leukocytes 24

description:
leukocytes DNA from health individual 24
leuko.24


title: DO mouse on HFCA Diet DO2.468


title: genomic DNA_leukocytes 23

description:
leukocytes DNA from health individual 23
leuko.23


title: genomic DNA_leukocytes 27

description:
leukocytes DNA from health individual 27
leuko.27


title: genomic DNA_leukocytes 35

description:
leukocytes DNA from health individual 35
leuko.35


title: genomic DNA_leukocytes 21

description:
leukocytes DNA from health individual 21
leuko.21


title: genomic DNA_leukocytes 32

description:
leukocytes DNA from health individual 32
leuko.32


title: genomic DNA_leukocytes 20

description:
leukocytes DNA from health individual 20
leuko.20


title: genomic DNA_leukocytes 19

description:
leukocytes DNA from health individual 19
leuko.19


title: DO mouse on HFCA Diet, Sample 467 replicate on plate 2 DO2.467

description: Gene expression in homogenized liver of DO mouse


title: genomic DNA_leukocytes 22

description:
leukocytes DNA from health individual 22
leuko.22


title: genomic DNA_leukocytes 17

description:
leukocytes DNA from health individual 17
leuko.17


title: genomic DNA_leukocytes 15

description:
leukocytes DNA from health individual 15
leuko.15


title: DO mouse on HFCA Diet DO2.469


title: genomic DNA_leukocytes 18

description:
leukocytes DNA from health individual 18
leuko.18


title: DO mouse on HFCA Diet, Sample 462 replicate on plate 2 DO2.462


title: DO mouse on HFCA Diet DO2.461


title: genomic DNA_leukocytes 14

description:
leukocytes DNA from health individual 14
leuko.14


title: DO mouse on HFCA Diet DO2.463


title: DO mouse on HFCA Diet DO2.466


title: DO mouse on HFCA Diet DO2.460


title: DO mouse on HFCA Diet DO2.464


title: DO mouse on HFCA Diet DO2.459


title: DO mouse on HFCA Diet DO2.465


title: DO mouse on HFCA Diet DO2.457


title: DO mouse on HFCA Diet DO2.458


title: genomic DNA_leukocytes 13

description:
leukocytes DNA from health individual 13
leuko.13


title: genomic DNA_leukocytes 16

description:
leukocytes DNA from health individual 16
leuko.16


title: genomic DNA_leukocytes 11

description:
leukocytes DNA from health individual 11
leuko.11


title: genomic DNA_leukocytes 12

description:
leukocytes DNA from health individual 12
leuko.12


title: genomic DNA_leukocytes 10

description:
leukocytes DNA from health individual 10
leuko.10


title: DO mouse on HFCA Diet DO2.453


title: DO mouse on HFCA Diet DO2.455


title: genomic DNA_leukocytes 9

description:
leukocytes DNA from health individual 9
leuko.9


title: DO mouse on HFCA Diet DO2.452


title: DO mouse on HFCA Diet DO2.454


title: DO mouse on HFCA Diet DO2.456


title: DO mouse on HFCA Diet DO2.450


title: DO mouse on HFCA Diet, Sample 451 replicate on plate 3 DO2.451