title: Breast tumor from Cohort 1 patient P_1

description:
SAMPLE 1
Breast tumor from Cohort 1 (methylation)


title: Breast tumor from Cohort 1 patient P_2

status: Public on Jul 16 2017

type: genomic

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description:
SAMPLE 2
Breast tumor from Cohort 1 (methylation)

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

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

data_processing: .idat files were loaded using methylumi R-package. High-detection p-value, SNP-containing, Cross-reactive and heterochromosomic probes were filtered out (replaced by null) and data were peak-based normalized using in-house R-scripts.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast tumor

label_protocol: Standard Infinium HD Methylation Assay protocol

extract_protocol: Genomic DNA was extracted with the Qiagen-DNeasy Blood &Tissue Kit (Qiagen, Hilden, Germany) or the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany)

tag: tissue

value: breast tumor

tag: cohort id

tag: itu-ly

tag: str-ly

tag: grade

tag: rfs_time (years)

tag: rfs_time_censored (years)

tag: os_time (years)


title: Breast tumor from Cohort 1 patient P_5

description:
SAMPLE 5
Breast tumor from Cohort 1 (methylation)

value: Basal


title: Breast tumor from Cohort 1 patient P_3

description:
SAMPLE 3
Breast tumor from Cohort 1 (methylation)

value: LumB


title: WT_DR_14h_mouse3

status: Public on Jul 14 2017

type: RNA

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

description: the reference pool was a mix of cDNAs from the samples

hyb_protocol: labelled samples were mixed with the reagents from Gene Expression Hybridisation kit (Agilent Technologies), hybridised overnight and washed according to the manufecturer instructions

scan_protocol: scanned using Agilent DNA Microarray Scanner with Surescan High-resolution Technology

data_processing:
Images were processed using Agilent Feature Extraction Software (v10.7.3.1).
log 2 difference between green and red dye intesity, background corrected and normalised between the arrays (LOESS normalisation) using limma R package

molecule: total RNA

organism: Plasmodium berghei

source_name: DR 14hpi

label_protocol: cDNA aminoallyl labelling as desribed on http://www.molbio1.princeton.edu/labs/llinas/protocols.html

growth_protocol: Plasmodium berghei ANKA parasites were propagated in BALB/c mice

extract_protocol: The total mRNA was extracted using the Trizol reagent

treatment_protocol: BALB/c mice were on a moderate dietary restriction protocol (food intake decreased by 30-40%) prior and during P. berghei infection

tag: mouse strain

value: BALB/c

tag: mouse dietary condition

value: dietary restriction (DR)

tag: hours post invasion (hpi)

source_name: reference pool

tag: sample type

value: pool of cDNAs


title: WT_DR_18h_mouse3

source_name: DR 18hpi


title: Brain 3

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

description: Gene expression from brain cell culture

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Canine Gene ST 1.0 GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Interrogating probes were imported, RMA normalized and RMA background corrected, Quantile normalization, Log probes using base 2 and Probeset summarization is Median Polish (Partek Genome Suite v6.6 (6.151022)

label: biotin

organism: Canis lupus familiaris

source_name: Brain cell culture

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

growth_protocol: Community-based dogs that underwent routine surgery at Struggletown Veterinary Clinic, Sydney had excess waste tissue (1-2 cm3) opportunistically harvested and donated by consenting owners. The use of canine tissue was approved by the Animal Care and Ethics Committee of The University of New South Wales.  Skin biopsies were immediately transferred in Phosphate-buffered saline (PBS; Thermo Fisher Scientific) and processed within 6 hours. The specimen was washed in PBS (Thermo Fisher Scientific) containing 1% Penicillin Streptomycin (Thermo Fisher Scientific), divided into 1-2 mm2 pieces and washed again. The tissue was digested with 0.1% Trypsin (Thermo Fisher Scientific) for 40 minutes at 37°C, followed by 0.1% DNAse (Roche Applied Science) digestion for 1 minute at room temperature. Then mechanically dissociated and passed through a 40 µm cell strainer (BD Bioscience).  The dissociated cells were then centrifuged at 180G for 5 minutes.     For fibroblast cell culture, the cells were re-suspended in 3:1 DMEM/F12 (Dulbecco's Modified Eagle Medium/Ham's F-12 Nutrient Mixture; Thermo Fisher Scientific) medium, containing 10% FBS (Thermo Fisher Scientific), 1% Glutamax (Thermo Fisher Scientific), and 1% Penicillin Streptomycin (Thermo Fisher Scientific). The cells were then plated onto non-tissue culture treated dishes at a density of 100,000 cells/cm2.    For SKN cell culture, following centrifugation, the cells were re-suspended in serum free complete medium containing 3:1 DMEM/F12 (Dulbecco's Modified Eagle Medium/Ham's F-12 Nutrient Mixture; Thermo Fisher Scientific) medium, 1% Penicillin Streptomycin (Thermo Fisher Scientific), 20 ng/mL Epidermal growth factor (EGF; BD Bioscience), 40 ng/mL β-Fibroblast growth factor (β-FGF; Thermo Fisher Scientific), and 2% B-27 (Thermo Fisher Scientific).  The cells were then plated non-tissue culture treated dishes at a density of 100,000 cells/cm2.    SKNs were initially cultured as neurospheres, which formed within 1-5 days after isolation. When most neurospheres reached >50 µm in diameter, they were collected and dissociated using TrypLE Select (Thermo Fisher Scientific) for 5 minutes at 37°C. The single cells suspension, diluted in complete medium, was then centrifuged at 180G for 5 minutes, re-suspended in complete medium and grown as an adherent monolayer by seeding at a density of 10,000 cells/cm2 on 0.1% gelatin coated flasks. SKNs were passaged when 80% confluent using TrypLE Select (Thermo Fisher Scientific).    For brain derived neural precursor cell culture, three recently euthanized dogs obtained from a local pound for use, as permissible under New South Wales law. Deceased animals were obtained within 4 hours post mortem and prior to routine cremation. The age of the subjects was not known, however all were mature adults. Tissue samples from the subventricular zone brain regions were diced then digested enzymatically with 0.1% Trypsin EDTA (Thermo Fisher Scientific) for 7 minutes at 37°C/5% CO2, washed with DMEM (Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (FBS: Thermo Fisher Scientific) – hereafter known as FDMEM, and then further mechanically dissociated. Cells were then washed again with FDMEM, centrifuged at 100rcf, and seeded in NeuroCult complete medium consisting of NeuroCult basal medium (Rat; Stem Cell Technologies) with the addition of NeuroCult NS-A proliferation supplements (Stem Cell Technologies), 2% FBS (Thermo Fisher Scientific), 2 µg/mL heparin (Sigma-Aldrich), 20 ng/mL EGF (BD Bioscience) and 10 ng/mL βFGF (Thermo Fisher Scientific). Neurospheres were collected after 14-21 days by centrifugation at 100rcf for 7 minutes. Following 0.1% trypsin EDTA (Thermo Fisher Scientific) for 2 minutes and repeated centrifugation, the single cell were re-suspended in complete medium and seeded at 10,000 cells/cm2 in 0.1% gelatin coated flasks.

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

treatment_protocol: The skin (SKN) cells, fibroblasts and brain derived neural precursor cells underwent no treatments prior to RNA extraction.

tag: primary cell culture type

value: Brain


title: Fibroblast 2

description: Gene expression from fibrobalst cell culture

source_name: fibroblast cell culture

value: Fibroblast


title: Brain 2

description: Gene expression from brain cell culture


title: WT_AL_18h_mouse3

source_name: control 18hpi

value: control diet


title: WT_DR_10h_mouse3

source_name: DR 10hpi


title: WT_DR_18h_mouse1


title: Fibroblast 3


title: Fibroblast 1


title: WT_DR_14h_mouse2


title: WT_DR_6h_mouse2

source_name: DR 6hpi


title: WT_DR_6h_mouse3


title: WT_AL_18h_mouse2


title: WT_DR_14h_mouse1


title: WT_AL_14h_mouse1

source_name: control 14hpi


title: WT_DR_10h_mouse1


title: WT_AL_6h_mouse3

source_name: control 6hpi


title: WT_DR_18h_mouse2


title: WT_DR_10h_mouse2


title: SKN 1

description: Gene expression from skin cell culture

source_name: Skin cell culture

value: Skin (SKN)


title: WT_DR_6h_mouse1


title: WT_AL_18h_mouse1


title: WT_AL_14h_mouse3


title: WT_AL_6h_mouse2


title: WT_AL_10h_mouse1

source_name: control 10hpi


title: MIN6, treated, biological replicate 3

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction,55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100µl were hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed according to manufacturer's intructions

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted .  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were normalized using bioconductor and limma package. Briefly, background substraction was performed using the normexp correction with an offset=1, then signals were normalized using quantile normalization. Only spots presenting a signal 10% brighter than the 95th percentile of the negative control are kept for statistical analysis

organism: Mus musculus

source_name: MIN6 incubated with EXO-HP purified from ex vivo muscle taken from mouse submitted to high fat diet

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol (Life Technologies) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

tag: cell type

value: pancreatic


title: WT_AL_10h_mouse3


title: WT_AL_6h_mouse1


title: MIN6, treated, biological replicate 1


title: WT_AL_14h_mouse2


title: Liver_Vehicle_29 days (10GR221_82)

city: groton

first: Petra

last: Koza-Taylor

state: CT

address: Eastern Point Road

country: USA

institute: Pfizer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with RMA normalization method. The trimmed mean target intensity of each array was arbitrarily set to 50.

source_name: Liver, Vehicle, 29 days

growth_protocol: For all three compounds, a time course study of  15  and  29  days was designed to determine when proliferative and/or hypoxic changes occur in the tissues where hemangiosarcomas develop. A roughly two-fold dose from the carcinogenicity high doses was used to maximize the potential to measure these changes.

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

treatment_protocol: Elmiron and troglitazone were administered by oral route, fenretinide was administered via diet daily  for up to 29 days.

tag: strain

value: Liver

tag: agent

value: Vehicle

tag: dose

tag: time

value: 29 days

tag: gender

value: Male


title: MIN6, treated, biological replicate 2


title: Liver_Elmiron_29 days (10GR221_93)

source_name: Liver, Elmiron, 29 days

tag: tissue

value: Elmiron


title: WT_AL_10h_mouse2


title: Liver_Elmiron_29 days (10GR221_95)


title: Liver_Elmiron_29 days (10GR221_94)


title: Liver_Vehicle_29 days (10GR221_81)


title: Liver_Elmiron_29 days (10GR221_91)


title: Liver_Vehicle_15 days (10GR221_42)

source_name: Liver, Vehicle, 15 days

value: 15 days


title: Liver_Vehicle_15 days (10GR221_47)


title: Liver_Elmiron_15 days (10GR221_55)

source_name: Liver, Elmiron, 15 days


title: Liver_Vehicle_29 days (10GR221_85)


title: Liver_Elmiron_15 days (10GR221_54)


title: Liver_Vehicle_29 days (10GR221_84)


title: Liver_Vehicle_29 days (10GR221_83)


title: Liver_Vehicle_15 days (10GR221_46)


title: MIN6, control, biological replicate 2

source_name: MIN6 incubated with Exo-STD purified from ex vivo muscle taken from mouse submitted to standard diet


title: Liver_Elmiron_15 days (10GR221_51)


title: Liver_Vehicle_15 days (10GR221_44)


title: Liver_Vehicle_15 days (10GR221_41)


title: Liver_Elmiron_15 days (10GR221_52)


title: Liver_Elmiron_15 days (10GR221_53)


title: MIN6, control, biological replicate 1


title: Liver_Elmiron_29 days (10GR221_92)


title: Liver_Troglitazone_29 days (10GR202_94)

source_name: Liver, Troglitazone, 29 days

value: Troglitazone


title: Adipose;Brown_Troglitazone_29 days (10GR202_91)

source_name: Adipose, Brown, Troglitazone, 29 days

value: Adipose, Brown


title: Liver_Troglitazone_29 days (10GR202_95)


title: Adipose;Brown_Troglitazone_29 days (10GR202_94)


title: Liver_Troglitazone_29 days (10GR202_96)


title: Liver_Vehicle_29 days (10GR202_87)


title: Adipose;Brown_Troglitazone_29 days (10GR202_93)


title: Liver_Vehicle_29 days (10GR202_88)


title: Adipose;Brown_Vehicle_29 days (10GR202_83)

source_name: Adipose, Brown, Vehicle, 29 days


title: Liver_Vehicle_29 days (10GR202_86)


title: Adipose;Brown_Vehicle_29 days (10GR202_82)


title: Adipose;Brown_Vehicle_29 days (10GR202_84)


title: Adipose;Brown_Vehicle_29 days (10GR202_86)


title: Liver_Vehicle_29 days (10GR202_85)


title: Liver_Troglitazone_15 days (10GR202_56)

source_name: Liver, Troglitazone, 15 days


title: Liver_Troglitazone_29 days (10GR202_92)


title: Adipose;Brown_Troglitazone_29 days (10GR202_95)


title: Liver_Troglitazone_29 days (10GR202_93)


title: Adipose;Brown_Troglitazone_15 days (10GR202_52)

source_name: Adipose, Brown, Troglitazone, 15 days


title: Adipose;Brown_Troglitazone_29 days (10GR202_92)


title: Adipose;Brown_Vehicle_29 days (10GR202_85)


title: Adipose;Brown_Troglitazone_15 days (10GR202_55)


title: Adipose;Brown_Troglitazone_15 days (10GR202_53)


title: Adipose;Brown_Troglitazone_15 days (10GR202_54)


title: Liver_Troglitazone_15 days (10GR202_55)


title: Liver_Troglitazone_15 days (10GR202_52)


title: Liver_Troglitazone_15 days (10GR202_54)


title: Liver_Troglitazone_15 days (10GR202_53)


title: Adipose;Brown_Troglitazone_15 days (10GR202_51)


title: Liver_Vehicle_29 days (10GR202_83)


title: Liver_Vehicle_15 days (10GR202_45)


title: Adipose;Brown_Vehicle_15 days (10GR202_45)

source_name: Adipose, Brown, Vehicle, 15 days


title: Adipose;White_Vehicle_29 days (10GR145_86)

source_name: Adipose, White, Vehicle, 29 days

value: Adipose, White


title: Adipose;White_Fenretinide_29 days (10GR145_93)

source_name: Adipose, White, Fenretinide, 29 days

value: Fenretinide


title: Adipose;White_Fenretinide_29 days (10GR145_95)


title: Liver_Vehicle_15 days (10GR202_46)


title: Liver_Vehicle_15 days (10GR202_44)


title: Adipose;White_Fenretinide_29 days (10GR145_91)


title: Adipose;White_Fenretinide_29 days (10GR145_94)


title: Adipose;Brown_Vehicle_15 days (10GR202_42)


title: Adipose;Brown_Vehicle_15 days (10GR202_44)


title: Adipose;Brown_Vehicle_15 days (10GR202_41)


title: Adipose;Brown_Vehicle_15 days (10GR202_43)


title: Adipose;White_Fenretinide_15 days (10GR145_58)

source_name: Adipose, White, Fenretinide, 15 days


title: Liver_Vehicle_15 days (10GR202_42)


title: Adipose;White_Vehicle_29 days (10GR145_83)


title: Adipose;White_Fenretinide_15 days (10GR145_57)


title: Adipose;White_Vehicle_15 days (10GR145_50)

source_name: Adipose, White, Vehicle, 15 days


title: Adipose;White_Fenretinide_15 days (10GR145_59)


title: Adipose;White_Vehicle_29 days (10GR145_85)


title: Adipose;White_Vehicle_29 days (10GR145_81)


title: Liver_Vehicle_15 days (10GR202_43)


title: Control male liver pool 1_rRNA-depleted_G138_M10

type: SRA

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: Ribosomal RNA-depleted, strand-specific library

library_source: transcriptomic

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) mRNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene, Primary RNA transcripts (hnRNA) were quantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; it thus excludes sequences found in an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics),
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and differential expression results comparing intact females and GH-treated male mouse livers compared to sham-treated male mouse livers.

source_name: liver tissue

extract_protocol:
RNA was extracted from flash fozen mouse liver using Trizol per the manufacturer's instructions.
RNA was depleted of rRNA using the NEB rRNA depletion kit (NEB, Ipswich, MA, Cat# E6310). Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, Cat# E7420) and multiplexed using NEBNext Multiplex Oligos for Illumina (NEB, Cat# E7335, E7500), according to the manufacturer's instructions.

treatment_protocol: Male and female CD1 mice, 8-9 weeks of age, were purchased from Charles River Laboratories  (Crl:CD1(ICR)). Alzet osmotic pumps (model 1007D) were filled with recombinant rat GH and were implanted subcutaneously under ketamine and xylazine anesthesia. GH was infused at a rate of 25 ng/g body weight/h for 10 h or 1 d. Sham treated males were used as controls.

value: Crl:CD1(ICR) (Charles River, strain code #022)

tag: treatment

value: Sham pump

tag: Sex

tag: age

value: 8 weeks


title: GH infusion_1d male liver pool 1_rRNA-depleted_G137_M13

value: Continuous GH infusion for 1 day


title: Het Liver 2

city: La Jolla

first: Mei Yee

last: Koh

state: CA

address: 10901 N Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

hyb_protocol: This was performed as described in the 3' IVT PLUS Reagent Kit (Affymetrix, P/N 902416):Hhybridization cocktail is prepared, including the fragmented target (cRNA) and Hybridization controls (included in the kit). Then, the sample is hybridized to the probe array (Affymetrix  GeneChip Mouse 430 2.0 Array) for 16-hours at 45°C in the GeneChip  hybridization oven 645 with rotation at 60 rpm. Immediately following hybridization, the probe array undergoes an automated washing and staining protocol on the GeneChip fluidics station 450.

scan_protocol: scanned using the GeneChip® Scanner 3000 7G, controlled by Affymetrix® Expression  Console  1.3.

data_processing: Affymetrix Gene Expression Console algorithm version 1.3.1.187, scale parameters log2, processing algorithm RMA

label: Biotin

source_name: Adjacent liver from SART1+/- mouse

label_protocol: 3'IVT Plus reagent kit

growth_protocol: Wild-type or SART1+/- were maintained on regular chow

extract_protocol: RNAEasy kit used to extract total RNA

treatment_protocol: No treatment was carried out. The male SART1+/- mice spontaneously developed liver tumors (hepatocellular carcinoma) from age 10 months

tag: genotype

value: liver

tag: diagnosis

value: Cellular alteration + severe steatosis

value: male

value: 12 months


title: GH infusion_1d male liver pool 3_rRNA-depleted_G137_M15


title: Intact female liver pool 1_rRNA-depleted_G138_M13

value: No treatment

value: Female


title: GH infusion_1d male liver pool 2_rRNA-depleted_G137_M14

value: Male


title: GH infusion_10h male liver pool 3_rRNA-depleted_G137_M12

value: Continuous GH infusion for 10 hours


title: Control male liver pool 3_rRNA-depleted_G138_M12


title: GH infusion_10h male liver pool 2_rRNA-depleted_G137_M11


title: Adipose;White_Vehicle_15 days (10GR145_48)

value: Vehicle

value: 15 days


title: Het Tumor 1

source_name: Liver tumor from SART1+/- mouse

value: Hepatocellular carcinoma + severe steatosis


title: Het Tumor 2


title: Het Liver 1


title: Intact female liver pool 2_rRNA-depleted_G138_M14


title: Intact female liver pool 3_rRNA-depleted_G138_M15


title: Adipose;White_Vehicle_15 days (10GR145_49)

value: Adipose, White


title: Het Tumor 3


title: Normal 2

source_name: Normal liver from wild-type mouse

value: wildtype

value: Normal+ mild Steatosis


title: Het Liver 3


title: GH infusion_10h male liver pool 1_rRNA-depleted_G137_M10

value: Crl:CD1(ICR) (Charles River, strain code #022)


title: Normal 3


title: Roundup (1 ppb G)_rep_2

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

hyb_protocol: Hybridisation cocktails were prepared of the fragmented labelled-cDNA according to Nugen's recommendations and hybridised at 45°C overnight. The arrays were washed and stained using wash protocol FS450_0001 recommended for Affymetrix Human Transcriptome 2.0 Arrays on the GeneChip Fluidics station 450.

scan_protocol: Arrays were scanned using the GCS3000 7G scanner (Affymetrix) following manufacturer's protocols.

data_processing: CEL files were imported into Expression Console software (Affymetrix) and normalised using RMA-sketch (gene-level).

source_name: Breast cancer cell line

label_protocol: Single Primer Isothermal Amplified (SPIA) cDNA was generated using the Ovation Pico WTA System V2 kit from Nugen, following the manufacturer's instructions. The SPIA cDNA was fragmented and Biotin-labelled using the Encore Biotin Module from Nugen according to the manufacturer instructions.

extract_protocol: RNA extraction was performed using the Agencourt RNAdvance Cell V2 kit according to the manufacturer's instructions.

treatment_protocol: MCF-7 cells were seeded into 96-well plates with DMEM medium containing 10% FBS at a density of 20,000 cells per well. After 24 h of steroid deprivation in hormone free medium (charcoal stripped FBS), the cells were stimulated with test substances for 48 h in triplicate in three independent experiments.

tag: exposure time

tag: experimental group

value: Roundup (1 ppb G)

value: Roundup

tag: concentration (µg/l)


title: Roundup (1 ppb G)_rep_3


title: Roundup (1 ppb G)_rep_1


title: Roundup (1 ppm G)_rep_2

value: Roundup (1 ppm G)


title: Roundup (100 ppb G)_rep_3

value: Roundup (100 ppb G)


title: Roundup (100 ppb G)_rep_1


title: Roundup (1 ppm G)_rep_3


title: Normal 1

value: liver

value: male


title: Roundup (1 ppm G)_rep_1


title: POEA (10 ppb)_rep_3

value: POEA (10 ppb)

value: POEA


title: POEA (100 ppb)_rep_2

value: POEA (100 ppb)


title: Roundup (100 ppb G)_rep_2


title: POEA (10 ppb)_rep_2


title: POEA (100 ppb)_rep_3


title: Control_rep_1

value: Control


title: Glyphosate (100 ppb)_rep_1

value: Glyphosate (100 ppb)

value: Glyphosate


title: Control_rep_3


title: E2_10pM_rep_3

value: Estradiol


title: Glyphosate (10 ppm)_rep_1

value: Glyphosate (10 ppm)


title: Glyphosate (10 ppm)_rep_3


title: Glyphosate (1 ppb)_rep_2

value: Glyphosate (1 ppb)


title: Glyphosate (10 ppm)_rep_2


title: Glyphosate (100 ppb)_rep_3


title: Glyphosate (100 ppb)_rep_2


title: Glyphosate (1 ppb)_rep_3


title: POEA (10 ppb)_rep_1


title: Glyphosate (1 ppb)_rep_1


title: POEA (100 ppb)_rep_1


title: Control_rep_2


title: E2_10pM_rep_1


title: E2_100pM_rep_3


title: E2_1nM_rep_3


title: E2_10pM_rep_2


title: Arabidopsis rdr1/2/6 in Dry -2F

status: Public on Jul 13 2017

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

description: Drought stress-treated rdr1/2/6 plants, biological rep2

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array for 18 hr  at 45°C  using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned at 0.7 mm resolution using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
For the analysis of transcriptional activities in whole genome, intensities of a total of 3.2 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 1.6 millions PM and 1.6 millions MM probes, of individual replicates for all samples were normalized via quantile normalization.
The intensities of (PM-MM) were used in all subsequent data analyses.

organism: Arabidopsis thaliana

source_name: Drought stress treated Arabidopsis rdr1/2/6 plants

label_protocol:
Eight to fifteen mg of total RNA per one sample was used for synthesis of double-stranded cDNA by the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) using an oligo(dT) primer containing the T7 RNA polymerase promoter.
Biotin-labeled cRNA was generated from the cDNA by in vivo transcription using the GeneChIP IVT Labeling Kit (Affymetrix).

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes (30 plants per plastic dish) containing GM agar (0.8%) medium supplemented with 1% sucrose for 14 days under 16-h-light/8-h-dark (40-80 mmol photons m-2 sec-1) essentially as described previously (Oono et al. 2003, Plant J. 34: 868-887).

extract_protocol: Total RNA extraction using Plant RNA Isolation Reagent (Life technologies) from seedling samples was performed according to the manufacturer's instructions.

tag: genotype/variation

value: rdr1/2/6 mutant


title: Arabidopsis rdr1/2/6 in control -3F

description: Untreated rdr1/2/6 plants, biological rep3

source_name: Untreated Arabidopsis rdr1/2/6 plants


title: Arabidopsis rdr1/2/6 in Dry -3F

description: Drought stress-treated rdr1/2/6 plants, biological rep3


title: Arabidopsis rdr1/2/6 in Dry -1F

description: Drought stress-treated  rdr1/2/6 plants, biological rep1


title: Arabidopsis rdr1/2/6 in control -2F

description: Untreated rdr1/2/6 plants, biological rep2


title: Arabidopsis rdr1/2/6 in control -1F

description: Untreated rdr1/2/6 plants, biological rep1


title: Arabidopsis WT in Dry -1F

description: Drought stress-treated WT plants, biological rep1

source_name: Drought stress treated Arabidopsis WT plants

value: wild type


title: Arabidopsis WT in Dry -2F

description: Drought stress-treated WT plants, biological rep2


title: E2_1nM_rep_1

tag: cell line


title: E2_1nM_rep_2


title: E2_100pM_rep_2


title: Arabidopsis WT in control -3F

description: Untreated WT plants, biological rep3

source_name: Untreated Arabidopsis WT plants


title: Arabidopsis WT in Dry -3F

description: Drought stress-treated WT plants, biological rep3


title: Arabidopsis WT in control -1F

description: Untreated WT plants, biological rep1


title: Bisphenol A_rep_1

value: Bisphenol A


title: Arabidopsis rdr1/2/6 in control -2R


title: GNS-day0-rep1

city: Toronto

first: Peter

middle: B

last: Dirks

state: ON

address: 686 Bay St

department: Arthur and Sonia Labatt Brain Tumour Research Centre and Division of Neurosurgery

country: Canada

institute: The Hospital for Sick Children

description: differentiation incompetent

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and washed using the protocol FS450_0001

scan_protocol: GeneChip Scanner 3000

data_processing:
Data was processed using Expression Console and Partek Genomic Suite (v.6.5) software. RMA was applied to probe intensities, gene level expression were summarized from the corrected intensities and then log2 transformed
HuEx-1_0-st-v2.r2.dt1.hg18.full.ps
HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: tumor neural stem cells, neural stem cell conditions

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

growth_protocol: Cells were grown under conditions for promoting expansion of neural stem cells (containing EGF and FGF)

extract_protocol: Rneasy Mini Kit (Qiagen)

treatment_protocol: Cells were extracted 2 days after each growth-factor withdrawal

value: glioblastoma

tag: timepoint


title: Arabidopsis WT in Dry -2R


title: Arabidopsis rdr1/2/6 in Dry -2R

description: Drought stress treated rdr1/2/6 plants, biological rep2


title: Arabidopsis rdr1/2/6 in Dry -3R

description: Drought stress treated rdr1/2/6 plants, biological rep3


title: HFNS-day2-rep2

description: differentiation competent

source_name: normal neural stem cells, EGF withdrawal

value: human fetal brain


title: GNS-day9-rep2

description: differentiation incompetent

source_name: tumor neural stem cells, FGF withdrawal


title: Arabidopsis rdr1/2/6 in control -1R


title: HFNS-day0-rep2

description: differentiation competent

source_name: normal neural stem cells, neural stem cell conditions


title: Arabidopsis rdr1/2/6 in control -3R


title: Arabidopsis rdr1/2/6 in Dry -1R

description: Drought stress treated rdr1/2/6 plants, biological rep1


title: Arabidopsis WT in Dry -3R


title: Arabidopsis WT in control -2F

description: Untreated WT plants, biological rep2


title: Arabidopsis WT in control -3R

description: Untreated WT plants, biological rep3


title: Arabidopsis WT in control -2R

description: Untreated WT plants, biological rep2


title: GNS-day2-rep1

description: differentiation incompetent

source_name: tumor neural stem cells, EGF withdrawal


title: HFNS-day9-rep2

description: differentiation competent

source_name: normal neural stem cells, FGF withdrawal


title: GNS-day9-rep1

description: differentiation incompetent


title: Arabidopsis WT in control -1R

description: Untreated WT plants, biological rep1


title: Arabidopsis WT in Dry -1R


title: GNS-day2-rep2

description: differentiation incompetent


title: HFNS-day2-rep1

description: differentiation competent


title: Bisphenol A_rep_3


title: GNS-day0-rep2

description: differentiation incompetent


title: HFNS-day9-rep1

description: differentiation competent


title: HFNS-day0-rep1

description: differentiation competent


title: E2_100pM_rep_1


title: GATA6-shRNA Day 4 definitive endoderm cells-Replicate 1

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

description: Gene Expression

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: The data were analyzed with Partek Genomics Suite Statistical Analysis Software version 6.6 using Affymetrix default analysis settings

source_name: H1 huES-derived day 4 definitive endoderm cells containing lentiviral-shRNA targeting GATA6

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3' IVT Express kit from 100ng total RNA

growth_protocol: Samples collected were either pluripotent cells  (Day 0) or pluripotent cells that were differentiated for 2 Days with 50ng/ml Activin A, 10ng/ml BMP4, and 20ng/ml FGF2 followed by 1 day (Day 3 Samples), 2 days (Day 4 Samples), or 3 days (Day 5 Samples) of 50ng/ml Activin A to generate different stages of Definitive Endoderm.  The same growth conditions were used for the Rescue Day 5 samples except cells containing a doxycycline-inducible hGATA6 trangene were treated with dox for 4 days prior to collection.

extract_protocol: Qiagen RNeasy Total RNA Kit According to Manufacturer's Protocol

treatment_protocol: Cells were liberated with accutase, pelleted, flash frozen, and suspended in RLT Buffer with BME from the Qiagen RNeasy Mini Kit

value: H1 huES

tag: doxycycline

tag: vector

value: lentiviral-shRNA targeting GATA6


title: Empty Vector Pluripotent cells-Replicate 1

description: Gene Expression

source_name: Pluripotent H1 huES cells

value: empty


title: GATA6-shRNA + shRNA-resistant GATA6 Day 5 definitive endoderm-Replicate 1

description: Gene Expression

source_name: H1 huES-derived definitive endoderm cells differentiated in the presence of Dox for 96 hours


title: Empty Vector Day 4 definitive endoderm cells-Replicate 2

description: Gene Expression

source_name: H1 huES-derived day 4 definitive endoderm cells containing empty lentiviral vector

value: empty lentiviral


title: Empty Vector Pluripotent cells-Replicate 2

description: Gene Expression


title: Empty Vector Day 5 definitive endoderm cells-Replicate 1

description: Gene Expression

source_name: H1 huES-derived day 5 definitive endoderm cells containing empty lentiviral vector


title: GATA6-shRNA Day 4 definitive endoderm cells-Replicate 2

description: Gene Expression


title: GATA6-shRNA Day 5 definitive endoderm cells-Replicate 2

description: Gene Expression

source_name: H1 huES-derived day 5 definitive endoderm cells containing lentiviral-shRNA targeting GATA6


title: GATA6-shRNA Day 3 definitive endoderm cells-Replicate 2

description: Gene Expression

source_name: H1 huES-derived day 3 definitive endoderm cells containing lentiviral-shRNA targeting GATA6


title: GATA6-shRNA + shRNA-resistant GATA6 Day 5 definitive endoderm-Replicate 2

description: Gene Expression


title: Empty Vector Day 5 definitive endoderm cells-Replicate 2

description: Gene Expression


title: Empty Vector Day 3 definitive endoderm cells-Replicate 1

description: Gene Expression

source_name: H1 huES-derived day 3 definitive endoderm cells containing empty lentiviral vector


title: GATA6-shRNA Day 3 definitive endoderm cells-Replicate 1

description: Gene Expression


title: GATA6-shRNA Day 5 definitive endoderm cells-Replicate 1

description: Gene Expression


title: Empty Vector Day 4 definitive endoderm cells-Replicate 1

description: Gene Expression


title: Empty Vector Day 3 definitive endoderm cells-Replicate 2

description: Gene Expression


title: control-2

city: Hiroshima

first: Yasushi

last: Horimasu

address: 1-2-3 Kasumi, Minami-ku

institute: Hiroshima University

description:
normal
SAMPLE 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio v3 software

source_name: Human lung

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep RNA amplification kit

extract_protocol: RNA was extracted from frozen lung tissue specimens and RNA quality was verified 1 using the RNA6000 Nano Assay on an Agilent 2100 Bioanalyzer.

value: normal


title: F-24-3_2

description:
nonspecific interstitial pneumonia
SAMPLE 9

value: Female

tag: smoking

value: no

value: NSIP


title: F12-2

description:
nonspecific interstitial pneumonia
SAMPLE 11

value: Male

value: yes


title: F-30-2

description:
idiopathic pulmonary fibrosis
SAMPLE 4

value: IPF


title: control-1

description:
normal
SAMPLE 5


title: F-7-2_3

description:
idiopathic pulmonary fibrosis
SAMPLE 6


title: F-35-2_2

description:
nonspecific interstitial pneumonia
SAMPLE 12


title: F-26-3_2

description:
nonspecific interstitial pneumonia
SAMPLE 14


title: F-39-3

description:
nonspecific interstitial pneumonia
SAMPLE 13


title: F40

description:
idiopathic pulmonary fibrosis
SAMPLE 8


title: F41

description:
idiopathic pulmonary fibrosis
SAMPLE 7


title: Alveolar macrophage from Tuberculosis patient 3

city: Medellín

first: LELIA

last: LAVALETT

state: Antioquia

department: Antioquia

country: Colombia

institute: Universidad de antioquia

description:
replicate 3
Sample 61

data_processing: Data were extracted with Illumina GenomeStudio v2011.1  software. Probes signal value was transformed by logarithm and normalized by Z-ratio method. The data were normalised using quantile normalisation with Lumi package in R

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

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

tag: subject status

value: Tuberculosis patient

tag: sample source

value: bronchoalveolar lavage

tag: cell type

value: Human alveolar macrophage


title: control-3

description:
normal
SAMPLE 15


title: Bisphenol A_rep_2

source_name: Breast cancer cell line

value: Bisphenol A

tag: treatment


title: Alveolar macrophage from Tuberculosis patient 2

description:
replicate 2
Sample 58


title: Alveolar macrophage from Tuberculosis patient 1

description:
replicate 1
Sample 52


title: Primary PDGF-driven GBM 4

status: Public on Jul 12 2017

first: Gilbert

middle: Joseph

last: Rahme

address: 365 Longwood Ave.

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: SAMPLE 4

data_processing: variance stabilizing transformation followed by robust spline normalization through the lumi package

source_name: GBM Tissue

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

growth_protocol: Tumor tissues were collected from mice exhibiting neurological symptoms or that were moribund.

extract_protocol: RNA was extracted using the Trizol method.

treatment_protocol: Tumor tissues were washed twice in PBS (without calcium and magnesium) and then frozen at -80  ͦC.

tag: strain

value: mixed background

tag: tissue

value: glioblastoma (GBM)


title: F-1-5_2

description:
idiopathic pulmonary fibrosis
SAMPLE 1

tag: gender

tag: age


title: Alveolar macrophage from control 1

description:
replicate 1
Sample 64

source_name: Alveolar macrophage from control

value: control


title: Primary PDGF-driven GBM 1

description: SAMPLE 1

tag: genotype


title: Alveolar macrophage from control 4

description:
replicate 4
Sample 76


title: F-4-3

description:
idiopathic pulmonary fibrosis
SAMPLE 2

tag: diagnosis


title: Alveolar macrophage from control 2

description:
replicate 2
Sample 70


title: Primary PDGF-driven GBM 8

description: SAMPLE 8


title: Primary PDGF-driven GBM 6

description: SAMPLE 6


title: Alveolar macrophage from control 3

description:
replicate 3
Sample 73


title: Primary PDGF-driven GBM 5

description: SAMPLE 5


title: Primary PDGF-driven GBM 7

description: SAMPLE 7


title: Primary PDGF-driven GBM 3

description: SAMPLE 3


title: Primary PDGF-driven GBM 2

description: SAMPLE 2


title: F-13-2

description:
idiopathic pulmonary fibrosis
SAMPLE 3


title: Induced tissue bio repeat 3

first: Andrea

last: Streit

address: Centre for Craniofacial & Regenerative Biology, King's College London

description: Mesoderm induced epiblast 3

hyb_protocol: Following fragmentation, 6 µg of cDNA were hybridized for 18 Hours at 45oC on GeneChip Gallus Gallus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. as per Nugen Inc Instructions for Nugen Ovation V2

scan_protocol: Affymetrix Scanner 3000 7G

data_processing: Probe set values were generated with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and a user defined scale factor of 1.0

organism: Gallus gallus

source_name: Induced epiblast excised after 12hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Host Embryos were incubated for 12 hours, the mesoderm induced ectoderm was dissected manually using fine insect pins and stored on ice until processing.

treatment_protocol: Tissue was dissected from host embryos after 12 hours

value: Induced epiblast from area opaca after 12 hours of exposure to lateral head mesoderm


title: Induced tissue bio repeat 2

department: Centre for Craniofacial & Regenerative Biology

description: Mesoderm induced epiblast 2


title: siControl_gene3

city: Suita

first: Yukio

last: Kawahara

state: Osaka

address: 2-2 Yamada-oka

department: Graduate School of Medicine

institute: Osaka University

description: Gene expression  48 hr after electroporation of negative control siRNA

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 hr at 45°C  on GeneChip Human transcriptome array using GeneChip Hybridization,Wash,and Stain Kit (Affymetrix) according to manufacturer's instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix) .

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

data_processing: The data were analyzed with GeneChip Command Console Softwere (Affymetrix) and normalized using Expression Console Softwere (Affymetrix) with default parameters (Gene level: SST-RMA, Exon level: SST- Alt Splice Analysis).

source_name: SH-SY5Y, NC-siRNA replicate3,Gene level

label_protocol: Biotynilated cDNA were synthesized from 100 ng of total RNA using Genechip WT PLUS Reagent Kit (Affymetrix) according to manufacturer's instructions.

growth_protocol: SH-SY5Y cells were grown at 37°C and 5% CO2 in DMEM/F-12 medium (Thermo Fisher Scientific) supplemented with 15% FBS.

extract_protocol: Forty eight hours after electroporation, total RNA was extracted and purified from cells treated with siRNA targeting Matrin3 or negative control siRNA using TRIzol® reagent and Purelink® RNA mini kit (Thermo Fisher Scientific). The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SH-SY5Y cells were splitted with trypsin, and 5×10^6 cells were washed with PBS two times before resuspension in buffer R containing 0.2 M siRNA.  One hundred ul of the suspension were electroporated with Neon® Transfection System Kits and device (Thermo Fisher Scientific; 1100 V; pulse width: 50 ms; number of pulses: 1). Electroporated cells were resuspended and cultured in 2 ml of DMEM/F-12 medium in 6 well plates.  Twenty- four after electroporation, medium was changed.

value: Negative control siRNA


title: Control tissue bio repeat 3

description: Control area opaca 3

source_name: area opaca excised after 12hrs

value: Area opaca


title: siControl_gene2

source_name: SH-SY5Y, NC-siRNA replicate2,Gene level


title: Induced tissue bio repeat 1

description: Mesoderm induced epiblast 1


title: siMatrin3_gene3

description: Gene expression  48 hr after electroporation of Matrin3

source_name: SH-SY5Y, Matrin3-siRNA replicate3,Gene level

value: Matrin3 siRNA


title: siControl_gene1

source_name: SH-SY5Y, NC-siRNA replicate1,Gene level


title: Control tissue bio repeat 2

description: Control area opaca 2


title: siMatrin3_gene2

source_name: SH-SY5Y, Matrin3-siRNA replicate2,Gene level


title: Control tissue bio repeat 1

description: Control area opaca 1


title: siMatrin3_gene1

source_name: SH-SY5Y, Matrin3-siRNA replicate1,Gene level


title: PT_31

city: Padova

first: Luca

last: Trentin

address: Via Giustiniani, 3

department: Department of Women's and Children's Health

country: Italy

institute: University of Padova

description: Gene expression data from Jurkat  untreated  in vitro for 24h

hyb_protocol: 15 ug were fragmented; following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA

source_name: Jurkat cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting  from 100ng of Total RNA using the Affymetrix 3' IVT Plus Kit

growth_protocol: leukemia cells were cultured in RPMI-1640

extract_protocol: RNA was extracted using the QIAGEN RNeasy Kit.

treatment_protocol: Panobinostat (LBH589, 5nM) or control, for  24h

value: Control

tag: replicate


title: PT_28

description: Gene expression data from KOPN8 treated with  LBH589 5nM in vitro for 24h

source_name: KOPN8 cell line with the t(11;19)


title: PT_27

description: Gene expression data from KOPN8  untreated  in vitro for 24h


title: PT_29

description: Gene expression data from REH  untreated  in vitro for 24h

source_name: REH cell line with the t(12;21)


title: PT_30

description: Gene expression data from REH treated with  LBH589 5nM in vitro for 24h


title: PT_22


title: PT_17

description: Gene expression data from SEM untreated  in vitro for 24h

source_name: SEM cell line with the t(4;11)


title: PT_19


title: PT_24

description: Gene expression data from Jurkat treated with  LBH589 5nM in vitro for 24h


title: PT_15


title: PT_20


title: PT_32


title: PT_26

description: Gene expression data from SEM treated with  LBH589 5nM in vitro for 24h


title: PT_18


title: PT_23


title: PT_11


title: PT_13


title: PT_10


title: PT_14


title: PT_9


title: PT_12


title: PT_6


title: PT_4


title: Mammary gland biopsy_dam’s milk_rep8

city: Zaragoza

first: Jorge

middle: H

last: Calvo

address: Avd. Montañana 930

department: Producción y Sanidad animal

country: Spain

institute: CITA

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol using GCOS

data_processing: Expression data were generated with GeneChip Operating Software (GCOS, Affymetrix) and normalization was carried out with Robust Multi-Array Average (RMA) algorithm with quantile normalization.

organism: Bos taurus

source_name: Mammary gland, biopsy, end of first lactation

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

growth_protocol: Sixteen Parda de Montaña heifers, were randomly but equally assigned at birth to one of four management strategies, in a 2 x 2 factorial experiment. In the pre-weaning period (0-6 months of age), all the heifers suckled their dams twice daily for 30 minutes. Half of the heifers (n=8) were supplemented a starter concentrate (CON) while the other half only had access to their dam’s milk (NOCON). In the post-weaning period (6-15 months), half of the heifers of each pre-weaning feeding treatment received alfalfa hay ad libitum plus concentrates, with a different forage to concentrate ratio (F:C), 67:33 (67F:33C) or 87:13 (87F:13C).Mammary tissue samples were taken by biopsy at weaning at the end of first lactation.

extract_protocol: RNeasy Tissue isolation kit (QIAGEN, Madrid, Spain)

treatment_protocol: Mammary gland tissue samples obtained with an  human Tru-Cut biopsy needle (CareFusion, France). Immediately after biopsy, the mammary tissue sample was stored in RNA later solution (QIAGEN, Madrid, Spain) and then frozen and stored at −80°C until processing for RNA extraction

value: female

tag: breed

value: Parda de Montaña

value: dam’s milk

value: mammary gland


title: PT_5


title: PT_16


title: PT_2


title: PT_1


title: PT_3


title: PT_8


title: PT_21


title: Mammary gland biopsy_dam’s milk_rep3


title: Mammary gland biopsy_dam’s milk_rep2


title: Expression data of UC_m27

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

institute: University of Tokyo

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: MAS5-calculated signal intensity were 'per chip' normalized (normalize to median of the measurements taken from that chip), 'per gene' normalized (normalize to median of the measurments for that gene), and log2 transformed.

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Samples obtained from surgically resected specimens or during surveillance colonoscopy were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatsworth,CA) according to the manufacturer's instructions.

tag: disease state

value: ulcerative colitis

value: Colorectal mucosa

tag: mitochondrial dna copy number

value: mtDNA-Low


title: Mammary gland biopsy_dam’s milk_rep6


title: Mammary gland biopsy_dam’s milk_rep5


title: Expression data of UC_m30

value: mtDNA-High


title: PT_7


title: Mammary gland biopsy_dam’s milk_rep7


title: Expression data of UC_m28


title: Mammary gland biopsy_dam’s milk_rep4


title: Mammary gland biopsy_dam’s milk+starter concentrate_rep5

value: dam’s milk+starter concentrate


title: Expression data of UC_m26


title: Mammary gland biopsy_dam’s milk_rep1


title: Mammary gland biopsy_dam’s milk+starter concentrate_rep7


title: Expression data of UC_m29


title: Mammary gland biopsy_dam’s milk+starter concentrate_rep4


title: Mammary gland biopsy_dam’s milk+starter concentrate_rep8


title: Mammary gland biopsy_dam’s milk+starter concentrate_rep6


title: Expression data of UC_m25


title: PT_25


title: Expression data of UC_m24


title: Mammary gland biopsy_dam’s milk+starter concentrate_rep3


title: Mammary gland biopsy_dam’s milk+starter concentrate_rep2


title: Expression data of UC_m23


title: Expression data of UC_m19


title: Expression data of UC_m22


title: Expression data of UC_m20


title: Expression data of UC_m18


title: Expression data of UC_m21


title: cluster-rep2

city: Gainesville

first: Rolf

middle: F

last: Renne

state: FL

address: 2033 Mowry Road

department: Molecular Genetics & Microbiology

institute: University of Florida

description: LncRNA expression of cells latently infected with Δcluster-KSHV.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, and fixed. and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: The hybridized arrays were scanned with the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs with at least 3 out of 9 samples having flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1).

source_name: TIVE cells,infected with Δcluster-KSHV,technical replicate 2

label_protocol: RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: TIVE cells were grown in complete Medium-199 (1% Pen-Strep, 20% FBS), supplemented with Endothelial cell growth supplement (Sigma E2759).

extract_protocol: Total RNA was isolated with RNA-Bee (Tel-Test Inc.) using the protocol provided by the manufacturer. Total RNA (5-10 µg) was treated with DNase I (NEB) according to the manufacturer’s instructions and ethanol precipitated overnight.

treatment_protocol: Latently-infected TIVE cells were maintained in the presence of hygromycin (10 µg/mL) to prevent loss of KSHV episomes.

tag: tissue culture cell line

value: telomerase-immortalized vein endothelial cells

tag: virus

value: Δcluster-KSHV, latent infection


title: Expression data of UC_m17


title: Mammary gland biopsy_dam’s milk+starter concentrate_rep1


title: cluster-rep3

source_name: TIVE cells,infected with Δcluster-KSHV,technical replicate 3


title: cluster-rep1

source_name: TIVE cells,infected with Δcluster-KSHV,technical replicate 1


title: Expression data of UC_m15


title: KSHV-rep3

description: LncRNA expression of cells latently infected with wt-KSHV.

source_name: TIVE cells,infected with wt-KSHV,technical replicate 3

value: wt-KSHV, latent infection


title: Expression data of UC_m16


title: KSHV-rep1

source_name: TIVE cells,infected with wt-KSHV,technical replicate 1


title: Mock-rep3

description: LncRNA expression of uninfected cells

source_name: TIVE cells,uninfected,technical replicate 3

value: uninfected (mock)


title: Expression data of UC_m13


title: Expression data of UC_m12


title: KSHV-rep2

source_name: TIVE cells,infected with wt-KSHV,technical replicate 2


title: Mock-rep2

description: LncRNA expression of uninfected cells

source_name: TIVE cells,uninfected,technical replicate 2


title: Expression data of UC_m09


title: Expression data of UC_m14


title: Expression data of UC_m08


title: Expression data of UC_m10


title: Expression data of UC_m11


title: Expression data of UC_m07


title: Expression data of UC_m06


title: 7 T1_1

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: For FFPE samples: 50ng of totalRNA were amplified and labeled using the SensationPlus FFPE Amplification and 3′ IVT Labeling kit (Catalog Number 902039, Affymetrix, Santa Clara, CA).

scan_protocol: Affymetrix GeneChip® Rat 230 2.0 arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Labeling Assay User Manual (Fluidics Protocol FS450_0002)

data_processing: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G

organism: Rattus norvegicus

source_name: Tumor tissue (Adenom) FFPE

label_protocol: For conv. Isolated samples: 250ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Express Kit (Catalog Number 901229, Affymetrix, Santa Clara,CA)

growth_protocol: Han-Wistar rats were obtained from Charles River (FRA). They were kept under standardized SPF-conditions. All experiments were approved by the “Committee of Animal Protection” of the Austrian government and performed according to  Austrian regulations.

extract_protocol: Frozen liver samples were homogenized in TRIzol reagent (Invitrogen) and subsequently extracted with the miRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. Formalin-fixed liver samples were isolated via laser capture microdissection and extracted with the RNeasy FFPE Kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer. RNA was stored at −80°C until GeneChip® experiment analysis.

treatment_protocol: Male rats were treated once with N-nitrosomorpholine (250mg/kg bw) and after a recovery period of 3 weeks they got 50mg PB per kg body weight (5-ethyl-5-phenylbarbituric acid sodium salt; Sigma, St. Louis, MO) via drinking water for a period of up to 17 months.

value: Wistar

value: Male

value: Tumor tissue (Adenom) FFPE

tag: group

value: 7 N

value: Phenobarbital

value: 50 mg/kg/day

value: 17 months

tag: fixation

value: FFPE


title: 7 N_1

source_name: Surrounding tissue - FFPE

value: Surrounding tissue - FFPE


title: Normal_3_1

source_name: Surrounding tissue

value: Surrounding tissue


title: Normal_2_1


title: 23 T4_1

source_name: Tumor tissue (Carcinom - bCatenin Mut)

value: Tumor tissue (Carcinom - bCatenin Mut)


title: 23 T6_1

source_name: Tumor tissue (Adenom)

value: Tumor tissue (Adenom)

value: Adenoma


title: Normal_1_1


title: Expression data of UC_m03

value: ulcerative colitis

value: Colorectal mucosa

value: mtDNA-Low


title: 7 F1_1

source_name: Tumor tissue (Focus) - FFPE

value: Tumor tissue (Focus) - FFPE


title: Mock-rep1

description: LncRNA expression of uninfected cells

source_name: TIVE cells,uninfected,technical replicate 1

value: telomerase-immortalized vein endothelial cells

value: uninfected (mock)


title: Expression data of UC_m02

value: mtDNA-High


title: Expression data of UC_m04


title: Expression data of UC_m05


title: 23 T5_1

value: Wistar

value: Male


title: 7 F2_1

value: 7 N

value: Phenobarbital

value: 50 mg/kg/day


title: Expression data of UC_m01


title: 7 F4_1

value: 17 months

value: FFPE


title: 23 T3_1

source_name: Tumor tissue (Carcinom)

value: Tumor tissue (Carcinom)

value: Carcinoma


title: 23 T1_1

value: Tumor tissue (Adenom)

value: Adenoma


title: 23 N_2_1

value: Surrounding tissue


title: 23 N_1_1


title: 23 T2_1

value: Tumor tissue (Carcinom - bCatenin Mut)


title: 21 T6_1


title: siControl_exon3

source_name: SH-SY5Y, NC-siRNA replicate3,exon level

tag: cell line

value: Negative control siRNA


title: siControl_exon1

source_name: SH-SY5Y, NC-siRNA replicate1,exon level


title: siMatrin3_exon3

source_name: SH-SY5Y, Matrin3-siRNA replicate3,exon level

value: Matrin3 siRNA


title: siControl_exon2

source_name: SH-SY5Y, NC-siRNA replicate2,exon level


title: siMatrin3_exon2

source_name: SH-SY5Y, Matrin3-siRNA replicate2,exon level


title: siMatrin3_exon1

source_name: SH-SY5Y, Matrin3-siRNA replicate1,exon level


title: 21 T1_1


title: 18 N_1

value: Surrounding tissue - FFPE


title: 21 T5_1


title: 18 F2_1

value: Tumor tissue (Focus) - FFPE


title: 14 T5_2_1

value: Wistar


title: 14 T4_2_1

value: Male

value: Tumor tissue (Adenom) FFPE


title: 14 N_1_1

value: Phenobarbital


title: 14 MT_1

source_name: Tumor tissue (Minitumor)

value: Tumor tissue (Minitumor)

value: Nodule

value: 50 mg/kg/day


title: 11 MT2_1

value: 17 months


title: 18 F3_1

value: FFPE


title: 10 T2_1

value: Tumor tissue (Carcinom)

value: Carcinoma


title: 10 T4_1


title: 14 T5_1_1

value: Tumor tissue (Adenom)

value: Adenoma


title: 14 N_2_1


title: 11 MT1_1


title: 14 T3_1


title: 21 N_1

value: Surrounding tissue


title: 10 N_1_1


title: 10 N_3_1


title: 11 N_1


title: 10 T3_1


title: 18 F1_1


title: 14 T4_1_1


title: 10 MT2_1


title: 10 N_2_1


title: 10 T1_1


title: 10 MT1_1


title: 10 F3_1


title: 10 F1_1


title: 10 F2_1


title: MC_PB_24h_3

hyb_protocol: Affymetrix GeneChip® Rat 230 2.0 arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Labeling Assay User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

source_name: Mesenchymal cell, Phenobarbital, 24 hours

label_protocol: 250ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Express Kit (Catalog Number 901229, Affymetrix, Santa Clara,CA)

extract_protocol: Cells were homogenized with Qiazol (Qiagen, Ger) and total RNA was subsequently extracted with the miRNeasy Mini Kit (Qiagen, Ger) according to the manufacturer's instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer. RNA was stored at −80°C until GeneChip® experiment analysis.

treatment_protocol: Male rats were treated with 50mg PB per 1000g body weight (5-ethyl-5-phenylbarbituric acid sodium salt; Sigma, St. Louis, MO) by a single gavage or via drinking water for a period of 14 days. Female Wistar rats were treated with 100mg CPA per kg body weight (Cyproterone acetate; Sigma, St. Louis, MO) by a single gavage on one day or on 6 consecutive days. Oil-treated rats served as control.

value: Female

value: Mesenchymal cell

value: 50 mg/kg

value: 24 hours


title: MC_PB_14d_3

source_name: Mesenchymal cell, Phenobarbital, 14 days

value: Wistar

value: Male

value: 14 days


title: HC_H2O_24h_2

source_name: Hepatocytes, Vehicle (Water), 24 hours

value: Hepatocytes

value: Vehicle (Water)

value: 0 mg/kg


title: MC_H2O_14d_2

source_name: Mesenchymal cell, Vehicle (Water), 14 days


title: HC_H2O_14d_2

source_name: Hepatocytes, Vehicle (Water), 14 days


title: MC_H2O_14d_3


title: MC_PB_14d_1

value: Phenobarbital


title: MC_PB_24h_1


title: MC_CPA_6d_2

source_name: Mesenchymal cell, Cyproterone Acetate, 6 days

value: Cyproterone Acetate

value: 100 mg/kg

value: 6 days


title: MC_PB_24h_2


title: MC_H2O_24h_3

source_name: Mesenchymal cell, Vehicle (Water), 24 hours


title: MC_PB_14d_2


title: HC_PB_24h_2

source_name: Hepatocytes, Phenobarbital, 24 hours


title: HC_PB_24h_3


title: HC_PB_24h_1


title: HC_PB_14d_2

source_name: Hepatocytes, Phenobarbital, 14 days


title: HC_PB_14d_1


title: HC_H2O_14d_1


title: HC_H2O_14d_3


title: HC_H2O_24h_1


title: MC_H2O_24h_1


title: HC_H2O_24h_3


title: MC_CPA_24h_3

source_name: Mesenchymal cell, Cyproterone Acetate, 24 hours


title: HC_PB_14d_3


title: HC_CPA_6d_3

source_name: Hepatocytes, Cyproterone Acetate, 6 days


title: MC_CPA_24h_1


title: MC_CPA_24h_2


title: MC_CPA_6d_1


title: MC_H2O_14d_1


title: MC_CPA_6d_3


title: MC_CO_Co_24h_3

source_name: Mesenchymal cell, Vehicle (Corn Oil), 24 hours

value: Vehicle (Corn Oil)

value: 10 ml/kg


title: HC_CPA_24h_3

source_name: Hepatocytes, Cyproterone Acetate, 24 hours


title: MC_CO_Co_24h_4


title: MC_CO_Co_24h_2


title: MC_CO_24h_5


title: MC_CO_6d_1

source_name: Mesenchymal cell, Vehicle (Corn Oil), 6 days


title: HC_CPA_24h_2


title: MC_CO_24h_1


title: MC_CO_6d_3


title: HC_CPA_6d_1


title: HC_CO_24h_4

source_name: Hepatocytes, Vehicle (Corn Oil), 24 hours


title: MC_CO_Co_24h_1


title: HC_CO_6d_3

source_name: Hepatocytes, Vehicle (Corn Oil), 6 days


title: MC_CO_24h_4


title: HC_CO_6d_2


title: HC_CO_Co_24h_1


title: HC_CO_Co_24h_4


title: HC_CO_Co_24h_2


title: HC_CO_24h_3


title: HC_CPA_6d_2


title: HC_CO_6d_1


title: HC_CO_24h_5


title: MC_CO_24h_3


title: MC_CO_6d_2


title: HC_CO_Co_24h_3


title: HC_CPA_24h_1


title: HC_CO_24h_2


title: MC_CO_24h_2


title: HC_CO_24h_1


title: L1S

city: Shanghai

first: haibin

last: wei

address: 294 Taiyuan Road

department: Institute for Nutritional Sciences

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

organism: Oryza sativa

source_name: roots

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

growth_protocol: Rice grew in greenhouse at normal planting environment.

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

treatment_protocol: No special treatments.

value: shallow roots


title: L1D

value: deep roots


title: H32D


title: L16D


title: L44D


title: L44S


title: H41S


title: H11S


title: L16S


title: H41D


title: H11D


title: M2 Macrophages_Normal_IL4_4

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description:
Monocytes cultured in normal glucose (5mM) for 6days, IL4 (10ng/ml)
Normal_IL4_4

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Hugene-1_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays.The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Primary monocytes cultured in normal glucose, IL4

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

growth_protocol: Primary human monocytes were cultured in serum free medium supplemented by M-CSF (5ng/ml) for 6 days with specific cytokine stimulations in order to differentiate in to different sub-types of macrophage population (M0,M1 and M2).

extract_protocol: RNA was isolated by using E.Z.N.A. total RNA kit. Extraction procedure was according to E.Z.N.A. total RNA kit

treatment_protocol: After isolating monocytes from buffy coats, these cells were cultured with IFNg (100ng/ml), IL4 (10ng/ml) and control (without cytokine) for 6 days

tag: patientno

tag: glucose

value: NG

tag: cell type

value: monocyte-derived macrophages

tag: cell subtype


title: M1 Macrophages_High_IFNg_3

description:
Monocytes cultured in high glucose (25mM) for 6days, IFNgamma (100ng/ml)
High_IFNg_3

source_name: Primary monocytes cultured in high glucose, IFNgamma

tag: treatment

value: IFNg

value: HG


title: M0 Macrophages_Normal_NS_4

description:
Monocytes cultured in normal glucose (5mM) for 6days
Normal_NS_4

source_name: Primary monocytes cultured in normal glucose

value: NS


title: M2 Macrophages_High_IL4_4

description:
Monocytes cultured in high glucose (25mM) for 6days, IL4 (10ng/ml)
High_IL4_4

source_name: Primary monocytes cultured in high glucose, IL4


title: M1 Macrophages_Normal_IFNg_4

description:
Monocytes cultured in normal glucose (5mM) for 6days, IFNgamma (100ng/ml)
Normal_IFNg_4

source_name: Primary monocytes cultured in normal glucose, IFNgamma


title: M0 Macrophages_Normal_NS_3

description:
Monocytes cultured in normal glucose (5mM) for 6days
Normal_NS_3


title: M1 Macrophages_High_IFNg_4

description:
Monocytes cultured in high glucose (25mM) for 6days, IFNgamma (100ng/ml)
High_IFNg_4


title: MC_H2O_24h_2

tag: strain

value: Wistar

tag: gender

value: Male

tag: tissue

value: Mesenchymal cell

value: 24 hours


title: M0 Macrophages_High_NS_4

description:
Monocytes cultured in high glucose (25mM) for 6days
High_NS_4

source_name: Primary monocytes cultured in high glucose


title: M0 Macrophages_Normal_NS_2

description:
Monocytes cultured in normal glucose (5mM) for 6days
Normal_NS_2


title: M2 Macrophages_High_IL4_3

description:
Monocytes cultured in high glucose (25mM) for 6days, IL4 (10ng/ml)
High_IL4_3


title: CAP treated MCF-7/TamR

city: goyang

first: seungyeon

last: lee

address: dongguk-ro 32

department: life science

country: South Korea

institute: dongguk unversity

description:
Cold athmospheric plasma treated MCF-7/TamR
SAMPLE 3

hyb_protocol: Following fragmentation, 0.75ug of cRNA were hybridized to the Illumina HumanHT-12 Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina Genomestudio v2011.1(Gene Expresion Module v1.9.0)

source_name: Mammary epithelial cell line

label_protocol: Biotinylated cRNA were prepared from 2ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

growth_protocol: All cell lines were maintained in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin under humidified 5% CO2 condition.

extract_protocol: The total RNA was isolated using the ZR-Duet DNA/RNA MiniPrep kit  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The tamoxifen resistant MCF-7 cell line (MCF-7/TamR) was generated by sequentially exposing to increasing doses of 4-hydroxytamoxifen.  The cells with 50% confluence in 60 mm plate were irradiated 10 times for 30 seconds every hour prior RNA extraction.


title: MCF-7/TamR

description:
Tamoxifen resistant MCF-7 (MCF-7/TamR)
SAMPLE 2


title: M2 Macrophages_Normal_IL4_3

description:
Monocytes cultured in normal glucose (5mM) for 6days, IL4 (10ng/ml)
Normal_IL4_3


title: M0 Macrophages_High_NS_3

description:
Monocytes cultured in high glucose (25mM) for 6days
High_NS_3


title: MCF-7

description:
Original MCF-7
SAMPLE 1


title: M1 Macrophages_Normal_IFNg_3

description:
Monocytes cultured in normal glucose (5mM) for 6days, IFNgamma (100ng/ml)
Normal_IFNg_3


title: M2 Macrophages_High_IL4_2

description:
Monocytes cultured in high glucose (25mM) for 6days, IL4 (10ng/ml)
High_IL4_2


title: M0 Macrophages_High_NS_2

description:
Monocytes cultured in high glucose (25mM) for 6days
High_NS_2


title: M0 Macrophages_Normal_NS_1

description:
Monocytes cultured in normal glucose (5mM) for 6days
Normal_NS_1


title: M2 Macrophages_Normal_IL4_2

description:
Monocytes cultured in normal glucose (5mM) for 6days, IL4 (10ng/ml)
Normal_IL4_2


title: M1 Macrophages_High_IFNg_2

description:
Monocytes cultured in high glucose (25mM) for 6days, IFNgamma (100ng/ml)
High_IFNg_2


title: M2 Macrophages_Normal_IL4_1

description:
Monocytes cultured in normal glucose (5mM) for 6days, IL4 (10ng/ml)
Normal_IL4_1


title: M2 Macrophages_High_IL4_1

description:
Monocytes cultured in high glucose (25mM) for 6days, IL4 (10ng/ml)
High_IL4_1


title: M1 Macrophages_High_IFNg_1

description:
Monocytes cultured in high glucose (25mM) for 6days, IFNgamma (100ng/ml)
High_IFNg_1


title: M1 Macrophages_Normal_IFNg_2

description:
Monocytes cultured in normal glucose (5mM) for 6days, IFNgamma (100ng/ml)
Normal_IFNg_2


title: M1 Macrophages_Normal_IFNg_1

description:
Monocytes cultured in normal glucose (5mM) for 6days, IFNgamma (100ng/ml)
Normal_IFNg_1


title: STD_T1_rep2

city: Rotondella

first: loretta

last: daddiego

state: MT

institute: ENEA C.R. Trisaia

description: Arrays include around 500 quality control spots

hyb_protocol: The fragmented Cy5-cRNAs were added to the hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% formamide, 100 ng/μl salmon sperm DNA, 0.04% SDS) and poured in the hybridization chambers of the pre-hybridized microarrays, following the CombiMatrix Hybridization protocol. After an overnight incubation at 45°C in a rotating rotisserie oven, microarrays were treated with six washing steps: firstly in 6X SSPE and 0.05% Tween-20 for 5’ at 45°C, then with 3X and 0.5X SSPE and 0.05% Tween-20 for 1’ at room temperature, with 2X PBS and 0.1% Tween-20 and finally twice with 2X PBS for 1’ at room temperature.

scan_protocol: Microarray slides were scanned with the GenePix Pro microarray scanner (Axon Instruments) and data processed with the CombiMatrix Microarray Imager software (CombiMatrix). A maximum threshold of 0.20 for the coefficient of variance (of the spots corresponding to identical probes) was applied to control intra-chip hybridization variability. The correlation among the three technical replicates for each experimental condition was assured by a minimum Pearson coefficient (R) of 0.99.

data_processing: Raw values were normalized on the median of the intensities by the CombiMatrix Probe Weaver software using the quantile algorithm. Pairwise analysis of differential expression was assessed with a Welch's t-test, followed by a Bonferroni-Hochberg FDR adjustment with a cut off p-value of 0.05, using R. To filter lowly expressed sequences, we calculated the average and standard deviation of the expression value of all empty and negative controls and set as threshold the mean value plus two times the standard deviation. Of the filtered significantly differentially expressed probes, only those with greater than 1.5-fold increase or 1.5-fold decrease in expression compared to the control condition were used for further analysis.

organism: Lactuca sativa

source_name: leaves

label_protocol: Two μg of total RNA were retrotranscribed using the RNA ampULSe Amplification and Labeling Kit for CombiMatrix arrays (Kreatech Biotechnology). cRNA labeling was carried out with the Cy5-ULS (Cyanine-Universal Linkage System). Unincorporated dye was removed with KREApure purification columns (Agilent). Labeling yield and quality were assessed using a NanoDrop 1000 (Thermo Scientific). cRNAs were fragmented for 20 min at 95°C in 200 mM Tris Acetate (pH 8.1), 500 mM potassium acetate and 150 mM molybdenum acetate

extract_protocol: Total RNA was isolated from 500 mg of finely ground lettuce leaves. A purification step was performed in a 1:1:5(v/v/v) solution of phenol, chloroform and RNA Extraction Buffer (1 M Tris-Borate pH 7.5,  0.5 M EDTA pH 8.0, 10% SDS) twice, followed by a phase separation with  KAc 5M and Ethanol. RNA was isolated from the aqueous phase by  Lithium chloride precipitation

value: SH-treated


title: M0 Macrophages_High_NS_1

description:
Monocytes cultured in high glucose (25mM) for 6days
High_NS_1


title: MC_PB_3

hyb_protocol: Affymetrix GeneChip® Mouse 430A 2.0  arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Labeling Assay User Manual (Fluidics Protocol FS450_0002)

source_name: Mesenchymal cell, Phenobarbital, 14 days

growth_protocol: Male C57BL/6N mice were obtained from Harlan Laboratories (USA). They were kept under standardized SPF-conditions. All experiments were approved by the “Committee of Animal Protection” of the Austrian government and performed according to  Austrian regulations.

treatment_protocol: Phenobarbital (Sigma 50mg/kg bw) was administered via drinking water for a period of 14 days. Controls received tap water only.

value: Phenobarbital

value: 50 mg/kg

value: 14 days


title: STD_T1_rep3


title: STD_T3_rep3


title: MC_H2O_3

source_name: Mesenchymal cell, vehicle, 14 days

value: vehicle

value: 0 mg/kg


title: STD_T3_rep2


title: HC_PB_3

source_name: Hepatocytes, Phenobarbital, 14 days

value: Hepatocytes


title: STD_T6_rep1


title: STD_T3_rep1


title: STD_T6_rep2


title: HC_PB_2


title: HC_PB_1


title: MC_PB_1


title: STD_T6_rep3


title: MC_PB_2


title: MC_H2O_1


title: MC_H2O_2


title: HC_H2O_2

source_name: Hepatocytes, vehicle, 14 days


title: HC_H2O_3


title: HC_H2O_1


title: PAA_T6_rep1

value: PAA-treated


title: PAA_T6_rep2


title: STD_T1_rep1


title: PAA_T1_rep2


title: PAA_T3_rep3


title: Western_diet_dabigatran_Replicate 0

city: East Lansing

first: James

last: Luyendyk

state: MI

address: 1129 Farm Lane

department: Pathobiology and Diagnostic Investigation

institute: Michigan State University

data_processing:
Raw BCL files are converted to fastQ files using the Illumina Casava software
The RNA sequence reads were mapped to the mouse reference transcriptome sequence (mm10) using TopHat version 2.0.4.
Parameters for TopHat included the --b2-fast, --transcriptome-only, and passing the refFlat.txt file through the –G parameter.
Differential expression was performed using the CuffDiff algorithm.
CummeRBund was used to visualize and categorize the data from CuffDiff into tables of differentially expressed genes using R (version 2.15.1).
Significant results are represented as fold change of HFD with dabigatran relative to HFD alone, with a q-value less than 0.05, where q-value is the false discovery rate (FDR) version of a p-value, such that a q-value <0.05 is equivalent to controlling the FDR at the 5% rate.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: FPKM files output from CuffDiff

source_name: Liver, High fat diet+dabigatran 3 months

extract_protocol:
Total RNA was isolated from approximately 50 mg of snap frozen liver using TRI Reagent (Molecular Research Center) per the manufacturers instructions
The RNA-seq library preparation was performed using the TruSeq RNA Sample Preparation Kit (illumina FC-122-1001).

value: liver

value: High fat diet+dabigatran 3 months


title: PAA_T3_rep1


title: PAA_T6_rep3


title: PAA_T3_rep2


title: Mice_High_Brain

city: Sapporo

first: Shouta

last: Nakayama

address: Kita18, Nishi9

institute: Hokkaido Univ

description:
Gene expression in high-dose brain
MHBr1

hyb_protocol: Gene Expression (GE) Hybridization Kit (Agilent Technologies) was used for labeling. 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse 8 x 60K ver.2.0 for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting (Agilent Technologies, Scan Resolution; 3 μm, TIFF file dynamic range; 20bit).

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

label: Cy 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from small pieces of liver, kidney, and brain soaked in RNAlater stabilizing solution (Sigma-Aldrich) using Nucleo spin (Takara bio, Shiga, Japan). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Two different concentrations of lead acetate (100 mg/L and 1,000 mg/L) were given to two of the groups (the low and high dosage groups, respectively) in the drinking water for three weeks. The control groups were provided with distilled water. Gene expression in the brain, kidney and liver of mice were examined.

value: Brain

value: male

tag: agent

value: lead acetate

tag: dose

value: High


title: Mice_Control_Kidney

description:
Gene expression in control kidney
MCKid1

value: Kidney

value: Control


title: Mice_High_Liver

description:
Gene expression in high-dose liver
MHLiv1

value: Liver


title: H32S

value: shallow roots


title: Mice_Control_Brain

description:
Gene expression in control brain
MCBr1


title: PAA_T1_rep1


title: Mice_Low_Brain

description:
Gene expression in low-dose brain
MLBr1

value: Low


title: liver biopsy 245

status: Public on Jul 11 2017

city: Lille

first: Lefebvre

last: Philippe

address: Bld Pr Jules Leclerc

institute: Inserm

hyb_protocol: Following fragmentation, 5.5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip®Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: NASH liver baseline

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Clean-up RNA with DNAse treatment were performed with Rneasy microkit Qiagen according to the manufacturer's instructions

tag: sample name

value: patient 245

tag: liver status

value: NASH

tag: type of intervention

value: Diet

tag: time

value: baseline

tag: age

value: female

tag: scan date

value: liver biopsy


title: Mice_Low_Kidney

description:
Gene expression in low-dose kidney
MLKid1


title: liver biopsy 247

source_name: no NASH liver baseline

value: patient 247

value: no NASH

value: BS


title: liver biopsy 236

value: patient 236

value: male


title: Mice_High_Kidney

description:
Gene expression in high-dose kidney
MHKid1

value: lead acetate

value: High


title: liver biopsy 244 (230)

source_name: no NASH liver follow-up

value: follow-up


title: liver biopsy 240

value: patient 240


title: liver biopsy 239

value: patient 239


title: liver biopsy 237

value: patient 237


title: liver biopsy 243

value: patient 243


title: liver biopsy 238

value: patient 238

value: NASH


title: Mice_Control_Liver

description:
Gene expression in control liver
MCLiv1

value: Liver

value: Control


title: liver biopsy 241

value: patient 241

value: baseline

value: female

value: liver biopsy


title: liver biopsy 235

value: patient 235

value: BS


title: liver biopsy 232

value: patient 232

value: no NASH


title: liver biopsy 230

value: patient 230


title: liver biopsy 231

value: patient 231

value: male


title: liver biopsy 234

value: patient 234


title: liver biopsy 229

value: patient 229


title: liver biopsy 227

value: patient 227

value: Diet


title: liver biopsy 225

value: patient 225


title: liver biopsy 228

value: patient 228

value: NASH


title: liver biopsy 233

value: patient 233

value: baseline


title: liver biopsy 222

value: patient 222

value: female

value: liver biopsy


title: liver biopsy 223

value: patient 223


title: liver biopsy 224

value: patient 224

value: no NASH

value: BS


title: liver biopsy 220

value: patient 220

value: male


title: liver biopsy 217

value: patient 217

value: follow-up


title: liver biopsy 221

value: patient 221

value: Diet


title: liver biopsy 226

value: patient 226


title: liver biopsy 218

value: patient 218

value: NASH


title: liver biopsy 214

value: patient 214

value: baseline


title: liver biopsy 210

value: patient 210


title: liver biopsy 206

value: patient 206

value: female

value: liver biopsy


title: liver biopsy 216

value: patient 216

value: no NASH


title: liver biopsy 219

value: patient 219


title: liver biopsy 209

value: patient 209

value: BS

value: male


title: liver biopsy 201

value: patient 201


title: liver biopsy 207

value: patient 207

value: Diet


title: liver biopsy 213

value: patient 213


title: liver biopsy 208

value: patient 208

value: NASH


title: liver biopsy 198 (164)

value: follow-up


title: liver biopsy 197

value: patient 197

value: baseline


title: liver biopsy 203

value: patient 203


title: liver biopsy 215

value: patient 215

value: female

value: liver biopsy


title: liver biopsy 196

value: patient 196


title: liver biopsy 212

value: patient 212


title: liver biopsy 204

value: patient 204

value: BS


title: liver biopsy 192

value: patient 192


title: liver biopsy 199 (156)

value: no NASH


title: liver biopsy 185

value: patient 185

value: Diet


title: liver biopsy 194

value: patient 194

value: male


title: liver biopsy 187

value: patient 187

value: NASH


title: liver biopsy 184

value: patient 184

value: baseline


title: liver biopsy 186

value: patient 186


title: liver biopsy 181

value: patient 181

value: female


title: liver biopsy 182

value: patient 182

value: liver biopsy


title: liver biopsy 180

value: patient 180

value: follow-up


title: liver biopsy 189 (151)

value: BS


title: liver biopsy 190

value: patient 190

value: no NASH


title: liver biopsy 179

value: patient 179


title: liver biopsy 177

value: patient 177


title: liver biopsy 178

value: patient 178

value: male


title: liver biopsy 193 (139)


title: liver biopsy 175

value: patient 175

value: NASH


title: liver biopsy 176

value: patient 176

value: Diet

value: baseline


title: liver biopsy 171 (212)

value: female


title: liver biopsy 174

value: patient 174


title: liver biopsy 173

value: patient 173

value: liver biopsy


title: liver biopsy 168 (220)

value: follow-up


title: liver biopsy 169 (237)

source_name: NASH liver follow-up


title: liver biopsy 172

value: patient 172

value: BS


title: liver biopsy 165 (213)


title: liver biopsy 166

value: patient 166

value: no NASH


title: liver biopsy 170

value: patient 170


title: liver biopsy 162

value: patient 162


title: liver biopsy 159

value: patient 159

value: male


title: liver biopsy 160

value: patient 160

value: NASH


title: liver biopsy 163

value: patient 163

value: Diet


title: liver biopsy 157

value: patient 157

value: baseline


title: liver biopsy 152

value: patient 152

value: female


title: liver biopsy 156

value: patient 156

value: liver biopsy


title: liver biopsy 151

value: patient 151

value: BS


title: liver biopsy 161

value: patient 161

value: no NASH


title: liver biopsy 149

value: patient 149


title: liver biopsy 155

value: patient 155


title: liver biopsy 148

value: patient 148


title: liver biopsy 150

value: patient 150


title: liver biopsy 164

value: patient 164

value: NASH


title: liver biopsy 146

value: patient 146


title: liver biopsy 158

value: patient 158


title: liver biopsy 153

value: patient 153

value: baseline

value: male


title: liver biopsy 145

value: patient 145


title: liver biopsy 142 (160)

value: follow-up

value: liver biopsy


title: liver biopsy 147

value: patient 147

value: Diet

value: female


title: liver biopsy 167

value: patient 167

value: no NASH


title: liver biopsy 139

value: patient 139

value: BS


title: liver biopsy 141

value: patient 141


title: liver biopsy 144 (208)


title: liver biopsy 138

value: patient 138

value: NASH


title: liver biopsy 136

value: patient 136


title: liver biopsy 134

value: patient 134


title: liver biopsy 137

value: patient 137

value: baseline


title: liver biopsy 132 (133)

value: male


title: liver biopsy 135

value: patient 135


title: liver biopsy 133

value: patient 133

value: liver biopsy


title: liver biopsy 195

value: patient 195

value: Diet


title: liver biopsy 131

value: patient 131

value: female


title: liver biopsy 126

value: patient 126


title: liver biopsy 129 (26)

value: patient 129 (26)

value: no NASH

value: BS

value: follow-up


title: liver biopsy 140

value: patient 140

value: NASH


title: liver biopsy 128

value: patient 128


title: liver biopsy 127 (136)


title: liver biopsy 125 (124)


title: liver biopsy 143

value: patient 143

value: baseline


title: liver biopsy 124

source_name: undefined liver baseline

value: patient 124

value: undefined


title: liver biopsy 119

value: patient 119

value: liver biopsy


title: liver biopsy 115 (90)

value: patient 115 (90)

value: male


title: liver biopsy 118 (128)

value: Diet

value: female


title: liver biopsy 123 (99)

value: patient 123 (99)


title: liver biopsy 112

value: patient 112

value: no NASH


title: liver biopsy 116

value: patient 116


title: liver biopsy 121

value: patient 121

value: BS


title: liver biopsy 113

value: patient 113

value: NASH


title: liver biopsy 109

value: patient 109

value: baseline


title: liver biopsy 111 (108)

value: follow-up


title: liver biopsy 117

value: patient 117


title: liver biopsy 105 (126)

value: liver biopsy


title: liver biopsy 110

value: patient 110


title: liver biopsy 102

value: patient 102


title: liver biopsy 106 (83)

value: patient 106 (83)

value: Diet


title: liver biopsy 107

value: patient 107

value: undefined

value: male


title: liver biopsy 104

value: patient 104

value: no NASH

value: female


title: liver biopsy 188

value: patient 188

value: BS


title: liver biopsy 183

value: patient 183

value: NASH


title: liver biopsy 103

value: patient 103

value: baseline


title: liver biopsy 96 (74)

value: patient 96 (74)

value: follow-up

value: liver biopsy


title: liver biopsy 97

value: patient 97


title: liver biopsy 100

value: patient 100


title: liver biopsy 94

value: patient 94

value: Diet


title: liver biopsy 101 (121)


title: liver biopsy 99

value: patient 99


title: liver biopsy 108

value: patient 108


title: liver biopsy 98

value: patient 98

value: male


title: liver biopsy 95

value: patient 95

value: no NASH

value: female


title: liver biopsy 87

value: patient 87


title: liver biopsy 93 (137)

value: patient 93 (137)

value: NASH


title: liver biopsy 85

value: patient 85

value: baseline


title: liver biopsy 84

value: patient 84

value: liver biopsy


title: liver biopsy 91

value: patient 91


title: liver biopsy 86 (112)

value: patient 86 (112)

value: BS

value: follow-up


title: liver biopsy 92 (91)

value: patient 92 (91)

value: Diet


title: liver biopsy 88

value: patient 88

value: male


title: liver biopsy 90

value: patient 90


title: liver biopsy 83

value: patient 83

value: female


title: liver biopsy 81 (22)

source_name: undefined liver follow-up

value: patient 81 (22)

value: undefined


title: liver biopsy 76 (77)

value: patient 76 (77)

value: no NASH


title: liver biopsy 75 (25)

value: patient 75 (25)

value: NASH


title: liver biopsy 82

value: patient 82

value: liver biopsy


title: liver biopsy 89 (59)

value: patient 89 (59)

value: BS


title: liver biopsy 77

value: patient 77

value: baseline


title: liver biopsy 79 (37)

value: patient 79 (37)

value: Diet

value: follow-up


title: liver biopsy 71 (34)

value: patient 71 (34)


title: liver biopsy 72 (21)

value: patient 72 (21)

value: male


title: liver biopsy 68

value: patient 68

value: female


title: liver biopsy 67

value: patient 67

value: no NASH


title: liver biopsy 80 (2)

value: patient 80 (2)


title: liver biopsy 70

value: patient 70


title: liver biopsy 66

value: patient 66

value: liver biopsy


title: liver biopsy 74

value: patient 74

value: NASH


title: liver biopsy 64 (117)

value: patient 64 (117)

value: BS


title: liver biopsy 60 (46)

value: patient 60 (46)

value: Diet


title: liver biopsy 57

value: patient 57

value: baseline


title: liver biopsy 62 (116)

value: patient 62 (116)

value: follow-up


title: liver biopsy 69

value: patient 69

value: female


title: liver biopsy 58 (113)

value: patient 58 (113)

value: male


title: liver biopsy 59

value: patient 59


title: liver biopsy 56

value: patient 56

value: no NASH


title: liver biopsy 47 (97)

value: patient 47 (97)

value: liver biopsy


title: liver biopsy 54

value: patient 54

value: NASH


title: liver biopsy 45

value: patient 45


title: liver biopsy 51

value: patient 51

value: Diet


title: liver biopsy 46

value: patient 46

value: baseline


title: liver biopsy 52

value: patient 52

value: BS

value: follow-up


title: liver biopsy 49

value: patient 49

value: female


title: liver biopsy 48 (135)

value: patient 48 (135)

value: male


title: liver biopsy 63 (30)

value: patient 63 (30)


title: liver biopsy 55 (29)

value: patient 55 (29)

value: no NASH


title: liver biopsy 50

value: patient 50

value: liver biopsy


title: liver biopsy 61

value: patient 61


title: liver biopsy 53

value: patient 53

value: NASH


title: liver biopsy 44

value: patient 44


title: liver biopsy 41

value: patient 41

value: baseline


title: liver biopsy 42

value: patient 42

value: BS


title: liver biopsy 37

value: patient 37

value: Diet


title: liver biopsy 38

value: patient 38


title: liver biopsy 43 (70)

value: patient 43 (70)

value: follow-up

value: female


title: liver biopsy 35 (17)

value: patient 35 (17)


title: liver biopsy 40 (57)

value: patient 40 (57)


title: liver biopsy 34

value: patient 34

value: no NASH

value: liver biopsy


title: liver biopsy 32 (109)

value: patient 32 (109)

value: male


title: liver biopsy 39 (53)

value: patient 39 (53)

value: NASH


title: liver biopsy 31 (95)

value: patient 31 (95)


title: liver biopsy 33

value: patient 33

value: baseline


title: liver biopsy 30

value: patient 30

value: Diet


title: liver biopsy 28 (41)

value: patient 28 (41)

value: BS


title: liver biopsy 22

value: patient 22


title: liver biopsy 19 (69)

value: patient 19 (69)

value: follow-up

value: female


title: liver biopsy 23

value: patient 23

value: no NASH


title: liver biopsy 27 (13)

value: patient 27 (13)

value: liver biopsy


title: liver biopsy 24 (33)

value: patient 24 (33)


title: liver biopsy 21

value: patient 21

value: male


title: liver biopsy 29

value: patient 29


title: liver biopsy 114 (131)


title: liver biopsy 18

value: patient 18

value: NASH

value: baseline


title: liver biopsy 20 (107)

value: patient 20 (107)

value: undefined

value: Diet


title: liver biopsy 26

value: patient 26

value: BS


title: liver biopsy 16 (94)

value: patient 16 (94)

value: follow-up


title: liver biopsy 9

value: patient 9

value: female


title: liver biopsy 17

value: patient 17

value: no NASH

value: liver biopsy


title: liver biopsy 13

value: patient 13


title: liver biopsy 11

value: patient 11

value: male


title: liver biopsy 1

value: patient 1


title: liver biopsy 12 (42)

value: patient 12 (42)


title: liver biopsy 6

value: patient 6

value: NASH

value: baseline


title: liver biopsy 4

value: patient 4


title: liver biopsy 7 (9)

value: patient 7 (9)

value: Diet


title: liver biopsy 15 (45)

value: patient 15 (45)

value: follow-up


title: liver biopsy 8 (1)

value: patient 8 (1)

value: BS

value: female


title: liver biopsy 25

value: patient 25

value: liver biopsy


title: liver biopsy 2

value: patient 2


title: liver biopsy 3

value: patient 3

value: no NASH