title: TN8

city: Brussels

first: Eric

middle: Stephane

last: Raspe

address: 808, route de Lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

description: Gene expression data from breast tumor sample

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG133 Plus 2 Array, Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner GCS3000.

data_processing:
The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization as impletemented in the R/Bioconductor package frma.
The asfRMA option of the fRMA R package was used. In this option, only the probes common to GPL570 and GPL96 are considered.

source_name: Breast tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (HuGen U133 Plus 2 array, Affymetrix).

growth_protocol: Not applicable

treatment_protocol: Not applicable

tag: grade

tag: er

tag: pr

tag: cellularity

value: breast cancer tumor

tag: molecular subtype

value: TN


title: Barley-2leaf-negative-rep1

status: Public on Jan 01 2017

type: RNA

city: Canberra

first: Ben

last: Trevaskis

state: ACT

address: Clunies Ross Drive

department: Plant Industry

country: Australia

institute: CSIRO

description:
Sibling null control
af1c4168-1-a1-190312

hyb_protocol: Hybridization performed by Australian Genome Research Facility according to AFFYMETRIX protocols

scan_protocol: Scanning performed by Australian Genome Research Facility according to AFFYMETRIX protocols

data_processing: Data was processed in R, using the Bioconductor suite, RNA normalization.

label: biotin

molecule: total RNA

organism: Hordeum vulgare

label_protocol: Labelling performed by Australian Genome Research Facility according to AFFYMETRIX protocols

growth_protocol: Glasshouse, avg temperature 20 degrees, 16 hours light

extract_protocol: Pine Tree extraction method (Chang 1993), followed by Qiagen RNAeasy column clean-up step.

tag: genotype/variation

value: control

tag: tissue

value: seedling (minus roots, at the 2-leaf stage)


title: Barley-2leaf-positive-rep3

description:
VRN1-HA transgene
af1c4168-6-b3-190312

value: VRN1-HA transgene


title: Barley-2leaf-negative-rep3

description:
Sibling null control
af1c4168-3-a3-190312


title: LumB4

organism: Homo sapiens

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

value: LumB


title: TN1


title: Barley-2leaf-positive-rep2

description:
VRN1-HA transgene
af1c4168-5-b2-190312


title: LumB9


title: TN5


title: TN2


title: LumB8


title: TN4


title: LumB10


title: Barley-2leaf-positive-rep1

description:
VRN1-HA transgene
af1c4168-4-b1-190312


title: TN7


title: LumB5


title: TN10


title: LumB3


title: LumA7

value: LumA


title: TN6


title: LumB1


title: LumB7


title: Barley-2leaf-negative-rep2

description:
Sibling null control
af1c4168-2-a2-190312


title: TN9


title: LumA4


title: LumA3


title: TN3


title: LumA9


title: LumB6


title: LumA8


title: Her2_6


title: Her2_8


title: Her2_4


title: Her2_7


title: Her2_3


title: ZR751

description: Gene expression data from breast cancer cell lines

data_processing:
The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization as implemented in the R/Bioconductor package frma.
The asfRMA option of the fRMA R package was used. In this option, only the probes common to GPL570 and GPL96 are considered.

source_name: ATCC

growth_protocol: Cells lines were cultured in the indicated medium and split following the indicated ratios (see characteristics). Cells were incubated in 10-cm petri dishes at 37 ºC at 5% CO2 until 70% confluency was reached. Pellets were harvested, flash frozen, and stored at -80 ºC for no more than one week until nucleic acid extraction.

treatment_protocol: Cells were kept in normal culture medium without treatment.

tag: cell line

value: ZR751 breast cancer cell line

tag: culture medium used

value: RPMI 10% serum

tag: split ratio

value: 1 out of 3


title: T47D

value: T47D breast cancer cell line

value: Lum


title: MDAMB134VI

value: MDAMB134VI breast cancer cell line


title: BT20

value: BT20 breast cancer cell line

value: DMEM 10 % serum

value: Basal


title: Her2_2


title: HCC38

value: HCC38 breast cancer cell line


title: SKBR3

value: SKBR3 breast cancer cell line


title: MDAMB436

value: MDAMB436 breast cancer cell line

value: 1 out of 5


title: HCC1500

value: HCC1500 breast cancer cell line


title: HCC1937

value: HCC1937 breast cancer cell line


title: [a] MPCCs_7day_DMSO (II)

city: Chicago

first: Brenton

middle: Robert

last: Ware

state: IL

address: 851 S Morgan St

department: Biomedical Engineering

country: USA

institute: University of Illinois at Chicago

description: Gene expression data from MPCCs treated with 0.1% DMSO for 7 days.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 microarray following manufacturer protocols.

scan_protocol: GeneChips were scanned using the Agilent Microarray Scanner BA.

data_processing: The data were normalized, modeled, and compared using the DNA Chip (dChip) Analyzer software.  Data from all chips were normalized to MPCCs treated with DMSO for 7 days (invariant set normalization).  Probe sets marked as 'present' on the 3T3-J2-only control chip were omitted from further analysis. Differentially expressed genes at each time-point were defined as those transcripts with |fold change| > 2.0 and |difference in expression| > 100 in drug-treated MPCCs relative to DMSO-only controls.

label: Biotin

source_name: MPCCs treated with DMSO for 7 days

label_protocol: Biotinylated cRNA was synthesized using the BioArray HighYield RNA Transcript Labeling Kit, purified over RNeasy columns (Qiagen), eluted, and then fragmented.

extract_protocol: Total RNA was extracted from cultures with the Rneasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

value: Plated cells

tag: treatment

value: 0.1% DMSO

tag: duration

value: 7 days


title: BT474

value: BT474 breast cancer cell line

value: RPMI 10% serum


title: Her2_1

value: breast cancer tumor


title: HCC1954

value: HCC1954 breast cancer cell line


title: HCC202

value: HCC202 breast cancer cell line

value: 1 out of 2


title: MDAMB361

value: MDAMB361 breast cancer cell line

value: DMEM 10 % serum

value: 1 out of 3


title: BT549

value: BT549 breast cancer cell line

value: Basal


title: HCC1806

value: HCC1806 breast cancer cell line

value: 1 out of 5


title: MCF7

value: MCF7 breast cancer cell line

value: Lum


title: MDAMB231

value: MDAMB231 breast cancer cell line


title: [a] MPCCs_7day_troglitazone (II)

description: Gene expression data from MPCCs treated with 2.82 µg/mL troglitazone for 7 days.

source_name: MPCCs treated with troglitazone for 7 days

value: Plated cells

value: 2.82 µg/mL troglitazone

value: 7 days


title: [a] MPCCs_7day_rosiglitazone_elevated

description: Gene expression data from MPCCs treated with 2.82 µg/mL rosiglitazone for 7 days.

source_name: MPCCs treated with an elevated rosiglitazone dose for 7 days

value: 2.82 µg/mL rosiglitazone


title: HCC70

value: HCC70 breast cancer cell line

value: RPMI 10% serum

value: 1 out of 4


title: HCC1569

value: HCC1569 breast cancer cell line


title: MDAMB468

value: MDAMB468 breast cancer cell line

value: DMEM 10 % serum


title: [a] MPCCs_14day_troglitazone

description: Gene expression data from MPCCs treated with 2.82 µg/mL troglitazone for 14 days.

source_name: MPCCs treated with troglitazone for 14 days

value: 14 days


title: [a] MPCCs_14day_rosiglitazone

description: Gene expression data from MPCCs treated with 0.373 µg/mL rosiglitazone for 14 days.

source_name: MPCCs treated with rosiglitazone for 14 days

value: 0.373 µg/mL rosiglitazone


title: [a] MPCCs_7day_troglitazone


title: [a] MPCCs_14day_DMSO

description: Gene expression data from MPCCs treated with 0.1% DMSO for 14 days.

source_name: MPCCs treated with DMSO for 14 days

value: 0.1% DMSO


title: [a] MPCCs_24hr_troglitazone

description: Gene expression data from MPCCs treated with 2.82 µg/mL troglitazone for 24 hours.

source_name: MPCCs treated with troglitazone for 24 hours

value: 24 hours


title: [a] MPCCs_24hr_DMSO

description: Gene expression data from MPCCs treated with 0.1% DMSO for 24 hours.

source_name: MPCCs treated with DMSO for 24 hours


title: HT29_rho0n_Xenograft_rep3

city: Tokyo

first: Masaru

last: Koido

address: 4-6-1, Shirokanedai, Minato-ku

country: Japan

institute: Institute of Medical Science, The University of Tokyo

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C 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 GeneChip Scanner 3000.

data_processing: Normalization of microarray data was carried out using Frozen Robust Multiarray Analysis (fRMA) using the R package ‘frma’ (version 1.14.0) with default parameters.

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

growth_protocol: Cells were cultured in PRMI-1640 (WAKO, Osaka, Japan), supplemented with 10% heat-inactivated FBS and 100 ug/ml of kanamycin (growth medium). To culture rho0 cells, 50 ug/mL uridine (SIGMA, St. Louis, MO, USA) and 1mM sodium pyruvate (SIGMA) were supplemented in growth medium (rho0 growth medium). In order to compare rho0 cells with parental cells under the same conditions, parental cells were also cultured in rho0 growth medium after preculture.

extract_protocol: Total RNA was extracted from cultured cells using a QIAshredder (QIAGEN, CA, USA) and RNeasy Mini Kit (QIAGEN, CA, USA).

treatment_protocol: AnaeroPack-Kenki 5% (Mitsubishi Gas Chemical, Tokyo, Japan) was used to create an hypoxic condition in an AnaeroPack-Rectangular Jar 2.5L (Mitsubishi Gas Chemical). Bortezomib (Millennium Pharmaceuticals) was used at the concentration of 100 nM.

value: HT-29 rho0n

tag: culture

value: xenograft

tag: stress

tag: mtdna

value: deficient


title: HT29_rho0x_Xenograft_rep2

value: HT-29 rho0x


title: [a] MPCCs_7day_rosiglitazone

description: Gene expression data from MPCCs treated with 0.373 µg/mL rosiglitazone for 7 days.

source_name: MPCCs treated with rosiglitazone for 7 days

value: Plated cells


title: HT29_rho0x_Xenograft_rep1


title: HT29_rho0n_Xenograft_rep2


title: Guadecitabine 3

city: Urbana

first: Michael

last: Spinella

address: 2001 South Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois

description: Guadecitabine treated 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GenomeStudio

source_name: Excised cell line xenograft tumor_Guadecitabine

label_protocol: Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illunima arrays

extract_protocol: Tumor was dissected free from stroma and mouse tissue.  RNA was extracted using an RNAeasy Mini Kit (Qiagen) and quality control was performed with the Agilent Bioanalyzer and RNA quantitated by Qubit (Thermo Fisher)

treatment_protocol: Mice with tumors were treated either with PBS or drug as indicated for each sample.

value: Xenograft from human testicular cancer cell line NT2/D1-R1


title: HT29_Xenograft_rep2

value: wild


title: [a] MPCCs_7day_DMSO

value: 7 days


title: HT29_Xenograft_rep1


title: HT29_rho0x_HYP_18h

source_name: HT29_rho0x_HYP, 18h

value: vitro

value: HYP


title: Guadecitabine 2

description: Guadecitabine treated 2


title: Control treated 1

description: Control treated 1

source_name: Excised cell line xenograft tumor_control


title: Control treated 3

description: Control treated 3


title: Control treated 2

description: Control treated 2


title: U266 JP11646 200 nM for 24 h_3

city: Bethesda

first: Jayakumar

middle: R

last: Nair

state: MD

address: 10 center drive

department: Women malignancies Branch

institute: National Cancer Institute

description:
Multiple myeloma - treated with JP11646 200 nM
U266-24hLC50_3

hyb_protocol: According to Genomics facility at Roswell Park Cancer Institute protocol.

data_processing:
Gene expression values for each gene (average of all the probesets) was normalized, quantile transformed and background corrected:
GSGX Version: 1.9.0
Report Date: 42069.456087963
Project: Lee_FINAL_030615
Group Set: all
Analysis: all_quantile_bkgd
Normalization: quantile

source_name: Cell line

growth_protocol: Cell lines were maintained in RPMI 1640 media (Mediatech Inc, Manassas, VA) containing 10% FBS (Hyclone Inc., Logan, UT), 1000 U/ml penicillin/streptomycin, 4 mM L-glutamine, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate. Recombinant IL-6 was purchased from R&D Systems (Minneapolis, MN).

treatment_protocol: JP11646 was made up as 10 mM stocks in DMSO and diluted in media before use.  Cells were harvested, washed and treated with LC50 concentrations of the drug for 24 hours, harvested and RNA used for hybridization to Illumina gene expression arrays.

value: MM cell line U266

tag: agent

tag: dose


title: U266 JP11646 200 nM for 24 h_1

description:
Multiple myeloma - treated with JP11646 200 nM
U266-24hLC50_1

scan_protocol: According to Genomics facility at Roswell Park Cancer Institute protocol.


title: HT29_rho0n_NOR_18h

source_name: HT29_rho0n_NOR, 18h


title: [a] MPCCs_24hr_rosiglitazone

description: Gene expression data from MPCCs treated with 0.373 µg/mL rosiglitazone for 24 hours.

source_name: MPCCs treated with rosiglitazone for 24 hours


title: Guadecitabine 1

description: Guadecitabine treated 1


title: HT29_rho0n_HYP_18h

source_name: HT29_rho0n_HYP, 18h


title: HT29_rho0x_NOR18h

source_name: HT29_rho0x_NOR, 18h


title: U266 JP11646 200 nM for 24 h_2

description:
Multiple myeloma - treated with JP11646 200 nM
U266-24hLC50_2

label_protocol: According to Genomics facility at Roswell Park Cancer Institute protocol.


title: [a] embryo at T0, biological rep1

description: Gene expression data from pure 3T3-J2 fibroblasts before inclusion in MPCCs.

source_name: Pure 3T3-J2s for background


title: U266 untreated_3

description:
Multiple myeloma - untreated
U266-con_3

extract_protocol: According to Genomics facility at Roswell Park Cancer Institute protocol.

value: untreated


title: HT29_rho0n_Xenograft_rep1


title: HT29_Pt_NOR_18h

source_name: HT29_NOR, 18h


title: U266 untreated_2

description:
Multiple myeloma - untreated
U266-con_2


title: U266 untreated_1

description:
Multiple myeloma - untreated
U266-con_1


title: MM1.S JP11646 20 nM for 24 h_3

description:
Multiple myeloma - treated with JP11646 20 nM for 24 hrs
MM1S-24hLC50_3

value: MM cell line MM.1S

value: 20 nM


title: MM1.S JP11646 20 nM for 24 h_1

description:
Multiple myeloma - treated with JP11646 20 nM for 24 hrs
MM1S-24hLC50_1


title: HT29_NOR_18h

description:
This sample is acquired in the series of  experiment using BZM.
GR_HT29_Cont_18h


title: MM1.S untreated_3

description:
Multiple myeloma - untreated
MM1S-con_3


title: HT29_HYP_18h

description:
This sample is acquired in the series of  experiment using BZM.
GR_HT29_Hypoxia_18h

source_name: HT29_HYP, 18h


title: OCI-Ly7_V3

city: Houston

first: R. Eric

last: Davis

state: Texas

address: 1515 Holcombe Blvd, Unit 0903

department: Lymphoma and Myeloma

institute: The UT MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

label_protocol: 300 ng of total RNA was reverse-transcribed, amplified, and biotin-labeled using an Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: Cell lines were cultured at 37°C with 5% CO2 in RPMI media with L-glutamine supplemented with: Fetal Bovine Serum (final concentration 10%), HEPES buffer (final concentration 20 mM), sodium pyruvate (final concentration 1 mM), gentamicin (final concentration 10 µg/ml), and penicillin/streptomycin (final concentration 100 U/ml and 100 µg/ml, respectively). To create BCR KO cells, we electroporated CRISPR/Cas9 system plasmid pX330 expressing Cas9 protein and a guide RNA (gRNA) sequence. For each cell line, 3 to 4 different target sequences in the immunoglobulin heavy chain hypervariable region (indicated by HV) or constant region (indicated by C) were used as replicates. Control cells were either unmanipulated (indicated by WT in column B, and N/A in column H), or were electroporated with empty pX458 vector (expressing Cas9 and GFP without a gRNA, indicated by EV in column B, and N/A in column H), for sorting of GFP-positive cells as a control for cell handling.

extract_protocol: BCR KO cells were isolated from mixed cultures on day 4-7 after electroporation using flow cytometry-assisted cell sorting, and rested in cell culture for 1-7 days before harvest. EV cells underwent similar sorting to isolate GFP+ cells, and resting in parallel. Total RNA was isolated from harvested cells with the RNAqueous Total RNA Isolation Kit (Thermo Scientific, catalog#: AM1912) with subsequent RNA quality assessment using an Agilent 2100 Bioanalyzer.

tag: bcr ko/control

value: BCR KO

tag: used grna


title: OCI-Ly7_WT2

value: Control


title: MM1.S JP11646 20 nM for 24 h_2

description:
Multiple myeloma - treated with JP11646 20 nM for 24 hrs
MM1S-24hLC50_2


title: HT29_Pt_HYP_18h


title: MM1.S untreated_2

description:
Multiple myeloma - untreated
MM1S-con_2


title: MM1.S untreated_1

description:
Multiple myeloma - untreated
MM1S-con_1


title: SUDHL-4_GC5


title: KM04

city: Frankfurt

first: Evelyn

last: Ullrich

address: Theodor-Stern-Kai 7

department: Childrens Hospital

country: Germany

institute: Goethe University

description: Gene expression of freshly sorted NK cells.

hyb_protocol: GeneChip Hybridization, Wash and Stain.

scan_protocol: GeneChip Scan 3000 7G.

data_processing: RMA normalization algorithm was applied through the affy package from R. The limma package from R was used for statistical calculations.

source_name: bone marrow NK cells

label_protocol: 3' IVT Express.

growth_protocol: Prior to MoFlo sorting, single cell suspensions were stained with the following antibodies: FITC-conjugated anti-CD56 (HCD56) (Biolegend, San Diego, USA), PE-conjugated anti-CD16 (368) (Biolegend, San Diego, USA) APC-conjugated anti-CD3 (UCHT1) (Biolegend, San Diego, USA) PE-Cy7-conjugated anti-CD19 (HIB19) (Biolegend, San Diego, USA). NK cell purity, functional properties and subset distribution was analyzed by FACS Canto II (BD Biosciences, Heidelberg, Germany) and use of the FlowJo Software (Treestar, Ashland, Oregon, USA).

extract_protocol: RNA was isolated from freshly sorted NK subsets using the RNeasy Mini/Micro Kit (QIAGEN, Hilden, Germany) according to the manufacturer's instructions. RNA quality was checked using the Agilent 2100 Bioanalyzer.

value: bone marrow

tag: cell type

value: natural killer (NK) cells


title: KM03


title: OCI-Ly7_WT1


title: SUDHL-4_GC4


title: HT29_BZM_18h

value: BZM


title: KM05


title: OCI-Ly7_V4


title: HT29_BZM+HYP_18h

source_name: HT29_BZM_100nM+HYP, 18h

value: BZM+HYP


title: KM06


title: SUDHL-4_EV2


title: SUDHL-4_EV1


title: KM02


title: OCI-Ly7_V2


title: SUDHL-6_V2_B


title: SUDHL-6_V4


title: SUDHL-4_GC6


title: SUDHL-6_V3


title: SUDHL-6_EV2


title: SUDHL-6_V2_A


title: T06

source_name: thymus NK cells

value: thymus


title: KM01


title: OCI-Ly19_V3


title: SUDHL-6_EV1


title: T05


title: OCI-Ly19_V5


title: OCI-Ly19_WT2


title: T03


title: T04


title: T02


title: OCI-Ly19_V2


title: OCI-Ly19_V4


title: DB_GC5

value: DB


title: OCI-Ly19_WT1


title: T01


title: DB_GC4


title: DB_GC6


title: DB_WT2


title: DB_WT1_B


title: PB16

source_name: peripheral blood NK cells

value: peripheral blood


title: OCI-Ly8_MC5


title: OCI-Ly8_WT2


title: DB_WT1_A


title: OCI-Ly8_MC6


title: PB15


title: PB12


title: PB11


title: SUDHL-7_GC6


title: SUDHL-7_GC5


title: OCI-Ly8_MC4


title: PB10


title: SUDHL-7_WT2


title: SUDHL-10_EV2


title: SUDHL-10_GC4


title: OCI-Ly8_WT1


title: SUDHL-7_GC4


title: SUDHL-10_GC5


title: SUDHL-10_GC6


title: SUDHL-10_EV1


title: 1,25D3_1

city: La tronche

first: didier

last: wion

address: fortuné ferrini

country: France

institute: INSERM

description: Gene expression from brain pericytes cell culture with 1,25D3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Expression console Suite (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: cell culture of pericyte with 1,25D3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300ng total RNA.

growth_protocol: Cells were cultured on poly-lysine coated culture dishes.The growth medium for pericytes was made with Pericyte Basal Culture Medium supplemented with 2% fetal bovine serum, with Pericyte Cell Growth Supplement and with penicillin and streptomycin.

extract_protocol: Total RNA were extracted from Brain pericyte with MirVana Isolation kit (according to the manufacter's instructions).

treatment_protocol: Cells were treated 24hours with 1.25D3 at 10 -8 M

tag: cells

value: Brain pericytes

value: 24 hours with 1.25D3 at 10 -8 M


title: PB09


title: Control_2

description: Gene expression from brain pericytes cell culture

source_name: cell culture of pericyte without 1,25D3


title: SUDHL-7_WT1


title: OCI-Ly18_MC4


title: OCI-Ly18_MC5


title: 1,25D3_2


title: OCI-Ly18_EV1


title: OCI-Ly18_EV2


title: Pfeiffer_GC5

value: Pfeiffer


title: Pfeiffer_GC6


title: Control_1


title: Non Responder - sample 42

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description: Gene expression data from CRC patients at diagnosis

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

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: The data were normalized using R software [www.r-project.org] with BioConductor package [www.bioconductor.org] "affy" (RMA normalization).

source_name: Pre Treatment biopsies

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

growth_protocol: No growth protocols were used

extract_protocol: RNA was extracted by phenol/chloroform extraction (TRIzol; Invitrogen) prior to further purification by column chromatography (RNeasy Mini kit; Qiagen). RNA integrity was then assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol: Pre CRT research biopsies (2-3 mm3) were collected during the initial diagnostic endoscopy, immediately frozen and stored in a liquid nitrogen tank.

value: CRC sample

tag: disease state

value: Rectal cancer

tag: name

tag: age

tag: Sex

value: Male

tag: class

value: Non Responder


title: Pfeiffer_GC4

tag: cell line


title: Non Responder - sample 41

tag: tissue


title: Pfeiffer_EV2


title: Non Responder - sample 40


title: Pfeiffer_EV1


title: PDLF + KSV

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

description: SAMPLE 2

hyb_protocol: Hybridization using standard hybridization protocols from Illumina

scan_protocol: Standard Illumina protocols for HumanHT-12 chip v4.0 from Illumina using the Illumina BeadArray Reader

data_processing: The data were normalised using the cubic spline algorithm (GenomeStudio) and background removed with the GenomeStudio's Detection P-value algorithm

source_name: human periodontal ligament fibroblasts (PDLF)

label_protocol: cRNA was labeled with the TargetAmp Nano Labeling kit for Illumina Expression BeadChip (Epicentre Catalog Number TAN07924)

growth_protocol: These cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Mediatech) supplemented with 10% FBS, 10 mM HEPES (pH 7.5), 100 U/mL of penicillin, 100 μg/mL streptomycin, and 0.25 μg/mL amphotericin B.  All cells were cultured at 37°C in 5% CO2. All experiments were carried out using cells harvested at low (< 20) passages

extract_protocol: RNA was extracted using  RNeasy Mini kit (Qiagen) including the DNAseI treatment

treatment_protocol: The cells were infected by KSHV (MOI=10) for 48 h

value: periodontal ligament fibroblasts

tag: kshv infection status

value: KSV infected


title: OCI-Ly18_MC6

value: BCR KO


title: Non Responder - sample 39

value: Female


title: Non Responder - sample 36


title: PDLF

description: SAMPLE 1

value: Control (not infected)


title: HGF + KSV

description: SAMPLE 4

source_name: human gingival fibroblasts (HGF)

value: gingival fibroblasts


title: patient 10 Day 1

city: Westmead

first: Linda

last: Bendall

state: NSW

address: 176 Hawkesbury ave

department: Center for Cancer Research

institute: Westmead Millennium Institute

description: 10 d1

data_processing: Data were normalised with Average normalisation in Genome Studio

source_name: patient_after treatment

label_protocol: Samples labelled with TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip.

extract_protocol: Samples extracted using TRizol reagent (invitrogen) using manufacturers guidelines. Quality control was performed with Agilent Bioanalyser.

tag: diagnosis

value: Relapsed/Refractory Acute Lymphoblastic Leukemia

tag: patient id

value: patient 10

tag: time point

value: 24 hrs after treatment with everolimus


title: HGF

description: SAMPLE 3


title: patient 7 Day 1

description: 7 d1

value: patient 7

value: peripheral blood


title: patient 7 Day 0

description: 7 d0

source_name: patient_before treatment

value: before treatment with everolimus


title: Non Responder - sample 37


title: patient 6 Day 0

description: 6 d0

value: patient 6


title: Non Responder - sample 33

value: CRC sample


title: patient 9 Day 0

description: 9 d0

value: patient 9


title: Responder - sample 34

value: Rectal cancer

value: Male

value: Responder


title: patient 11 Day 1

description: 11 d1

value: patient 11


title: patient 9 Day 1

description: 9 d1


title: Non Responder - sample 35

value: Non Responder


title: patient 10 Day 0

description: 10 d0


title: Non Responder - sample 38


title: Responder - sample 31

value: Female


title: patient 11 Day 0

description: 11 d0


title: Responder - sample 30


title: patient 6 Day 1

description: 6 d1


title: Non Responder - sample 32


title: Non Responder - sample 25


title: Non Responder - sample 26


title: CD4 HIV+ Acute Treated 7

city: Cambridge

first: Xu

middle: G

last: Yu

state: Massachusetts

address: 400 Technology sqr

institute: Ragon Institute of MGH, MIT and Harvard

description:
AT7
long term HAART treated patient 7 after the acute phase of the infection

hyb_protocol: Illumina standard iSCAN protocol

scan_protocol: Illumina standard iSCAN protocol

data_processing: Quantile Normalized, Background Corrected (BeadStudio).

source_name: CD4 T cells

label_protocol: Illumina Whole Genome DASL assay per manufacturer protocol

extract_protocol: mirVana™ miRNA Isolation Kit, Ambion

value: CD4 T cells

tag: infection status

value: Acute Treated

tag: treatment

value: HAART


title: CD4 HIV+ Acute Treated 6

description:
AT6
long term HAART treated patient 6 after the acute phase of the infection


title: Responder - sample 29


title: CD4 HIV+ Acute Treated 5

description:
AT5
long term HAART treated patient 5 after the acute phase of the infection


title: CD4 HIV Elite Controller 7

description:
EC7
elite controllers 7

value: Elite Controller

value: NO Treatment


title: CD4 HIV Elite Controller 1

description:
EC1
elite controllers 1


title: CD4 HIV+ Acute Treated 2

description:
AT2
long term HAART treated patient 2 after the acute phase of the infection


title: CD4 HIV Elite Controller 3

description:
EC3
elite controllers 3


title: Responder - sample 24


title: Biological replicate of CD4 HIV Elite Controller 1

description:
EC1_rep
biological replicate of elite controllers 1


title: CD4 HIV+ Acute Treated 3

description:
AT3
long term HAART treated patient 3 after the acute phase of the infection


title: Responder - sample 28


title: CD4 HIV+ Acute Treated 8

description:
AT8
long term HAART treated patient 8 after the acute phase of the infection


title: CD4 HIV+ Acute Treated 4

description:
AT4
long term HAART treated patient 4after the acute phase of the infection


title: CD4 HIV Elite Controller 8

description:
EC8
elite controllers 8


title: CD4 HIV Elite Controller 10

description:
EC10
elite controllers 10


title: Biological replicate of CD4 HIV+ Acute Treated 3

description:
AT3_rep
biological replicate of long term HAART treated patient 3 after the acute phase of the infection


title: CD4 HIV Elite Controller 4

description:
EC4
elite controllers 4


title: CD4 HIV Elite Controller 6

description:
EC6
elite controllers 6


title: CD4 HIV+ Acute Treated 1

description:
AT1
long term HAART treated patient 1 after the acute phase of the infection


title: Responder - sample 22


title: CD4 HIV Elite Controller 9

description:
EC9
elite controllers 9


title: CD4 HIV Elite Controller 5

description:
EC5
elite controllers 5


title: Non Responder - sample 23


title: CD4 HIV+ Chronic Treated 7

description:
CT7
long term HAART treated patient 7 after the chronic phase of the infection

value: Chronic Treated


title: CD4 HIV Elite Controller 2

description:
EC2
elite controllers 2


title: CD4 HIV+ Chronic Treated 8

description:
CT8
long term HAART treated patient 8 after the chronic phase of the infection


title: Non Responder - sample 19


title: Responder - sample 20


title: CD4 HIV+ Chronic Treated 9

description:
CT9
long term HAART treated patient 9 after the chronic phase of the infection


title: CD4 HIV+ Chronic Treated 1

description:
CT1
long term HAART treated patient 1 after the chronic phase of the infection


title: CD4 HIV+ Chronic Treated 3

description:
CT3
long term HAART treated patient 3 after the chronic phase of the infection


title: CD4 HIV+ Chronic Treated 5

description:
CT5
long term HAART treated patient 5 after the chronic phase of the infection


title: Non Responder - sample 18

description: Gene expression data from CRC patients at diagnosis


title: Non Responder - sample 21


title: Non Responder - sample 27


title: Non Responder - sample 17


title: CD4 HIV+ Chronic Treated 2

description:
CT2
long term HAART treated patient 2 after the chronic phase of the infection


title: CD4 HIV+ Chronic Treated 10

description:
CT10
long term HAART treated patient 10 after the chronic phase of the infection


title: CD4 HIV+ Chronic Treated 4

description:
CT4
long term HAART treated patient 4 after the chronic phase of the infection


title: CD4 HIV+ Chronic Treated 6

description:
CT6
long term HAART treated patient 6 after the chronic phase of the infection


title: Responder - sample 16


title: Responder - sample 12


title: Responder - sample 11


title: siROR2_rep1

city: Wako

first: Kota

last: Tamada

state: Saitama

address: Hirosawa 2-1

department: BSI

institute: RIKEN

hyb_protocol: 10 ug of digoxigenin-labeled cRNA samples were fragmented for 30 min at 60℃ and hybridized for 16h to Human Genome Survey Microarrays V2.0 (Applied Biosystems) at a temperature of 55℃. After several washing steps of increasing stringency, an anti-digoxigenin-antibody conjugated to alkaline phosphatase (Roche Diagnostics) was added.

scan_protocol: Chemiluminescence and fluorescence signals were detected on an AB1700 microarray reader. Reagents from the Chemiluminescence Detection Kit (Applied Biosystems) were used in this procedure. Human Genome Survey Microarrays V2.0 feature numerous control probes and 32878 target gene specific 60 mer probes detecting more than 27000 different genes.

data_processing: Detectable probes were determined by a signal to noise ratio (S/N) > 3 and quality flag < 5,000 determined by the AB1700 microarray software tool. Global median normalization method was used for calculating the normalized value for each array.

label: Digoxigenin

source_name: SaOS2, osteosarcoma cell line

label_protocol: 1-2 ug total RNA were introduced into an RT-IVT reaction: the RNA was reverse-transcribed into ds-cDNA and then converted into labelled cRNA by in vitro transcription (Nano-Amp RT-IVT Labeling Kit, Applied Biosystems) using digoxigenin-conjugated UTP nucleotides (Roche).

growth_protocol: SaOS-2 cells were cultured in DMEM (Nissui, Tokyo, Japan) containing 10% (v/v) fetal bovine serum (FBS) (BioWest, Nuaillé, France).

extract_protocol: Total RNA was isolated from SaOS2 cells using SV total RNA Isolation Kit (Promega) according to the manufacturer’s instructions. The purity and integrity of the RNAs were assessed by the Agilent 2100 Bioanalyzer (Agilent Technologies) and the quantities were determined by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: For siRNA transfection, GeneSilencer siRNA Transfection Reagent (GenLantis, San Diego, CA) was used, according to the manufacturers’ instructions.

tag: sirna knock-down treatment

tag: trial


title: siCTL_rep1

value: siCTL


title: Responder - sample 14


title: Responder - sample 15


title: siROR2_rep2


title: siCTL_rep2


title: Responder - sample 13


title: Non Responder - sample 10


title: TT1

city: Graz

first: Silvija

last: Tokic

address: Auenbruggerplatz 14

country: Austria

institute: Medical University of Graz

description: total RNA

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw data were normalized globally and processed with Microarray Suite, version 5.0 (Affymetrix) and Data Mining Tool (Affymetrix) software.

source_name: Isolated and in vitro cultured placental trophoblasts

label_protocol: cDNA was synthesized with SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen); cDNA was in vitro transcribed with the RNA Transcript Labeling Kit from Enzo diagnostics

growth_protocol: Prior to microarray analysis 800,000 trophoblasts  in flasks (25 cm^²) using DMEM Medium with 5% FCS. Cells were cultured for 48 h at 21% O2/5% CO2 environment at 37°C.

extract_protocol: RNA isolation with TRI REAGENT according to manufacturer

tag: cell type

value: trophoblasts

value: placenta


title: TT2

description: total RNA


title: OA_patient_50

city: New York

first: Hua

last: Zhou

state: NY

address: 550 First Avenue, Smilow 1307

department: PATHOLOGY

institute: NYU SCHOOL OF MEDICINE

description: Gene expression data for OA patients

hyb_protocol: 20ug of cRNA was  fragmented at 95°C for 35 minutes, samples were hybridized against the Human Genome U133A microarray.

scan_protocol: Array scaning was performed following manufacturer's instructions(Affymetrix).

data_processing: Raw expression data from array scans were preprocessed using the Affy package from Bioconductor, normalized using the robust multichip average (RMA) method.  Genes with <70% reliable expression measurement were filtered out, leaving 8,700 genes for analysis.

source_name: Patient 50 with OA

label_protocol: Complementary RNA was synthesized using an Enzo kit (Affymetrix) and purified using the Qiagen Rneasy kit, 5 ug of total RNA was used.

growth_protocol: Blood samples were collected in pyrogen-free heparinized tubes for isolation of PBLs susing ficoll gradient. Blood samples were processed within 2hr of collection. Total number of cells were estimated and lysed in Trizol (1ml of TRIzol for 10 x7 cells) and stored immediately in -70C for RNA isolation at a later time.

extract_protocol: Total RNA from PBLs were isolated using Qiagen micro RNeasy column.

value: peripheral blood mononuclear cells

tag: phenotype

value: symptomatic knee osteroarthritis

tag: age at the time of collection

tag: gender

value: F

tag: bmi


title: OA_patient_48b

description: Gene expression data for OA patients

source_name: Patient 48b with OA

value: M


title: OA_patient_46

description: Gene expression data for OA patients

source_name: Patient 46 with OA


title: OA_patient_49

description: Gene expression data for OA patients

source_name: Patient 49 with OA


title: OA_patient_45

description: Gene expression data for OA patients

source_name: Patient 45 with OA


title: OA_patient_47

description: Gene expression data for OA patients

source_name: Patient 47 with OA


title: Non Responder - sample 7

value: CRC sample

tag: disease state

value: Rectal cancer

tag: name

tag: age

tag: Sex


title: OA_patient_44

description: Gene expression data for OA patients

source_name: Patient 44 with OA

tag: tissue


title: OA_patient_43

description: Gene expression data for OA patients

source_name: Patient 43 with OA


title: OA_patient_48a

description: Gene expression data for OA patients

source_name: Patient 48a with OA


title: Responder - sample 8

source_name: Pre Treatment biopsies

tag: class

value: Responder


title: Responder - sample 6

value: Female


title: Non Responder - sample 5

value: Non Responder


title: Non Responder - sample 9

value: Male


title: OA_patient_41

description: Gene expression data for OA patients

source_name: Patient 41 with OA


title: OA_patient_42

description: Gene expression data for OA patients

source_name: Patient 42 with OA


title: Responder - sample 4


title: OA_patient_35

description: Gene expression data for OA patients

source_name: Patient 35 with OA


title: Responder - sample 3


title: OA_patient_37

description: Gene expression data for OA patients

source_name: Patient 37 with OA


title: OA_patient_40

description: Gene expression data for OA patients

source_name: Patient 40 with OA


title: OA_patient_33

description: Gene expression data for OA patients

source_name: Patient 33 with OA


title: Non Responder - sample 2


title: OA_patient_39

description: Gene expression data for OA patients

source_name: Patient 39 with OA


title: OA_patient_38

description: Gene expression data for OA patients

source_name: Patient 38 with OA


title: OA_patient_34

description: Gene expression data for OA patients

source_name: Patient 34 with OA


title: Responder - sample 1


title: OA_patient_32

description: Gene expression data for OA patients

source_name: Patient 32 with OA


title: OA_patient_30

description: Gene expression data for OA patients

source_name: Patient 30 with OA


title: OA_patient_29

description: Gene expression data for OA patients

source_name: Patient 29 with OA


title: OA_patient_24

description: Gene expression data for OA patients

source_name: Patient 24 with OA


title: OA_patient_26

description: Gene expression data for OA patients

source_name: Patient 26 with OA


title: OA_patient_28

description: Gene expression data for OA patients

source_name: Patient 28 with OA


title: OA_patient_22

description: Gene expression data for OA patients

source_name: Patient 22 with OA


title: OA_patient_17

description: Gene expression data for OA patients

source_name: Patient 17 with OA


title: OA_patient_16

description: Gene expression data for OA patients

source_name: Patient 16 with OA


title: OA_patient_20

description: Gene expression data for OA patients

source_name: Patient 20 with OA


title: OA_patient_19

description: Gene expression data for OA patients

source_name: Patient 19 with OA


title: OA_patient_18

description: Gene expression data for OA patients

source_name: Patient 18 with OA


title: 0MONTH_PCB_CHILD-B9

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

description: Gene expression data from the Child with prenatal exposure of PCBs.

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

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 150.

source_name: 0 Month SLovak Child.

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

extract_protocol: Cord blood  (2.5cc) blood was collected for gene expression by needle aspiration of the fetal vessels on the fetal placental surface. Dripping the placental blood directly into the Collection Tube of PAXgene Blood RNA Kit IVD for total RNA extraction.

treatment_protocol: Child with Prenatal PCBs Exposure

value: male

value: 0 month child


title: OA_patient_21

description: Gene expression data for OA patients

source_name: Patient 21 with OA


title: OA_patient_23

description: Gene expression data for OA patients

source_name: Patient 23 with OA


title: 0MONTH_PCB_CHILD-B6


title: 0MONTH_PCB_CHILD-B10


title: 0MONTH_PCB_CHILD-B8


title: 0MONTH_PCB_CHILD-B11


title: 0MONTH_PCB_CHILD-B7


title: 0MONTH_PCB_CHILD-B12


title: 0MONTH_PCB_CHILD-B4


title: OA_patient_14

description: Gene expression data for OA patients

source_name: Patient 14 with OA


title: 0MONTH_PCB_CHILD-B5


title: OA_patient_15

description: Gene expression data for OA patients

source_name: Patient 15 with OA


title: OA_patient_25

description: Gene expression data for OA patients

source_name: Patient 25 with OA


title: WT - 21 mon, biological rep3

city: Guelph

first: Faisal

middle: James

last: Alibhai

state: ON

address: 50 Stone Rd East

department: Biomedical Sciences

country: Canada

institute: University of Guelph

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on miRNA 4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneSpring GX Software v. 11.5 using default Affymetrix settings.

organism: Mus musculus

source_name: WT - 21 mo

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA

growth_protocol: The mice were collected at 4 or 21 months of age at ZT 6 ( 6 hours into the light phase)

extract_protocol: Total RNA was extracted using the miRNeasy method according to the manufacturer's instructions.

treatment_protocol: The hearts were collected and snap frozen in liquid Nitrogen.

tag: background strain

tag: genotype/variation

value: Wild type

value: Ventricular


title: WT - 21 mon, biological rep2


title: OA_patient_13

description: Gene expression data for OA patients

source_name: Patient 13 with OA


title: OA_patient_6

description: Gene expression data for OA patients

source_name: Patient 06 with OA


title: OA_patient_10

description: Gene expression data for OA patients

source_name: Patient 10 with OA


title: WT - 21 mon, biological rep1

extract_protocol: Total RNA was extracted using the mIRNeasy method according to the manufacturer's instructions.


title: TT3

description: total RNA

source_name: Isolated and in vitro cultured placental trophoblasts


title: Clock Mutant - 21 mon, biological rep3

source_name: Clock - 21 mo

value: Clock delta 19/delta 19


title: 0MONTH_PCB_CHILD-B2


title: OA_patient_12

description: Gene expression data for OA patients

source_name: Patient 12 with OA


title: OA_patient_11

description: Gene expression data for OA patients

source_name: Patient 11 with OA


title: OA_patient_7

description: Gene expression data for OA patients

source_name: Patient 07 with OA


title: 0MONTH_PCB_CHILD-B3

value: female


title: Clock Mutant - 21 mon, biological rep2


title: OA_patient_3

description: Gene expression data for OA patients

source_name: Patient 03 with OA


title: OA_patient_5

description: Gene expression data for OA patients

source_name: Patient 05 with OA

value: missing


title: Non_OA_patient_31

description: Gene expression data for control patients

source_name: Patient 31 Control

value: peripheral blood mononuclear cells

value: control


title: 0MONTH_PCB_CHILD-B1

source_name: 0 Month SLovak Child.


title: 0MONTH_PCB_CHILD-G15


title: 0MONTH_PCB_CHILD-G17


title: 0MONTH_PCB_CHILD-G13


title: 0MONTH_PCB_CHILD-G14


title: OA_patient_2

description: Gene expression data for OA patients

source_name: Patient 02 with OA

value: symptomatic knee osteroarthritis

value: F


title: Clock Mutant - 21 mon, biological rep1


title: 0MONTH_PCB_CHILD-G12


title: WT - 4 mon, biological rep3

source_name: WT - 4 mo


title: 0MONTH_PCB_CHILD-G16


title: WT - 4 mon, biological rep2


title: Clock Mutant - 4 mon, biological rep3

source_name: Clock - 4 mo

value: ventricular


title: Non_OA_patient_30

source_name: Patient 30 Control


title: Clock Mutant - 4 mon, biological rep1


title: Non_OA_patient_29

source_name: Patient 29 Control


title: Clock Mutant - 4 mon, biological rep2


title: 0MONTH_PCB_CHILD-G9


title: Non_OA_patient_25

source_name: Patient 25 Control

value: M


title: Non_OA_patient_27

source_name: Patient 27 Control


title: 0MONTH_PCB_CHILD-G10


title: 0MONTH_PCB_CHILD-G5


title: Non_OA_patient_28

source_name: Patient 28 Control


title: Non_OA_patient_18

source_name: Patient 18 Control


title: Non_OA_patient_22

source_name: Patient 22 Control


title: 0MONTH_PCB_CHILD-G6


title: 0MONTH_PCB_CHILD-G7


title: 0MONTH_PCB_CHILD-G11


title: 0MONTH_PCB_CHILD-G8


title: Non_OA_patient_19

source_name: Patient 19 Control


title: Non_OA_patient_16

source_name: Patient 16 Control


title: 0MONTH_PCB_CHILD-G3


title: Non_OA_patient_23

source_name: Patient 23 Control


title: 0MONTH_PCB_CHILD-G4


title: 0MONTH_PCB_CHILD-G2


title: OA_patient_27

description: Gene expression data for OA patients

source_name: Patient 27 with OA


title: Non_OA_patient_14

source_name: Patient 14 Control


title: 0MONTH_PCB_CHILD-G1


title: Non_OA_patient_13

source_name: Patient 13 Control


title: Non_OA_patient_12

source_name: Patient 12 Control


title: Non_OA_patient_15

source_name: Patient 15 Control


title: CRC liver metastasis, patient 63

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Standard Illumina WG-DASL hybridization protocol

scan_protocol: Standard Illumina WG-DASL scanning protocol

data_processing: Scanned data were uploaded into GenomeStudio software version 2011.1 via the Whole Genome DASL gene expression module for further analysis. The average signal, detection P-value, Bead standard error and average beads were used to quantile normalize the data in the statistical language R (www.r-project.org) using the “lumi” package

source_name: Liver metastasis, FFPE

label_protocol: The WG-DASL assay was performed according to the manufacturer’s instructions.

extract_protocol: Depending on the size of the FFPE samples, total RNA was extracted from 3 to 6 x 20 μm sections. Following paraffin removal with xylene the high-pure RNA paraffin kit was used according the supplier's instructions (Roche, Mannheim, Germany). Following isolation, RNA was stored in RNase/DNase-free water at -80°C.

value: liver metastasis

tag: relapse

value: Yes <=12 months


title: Non_OA_patient_11

source_name: Patient 11 Control


title: CRC liver metastasis, patient 61

value: No >= 36 onths


title: CRC liver metastasis, patient 60


title: CRC liver metastasis, patient 59


title: Non_OA_patient_07

source_name: Patient 07 Control


title: Non_OA_patient_09

source_name: Patient 09 Control


title: CRC liver metastasis, patient 57


title: OA_patient_31

description: Gene expression data for OA patients

source_name: Patient 31 with OA


title: CRC liver metastasis, patient 62


title: Non_OA_patient_08

source_name: Patient 08 Control


title: Non_OA_patient_10

source_name: Patient 10 Control


title: Non_OA_patient_06

source_name: Patient 06 Control


title: CRC liver metastasis, patient 58


title: Non_OA_patient_03

source_name: Patient 03 Control


title: CRC liver metastasis, patient 54


title: CRC liver metastasis, patient 55


title: CRC liver metastasis, patient 56


title: CRC liver metastasis, patient 51


title: Non_OA_patient_04

source_name: Patient 04 Control


title: CRC liver metastasis, patient 49


title: CRC liver metastasis, patient 52


title: RLA4NL16

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description: Normal control

hyb_protocol: Hybridized to Affymetrix U133 2.0 microarrays as described in the Affymetrix GeneChip 3 IVT Express user manual

scan_protocol: Scanned using an Affymetrix GeneArray Scanner 3000 7G Plus

data_processing: CEL files were summarized using Affymetrix Expression Console (current version 1.1). CEL files were processed using Robust Multi-chip Average (RMA).

source_name: Human lung biopsy

label_protocol: Biotin-labeled amplified RNA was purified, fragmented as described in the Affymetrix GeneChip 3 IVT Express user manual

extract_protocol: Total RNA from human lung biopsy tissue was extracted using microRNeasy Mini Kits (Qiagen).

value: lung

value: Normal control

tag: patient


title: CRC liver metastasis, patient 46


title: CRC liver metastasis, patient 48


title: RLA3NL13

description: Normal control


title: Non_OA_patient_05

source_name: Patient 05 Control


title: RLA5SD01

description: SSc-ILD patient

value: SSc-ILD patient


title: CRC liver metastasis, patient 53


title: RLA2NL10

description: Normal control


title: CRC liver metastasis, patient 47


title: Non_OA_patient_02

source_name: Patient 02 Control


title: CRC liver metastasis, patient 50


title: Non_OA_patient_01

source_name: Patient 01 Control


title: RLA6SD05

description: SSc-ILD patient


title: RLA1NL09

description: Normal control


title: CRC liver metastasis, patient 45


title: RLA10SD11

description: SSc-ILD patient


title: WT - 4 mon, biological rep1

source_name: WT - 4 mo

value: Wild type


title: CRC liver metastasis, patient 44


title: RLA8SD07

description: SSc-ILD patient


title: CRC liver metastasis, patient 42


title: RLA7SD06

description: SSc-ILD patient


title: RLA9SD08

description: SSc-ILD patient


title: CRC liver metastasis, patient 43


title: RLA11SD13

description: SSc-ILD patient


title: CRC liver metastasis, patient 41


title: CRC liver metastasis, patient 40


title: CRC liver metastasis, patient 37


title: CRC liver metastasis, patient 38


title: RLB1SD17

description: SSc-ILD patient


title: UM-Chor1, IFN-gamma-treated, sample 3

first: Jacob

last: Richards

address: 10 Center Drive, Room 8B09, MSC 1750

description: Treated Sample 3

hyb_protocol: Three replicates of each group were hybridized to human Gene ST 2.0 GeneChip (Affymetrix)

scan_protocol: Samples were scanned on the GeneChip scanner 3000 (Affymetrix)

data_processing: Data were collected using Affymetrix AGCC software

source_name: UM-Chor1 cell line

label_protocol: Sense strand cDNA was fragmented and labeled using WT terminal labeling kit (Affymetrix, Santa Clara, CA)

growth_protocol: UM-Chor1 cells were maintained in Iscove’s modification of DMEM and RPMI1640 medium (4:1) supplemented with 10% fetal bovine serum, 1% of penicillin/streptomycin and non-essential amino acids

extract_protocol: total RNA was isolated using the RNAeasy Plus minikit (Qiagen, Valencia, CA)

treatment_protocol: UM-Chor1 cells were treated or untreated with 50 ng/mL of IFN-g for 24 hours

tag: cell line

tag: cancer

value: Chordoma


title: CRC liver metastasis, patient 39


title: RLA12SD14

description: SSc-ILD patient


title: RLB2SD22

description: SSc-ILD patient


title: KS vs DS

type: genomic

city: Hohhot

first: Li

last: Ru

address: Saihan Road 306

country: China

institute: Inner Mongolia University

description: CNV analysis of KS vs DS

hyb_protocol: Hybridization was processing overnight at 42°C in Roche-NimbleGen hybridization system12.

scan_protocol: Arrays were scanned on an Roche-NimbleGen MS200 scanner.

data_processing: Arrays were processed using NimbleScan,which transformed image signal to digital signal, following using segMNT algorithm to analyze the normalized signal ratio.

molecule: genomic DNA

organism: Ovis aries

source_name: KS DNA, adult female sheep

label_protocol: The sample labelling was using NimbleGen Dual-Color DNA Labeling Kit.

growth_protocol: adult female sheep

extract_protocol: The genomic DNA was extracted using the Axygen Genomic DNA Extraction Kit.

treatment_protocol: blood was directly dissected from sheep

tag: breed

value: Kazakh sheep

value: blood

source_name: DS DNA, adult female sheep

value: Dorper sheep


title: MS2 vs DS

description: CNV analysis of MS2 vs DS

source_name: MS2 DNA, adult female sheep

value: Mongolian sheep (from Mongolia)


title: RLB3SD23

description: SSc-ILD patient


title: CRC liver metastasis, patient 36

source_name: Liver metastasis, FFPE


title: UM-Chor1, untreated, sample 3

description: Sample Control 3


title: UM-Chor1, IFN-gamma-treated, sample 2

description: Treated Sample 2


title: CRC liver metastasis, patient 35


title: RLB4SD26

description: SSc-ILD patient


title: RLB6SD31

description: SSc-ILD patient


title: CRC liver metastasis, patient 34


title: TS vs DS

description: CNV analysis of TS vs DS

source_name: TS DNA, adult female sheep

value: Tibetan sheep


title: RLB5SD28

description: SSc-ILD patient


title: CRC liver metastasis, patient 33


title: MS1 vs DS

description: CNV analysis of MS1 vs DS

source_name: MS1 DNA, adult female sheep

value: Mongolian sheep (from Inner Mongolia of China)


title: HS vs DS

description: CNV analysis of HS vs DS

source_name: HS DNA, adult female sheep

value: Hu sheep


title: UM-Chor1, untreated, sample 2

description: Sample Control 2


title: CRC liver metastasis, patient 31


title: UM-Chor1, untreated, sample 1

description: Sample Control 1


title: UM-Chor1, IFN-gamma-treated, sample 1

description: Treated Sample 1


title: mutant intestinal stroma, biological rep2

city: Saint Louis

first: Ting-Lin

last: Yang

state: Missouri

address: 660 S. Euclid Ave., CB 8123

institute: Washington University of St Louis

description: Gene expression data from mTR-/- G4 intestinal stroma

hyb_protocol: 5.5 μg of labeled cDNA was hybridized to Mouse Gene 1.0ST GeneChips, stained with streptavidin-phycoerythrin

scan_protocol: GeneChips were visualized with the GeneChip 3000 7G scanner

data_processing: Affymetrix probe intensity (.cel) files were imported into Partek Genomics Suite (v6.6, Partek Inc., St. Louis, MO) where RMA normalization was applied.

source_name: Late-generation telomerase-deficient mus musculus intestinal stroma

label_protocol: All protocols were conducted as described in the Ambion WT Expression Manual and the Affymetrix GeneChip Expression Analysis Technical Manual, using 250 ng of total RNA for first-strand cDNA synthesis.

growth_protocol: Mice were housed in a standard animal care room with 12:12-h light-dark cycle with free access to food and water.

extract_protocol: Total RNA extraction was performed with the Qiagen miRNeasy Kit according to the manufacturer's instructions.

treatment_protocol: 8 cm of ileum was longitudinally cut and rinsed in cold PBS, followed by firm scraping of intestinal villi with hemacytometer coverslip, incubation in 10 ml 30 mM EDTA and 1.5 mM DTT in PBS on ice for 20 minutes. The intestine was transferred to 10 ml 30 mM EDTA in PBS at 37°C for 8 minutes, followed by 3 rounds of shaking per second for 30-40 seconds. The supernatant was centrifuged at 200 g for 1 minute at 4°C, followed by passage through a 70 μm cell strainer. The strained supernatant was spun down again at 130 g for 1 minute at 4°C to deplete single cells, and the crypt pellet was collected for RNA extraction. The remaining intestinal tissue is scraped with a coverslip to remove residual epithelial cells and is mechanically homogenized with a TissueRuptor (Qiagen) before RNA extraction.

value: Intestinal stroma

tag: genotype

value: mTR-/-

value: 6-8 month old


title: CRC liver metastasis, patient 32

value: liver metastasis


title: CRC liver metastasis, patient 27

value: Yes <=12 months


title: mutant intestinal stroma, biological rep3


title: wild-type intestinal stroma, biological rep2

description: Gene expression data from wild type intestinal stroma

source_name: Wild type mus musculus intestinal stroma


title: CRC liver metastasis, patient 26


title: CRC liver metastasis, patient 28

value: No >= 36 onths


title: mutant intestinal stroma, biological rep1


title: CRC liver metastasis, patient 30


title: CRC liver metastasis, patient 29


title: mutant intestinal crypt epithelium, biological rep3

description: Gene expression data from mTR-/- G4 intestinal crypt epithelium

source_name: Late-generation telomerase-deficient mus musculus intestinal crypt epithelium

value: Intestinal crypt epithelium


title: mutant intestinal crypt epithelium, biological rep2


title: CRC liver metastasis, patient 24


title: mutant intestinal stroma, biological rep4


title: CRC liver metastasis, patient 25


title: wild-type intestinal stroma, biological rep1


title: wild-type intestinal crypt epithelium, biological rep1

description: Gene expression data from wild type intestinal crypt epithelium

source_name: Wild type mus musculus intestinal crypt epithelium


title: CRC liver metastasis, patient 23


title: wild-type intestinal crypt epithelium, biological rep3


title: CRC liver metastasis, patient 21


title: CRC liver metastasis, patient 20


title: mutant intestinal crypt epithelium, biological rep1


title: tumoral8

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

institute: University Ghent

description: Gene expression data from tumoral CD11b+ DCs

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).  To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).  To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: xps 1.12.1 package of BioConductor

source_name: CD11b+ DCs from tumoral lung tissue

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: CD11c+/MHC2+/CD11b+ myeloid cells from peritumoral lung tissue versus lung tumor

extract_protocol: Total RNA was extracted from DCs using the miRNeasy kit (Qiagen) according to manufacturers instruction. Quality checks were performed on an Experion automated electrophoresis system (RQI).

treatment_protocol: For mouse gene expression analysis of tumor-exposed DCs, DCs were FACS-sorted from tumor and peritumoral lung tissue from tumor-bearing mice.

tag: strain

value: orthotopic model of lung cancer by inoculating Lewis lung carcinoma (LLC) cells into the airways of immunocompetent syngeneic C57BL/6 hosts

value: lung


title: CRC liver metastasis, patient 22


title: CRC liver metastasis, patient 19


title: wild-type intestinal crypt epithelium, biological rep2

value: Wild type


title: 3-2

city: Ningbo

first: Junming

last: Guo

address: 818 Fenghua Road

department: Department of Biochemistry and Molecular Biology, and Zhejiang Provincial Key Laboratory of Pathophysiology

institute: Ningbo University

description: This sample is paired paracancerous tissue from a patient with gastric cancer

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 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned at 5 µm/pixel resolution using a GenePix 4000B scanner piloted by GenePix Pro 6.0 software (Axon Instruments, Union City, CA). Scanned images were then imported into NimbleScan software (version 2.5) for grid alignment and raw intensity extraction.

data_processing: The raw microarray data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.

source_name: Paracancerous tissue

label_protocol: CircRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). 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.

extract_protocol: Total RNA was extracted by using TRIzol (Life Technologies, Inc., Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrohoresis.

value: Gastric paracancerous tissue


title: tumoral6


title: tumoral7


title: CRC liver metastasis, patient 16


title: 3-1

description: This sample is cancer tissue from a patient with gastric cancer

source_name: Gastric cancer tissue

value: Gastric cancer tissue


title: CRC liver metastasis, patient 18


title: tumoral4


title: 2-1


title: 1-2


title: 2-2


title: tumoral5


title: tumoral1


title: CRC liver metastasis, patient 14


title: CRC liver metastasis, patient 12


title: tumoral3


title: CRC liver metastasis, patient 15


title: CRC liver metastasis, patient 13


title: tumoral2


title: peritumoral8

description: Gene expression data from peritumoral CD11b+ DCs

source_name: CD11b+ DCs from peritumoral lung tissue


title: 1-1


title: CRC liver metastasis, patient 9


title: CRC liver metastasis, patient 8


title: T.gondii infected HFF cell group

city: Wenzhou

first: liyang

last: huang

institute: Wenzhou Medical College

description: Biological replicate for three timas. HFF group, ITF group , TGI groups after several passages.

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

scan_protocol: Images were quantified using Agilent Feature Extraction Software (v10.7)

data_processing: Agilent Feature Extraction Software (v10.7) was used for background subtraction and LOWESS normalization.

source_name: Toxoplasma gondii infected HFF cell

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

growth_protocol: HFF cells were cultured in medium(DMEM) and were supplemented with 10% fetal bovine serum (Invitrogen,USA) with 1% antibiotics(100 U/ml penicillin and 100μg/ml streptomycin sulfate) at 37 °C in a 5 % CO2 atmosphere.

extract_protocol: Total RNA was extraction individually from the cell samples which were cryo-preserved at −80 °C using TRIzol Reagent(Invitrogen, CA, USA) according to the manufacturer's protocol.

treatment_protocol: When the cell density had grown to 8×107in 75 cm2 , experimental design was divided into three groups. For the infected group, they were infected with ME49 strain tachyzoites and ensure that the ME49 and the cell ratio was 1:5; For the control group, they were infected with inactivated ME49 strain tachyzoites (60°C water bath for 10 minutes); The last group was the normal cell group

value: 48 hours

value: foreskin


title: peritumoral6


title: peritumoral5


title: Inactived tachyzoites group

source_name: Inactived tachyzoites infected HFF cell


title: CRC liver metastasis, patient 11


title: CRC liver metastasis, patient 5


title: peritumoral3


title: CRC liver metastasis, patient 10


title: [H, H1]

city: Kualalumpour

first: sanaz

last: koosha

address: Department of pharmacology, faculty of medicine, UM

department: pharmacology

country: Malaysia

institute: university of Malaya

description: Non-Alcoholic Fatty Liver Disease (NAFLD)

hyb_protocol: Hybridization mix was prepared. The target was denatured and the mixture was incubated. The Agilent SureHyb Gasket was placed into an Agilent Chamber base. Immediately, hybridisation mix was pipetted onto the gasket slide. Array was placed onto the Gasket slide. The hybridisation chamber was placed in the hybridisation oven and hybridised. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Data were extracted using Feature Extraction Software (version 10.7.3.1) and uploaded into the CytoSure™ Interpret software (version 4.2.5), normalized and converted into .cgh files. The data were segmented using a modified Circular Binary Segmentation (CBS) algorithm.

source_name: high fat diet

label_protocol: Reaction tubes were prepared as a mixture of 18 μL of c DNA sample (or reference), 10 μL of random primer and 10 μL of reaction buffer. The reactions were mixed and centrifuged for 15 s, followed by denaturation in a PCR block with a heated lid at 99°C for 20 min. Immediately after, the tubes were placed on ice for 5 min. On ice, the followings were added to the tubes: 10 μL of dCTP labelling mix, 1 μL of Cy3-dCTP (for sample) / 1 μL of Cy3-dCTP (for reference), and 1 μL of Klenow. The mixture was centrifuged for 15 s and incubated at 37°C for 2 h. Following that, the mixture was incubated at 65°C for 10 min, then placed on ice for 5 min. The mixture was centrifuged for 15 s.

growth_protocol: Male healthy wild type mice (C57BL/6) will be obtained from Animal House Unit, Faculty of Medicine, University of Malaya, Malaysia. They will be singly housed in wire bottomed cages at 25 ± 3 oC temperature, 50-60 % humidity, and a 12 h light–dark cycle. They will be maintained at standard housing conditions and free access to standard diet and water ad libitum during the experiment.

extract_protocol: total RNA extrated by QIAamp RNA Mini Kit

treatment_protocol: Group 2 (H3,H4,H6,H1): High fat diet group (positive control group) will be feed with high fat diet (60 % kcal % fat) plus 1 % cholesterol and 30 % fructose in drinking water to induce NAFLD.

tag: group

value: high fat

value: liver

value: 7-8 weeks

tag: gender

value: male


title: CRC liver metastasis, patient 7


title: peritumoral7


title: peritumoral4


title: peritumoral1


title: [H, H6]


title: HuH7 MKL1/2 KD, biological rep 2

city: Munich

first: Constanze

last: Mittermeier

address: Goethestr. 33

department: Walther Straub Institute of Pharmacology and Toxicology

institute: LMU Munich

description: HuH7 MKL1/2 KD 2

hyb_protocol: After fragmentation, cRNA was hybridized to the GeneChip Human Gene 1.0 ST array at 45°C for 17 hours.

scan_protocol: GeneChips were scanned by a Affymetrix laser scanner.

data_processing: Data were analyzed with the Partek Genomics Suite software. The used algorithm was one-way between-subject ANOVA (unpaired).

source_name: HuH7_MKL1/2 shRNA

label_protocol: cDNA was labeled by using the GeneChip WT Terminal Labeling and Hybridization Kit according to the manufacturer's instructions.

growth_protocol: HuH7 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were grown at 37°C and 5% CO2.

extract_protocol: Total RNA from HuH7 cells was isolated by using the RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: For the stable MKL1 and MKL2 knockdown, the appropriate sequence was cloned into the pLKO.1 vector. Plasmids expressing control shRNA or shRNA directed against MKL1 and MKL2 were cotransfected with the packaging plasmids into HEK293T cells. The virus containing supernatant was filtered and HuH7 cells were infected with the viral supernatant and selected with puromycin for 7 days.

tag: cell line background

tag: cell type

value: hepatocellular carcinoma (HCC)

value: stably expressing MKL1/2 shRNA

tag: passage

value: < 10 passages


title: [H, H3]

tag: age


title: [M, M4]

source_name: Methionine choline deficient diet

treatment_protocol: Group 7 (M3,M4,M8): Methionine choline deficient (MCD) diet group (second positive control group) will be feed with MCD diet to induce NASH.

tag: tissue


title: CRC liver metastasis, patient 3

source_name: Liver metastasis, FFPE

value: liver metastasis

value: Yes <=12 months


title: Normal HFF cell group

source_name: Normal HFF cell


title: [M, M8]


title: [H, H4]


title: CRC liver metastasis, patient 4

value: No >= 36 onths


title: peritumoral2

value: orthotopic model of lung cancer by inoculating Lewis lung carcinoma (LLC) cells into the airways of immunocompetent syngeneic C57BL/6 hosts


title: CRC liver metastasis, patient 6


title: HuH7 ctrl, biological rep 2

description: HuH7 ctrl 2

source_name: HuH7_negative control shRNA

value: stably expressing a control shRNA


title: CRC liver metastasis, patient 1


title: [M, M3]


title: HuH7 ctrl, biological rep 1

description: HuH7 ctrl 1


title: HuH7 MKL1/2 KD, biological rep 1

description: HuH7 MKL1/2 KD 1


title: CRC liver metastasis, patient 2


title: [L, L6]

source_name: low fat diet

treatment_protocol: Group 1 (L1,L3,L4,L6): Normal diet group (normal control group) will be feed with standard pellet diet.

value: low fat


title: [L, L1]


title: PG35 irradiated replicate 3

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

description: Glioblastoma tumor cells.

hyb_protocol: 5μg of fragmented, labeled cRNA was hybridized at 45°C for 16h onto GeneChip® Human Gene 1.0 ST arrays, then washed and stained using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 7G scanner.

data_processing: Raw data were RMA normalized using the Affymetrix Power Tools software package with default parameters.

source_name: Non-GICs, irradiated

label_protocol: Biotinylated cRNA was prepared from an input of 100-300 ng RNA using an Ambion WT kit followed by the Affymetrix terminal labelling kit according to the manufacturer's instructions.

growth_protocol: Standard cell culture conditions, 37°C humidified 5% CO2 incubator.

extract_protocol: Total RNA was extracted using a Qiagen miRNeasy Mini kit according to the manufacturer's protocol. RNA integrity was assessed using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Control (non-irradiated) versus irradiated with fractionated radiotherapy at a dose of 2Gy/day up to 8Gy.

tag: treatment

value: fractionated radiotherapy

tag: dose

value: 2Gy/day up to 8Gy


title: PG35 irradiated replicate 2

description: Glioblastoma tumor cells.


title: hsp70:HRAS_3d_rep2

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

institute: Institute of Biology, Leiden University

description:
Biological replicate 2 of 3: hsp:HRAS versus control, heat-shocked at 3 dpf, sample taken 6 hours later
252043010013_5u20b_S02_GE2_107_Sep09_1_2

hyb_protocol: The dual colour hybridization of the microarray chips was performed according to Agilent protocol GE2-v5_95_Feb07 and GE2_105_Jan09 (www.Agilent.com) for two-color microarray-based gene expression analysis except that hybridization and washing was performed at 37 ◦C.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.1 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

label_protocol: RNA labeling was carried out with miRCURY™ LNA microRNA, Hy3™/Hy5™ Power Labeling kit (Exiqon) using 1 microgram of total RNA according to the manufacturer’s instructions.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Larvae or adult fins for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Total RNA was isolated using the miRNeasy Mini kit (qiagen) to preserve small RNA pieces.

treatment_protocol: 15 3dpf, 15 7dpf and 5 14dpf larvae were pooled to obtain each sample. Replicates for each experiment were obtained by pooling larvae obtained from different parents. Controls for 3-7-14 dpf larvae kita:HRAS and zic:HRAS were AB wild type embryos. Heat-shock induction of hsp70:RAS was performed at 37°C for 30min at 3dpf and RNA was isolated after 6 hours. Controls for hsp70:HRAS were AB wild type larvae heat-shocked at 37°C for 30min at 3dpf. Adult samples are individual fins with tumor from kita:HRAS fish. Control for adult samples are individual fins from AB wild type fish.

tag: genotype/variation

tag: developmental stage

value: larvae heat-shocked at 3 dpf, sample taken 6 hours later

value: control


title: hsp70:HRAS_3d_rep1

description:
Biological replicate 1 of 3: hsp:HRAS versus control, heat-shocked at 3 dpf, sample taken 6 hours later
252043010013_5u20b_S02_GE2_107_Sep09_1_1


title: [L, L3]


title: IRF4 knockout DT40 B cells rep3

city: Turku

first: Paulina

last: Budzynska

address: Kiinamyllynkatu 13

country: Finland

institute: University of Turku

hyb_protocol: 1.65 ug of Cy-3 labeled sample was hybridized onto Agilent’s 4x44K Chicken V2 array (Design ID 026441) at 65 °C overnight using Agilent’s GE Hybridization Kit (Product number 5188-5242) following manufacturer's instructions.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2565CA. Scan Profile:  AgilentHD_GX_1Color.

data_processing: gProcessedSignal column in the Agilent raw data files was used as the input for the analysis. The data were normalised using quantile normalisation with limma package in R/Bioconductor tool (Bioconductor version 2.7, R version 2.12.0)

organism: Gallus gallus

source_name: IRF4 knockout DT40 B cells

label_protocol: Cy3-labeled with Agilent’s one-color Low Input Quick Amp Labeling kit, one-color according to manufacturer's instructions.

extract_protocol: Total RNA was prepared from 5x10^6 cells of three independent cultures of WT and IRF4KO cells with RNeasy Mini Kit (Qiagen) with RNase- Free DNase treatment according to manufacturer’s instructions.


title: hsp70:HRAS_3d_rep3

description:
Biological replicate 3 of 3: hsp:HRAS versus control, heat-shocked at 3 dpf, sample taken 6 hours later
252043010013_5u20b_S02_GE2_107_Sep09_1_3


title: zic:HRAS_3d_rep2

description:
Biological replicate 2 of 3: zic:HRAS versus control, 3 dpf
252043010013_5u20b_S02_GE2_107_Sep09_2_1

value: larvae at 3 dpf


title: [L, L4]

value: liver


title: PG35s irradiated replicate 1

description: Glioblastoma tumor cells.

source_name: GICs, irradiated

value: glioblastoma-initiating cells (GICs)


title: PG35 irradiated replicate 1

description: Glioblastoma tumor cells.


title: PG35s irradiated replicate 3

description: Glioblastoma tumor cells.


title: zic:HRAS_3d_rep3

description:
Biological replicate 3 of 3: zic:HRAS versus control, 3 dpf
252043010013_5u20b_S02_GE2_107_Sep09_2_2


title: zic:HRAS_3d_rep1

description:
Biological replicate 1 of 3: zic:HRAS versus control, 3 dpf
252043010013_5u20b_S02_GE2_107_Sep09_1_4


title: IRF4 knockout DT40 B cells rep1


title: [E, E4]

source_name: treated with EGCG

treatment_protocol: Group 5 (E2,E4,E6): High fat diet + 20mg/kg EGCG group (active compound of green tea treatment group) will be orally administrated.

value: high fat

value: 7-8 weeks

value: male


title: IRF4 knockout DT40 B cells rep2


title: PG35s irradiated replicate 2

description: Glioblastoma tumor cells.


title: [E, E6]


title: [E, E2]


title: [A, A8]

source_name: treated with atorvastatin

treatment_protocol: Group 6 (A10,A7,A8): High fat diet + atorvastatin (reference group) will be feed on 20 mg/kg atorvastatin (Hatzitolios et al., 2004).


title: kita:HRAS_adult_tail_rep3

description:
Biological replicate 3 of 3: kita:HRAS adult fin with tumor tissue versus fin tissue from control adult
test__252043010010_S01_GE2_107_Sep09_1_1

value: adult tail fin with tumor tissue

value: adult tail fin


title: R. sphaeroides WT 2.4.1_pRKSorX144 versus pRK415 after 7 min of singlet oxygen stress_technical replicate 1

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description: biological sample 1-3

hyb_protocol: Total RNA of three independent experiments of Rhodobacter sphaeroides 2.4.1 pRKSorX144 and pRK415 were pooled and hybridized to one array. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

scan_protocol: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: LOESS normalization with Limma package for Bioconductor in R was applied for dye-bias correction.

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides crude extracts_pRKSorX144 7 min

label_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation.

growth_protocol: R. sphaeroides strains were grown under aerobic conditions (100% oxygen) to an OD660 of 0.4 and stressed with 0.2 µM methylene blue in the presence of 800 W m-2 high light for 7 min.

extract_protocol: Total RNA was isolated by the hot phenol method (Janzon et al., 1986). After DNaseI treatment, RNA was purified by phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen).

source_name: R. sphaeroides crude extracts_pRK415 7 min


title: R. sphaeroides WT 2.4.1_pRKSorX144 versus pRK415 after 7 min of singlet oxygen stress_biological replicate 2

description: biological sample 4-6


title: kita:HRAS_adult_tail_rep2

description:
Biological replicate 2 of 3: kita:HRAS adult fin with tumor tissue versus fin tissue from control adult
test__252043010010_S01_GE2_107_Sep09_1_3


title: kita:HRAS_adult_tail_rep1

description:
Biological replicate 1 of 3: kita:HRAS adult fin with tumor tissue versus fin tissue from control adult
test__252043010010_S01_GE2_107_Sep09_1_2


title: CRC liver metastasis, patient 17

value: liver metastasis

tag: relapse


title: PG35s Double irradiated replicate 2

description: Glioblastoma tumor cells.

source_name: GICs, double irradiated

value: 2 cycles of fractionated radiotherapy


title: PG35s Double irradiated replicate 1

description: Glioblastoma tumor cells.


title: R. sphaeroides WT 2.4.1_pRKSorX144 versus pRK415 after 7 min of singlet oxygen stress_biological replicate 1

description: biological sample 1-3


title: [A, A10]


title: [2%, 2%7]

source_name: treated with 2% green tea extract

treatment_protocol: Group 4 (2%1,2%2,2%5,2%7): High fat diet + 200mg/kg Green tea extract group (high dose treatment group) will be orally administrated.


title: kita:HRAS_14d_rep1

description:
Biological replicate 1 of 3: kita:HRAS versus control, 14 dpf
US22502421_252043010012_S01_GE2_107_Sep09_2_4

value: larvae at 14 dpf


title: [2%, 2%5]


title: kita:HRAS_14d_rep2

description:
Biological replicate 2 of 3: kita:HRAS versus control, 14 dpf
US22502421_252043010012_S01_GE2_107_Sep09_2_3


title: kita:HRAS_14d_rep3

description:
Biological replicate 3 of 3: kita:HRAS versus control, 14 dpf
US22502421_252043010012_S01_GE2_107_Sep09_2_2


title: Ji_Batch6_39

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

description:
STANSUB_SLVP021-087-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

data_processing: Genespring GX 12.6., RMA normalization: median of all samples

value: whole blood

tag: time point

value: day 0 (before vaccination)

tag: Sex

value: Female

tag: race

value: Decline to answer


title: [A, A7]


title: PG35s Control replicate 3

description: Glioblastoma tumor cells.

source_name: GICs, not irradiated


title: [2%, 2%1]


title: PG35 Control replicate 3

description: Glioblastoma tumor cells.

source_name: Non-GICs, not irradiated


title: Ji_Batch6_42

description:
STANSUB_SLVP021-088-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Asian


title: PG35s Control replicate 1

description: Glioblastoma tumor cells.


title: PG35 Control replicate 2

description: Glioblastoma tumor cells.


title: Ji_Batch6_33

description:
STANSUB_SLVP021-085-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Caucasian or White


title: Ji_Batch6_44

description:
STANSUB_SLVP021-086-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record


title: PG35s Control replicate 2

description: Glioblastoma tumor cells.


title: kita:HRAS_7d_rep2

description:
Biological replicate 2 of 3: kita:HRAS versus control, 7 dpf
US22502421_252043010012_S01_GE2_107_Sep09_2_1

value: larvae at 7 dpf

value: control


title: kita:HRAS_7d_rep3

description:
Biological replicate 3 of 3: kita:HRAS versus control, 7 dpf
US22502421_252043010012_S01_GE2_107_Sep09_1_3


title: kita:HRAS_7d_rep1

description:
Biological replicate 1 of 3: kita:HRAS versus control, 7 dpf
US22502421_252043010012_S01_GE2_107_Sep09_1_4


title: PG35 Control replicate 1

description: Glioblastoma tumor cells.


title: [1%, 1%4]

description: Non-Alcoholic Fatty Liver Disease (NAFLD)

source_name: treated with1% green tea extract

treatment_protocol: Group 3 (1%2,1%3,1%4): High fat diet + 100mg/kg green tea extract group (low dose treatment group) will be orally administrated.

value: liver


title: Ji_Batch6_37

description:
STANSUB_SLVP021-084-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Male


title: kita:HRAS_3d_rep3

description:
Biological replicate 3 of 4: kita:HRAS versus control, 3 dpf
test__252043010010_S01_GE2_107_Sep09_2_2

value: larvae at 3 dpf


title: kita:HRAS_3d_rep4

description:
Biological replicate 4 of 4: kita:HRAS versus control, 3 dpf
test__252043010010_S01_GE2_107_Sep09_1_4


title: [1%, 1%2]

value: high fat

value: 7-8 weeks

value: male


title: kita:HRAS_3d_rep2

description:
Biological replicate 2 of 4: kita:HRAS versus control, 3 dpf
US22502421_252043010012_S01_GE2_107_Sep09_1_2


title: [1%, 1%3]


title: kita:HRAS_3d_rep1

description:
Biological replicate 1 of 4: kita:HRAS versus control, 3 dpf
US22502421_252043010012_S01_GE2_107_Sep09_1_1


title: zebrafish embryo 295

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

institute: University of Amsterdam

hyb_protocol: The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide). ). Hybridization took place for 17 hours at 65°C. In order to avoid confounding with spawn, samples have been randomized with respect to labeling batch and hybridization chamber.

scan_protocol: The microarrays were scanned in an ozone-free room with a DNA microarray scanner G2565CA (Agilent Technologies). Data was retrieved with Feature Extraction Software version 9.5.3 (Agilent Technologies).

data_processing: The quality of the microarray data was assessed via multiple quality-control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Handling, analysis and visualization of all data was performed in R (http://cran.r-project.org/) using the Bioconductor packages affy, limma and maanova (Gentleman et al. 2004). Log2 transformed Cy3 data was subjected to a procedure, similar to the one described in (Pagano et al. 2016, doi:10.1016/j.dib.2016.04.045), in which probes were identified as expressed or non-expressed probes. Here a log variance cut-off value of -2 was used to separate low and high variant probes and the per microarray cut-off for the likelihood of a probe to be expressed was set to 20%, thus avoiding too many false negatives. Hence, in this step for each array, individual probes were called ‘present’ or ‘not-present’. Next, we defined that a probe to be truthfully expressed must be called ‘present’ in at least 6 samples in one moving window of 30 with the samples ordered in epiboly stage to avoid false positives. Next all ‘present’ probes were quantile normalized and collapsed into transcripts using the R Bioconductor affy package. In the procedure no background removal was applied.

source_name: whole embryo

label_protocol: Amplification and labeling of RNA was done in an identical fashion as described in (de Jong et al. 2010, doi: 10.1186/1756-0500-3-73) in a one-round mRNA amplification per zebrafish embryo using the Amino-allyl MessageAmp II kit (Applied Biosystems). Test samples were labeled with Cy3 and a reference sample was labeled with Cy5. The reference sample was made by pooling equimolar amounts of RNA from test samples and is mentioned here for completeness only, since in the analysis a one dye approach has been applied. The yield and CyDye incorporation were again measured with the NanoDrop ND-1000

growth_protocol: Zebrafish were handled and maintained according to standard protocols (http://ZFIN.org). The local animal welfare committee (DEC) of the University of Leiden, the Netherlands specifically approved this study. All protocols adhered to the international guidelines specified by the EU Animal Protection Directive 86/609/EEC.

extract_protocol: RNA was extracted from single embryos using the procedure described in (de Jong et al. 2010, doi: 10.1186/1756-0500-3-73). The amount of RNA per μl was measured on the Nano- Drop ND-1000 (Thermo Scientific; Supplemental File S3). RNA integrity was assessed with the BioAnalyzer (Agilent Technologies) using the RNA pico 6000 kit (Agilent Technologies).

treatment_protocol: Embryos were obtained by placing a female and a male, both of genotype ABTL, overnight in a tank separated by transparent, but watertight division. Approximately 1 hour after the start of the light period the division was removed after which spawning and fertilization took place, generally in one or more pushes. Embryos were retrieved by transferring both animals to a different tank and sieving the remaining water. In total from 9 pairs, embryos were obtained ('Spawn'). Embryos were maintained at 28.5 °C in egg water (60 μg/ml Instant Ocean sea salts).

value: epiboly ~ 55

tag: spawn

tag: genotype

value: wild type ABTL

source_name: pool of whole embryos

value: late blastula, early gastrula

value: all


title: Ji_Batch6_34

description:
STANSUB_SLVP021-065-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: whole blood

value: day 0 (before vaccination)


title: zebrafish embryo 229

value: epiboly ~ 58


title: High fat+ high sugar rep6

city: Seoul

first: Jooyoung

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using background subtraction and quantile normalization with Illumina GenomeStudio Software v.2011.1.

source_name: Mouse liver

label_protocol: Biotinylated cRNA were prepared with the using Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: Total RNA was isolated from liver tissues with Ambion RNAqueous-4PCR Kits (Ambion, Austin, TX, USA) according to the manufacturer’s protocol. RNA concentrations were quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). The integrities of mRNA were confirmed by 1% agarose gel electrophoresis.

tag: strain

value: 16 weeks

tag: diet

value: High fat+ high sugar


title: High fat+ high sugar rep1

description: replicate 1

tag: gender


title: zebrafish embryo 267

value: epiboly ~ 43


title: High fat+ high sugar rep3

description: replicate 3


title: Ji_Batch6_30

description:
STANSUB_SLVP021-061-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Female

value: Asian


title: Ji_Batch6_38

description:
STANSUB_SLVP021-080-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Male

value: Caucasian or White


title: High-sugar rep6

description: replicate 6

value: High-sugar

value: liver


title: Ji_Batch6_48

description:
STANSUB_SLVP021-082-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record


title: High fat+ high sugar rep4

description: replicate 4


title: High fat+ high sugar rep2

description: replicate 2


title: High fat+ high sugar rep5

description: replicate 5


title: Ji_Batch6_52

description:
STANSUB_SLVP021-054-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record


title: Ji_Batch6_50

description:
STANSUB_SLVP021-052-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record


title: zebrafish embryo 343-2

value: epiboly ~ 51


title: zebrafish embryo 443

value: epiboly ~ 56


title: Ji_Batch6_29

description:
STANSUB_SLVP021-049-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record


title: BHK21 cell_Cirp−/−_72h_rep1

city: Chengdu

first: Cheng

last: TANG

state: Sichuan

address: No 16  Yihuan Lu South Sect.4,

institute: Southwest University for Nationalities

description: Cirp−/− BHK21 cell

hyb_protocol: Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5.26) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.

source_name: BHK21 cell,Cirp−/−,72h

label_protocol: Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

growth_protocol: Cirp−/−, or control BHK21 cells at a density of 2.0×105 cells/mL were inoculated into six-well plates containing 2.5 mL of Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and then cultured at 37 °C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA from Cirp−/− and control BHK21 cells at 24, 48, and 72 h was extracted using TRIzol reagent (Applied Biosystems Inc., Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: Before RNA extract, the cells were washed three times by the phosphate buffer solution (PBS).

tag: cell line

value: Cirp−/− knockdown

tag: time


title: BHK21 cell_Cirp−/−_72h_rep2

description: Cirp−/− BHK21 cell


title: zebrafish embryo 344

value: epiboly ~ 46

value: wild type ABTL

value: late blastula, early gastrula


title: BHK21 cell_Cirp−/−_72h_rep3

description: Cirp−/− BHK21 cell


title: zebrafish embryo 192

value: all


title: zebrafish embryo 358

data_processing:
The quality of the microarray data was assessed via multiple quality-control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Handling, analysis and visualization of all data was performed in R (http://cran.r-project.org/) using the Bioconductor packages affy, limma and maanova (Gentleman et al. 2004). Log2 transformed Cy3 data was subjected to a procedure, similar to the one described in (Pagano et al. 2016, doi:10.1016/j.dib.2016.04.045), in which probes were identified as expressed or non-expressed probes. Here a log variance cut-off value of -2 was used to separate low and high variant probes and the per microarray cut-off for the likelihood of a probe to be expressed was set to 20%, thus avoiding too many false negatives. Hence, in this step for each array, individual probes were called ‘present’ or ‘not-present’. Next, we defined that a probe to be truthfully expressed must be called ‘present’ in at least 6 samples in one moving window of 30 with the samples ordered in epiboly stage to avoid false positives. Next all ‘present’ probes were quantile normalized and collapsed into transcripts using the R Bioconductor affy package. In the procedure no background removal was applied.

This array did not meet quality standards and was not included in the final analysis. No processed/normalized data is available.

value: epiboly ~ 53


title: High-sugar rep5

description: replicate 5

tag: age

value: 16 weeks


title: Ji_Batch6_31

description:
STANSUB_SLVP021-030-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

tag: tissue

value: whole blood

value: day 0 (before vaccination)

value: Decline to answer


title: High-sugar rep3

description: replicate 3


title: BHK21 cell_Cirp−/−_48h_rep3

description: Cirp−/− BHK21 cell

source_name: BHK21 cell,Cirp−/−,48h

tag: treatment


title: zebrafish embryo 247

value: epiboly ~ 62


title: Ji_Batch6_51

description:
STANSUB_SLVP021-038-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Male


title: Ji_Batch6_36

description:
STANSUB_SLVP021-040-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Caucasian or White


title: zebrafish embryo 460

value: epiboly ~ 70


title: High-sugar rep1

description: replicate 1

value: High-sugar

value: liver