title: Marginal zone B-cell lymphoma patient sample 08-030

description:
08-030.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-030


title: Marginal zone B-cell lymphoma patient sample 08-032

status: Public on Feb 01 2011

type: genomic

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

description:
08-032.CEL
Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Data acquisition was performed using the GeneChip Operating Software (GCOS) v1.4 and Genotyping Analysis Software (GTYPE) v4.1. Genotype calls were calculated using the BRLMM algorithm. Mapping data for probes were derived from the National Center for Biotechnology Information (NCBI) Human Genome Build 36, as provided by Affymetrix, which was used for all subsequent analyses. The modified Bayesian Piecewise Regression (mBPCR) method was used to estimate the copy number (CN) starting from raw CN values obtained with Affymetrix CNAT 4.01 using a Gaussian bandwidth of 0 Kb and 46 Caucasian normal female samples of the HapMap Project as reference samples.
signal = log2ratio; loh = 0 or 1

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: MZL patient sample 08-032

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: All clinical specimens were derived from involved sites and obtained in the course of routine diagnostic procedures before therapy initiation. Cases were selected based upon the availability of frozen material with a fraction of neoplastic cells in the specimen representing >70% of overall cellularity as determined by morphologic and/or immunophenotypic studies. Genomic DNA was extracted using the QIAamp DNA Mini Kit.

tag: cell type

value: marginal zone lymphoma

tag: diagnosis

value: SMZL


title: GC resistant clone C7H2-R19E7 treated for 6 hours with GC

type: RNA

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description: GC resistant clone C7H2-R19E7 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

hyb_protocol: 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software.

data_processing: The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's gcrma package).

label: biotin

molecule: total RNA

label_protocol: Total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: Cell lines were cultured in RPMI 1640 supplemented with 10% fetal calf serum and 2mM L-glutamine at 37C, 5% carbon-dioxide and saturated humidity. The cells were free of mycoplamsa infection.

extract_protocol: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.

treatment_protocol: Cells were treated with 100nM dexametasone (Sigma, Vienna, Austria) or 0.1% ethanol as carrier control.

value: lymphoblastic leukemia

tag: gc resistant

value: TRUE

tag: treatment

value: GC


title: GC resistant clone C7H2-R19F2 treated for 6 hours with GC

description: GC resistant clone C7H2-R19F2 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).


title: Unsorted WM (patient 3)

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

country: USA

institute: University at Buffalo

hyb_protocol: Affy standard

scan_protocol: Affy standard using a HP scanner in 2003

data_processing: The analysis was performed using GCOS software and the CHP file generated using MAS5 algorithm.

source_name: Unsorted white matter dissociate

label_protocol: Affy small sample amplification protocol (v1, 100ng)

extract_protocol: Trizol followed by Qiagen RNeasy with On-column DNase

tag: gender

value: Male

tag: age

value: Epilepsy


title: Marginal zone B-cell lymphoma patient sample 08-023

description:
08-023.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-023

value: NMZL


title: GC sensitive clone C7H2-S11 treated for 6 hours with GC

description: GC sensitive clone C7H2-S11 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).

value: FALSE


title: A2B5+ WMPCs (patient 3)

source_name: A2B5-sorted white matter dissociate


title: GC sensitive clone C7H2-S12 treated for 6 hours with GC

description: GC sensitive clone C7H2-S12 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).


title: GC sensitive clone C7H2-S27 treated for 6 hours with GC

description: GC sensitive clone C7H2-S27 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).


title: GC resistant clone C7H2-R3B5 treated for 6 hours with GC

description: GC resistant clone C7H2-R3B5 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).


title: GC resistant clone C7H2-R9C10 treated for 6 hours with GC

description: GC resistant clone C7H2-R9C10 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).


title: Epilepsy patient E4, 6 hours GC treatment

description:
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E4 taken 6 hours after GC administration.

E4-6h

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.

data_processing: The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).

source_name: Mononuclear cells, epilepsy patient E4, 6 hours after GC administration

label_protocol: 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: None.

extract_protocol: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.

treatment_protocol: Single administration of the glucocorticoid dexamethasone (20 mg/m2).

tag: tissue

value: peripheral blood

value: mononuclear cells

tag: disease state

value: epilepsy, non-leukemic

value: dexamethasone

value: 6 hrs

tag: patient


title: Unsorted WM (patient 2)


title: Unsorted WM (patient 1)


title: Marginal zone B-cell lymphoma patient sample 08-026

description:
08-026.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-026

value: EMZL


title: A2B5+ WMPCs (patient 1)


title: A2B5+ WMPCs (patient 2)


title: GC resistant clone C7H2-R10E7 treated for 6 hours with GC

description: GC resistant clone C7H2-R10E7 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).


title: Marginal zone B-cell lymphoma patient sample 07-466

description:
07-466.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-466


title: GC resistant clone C7H2-R19E5 treated for 6 hours with GC

description: GC resistant clone C7H2-R19E5 treated for 6 hours with 100nM dexamethasone (a glucocorticoid).


title: GC sensitive clone C7H2-S15 treated for 6 hours with EtOH

description: GC sensitive clone C7H2-S15 treated for 6 hours with 0.1% ethanol (carrier control).

value: EtOH


title: Marginal zone B-cell lymphoma patient sample 08-021

description:
08-021.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-021


title: Marginal zone B-cell lymphoma patient sample 07-455

description:
07-455.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-455


title: Marginal zone B-cell lymphoma patient sample 08-020

description:
08-020.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-020


title: Marginal zone B-cell lymphoma patient sample 07-463

description:
07-463.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-463


title: Marginal zone B-cell lymphoma patient sample 07-452

description:
07-452.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-452


title: Marginal zone B-cell lymphoma patient sample 08-019

description:
08-019.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-019


title: Marginal zone B-cell lymphoma patient sample 07-453

description:
07-453.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-453


title: GC sensitive clone C7H2-S2 treated for 6 hours with EtOH

description: GC sensitive clone C7H2-S2 treated for 6 hours with 0.1% ethanol (carrier control).


title: Marginal zone B-cell lymphoma patient sample 07-451

description:
07-451.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-451


title: 3 hour DAPT treatment, biological rep2

city: Kansas City

first: Olivier

last: Pourquie

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

description:
Gene expression data from 3 hour DAPT treated embryos
3 hour DAPT treatment, biological rep2

hyb_protocol: Each chip was hybridized to 13 μg fragmented cRNA. Arrays were hybridized according to the manufacturer’s instructions.

scan_protocol: GeneChips were scanned with a Affymetrix GeneChip Scanner 3000 7G at the Microarray Core Facility of the Stowers Institute for Medical Research

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.

organism: Danio rerio

source_name: Zebrafish embryos paraxial mesoderm

label_protocol: Biotinylated cRNA were prepared by using Affymetrix GeneChip Expression 3'-Amplification Reagents for IVT Labeling kit.

growth_protocol: Embryos from AB line were grown at 24C° untill 12-somite stage.

extract_protocol: Trizol extraction of total RNA was performed.

treatment_protocol: Embryos are either incubated in drugs (RA, DMSO, DAPT) at room temperature (24C°) or heat-shocked at 37C° then transfered to 24C°. Embryos were manually dechorionated at 24C°. Selected embryos were transferred to a basket in L15 media. Embryos were manually dissected and the tissue sections were placed in the Trizol solution (Invitrogen) and frozen immediately on dry ice and stored at -80C°.

tag: protocol

value: 3 hour DAPT treatment

value: posterior PSM

tag: genotype

value: wild-type AB

value: 12-somite stage


title: WPE1-NB26

city: Ann Arbor

first: xiaosong

last: wang

state: MI

address: 1500 E. Medical Center Drive

institute: University of Michigan

scan_protocol: Agilent Technologies Scanner G2505B

data_processing: Agilent Feature Extraction Software. Values are the log 10 rProcessedSignal/gProcessedSignal.

source_name: WPE1-NB26 prostate cancer cell line

label_protocol: Fluorescence labeling (Agilent protocol for 105 K arrays, version 6.0, November 2008)

growth_protocol: grow in full serum under standard conditions

value: Prostate

tag: cell line

source_name: Human Adult Male Normal Genomic DNA

value: whole blood


title: VCaP

hyb_protocol: Agilent protocol for 105 K arrays, version 6.0, November 2008

source_name: VCaP prostate cancer cell line

value: VCaP


title: GC sensitive clone C7H2-S27(ZR) treated for 6 hours with EtOH

description: GC sensitive clone C7H2-S27(ZR) treated for 6 hours with 0.1% ethanol (carrier control).

value: lymphoblastic leukemia


title: 3 hour DAPT treatment, biological rep1

description:
Gene expression data from 3 hour DAPT treated embryos
3 hour DAPT treatment, biological rep1


title: GC sensitive clone C7H2-S12 treated for 6 hours with EtOH

description: GC sensitive clone C7H2-S12 treated for 6 hours with 0.1% ethanol (carrier control).


title: GC sensitive clone C7H2-S10 treated for 6 hours with EtOH

description: GC sensitive clone C7H2-S10 treated for 6 hours with 0.1% ethanol (carrier control).


title: GC sensitive clone C7H2-S11 treated for 6 hours with EtOH

description: GC sensitive clone C7H2-S11 treated for 6 hours with 0.1% ethanol (carrier control).


title: NCI660

source_name: NCI660 prostate cancer cell line

extract_protocol: Agilent protocol for 105 K arrays, version 6.0, November 2008


title: Marginal zone B-cell lymphoma patient sample 07-449

description:
07-449.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-449

value: marginal zone lymphoma

value: SMZL


title: Marginal zone B-cell lymphoma patient sample 07-450

description:
07-450.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-450


title: LAPC4

source_name: LAPC4 prostate cancer cell line


title: Marginal zone B-cell lymphoma patient sample 07-412

description:
07-412.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-412


title: GC resistant clone C7H2-R19E7 treated for 6 hours with EtOH

description: GC resistant clone C7H2-R19E7 treated for 6 hours with 0.1% ethanol (carrier control).

value: TRUE


title: MDAPCa-2b

source_name: MDAPCa-2b prostate cancer cell line


title: PC3

source_name: PC3 prostate cancer cell line


description:
Gene expression data from 3 hour DMSO treated embryos
3 hour DMSO treatment as a control for DAPT treatment, biological rep4

value: 3 hour DMSO treatment


title: GC resistant clone C7H2-R19F2 treated for 6 hours with EtOH

description: GC resistant clone C7H2-R19F2 treated for 6 hours with 0.1% ethanol (carrier control).


description:
Gene expression data from 3 hour DMSO treated embryos
3 hour DMSO treatment as a control for DAPT treatment, biological rep3


title: Marginal zone B-cell lymphoma patient sample 07-410

description:
07-410.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-410


title: GC resistant clone C7H2-R3B5 treated for 6 hours with EtOH

description: GC resistant clone C7H2-R3B5 treated for 6 hours with 0.1% ethanol (carrier control).


description:
Gene expression data from 3 hour DMSO treated embryos
3 hour DMSO treatment as a control for DAPT treatment, biological rep2


description:
Gene expression data from 1.5 hour DAPT treated embryos
1.5 hour DAPT treatment, biological rep3

value: 1.5 hour DAPT treatment


title: GC resistant clone C7H2-R9C10 treated for 6 hours with EtOH

description: GC resistant clone C7H2-R9C10 treated for 6 hours with 0.1% ethanol (carrier control).


description:
Gene expression data from 3 hour DMSO treated embryos
3 hour DMSO treatment as a control for DAPT treatment, biological rep1


title: Marginal zone B-cell lymphoma patient sample 07-446

description:
07-446.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-446


title: Marginal zone B-cell lymphoma patient sample 07-408

description:
07-408.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-408


title: S. oneidensis_O2_batch_rep3

city: Ithaca

first: Miriam

last: Rosenbaum

address: 325 Riley-Robb Hall

department: Biological and Environmental Engineering

institute: Cornell University

description: Gene expression data from wild-type S. oneidensis MR-1, grown aerobically on lactate with oxygen as electron acceptor; 5 g/L glycero-phosphate in medium.

hyb_protocol: 10 µg of RNA sample was used for cDNA synthesis, followed by reverse transcription, cDNA purification, and cDNA-fragmentation. This was followed by labeling of cDNA and 16 hours of hybridization at 45°C on S. oneidensis arrays. The labeled arrays were subjected to several cycles of washing and staining using Affymetrix Wash buffers A and B, Goat IgG, Streptavidin, Anti-streptavidin and SAPE according to the Affymetrix protocol for prokaryotic arrays in the Affymetrix Fluidics Station 400.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Shewanella oneidensis MR-1

source_name: S. oneidensis with oxygen, 20 h

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

growth_protocol: Cells were grown aerobically at 30°C for 20 hours with defined medium (modified M4), 20 mM lactate.

extract_protocol: 2 mL of each culture were combined with 2 mL RNA protect, vortexed, and centrifuged at 5,500g for 10 min. The pellets were resuspended in NAES buffer (50 mM sodium acetate buffer, 10 mM EDTA and 1 % SDS at pH 5). RNA was isolated with a phenol:chloroform extraction protocol. The isolated RNA was purified with Ambion DNase I treatment following the manufacturer’s instructions.

treatment_protocol: BES carbon paper electrodes from continuous BES operation were dipped in Qiagen RNA-protect and frozen at -80°C until total RNA extraction.

value: wild type

tag: culture type

value: 10 mL batch culture (20 hours) in defined medium (modified M4) with 20 mM lactate, aerobic; 5 g/L glycero-phosphate in medium


description:
Gene expression data from 1.5 hour DAPT treated embryos
1.5 hour DAPT treatment, biological rep1


description:
Gene expression data from 1.5 hour DAPT treated embryos
1.5 hour DAPT treatment, biological rep2


title: Marginal zone B-cell lymphoma patient sample 07-407

description:
07-407.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-407


title: DU145 replicate 1

source_name: DU145 prostate cancer cell line


title: DU145 replicate 2


title: C4-2B

source_name: C4-2B prostate cancer cell line


title: GC resistant clone C7H2-R19E5 treated for 6 hours with EtOH

description: GC resistant clone C7H2-R19E5 treated for 6 hours with 0.1% ethanol (carrier control).


title: CLL 379-01 LMP-420

city: Durham

first: Daphne

middle: R

last: Friedman

state: NC

address: 101 Science Drive, Room 2121, CIEMAS Bldg

institute: Duke University Medical Center

description: Treated cells

data_processing: R/Bioconductor; RMA normalization

source_name: CLL cells

label_protocol: According to standard Affymetrix protocol.  Affymetrix 1-step IVT

growth_protocol: 24 hour incubation in Hybridoma SFM media with 10% fetal bovine serum

extract_protocol: Qiashredder and RNeasy Mini Columns

treatment_protocol: Incubation with 2 uM LMP-420 or media alone

tag: agent

tag: selection protocol

value: negatively selected cells


title: Marginal zone B-cell lymphoma patient sample 08-022

description:
08-022.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 08-022

value: NMZL


title: S. oneidensis_O2_batch_rep2

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.


title: CLL 379-01 Control

description: Control cells

hyb_protocol: According to standard Affymetrix protocol.

value: Control


description:
Gene expression data from 1.5 hour DMSO treated embryos
1.5 hour DMSO treatment as a control for DAPT treatment, biological rep4

source_name: Zebrafish embryos paraxial mesoderm

value: 1.5 hour DMSO treatment

value: posterior PSM


title: CA-hpv-10

source_name: CA-hpv-10 prostate cancer cell line

source_name: Human Adult Male Normal Genomic DNA


title: Marginal zone B-cell lymphoma patient sample 07-406

description:
07-406.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-406


title: Marginal zone B-cell lymphoma patient sample 07-405

description:
07-405.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-405


title: Marginal zone B-cell lymphoma patient sample 07-404

description:
07-404.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-404


title: Marginal zone B-cell lymphoma patient sample 07-403

description:
07-403.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-403

value: EMZL


title: S. oneidensis_O2_batch_rep1


title: Marginal zone B-cell lymphoma patient sample 07-409

description:
07-409.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-409


description:
Gene expression data from 1.5 hour DMSO treated embryos
1.5 hour DMSO treatment as a control for DAPT treatment, biological rep2

value: wild-type AB

value: 12-somite stage


title: S. oneidensis_Fe(III)_batch_rep2

description: Gene expression data from wild-type S. oneidensis MR-1, grown anaerobically on lactate with Fe(III)citrate as electron acceptor; no glycero-phosphate in medium

source_name: S. oneidensis anaerobic with Fe(III)citrate, 20 h, no glycero-phosphate in medium

growth_protocol: Cells were grown anaerobically at 30°C for 20 hours with defined medium (modified M4), 20 mM lactate and 50 mM Fe(III)citrate; no glycero-phosphate in medium.

value: 10 mL batch culture (20 hours) in defined medium (modified M4) with 20 mM lactate, 50 mM Fe(III)citrate, no glycero-phosphate in medium


description:
Gene expression data from 1.5 hour DMSO treated embryos
1.5 hour DMSO treatment as a control for DAPT treatment, biological rep3


title: Marginal zone B-cell lymphoma patient sample 07-402

description:
07-402.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-402


title: S. oneidensis_Fe(III)GP_batch_rep2

description: Gene expression data from wild-type S. oneidensis MR-1, grown anaerobically on lactate with Fe(III)citrate as electron acceptor; 5 g/L glycero-phosphate in medium.

source_name: S. oneidensis anaerobic with Fe(III)citrate, 20 h, 5 g/L glycero-phosphate in medium

growth_protocol: Cells were grown anaerobically at 30°C for 20 hours with defined medium (modified M4), 20 mM lactate and 50 mM Fe(III)citrate; 5 g/L glycero-phosphate in medium.

value: 10 mL batch culture (20 hours) in defined medium (modified M4) with 20 mM lactate, 50 mM Fe(III)citrate; 5 g/L glycero-phosphate in medium.


title: S. oneidensis_Fe(III)_batch_rep1


title: CLL 377-01 LMP-420

description: Treated cells

scan_protocol: According to standard Affymetrix protocol.


description:
Gene expression data from 1.5 hour DMSO treated embryos
1.5 hour DMSO treatment as a control for DAPT treatment, biological rep1


title: CLL 378-01 Control

description: Control cells


title: CLL 377-01 Control

description: Control cells


title: CLL 378-01 LMP-420

description: Treated cells


title: Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 90 mins, biological rep4

description:
Gene expression data from heat-shocked embryos
Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 90 minutes ,  biological rep4

value: embryos heat-shocked for 1hr, posterior presomitic mesoderm dissected after 90 mins


title: Marginal zone B-cell lymphoma patient sample 07-401

description:
07-401.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-401

value: marginal zone lymphoma

value: SMZL


title: Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 90 mins, biological rep1

description:
Gene expression data from heat-shocked embryos
Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 90 minutes ,  biological rep1


title: Marginal zone B-cell lymphoma patient sample 07-034

description:
07-034.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-034


title: Marginal zone B-cell lymphoma patient sample 07-022

description:
07-022.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-022


title: CLL 361-01 LMP-420

description: Treated cells


title: CLL 161-04 LMP-420

description: Treated cells


title: Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 90 mins, biological rep2

description:
Gene expression data from heat-shocked embryos
Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 90 minutes ,  biological rep2


title: Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 90 mins, biological rep3

description:
Gene expression data from heat-shocked embryos
Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 90 minutes ,  biological rep3


title: Subject33_before

city: Maastricht

first: Dennie

last: Hebels

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

description: No intervention

hyb_protocol: Hybridization according to Agilent instructions on 4x44K human whole genome microarrays.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 was excited at a wavelengths of 532 nm. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 522 (Cy3), based on automatic establishment of ideal scan settings. Images were subsequently saved (resolution 5 micron, 16 bit tiff image).

data_processing: Bad and empty spots were flagged using the GenePix Pro software (version 6.0, Molecular Devices, Sunnyvale, CA). Quality control was performed in the statistical software environment R (version 2.10.1, The R Foundation for Statistical Computing, Vienna, Austria). Quantile normalization and subsequent data processing including background subtraction and Log2 transformation of spot intensities was performed in ArrayTrack (version 3.4, NCTR, Jefferson, AR).

source_name: Human colon biopsies before intervention

label_protocol: Dye-labeled cRNA (Cy3) was synthesized following the Agilent one-color Quick-Amp labeling protocol (Agilent Technologies, Amstelveen, The Netherlands).

extract_protocol: During a colonoscopic examination six biopsies were taken from mucosal tissue in visually non-inflamed regions of the colon (in most cases from the sigmoid and descending colon) which were immediately frozen in liquid nitrogen and stored at -80 °C until use. Three biopsies were separately dissolved in QIAzol® (Qiagen, Venlo, The Netherlands) using a tissue disruptor and subsequently pooled. Total RNA was subsequently extracted according to the manufacturer's instructions.

treatment_protocol: Subjects with a before AND after measurement participated in a 7-day red meat intervention study (300 grams of red meat per day). Subjects with only a before measurement did not participate in any intervention

tag: subject number

tag: disease status

value: IBD

value: male

tag: intervention status

value: before


title: 22RV1

source_name: 22RV1 prostate cancer cell line

value: Prostate

value: whole blood


title: Subject56_before

description: No intervention


title: CLL 161-04 Control

description: Control cells

source_name: CLL cells

value: negatively selected cells


title: CLL 361-01 Control

description: Control cells

value: Control


title: Marginal zone B-cell lymphoma patient sample 07-180

description:
07-180.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-180

tag: cell type

tag: diagnosis


title: GC resistant clone C7H2-R10E7 treated for 6 hours with EtOH

description: GC resistant clone C7H2-R10E7 treated for 6 hours with 0.1% ethanol (carrier control).

value: lymphoblastic leukemia

tag: gc resistant

value: TRUE

tag: treatment

value: EtOH


title: Marginal zone B-cell lymphoma patient sample 07-021

description:
07-021.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-021

value: NMZL


title: S. oneidensis_Fe(III)GP_batch_rep1

description: Gene expression data from wild-type S. oneidensis MR-1, grown anaerobically on lactate with Fe(III)citrate as electron acceptor; 5 g/L glycero-phosphate in medium

value: wild type

value: 10 mL batch culture (20 hours) in defined medium (modified M4) with 20 mM lactate, 50 mM Fe(III)citrate; 5 g/L glycero-phosphate in medium


title: Marginal zone B-cell lymphoma patient sample 07-023

description:
07-023.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-023


title: Subject31_after

description: Participated in red meat intervention

source_name: Human colon biopsies after intervention

value: IBS

tag: gender

value: female

tag: age

value: after


title: Marginal zone B-cell lymphoma patient sample 07-020

description:
07-020.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-020

value: marginal zone lymphoma

value: EMZL


title: CLL 119-09 Control

description: Control cells


title: CLL 149-05 LMP-420

description: Treated cells


title: Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 90 mins, biological rep2

description:
Gene expression data from heat-shocked embryos
Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 90 minutes ,  biological rep2

source_name: Zebrafish embryos paraxial mesoderm

value: embryos heat-shocked for 1hr, posterior presomitic mesoderm dissected after 90 mins

tag: tissue

value: posterior PSM

value: 12-somite stage


title: Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 90 mins, biological rep4

description:
Gene expression data from heat-shocked embryos
Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 90 minutes ,  biological rep4


title: Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 90 mins, biological rep3

description:
Gene expression data from heat-shocked embryos
Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 90 minutes ,  biological rep3


title: Subject29_before

description: No intervention

value: IBD

value: male

value: before


title: CLL 145-04 Control

description: Control cells

value: Control

value: negatively selected cells


title: Subject32_before

description: No intervention


title: Subject28_before

description: Participated in red meat intervention


title: CLL 119-09 LMP-420

description: Treated cells


title: Subject31_before

description: Participated in red meat intervention


title: Subject30_before

description: No intervention


title: Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 45 mins, biological rep2

description:
Gene expression data from heat-shocked embryos
Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 45 minutes ,  biological rep2

value: embryos heat-shocked for 1hr, posterior presomitic mesoderm dissected after 45 mins


title: Marginal zone B-cell lymphoma patient sample 07-019

description:
07-019.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-019


title: Marginal zone B-cell lymphoma patient sample 07-017

description:
07-017.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-017

value: SMZL


title: CLL 145-04 LMP-420

description: Treated cells


title: Marginal zone B-cell lymphoma patient sample 07-015

description:
07-015.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-015

value: NMZL


title: Marginal zone B-cell lymphoma patient sample 07-014

description:
07-014.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-014


title: CLL 149-05 Control

description: Control cells


title: Marginal zone B-cell lymphoma patient sample 07-011

description:
07-011.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-011


title: Subject27_after

description: Participated in red meat intervention


title: CLL 69-04 Control

description: Control cells


title: Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 45 mins, biological rep4

description:
Gene expression data from heat-shocked embryos
Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 45 minutes ,  biological rep4


title: Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 45 mins, biological rep3

description:
Gene expression data from heat-shocked embryos
Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 45 minutes ,  biological rep3


title: Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 45 mins, biological rep4

description:
Gene expression data from heat-shocked embryos
Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 45 minutes ,  biological rep4


title: Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 45 mins, biological rep1

description:
Gene expression data from heat-shocked embryos
Tg(UAS:myc-notch1a-intra)xTg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 45 minutes ,  biological rep1


title: Subject26_before

description: No intervention


title: Subject28_after

description: Participated in red meat intervention


title: Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 90 mins, biological rep1

description:
Gene expression data from heat-shocked embryos
Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 90 minutes ,  biological rep1


title: Subject25_before

description: No intervention


title: CLL 69-04 LMP-420

description: Treated cells


title: Marginal zone B-cell lymphoma patient sample 07-013

description:
07-013.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-013


title: CLL 141-08 LMP-420

description: Treated cells


title: Marginal zone B-cell lymphoma patient sample 07-008

description:
07-008.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-008


title: Subject27_before

description: Participated in red meat intervention


title: Subject24_before

description: No intervention


title: Marginal zone B-cell lymphoma patient sample 07-009

description:
07-009.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-009


title: Marginal zone B-cell lymphoma patient sample 07-010

description:
07-010.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-010


title: Marginal zone B-cell lymphoma patient sample 07-006

description:
07-006.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-006


title: Tg(hsp:70:dkk1-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep4

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:dkk1-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep4

value: embryos heat-shocked for 30 mins, posterior presomitic mesoderm dissected after 1 hour


title: CLL 11-18 Control

description: Control cells

source_name: CLL cells


title: CLL 141-08 Control

description: Control cells


title: CLL 164-02 LMP-420

description: Treated cells


title: Tg(hsp:70:dkk1-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep2

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:dkk1-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep2


title: Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 45 mins, biological rep2

description:
Gene expression data from heat-shocked embryos
Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 45 minutes ,  biological rep2


title: Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 45 mins, biological rep3

description:
Gene expression data from heat-shocked embryos
Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 45 minutes ,  biological rep3


title: CLL 38-11 LMP-420

description: Treated cells


title: CLL 38-11 Control

description: Control cells


title: wild type CTL+AktI, biological replicate 3

city: Dundee

first: maria

middle: carmen

last: feijoo

address: Dow Street

department: Cell biology and immunology

country: United Kingdom

institute: University of Dundee

description:
Gene expression data from wild-type CTL from mouse 3 treated with AktI
6_157IL2Akti

hyb_protocol: Each sample was hybridized to GeneChip®Mouse Genome 430 2.0 Array at +45°C overnight (16 h) according to GeneChip® Expression Analysis Technical Manual (With Specific Protocols for Using the GeneChip® Hybridization, Wash and Stain Kit) GeneChip Fluidics Station 450 was used to wash and stain the arrays.

scan_protocol: GeneChip Scanner 3000 7G with AutoLoader was used to scan the arrays.

data_processing:
Affymetrix GeneChip Command Console (AGCC) 1.1 was used to control GeneChip Fluidics Stations and Scanner and in summarizing probe cell intensity data (.CEL file generation).
After hybridization quality was checked with AGCC and Expression Console TM 1.1.
Data was normalized using the Affymetrix Expression Console v1.1 (Affymetrix) implementation of the robust multichip averaging algorithm using default analysis settings and quantile normalisation.

organism: Mus musculus

source_name: CTL made from wild type splenocytes and treated with AktI

label_protocol: Biotinylated cRNA were prepared from 2μg RNA according to the standard One-cycle target labelling protocol from GeneChip Expression Analysis Technical Manual (with specific protocols for using the GeneChip hybridization, Wash and Stain Kit)

growth_protocol:
CTL were generated by activating Splenic T-cells for 48h in RPMI 1640/10% heat-inactivated fetal calf serum (FCS) penicillin/streptomycin (Gibco), 50μM β-mercaptoethanol (β-ME) (Sigma)  with 0.5μg/ml CD3 antibody (2C11) in the presence of 20ng/ml IL2.
Cells were then washed free of activating agent and thereafter maintained in 20ng/ml IL2 at a density of approximately 0.3×106/ml at 37°C

extract_protocol: RNA was extracted from cells with the RNeasy RNA purification minikit (Qiagen) according to the manufactures protocol.

treatment_protocol:
C57BL/6GT(ROSA)26tm9(creEsr1)Arte (TamoxCre) and PDK1fl/fl C57BL/6GT(ROSA)26tm9(creEsr1)Arte (PDK1fl/fl TamoxCre) T-cells were activated for 48h and then cultured for 5days, supplimented with 0.6μM 4OHT for the last 72h of culture.
Alternatively T-cells from C57/B6 mice were were activated for 48h and then cultured for 5days with half the cells from each biological replicated being treated with 1μM AktI-1/2 for the last 48h of culture.

tag: strain

value: cytotoxic T-lymphocytes (CTL)

tag: genotype/variation

value: wild type

value: Akt inhibitor AktI-1/2


title: Subject23_before

description: No intervention

source_name: Human colon biopsies before intervention


title: Marginal zone B-cell lymphoma patient sample 07-007

description:
07-007.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-007

value: marginal zone lymphoma


title: Subject20_before

description: No intervention

value: female


title: Tg(hsp:70:wnt8a-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep4

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:wnt8a-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep4

tag: protocol

tag: genotype


title: Subject19_before

description: No intervention

value: IBS


title: Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour dissected after 45 mins, biological rep1

description:
Gene expression data from heat-shocked embryos
Tg(hsp70;gal4VP16) embryos heat-shocked for 1 hour and posterior presomitic mesoderm is dissected 45 minutes ,  biological rep1

value: posterior PSM


title: CLL 11-18 LMP-420

description: Treated cells


title: Subject22_before

description: No intervention


title: Subject18_before

description: No intervention


title: Marginal zone B-cell lymphoma patient sample 07-005

description:
07-005.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 07-005


title: wild type CTL, biological replicate 2

description:
Gene expression data from wild-type CTL from mouse 2
3_154IL2

source_name: CTL made from wild type splenocytes

value: control


title: wild type CTL+AktI, biological replicate 1

description:
Gene expression data from wild-type CTL from mouse 1 treated with AktI
2_153IL2Akti


title: Marginal zone B-cell lymphoma patient sample 06-R-389

description:
06-R-389.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 06-R-389


title: Tg(hsp:70:dkk1-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep3

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:dkk1-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep3

source_name: Zebrafish embryos paraxial mesoderm

value: 12-somite stage


title: Tg(hsp:70:DeltaTcF-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep3

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:DeltaTcF-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep3

value: heat-shocked for 30 mins, posterior presomitic mesoderm dissected after 1 hour


title: wild type CTL, biological replicate 1

description:
Gene expression data from wild-type CTL from mouse 1
1_152IL2


title: Subject21_before

description: No intervention

value: male

value: before


title: Tg(hsp:70:dkk1-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep1

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:dkk1-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep1


title: Tg(hsp:70:DeltaTcF-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep2

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:DeltaTcF-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep2


title: PDK1 null CTL, biological replicate 1

description:
Gene expression data from PDK1 null CTL ( C57BL/6GT(ROSA)26tm9(creEsr1)Arte PDK1fl/fl treated with 4OHT)
TamoxCrePDK1KC248

source_name: CTL made from PDK1fl/fl TamoxCre splenocytes and treated with 4OHT

value: PDK1 null


title: wild type CTL, biological replicate 3

description:
Gene expression data from wild-type CTL from mouse 3
5_156IL2


title: PDK1 null CTL, biological replicate 2

description:
Gene expression data from PDK1 null CTL ( C57BL/6GT(ROSA)26tm9(creEsr1)Arte PDK1fl/fl treated with 4OHT)
TamoxCrePDK1KC252


title: Subject15_before

description: No intervention

value: IBD


title: wild type CTL+AktI, biological replicate 2

description:
Gene expression data from wild-type CTL from mouse 2 treated with AktI
4_155IL2Akti


title: Marginal zone B-cell lymphoma patient sample 06-R-391

description:
06-R-391.CEL
Hybridized to 250K_Nsp

source_name: MZL patient sample 06-R-391

value: EMZL


title: Subject16_before

description: No intervention


title: Subject12_after

description: Participated in red meat intervention

source_name: Human colon biopsies after intervention

value: after


title: Tamoxifen Cre Control CTL, biological replicate 2

description:
Gene expression data from  C57BL/6GT(ROSA)26tm9(creEsr1)Arte (TamoxCre)  control CTL treated with 4OHT
TamoxCreKG168

source_name: CTL made from Tamox Cre splenocytes and treated with 4OHT


title: Tg(hsp:70:wnt8a-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep3

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:wnt8a-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep3

value: embryos heat-shocked for 30 mins, posterior presomitic mesoderm dissected after 1 hour


title: Wild-type embryos heat-shocked for 30 mins and posterior PSM dissected after 30 mins, biological rep3

description:
Gene expression data from heat-shocked embryos
Wild-type embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 30 minutes ,  biological rep3

value: embryos heat-shocked for 30 mins, posterior presomitic mesoderm dissected after 30 mins

value: wild-type AB


title: CLL 164-02 Control

description: Control cells

value: Control

value: negatively selected cells


title: Subject10_after

description: Participated in red meat intervention

value: female


title: Subject17_after

description: Participated in red meat intervention

value: IBS


title: Tg(hsp:70:wnt8a-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep2

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:wnt8a-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep2

value: posterior PSM


title: Wild-type embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep4

description:
Gene expression data from heat-shocked embryos
Wild-type embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep4


title: Liver sample of WT mouse 3

description: Expression profile of liver sample from control mouse, biological replicate 3.

hyb_protocol: 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix Mouse Genome 430 2.0 GeneChips.

data_processing: The raw signal intensities were proprocessed in R (version 2.9.1) using Bioconductor's gcrma package (version 2.16.0).

source_name: Six week old male C57BL/6 mouse.

growth_protocol: The animals were raised and cared for in accordance with the guidelines established by the Innsbruck Medical University, Austria

extract_protocol: Liver samples from 6 week old p14 KO and control mice (gender matched) were homogenized in 1ml of Trizol Reagent using a tissue hand-homogenizer (5 ml, Unilab Politakis OHG). The extraction of total RNA was performed according to the manufacturer's directions, and the RNA was subsequently purified by passage through Rneasy mini-columns (QIAGEN, Valencia, CA).

value: liver

value: p14 WT

tag: genetic background


title: Subject17_before

description: Participated in red meat intervention


title: Tg(hsp:70:wnt8a-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep1

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:wnt8a-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep1

value: 12-somite stage


title: Tg(hsp:70:DeltaTcF-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep4

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:DeltaTcF-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep4

value: heat-shocked for 30 mins, posterior presomitic mesoderm dissected after 1 hour


title: Wild-type embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep1

description:
Gene expression data from heat-shocked embryos
Wild-type embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep1


title: Liver sample of WT mouse 2

description: Expression profile of liver sample from control mouse, biological replicate 2.


title: PDK1 null CTL, biological replicate 3

description:
Gene expression data from PDK1 null CTL ( C57BL/6GT(ROSA)26tm9(creEsr1)Arte PDK1fl/fl treated with 4OHT)
TamoxCrePDK1KC283

value: cytotoxic T-lymphocytes (CTL)


title: Subject14_before

description: No intervention

value: before


title: Tamoxifen Cre Control CTL, biological replicate 3

description:
Gene expression data from  C57BL/6GT(ROSA)26tm9(creEsr1)Arte (TamoxCre)  control CTL treated with 4OHT
TamoxCreKG169

value: control


title: Subject8_before

description: Participated in red meat intervention


title: Subject7_after

description: Participated in red meat intervention

value: male


title: Subject7_before

description: Participated in red meat intervention


title: Wild-type embryos heat-shocked for 30 mins and posterior PSM dissected after 30 mins, biological rep4

description:
Gene expression data from heat-shocked embryos
Wild-type embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 30 minutes ,  biological rep4


title: Tg(hsp:70:DeltaTcF-gfp) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep1

description:
Gene expression data from heat-shocked embryos
Tg(hsp:70:DeltaTcF-gfp) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep1


title: Wild-type embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep2

description:
Gene expression data from heat-shocked embryos
Wild-type embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep2


title: Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep3

description:
Gene expression data from heat-shocked embryos
Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep3


title: Subject12_before

description: Participated in red meat intervention

value: IBD


title: Subject11_before

description: No intervention


title: Liver sample of p14 KO mouse 3

description: Expression profile of liver sample from p14 KO mouse, biological replicate 3.

source_name: Six week old male C57BL/6 mouse with conditional liver p14 knock out.

value: p14 KO


title: Subject6_after

description: Participated in red meat intervention

value: after


title: Wild-type embryos heat-shocked for 30 mins and posterior PSM dissected after 30 mins, biological rep2

description:
Gene expression data from heat-shocked embryos
Wild-type embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 30 minutes ,  biological rep2

value: embryos heat-shocked for 30 mins, posterior presomitic mesoderm dissected after 30 mins

value: wild-type AB


title: Wild-type embryos heat-shocked for 30 mins and posterior PSM dissected after 30 mins, biological rep1

description:
Gene expression data from heat-shocked embryos
Wild-type embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 30 minutes ,  biological rep1


title: Subject9_before

description: Participated in red meat intervention


title: Subject10_before

description: Participated in red meat intervention


title: 4FTSC L2

city: Bonn

first: Peter

last: Kuckenberg

address: Sigmund Freud Str. 25

department: Institut of Pathology

country: Germany

institute: University Medical School Bonn

hyb_protocol: Standard Affymetrix protocol

scan_protocol: After hybridization, arrays were washed and stained automatically on a GeneChip® Fluidics Station 450 (Affymetrix) and scanned with a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Normalization and statistical data analyses were performed by an RMA algorithm performed with GeneSpring GX 10 software (Agilent)

source_name: undifferentiated Oct4, Sox2, cMyc, Klf4 doxycycline inducible mouse trophoblast stem cells

label_protocol: Affymetrix GeneChip® Mouse Genome 430 2.0 arrays (Affymetrix) were hybridized with 15 µg biotin-labeled cRNA, obtained from 5 μg total RNA, using the GeneChip® One-Cycle labeling kit (Affymetrix).

growth_protocol: 4FTSCs were grown feeder free with 30% feeder conditioned medium, RPMI, FGF4 and heparin as per Tanaka et al, 1998 PMID:9851926

extract_protocol: Total RNA was extracted from cells using the RNAeasy Mini kit, including DNAse digestion (Qiagen)


title: Subject8_after

description: Participated in red meat intervention


title: Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep1

description:
Gene expression data from heat-shocked embryos
Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep1

value: embryos heat-shocked for 30 mins, posterior presomitic mesoderm dissected after 1 hour


title: ESC

source_name: undifferentiated mouse embryonic stem cells

growth_protocol: cells were cultured under embryonic stem cell condition with Lif


title: TSC-iPSC L2K1

source_name: trophoblast stem cell derived induced pluripotent stem cells line2, clone1


title: Wild-type embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep3

description:
Gene expression data from heat-shocked embryos
Wild-type embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep3


title: Liver sample of WT mouse 1

description: Expression profile of liver sample from control mouse, biological replicate 1.


title: Liver sample of p14 KO mouse 2

description: Expression profile of liver sample from p14 KO mouse, biological replicate 2.


title: Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep2

description:
Gene expression data from heat-shocked embryos
Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep2


title: 14120031 - UPRT-line12 repet2 vs. col0 repet2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Transcriptomic analysis of the overexpression of UPTR.

hyb_protocol: col0 repet2 Cy5 / UPRT-line12 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0. Cy3: pmt voltage 532nm, 480V, laser power 35%. Cy5: 635nm, pmt voltage 480V, laser power 30%.

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: Whole plant. Media=MS(1/2). Hygrometry=50%. Temperature=21°C. Light=16h light and 8h dark cycle.

extract_protocol: col0 repet2:10ug. Qiagen RNeasy kit.

treatment_protocol: Name: Mestradiol - compound based treatment - mestradiol,mannitol,mestradiol:. 11d-old-seedlings grown on MS(1/2) plates. Transfer into 6-well-plates filled with 3ml 0.01% silwet, 0.2% EtOH or 0.01% silwet, 40µ Mestradiol (from 500xstock in EtOH), seedlings gently transferred with forceps, placed into the wells. Most leaves are submerged.

tag: ecotype

value: Columbia

value: wt

value: whole plant

value: 11 days

extract_protocol: UPRT-line12 repet2:10ug. Qiagen RNeasy kit.

value: UPRT transgenic


title: Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 mins and posterior PSM dissected after 1 hour, biological rep4

description:
Gene expression data from heat-shocked embryos
Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 1 hour ,  biological rep4

value: posterior PSM

value: 12-somite stage


title: TSC-iPSC L2K2

source_name: trophoblast stem cell derived induced pluripotent stem cells line2, clone2


title: Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 mins and posterior PSM dissected after 30 mins, biological rep3

description:
Gene expression data from heat-shocked embryos
Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 30 minutes ,  biological rep3


title: Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 mins and posterior PSM dissected after 30 mins, biological rep4

description:
Gene expression data from heat-shocked embryos
Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 30 minutes ,  biological rep4


title: Liver sample of p14 KO mouse 1

description: Expression profile of liver sample from p14 KO mouse, biological replicate 1.

value: liver


title: CbCln6 mutant 3

city: Boston

first: Susan

last: Cotman

state: MA

address: 185 Cambridge Street

institute: MGH

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: gcRMA.

source_name: Immortalized cell line, C57BL6 Cln6 mutant

label_protocol: Standard Affymetrix protocol.

growth_protocol: DMEM, 10% FBS, 24mM KCl, pen/strep/glutamine, 200µg/ml G418, 5% CO2, 33˚C.

extract_protocol: Trizol extraction and Qiagen Rneasy mini coulmn clean up.

treatment_protocol: Untreated.

tag: phenotype

value: Cln6 mutant

value: Cln6 nclf/nclf

value: cerebellar cells, nestin-positive, GFAP-negative

tag: differentiation state

value: neuronal precursor cells


title: 14120030 - col0 repet2 vs. UPRT-line12 repet2

hyb_protocol: UPRT-line12 repet2 Cy5 / col0 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CbCln6 mutant 2


title: Tamoxifen Cre Control CTL, biological replicate 1

description:
Gene expression data from C57BL/6GT(ROSA)26tm9(creEsr1)Arte (TamoxCre) control CTL treated with 4OHT
TamoxCreKG167

value: cytotoxic T-lymphocytes (CTL)

value: control


title: Subject4_before

description: No intervention

source_name: Human colon biopsies before intervention

tag: subject number

tag: disease status

value: IBS

value: male

value: before


title: CbCln6 mutant 1

tag: cell type


title: Subject3_after

description: Participated in red meat intervention

value: female

tag: intervention status

value: after


title: Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 mins and posterior PSM dissected after 30 mins, biological rep2

description:
Gene expression data from heat-shocked embryos
Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 30 minutes ,  biological rep2

value: embryos heat-shocked for 30 mins, posterior presomitic mesoderm dissected after 30 mins


title: 14120029 - UPRT-line9 repet2 vs. col0 repet2

hyb_protocol: col0 repet2 Cy5 / UPRT-line9 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia

value: wt

value: whole plant

value: 11 days

extract_protocol: UPRT-line9 repet2:10ug. Qiagen RNeasy kit.


title: 14120025 - col0 repet2 vs. UPRT-line3 repet2

hyb_protocol: UPRT-line3 repet2 Cy5 / col0 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: UPRT-line3 repet2:10ug. Qiagen RNeasy kit.

value: UPRT transgenic


title: 14120024 - UPRT-line1 repet2 vs. col0 repet2

hyb_protocol: col0 repet2 Cy5 / UPRT-line1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: UPRT-line1 repet2:10ug. Qiagen RNeasy kit.


title: Subject3_before

description: Participated in red meat intervention


title: CbCln6 wild-type 2

source_name: Immortalized cell line, C57BL6 wild-type

value: wild-type


title: Subject5_before

description: No intervention

value: IBD


title: 14120028 - col0 repet2 vs. UPRT-line9 repet2

hyb_protocol: UPRT-line9 repet2 Cy5 / col0 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 3 hour RA treatment, biological rep3

description:
Gene expression data from 3 hour RA treated embryos
3 hour RA treatment, biological rep3

value: 3 hour RA treatment

value: posterior PSM

value: wild-type AB

value: 12-somite stage


title: 14120026 - UPRT-line3 repet2 vs. col0 repet2

hyb_protocol: col0 repet2 Cy5 / UPRT-line3 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Subject2_after

description: Participated in red meat intervention


title: Subject2_before

description: Participated in red meat intervention


title: CbCln6 wild-type 1

value: cerebellar cells, nestin-positive, GFAP-negative

value: neuronal precursor cells


title: 3 hour RA treatment, biological rep2

description:
Gene expression data from 3 hour RA treated embryos
3 hour RA treatment, biological rep2


title: Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 mins and posterior PSM dissected after 30 mins, biological rep1

description:
Gene expression data from heat-shocked embryos
Tg(hsp701;dnfgfr1-EGFP) embryos heat-shocked for 30 minutes and posterior presomitic mesoderm is dissected 30 minutes ,  biological rep1


title: CbCln6 wild-type 3


title: 14120022 - col0 repet2 vs. UPRT-line1 repet2

hyb_protocol: UPRT-line1 repet2 Cy5 / col0 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14120021 - UPRT-line12 repet1 vs. col0 repet1

hyb_protocol: col0 repet1 Cy5 / UPRT-line12 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: col0 repet1:10ug. Qiagen RNeasy kit.

extract_protocol: UPRT-line12 repet1:10ug. Qiagen RNeasy kit.


title: CbCln3 mutant 2

source_name: Immortalized cell line, CD1 Cln3 mutant

value: Cln3 mutant

value: Cln3 ∆ex7/8/∆ex7/8


title: 14120020 - col0 repet1 vs. UPRT-line12 repet1

hyb_protocol: UPRT-line12 repet1 Cy5 / col0 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 3 hour RA treatment, biological rep1

description:
Gene expression data from 3 hour RA treated embryos
3 hour RA treatment, biological rep1

hyb_protocol: Each chip was hybridized to 13 μg fragmented cRNA. Arrays were hybridized according to the manufacturer’s instructions.


title: shp53, replicate 3

city: Houston

first: Mien-chie

last: Hung

state: Texas

address: 1515 Holcomb Blvd

department: Molecular and Cellular Oncology

institute: M.D. Anderson Cancer Center

hyb_protocol: According to the Exiqon protocol.

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 was used to read the raw intensity of the image.

data_processing: The ratio of red signal to green signal was calculated after background subtraction and normalization using the non-linear regression algorithm.

source_name: MCF12A, shp53

label_protocol: According to the Exiqon protocol.

growth_protocol: Standard growth medium for the MCF12A cell line.

extract_protocol: Total RNA using the Rneasy mini plus kit according to the Qiagen protocol.

treatment_protocol: Retroviral infection with retrovirues expressing shp53 or shVector.

tag: cell line

tag: retroviral expression

source_name: MCF12A, shVector

value: shVector


title: Subject6_before

description: Participated in red meat intervention

hyb_protocol: Hybridization according to Agilent instructions on 4x44K human whole genome microarrays.

tag: gender

value: male

value: before


title: shp53, replicate 2


title: CbCln3 mutant 3


title: IgG(Cy5) vs. Input(Cy3)

city: wuhan

first: haifang

last: qiu

address: lion street 1

country: China

institute: Huazhong Agricultural University

hyb_protocol: Hybridization, and washing were carried out according to the manufacturer's instruction (Aviva, AK-0524).

scan_protocol: Slides were scanned with the DNA Microarray Scanner BA (Agilent Technologies, Santa Clara, CA, USA)

data_processing: Raw data (LSR files) were read into the R statistical computation environment for preprocessing and data analysis. Local background intensities were subtracted from raw signals and negative values were replaced with small positive ones. Signals were then normalized using a variance stabilization method described in (Gibbons et al., 2005; Huber et al., 2002) and implemented in the vsn Bioconductor package. Functional annotation of the target genes, including classification and pathway analysis, was carried out using the DAVID tool. Promoter sequences were analyzed for the presence of putative transcription factor binding sites using the TESS (Transcription Element Search System) web tool available from the Computational Biology and Informatics Laboratory at the University of Pennsylvania. The complete data matrix containing ratio values Ab/IgG, as well as the matrix with target genes of TEAD1 are supplied as supplementary files on the Series record.

source_name: Skeletal muscle_Mouse_Adult_IgG(Cy5)

label_protocol: The ChIP DNA samples were amplified and labeled by Aviva's ChIP-GLAS system. Briefly, ChIP, IgG, and input DNAs were biotinylated and annealed to the M8K-Oligo-Mix. The ChIP DNA samples were then amplified by ligation mediated PCR with T3 and T7 based primers (25 cycles), labeled with Atto 550 or 647, and hybridized onto the chip.

growth_protocol: Skeletal muscle tissues were collected from adult Kunming mice, then frozen in liquid  nitrogen, and stored at −80 °C.

extract_protocol: After lysis, samples were sonicated to an average DNA length of 1000 bp . Following chromatin sonication, the lysates were precipitated overnight using 5 μg of mouse anti-TEAD1 monoclonal antibody (BD) and anti-IgG antibody (BD) as a negative control. Two independent ChIP experiments were performed for each antibody. Protein A-agarose beads were added to purify immune complexes. Cross-linking was reversed by heating the samples overnight at 65 °C. RNA was degraded with RNase A for 4 h at 65 °C, and proteins were degraded by proteinase K treatment for 2 h at 45 °C. The DNA was further purified. The ChIP-captured DNA of samples, IgG DNA and the total input DNA consisting of genomic DNA prepared from control cross-linked tissues were prepared for amplification.

treatment_protocol: 1 g of tissue was fixed with formaldehyde, neutralized with glycine and rinsed with cold phosphate-buffered saline.

value: Kunming

tag: developmental stage

value: adult

value: skeletal muscle

tag: antibody

value: anti-IgG antibody (BD, 555787)

source_name: Skeletal muscle_Mouse_Adult_Input(Cy3)


title: CbCln3 mutant 1

tag: strain


title: Ab(Cy5) vs. Input(Cy3)

source_name: Skeletal muscle_Mouse_Adult_Ab(Cy5)

tag: tissue

value: anti-TEAD1 monoclonal antibody (BD, 610923)


title: 14120018 - col0 repet1 vs. UPRT-line9 repet1

hyb_protocol: UPRT-line9 repet1 Cy5 / col0 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: UPRT-line9 repet1:10ug. Qiagen RNeasy kit.

value: Columbia

value: UPRT transgenic

value: whole plant

tag: age

value: 11 days

value: wt


title: 14120019 - UPRT-line9 repet1 vs. col0 repet1

hyb_protocol: col0 repet1 Cy5 / UPRT-line9 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype


title: HMEC, replicate 3

source_name: HMEC CD24-CD44+

growth_protocol: Lonza medium for HMEC cultures. HMEC cells were provided by Dr. Robert Weinberg (Whitehead institute, MIT).

treatment_protocol: Sorted HMEC cells for CD24-CD44+ and non-CD24-CD44+ cell populations using flow cytometry.

value: human mammary epithelial cells

tag: cell population

source_name: HMEC non-CD24-CD44+


title: 14120016 - UPRT-line3 repet1 vs. col0 repet1

hyb_protocol: col0 repet1 Cy5 / UPRT-line3 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

extract_protocol: UPRT-line3 repet1:10ug. Qiagen RNeasy kit.


title: 14120015 - col0 repet1 vs. UPRT-line3 repet1

hyb_protocol: UPRT-line3 repet1 Cy5 / col0 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CbCln3 wild-type 3

hyb_protocol: Standard Affymetrix protocol.

source_name: Immortalized cell line, CD1 wild-type

tag: phenotype

value: wild-type

value: cerebellar cells, nestin-positive, GFAP-negative

value: neuronal precursor cells


title: CbCln3 wild-type 1

tag: differentiation state


title: CbCln3 wild-type 2


title: Subject9_after

description: Participated in red meat intervention

source_name: Human colon biopsies after intervention

tag: subject number

value: IBD

value: after


description:
Gene expression data from 3 hour DMSO treated embryos
3 hour DMSO treatment as a control for RA treatment, biological rep4

source_name: Zebrafish embryos paraxial mesoderm

extract_protocol: Trizol extraction of total RNA was performed.

tag: protocol

value: 3 hour DMSO treatment

value: posterior PSM

value: wild-type AB

value: 12-somite stage


title: 1.5 hour RA treatment, biological rep4

description:
Gene expression data from 1.5 hour RA treated embryos
1.5 hour RA treatment, biological rep4

value: 1.5 hour RA treatment


description:
Gene expression data from 3 hour DMSO treated embryos
3 hour DMSO treatment as a control for RA treatment, biological rep3


title: 1.5 hour RA treatment, biological rep3

description:
Gene expression data from 1.5 hour RA treated embryos
1.5 hour RA treatment, biological rep3


title: 14120014 - UPRT-line1 repet1 vs. col0 repet1

hyb_protocol: col0 repet1 Cy5 / UPRT-line1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: UPRT-line1 repet1:10ug. Qiagen RNeasy kit.


description:
Gene expression data from 3 hour DMSO treated embryos
3 hour DMSO treatment as a control for RA treatment, biological rep2


title: shp53, replicate 1

value: shVector


title: HMEC, replicate 2

tag: cell type


description:
Gene expression data from 3 hour DMSO treated embryos
3 hour DMSO treatment as a control for RA treatment, biological rep1


title: 14162197 - col0 repet1 vs. UPRT-line1 repet1

description: Transcriptomic analysis of the overexpression of UPTR.

hyb_protocol: UPRT-line1 repet1 Cy5 / col0 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Columbia


title: HMEC, replicate 1


title: 1.5 hour RA treatment, biological rep1

description:
Gene expression data from 1.5 hour RA treated embryos
1.5 hour RA treatment, biological rep1


description:
Gene expression data from 1.5 hour DMSO treated embryos
1.5 hour DMSO treatment as a control for RA treatment, biological rep4

value: 1.5 hour DMSO treatment


title: 1.5 hour RA treatment, biological rep2

description:
Gene expression data from 1.5 hour RA treated embryos
1.5 hour RA treatment, biological rep2


title: Induced 2

city: Braunschweig

first: Andre

last: Lemme

address: Inhoffenstr. 7

department: Cell Biology

institute: Helmholtz Centre for Infection Research

description: Biological replicate 1 of 2: CSP-induced cells compared to non-induced cells.

hyb_protocol: 450 ng of each Cy3- and Cy5-labeled RNA was fragmented and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the manufacturer’s instructions.

scan_protocol: The arrays were scanned using the Agilent DNA Microarray Scanner. Raw data were extracted using the Agilent Feature Extraction software.

data_processing: The algorithm of the Agilent software was used for background correction and normalization. Afterwards, the p-values for differential expression were adjusted for false-discovery rate using the method by Benjamini and Hochberg (BH).

organism: Streptococcus mutans

source_name: All cells with CSP

label_protocol: RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: S. mutans were grown in THBY medium at 37°C aerobical (5% CO2 enriched).

extract_protocol: RNA extraction was performed using the Rneasy micro kit (Qiagen).

treatment_protocol: Induction of competence by adding peptide CSP and separation of cells with FACS.

value: wildtype

tag: induction

value: competence-stimulating peptide (CSP)

value: unsorted

source_name: Cells not induced with CSP


title: Induced 1

description: Biological replicate 2 of 2: CSP-induced cells compared to non-induced cells.