title: T47D cells T6 hours Rep 1

description: Gene expression after 24 hours starvation and 6 hours R5020 control


title: T47D cells T0 hours Rep 2

status: Public on Dec 01 2015

type: RNA

city: Barcelona

first: Roni

last: Wright

address: C/ Doctor Aiguader, 88

country: Spain

institute: CRG-Centre de Regulació Genòmica

description: Gene expression after 24 hours starvation

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing:
The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

molecule: total RNA

organism: Homo sapiens

source_name: T47D cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: T47D were seeding in RPM1 minus phenol red, 10% CHS FCS, 24 hours prior to hormone addition cells were starved RPM1 minus phenol red minus FCS.

extract_protocol: Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions

treatment_protocol: Cells were treated with R5020 for 6 hours.

tag: tissue

value: breast

tag: cell line

tag: time hormone (r5020) hours


title: T47D cells T0 hours Rep 3 treated NUDIXsi

description: Gene expression after 24 hours starvation NUDIX5 inhibition

tag: treatment

value: NUDIX5 specific siRNA


title: T47D cells T6 hours Rep 2


title: T47D cells T0 hours Rep 1


title: T47D cells T6 hours Rep 1 treated NUDIXsi

description: Gene expression after 24 hours starvation and 6 hours R5020, presence NUDIX inhibition


title: siControl repeat 2

city: Bristol

first: James

last: Uney

address: Medical School, University Walk

department: School of Clinical Sciences

country: United Kingdom

institute: University of Bristol

description: siControl

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix GeneChip® Scanner

data_processing:
AltAnalyze processes raw Affymetrix image files (CEL files) using the RMA algorithm.
Ensembl build: Assembly build-34    genome build: hg16    AltAnalyze version number information: AltAnalyze version 2.0.7
HuEx-1_0-st-v2

label: biotin

source_name: SHSY-5Y cells

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

growth_protocol: Standard cell culture in DMEM:F12 media

extract_protocol: RNA was extracted with Ambion mirVana™ miRNA Isolation Kit using total RNA protocol.

treatment_protocol: Transfection with siRNA, harvest after 24 hrs.

tag: disease

value: Neuroblastoma


title: T47D cells T0 hours Rep 1 treated NUDIXsi


title: siControl repeat 1

description: siControl


title: Normal_DNA_17395

type: genomic

city: Novara

first: Valeria

last: Spina

state: NO

address: Solaroli, 17

department: Translational Medicine

country: Italy

institute: Amedeo Avogadro University of Eastern Piedmont

description:
22N
Hybridized to Cytoscan HD array Affymetrix

hyb_protocol: Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the diagested DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Affymetrix, Santa Clara, CA,US)  to obtain biotin labeled DNA, as per manufacturer’s instruction.

scan_protocol: The Arrays were washed using affymetrix fluidics stations FS450 and scanned using the Gene Chip Scanner 3000.

data_processing: Raw data passed quality control were further analyzed by Affymetrix® Chromosome Analysis Suite (Affymetrix, Santa Clara, CA, US). CEL files were generated from the scanned array image files by the Affymetrix GeneChip Command Console Software and were imported into the Affymetrix Chromosome Analysis Suite v1.2.0 Software. Copy number and genotyping data files (cyhd.cychp and cyhd.txt files) were generated using ChAS (cyhd.cychp files are displayed in the Sample data table below). The identification of regions of abnormal copy number was performed both by ChAs and by a pipeline that embed the circular binary segmentation as detailed in previously published papers: normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm (NMZL_cnmz.txt: matrix of the 35 NMZL and 23 paired normal DNAs). All the CNAs were visually inspected by dChip sopftware (https://sites.google.com/site/dchipsoft/).

label: Biotin

molecule: genomic DNA

source_name: genomic DNA extracted from tumor free bone marrow of patient 14054

growth_protocol: Not applicable

extract_protocol: Genomic DNA was purified by cell lysis followed by digestion with proteinase K, “salting out” extraction, and ethanol precipitation. DNA was quantified by the Quant-iT PicoGreen reagent (Invitrogen). All DNA samples were verified for integrity by 0.8% agarose gel electrophoresis.

treatment_protocol: Not applicable

tag: sample id

tag: disease state

value: NMZL

tag: individual

value: patient 14054

value: granulocytes


title: Normal_DNA_16712

description:
19N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 10864

label_protocol: Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the diagested DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Affymetrix, Santa Clara, CA,US)  to obtain biotin labeled DNA, as per manufacturer’s instruction.

value: patient 10864

value: tumor free bone marrow


title: Normal_DNA_17338

description:
23N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from tumor free bone marrow of patient 17189

value: patient 17189


title: Normal_DNA_16748

description:
20N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from granulocytes of patient 11323

value: patient 11323

value: saliva


title: Normal_DNA_17611

description:
13N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 17184

value: patient 17184


title: Normal_DNA_17999

description:
18N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 17931

value: patient 17931


title: Normal_DNA_18074

description:
12N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from tumor free bone marrow  of patient 14059

value: patient 14059


title: Normal_DNA_17336

description:
21N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from tumor free bone marrow of patient 17177

value: patient 17177


title: Normal_DNA_16747

description:
4N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from granulocytes of patient 9979

value: patient 9979


title: Normal_DNA_17575

description:
15N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from tumor free bone marrow of patient 14056

value: patient 14056


title: Normal_DNA_17705

description:
14N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from tumor free bone marrow of patient 17707

value: patient 17707


title: Nodal_Marginal_Zone_Lymphoma_17183

description:
32T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17183 affected by NMZL sampled at diagnosis

value: patient 17183

value: lymphonode sampled at diagnosis


title: Normal_DNA_16955

description:
8N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 11801

value: NMZL

value: patient 11801

value: T lymphocytes


title: Normal_DNA_16763

description:
5N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 10063

value: patient 10063


title: Normal_DNA_17935

description:
16N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 17933

value: patient 17933


title: Normal_DNA_16818

description:
9N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 16817

value: patient 16817


title: Normal_DNA_17863

description:
10N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from T lymphocytes of patient 16814

value: patient 16814

value: tumor free bone marrow


title: Nodal_Marginal_Zone_Lymphoma_17176

description:
30T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17176 affected by NMZL sampled at diagnosis

value: patient 17176


title: Normal_DNA_16716

description:
2N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 10347

value: patient 10347

value: saliva


title: Nodal_Marginal_Zone_Lymphoma_17930

description:
35T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17930 affected by NMZL sampled at diagnosis

value: patient 17930


title: Normal_DNA_15593

description:
11N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from granulocytes of patient 4723

value: patient 4723


title: Normal_DNA_16764

description:
6N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from granulocytes of patient 16781

value: patient 16781


title: Normal_DNA_16696

description:
7N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 16815

value: patient 16815

value: granulocytes


title: Normal_DNA_18001

description:
17N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 17932

value: patient 17932


title: Nodal_Marginal_Zone_Lymphoma_17188

description:
33T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17188 affected by NMZL sampled at diagnosis

value: NMZL

value: patient 17188

value: lymphonode sampled at diagnosis


title: Nodal_Marginal_Zone_Lymphoma_14053

description:
31T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 14053 affected by NMZL sampled at diagnosis

value: patient 14053


title: Nodal_Marginal_Zone_Lymphoma_17190

description:
34T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17190 affected by NMZL sampled at diagnosis

value: patient 17190


title: Normal_DNA_16751

description:
3N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 16240

value: patient 16240


title: Normal_DNA_16695

description:
1N
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from saliva of patient 4672

value: patient 4672


title: Nodal_Marginal_Zone_Lymphoma_16820

description:
29T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from axillary lymphonode of patient 16820 affected by NMZL sampled at diagnosis

value: patient 16820


title: Nodal_Marginal_Zone_Lymphoma_16819

description:
28T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lateral cervical lymphonode of patient 16819 affected by NMZL sampled at diagnosis

value: patient 16819


title: Nodal_Marginal_Zone_Lymphoma_14057

description:
25T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 14057 affected by NMZL sampled at diagnosis

value: patient 14057


title: Nodal_Marginal_Zone_Lymphoma_10864

description:
19T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 10864 affected by NMZL sampled at diagnosis

value: patient 10864


title: Nodal_Marginal_Zone_Lymphoma_11323

description:
20T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells  of patient 11323 affected by NMZL sampled at diagnosis

value: patient 11323


title: Nodal_Marginal_Zone_Lymphoma_14054

description:
22T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 14054 affected by NMZL sampled at diagnosis

value: patient 14054


title: Nodal_Marginal_Zone_Lymphoma_17177

description:
21T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17177 affected by NMZL sampled at diagnosis

value: patient 17177


title: Nodal_Marginal_Zone_Lymphoma_17184

description:
13T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17184 affected by NMZL sampled at diagnosis

value: patient 17184


title: Nodal_Marginal_Zone_Lymphoma_14055

description:
24T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 14055 affected by NMZL sampled at diagnosis

value: patient 14055


title: Nodal_Marginal_Zone_Lymphoma_17707

description:
14T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17707 affected by NMZL sampled at diagnosis

value: patient 17707


title: Nodal_Marginal_Zone_Lymphoma_16816

description:
27T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from supraclavicular lymphonode of patient 16816 affected by NMZL sampled at diagnosis

value: NMZL

value: patient 16816


title: Nodal_Marginal_Zone_Lymphoma_14058

description:
26T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 14058 affected by NMZL sampled at diagnosis

value: patient 14058

value: lymphonode sampled at diagnosis


title: Nodal_Marginal_Zone_Lymphoma_16815

description:
7T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from inguinal lymphonode of patient 16815 affected by NMZL sampled at diagnosis

value: patient 16815


title: Nodal_Marginal_Zone_Lymphoma_17933

description:
16T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17933 affected by NMZL sampled at diagnosis

value: patient 17933


title: Nodal_Marginal_Zone_Lymphoma_4723

description:
11T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 4723 affected by NMZL sampled at diagnosis

value: patient 4723


title: Nodal_Marginal_Zone_Lymphoma_11801

description:
8T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 11801 affected by NMZL sampled at diagnosis

value: patient 11801


title: Nodal_Marginal_Zone_Lymphoma_14056

description:
15T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 14056 affected by NMZL sampled at diagnosis

value: patient 14056


title: Nodal_Marginal_Zone_Lymphoma_16814

description:
10T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lateral cervical lymphonode of patient 16814 affected by NMZL sampled at diagnosis

value: patient 16814


title: Nodal_Marginal_Zone_Lymphoma_17932

description:
17T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17932 affected by NMZL sampled at diagnosis

value: patient 17932


title: Nodal_Marginal_Zone_Lymphoma_17931

description:
18T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17931 affected by NMZL sampled at diagnosis

value: patient 17931


title: Nodal_Marginal_Zone_Lymphoma_16781

description:
6T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 16781 affected by NMZL sampled at diagnosis

value: patient 16781


title: Nodal_Marginal_Zone_Lymphoma_9979

description:
4T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 9979 affected by NMZL sampled at diagnosis

value: patient 9979


title: Nodal_Marginal_Zone_Lymphoma_10063

description:
5T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from axillary lymphonode cells of patient 10063 affected by NMZL sampled at diagnosis

value: patient 10063


title: Nodal_Marginal_Zone_Lymphoma_14059

description:
12T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 14059 affected by NMZL sampled at diagnosis

value: patient 14059


title: Nodal_Marginal_Zone_Lymphoma_17189

description:
23T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 17189 affected by NMZL sampled at diagnosis

value: patient 17189


title: CMML_111_BM

first: Laura

last: Palomo

state: Barcelona

address: Carretera de Can Ruti, Camí de les Escoles, s/n

department: Campus ICO-GTiP

institute: Josep Carreras Leukemia Research Institute

description: Hybridized to Cytoscan_HD

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

scan_protocol: The Affymetrix 450 fluidics station and 3000 G7 gene scanner were used to wash, stain and scan the arrays

data_processing: SNP-A data were analyzed with Chromosome Analysis Suite Version 2.0.1.2 (Affymetrix), using annotations of genome version GRCh37 (hg19)

source_name: Bone marrow

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from whole bone marrow or whole peripheral blood samples using the QiaAmp DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose 1% gel electrophoresis.

value: chronic myelomonocytic leukemia


title: CMML_110_BM

description: Hybridized to Cytoscan_HD


title: Nodal_Marginal_Zone_Lymphoma_10347

description:
2T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 10347 affected by NMZL sampled at diagnosis

value: NMZL

value: patient 10347


title: Nodal_Marginal_Zone_Lymphoma_16240

description:
3T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 16240 affected by NMZL sampled at diagnosis

value: patient 16240

value: lymphonode sampled at diagnosis


title: Nodal_Marginal_Zone_Lymphoma_16817

description:
9T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from inguinal lymphonode of patient 16817 affected by NMZL sampled at diagnosis

value: patient 16817


title: CMML_109_BM

description: Hybridized to Cytoscan_HD


title: Replicate3_gcn2_mock treated_total

city: Knoxville

first: Albrecht

middle: G

last: von Arnim

state: TN

address: M407 Walters Life Science Building

department: Biochemistry, Cellular and Molecular Biology

country: USA

institute: The University of Tennessee

description: total RNA

hyb_protocol: Following fragmentation, cRNA were hybridized to Arabidopsis ATH1 Genome Arrays.

scan_protocol: Standard protocol and instrumentation

data_processing: Raw signal intensities for each probe set were extracted from CEL files using RMA using R/Bioconductor (http://www.r-project.org/, version 2.13.2, released on 09/30/2011), and the affy package. MAS5.0 was used to assign P(resent) calls indicating reliable gene detection.

organism: Arabidopsis thaliana

source_name: 10 day old seedling

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

growth_protocol: Medium:   GM medium with 1% sucrose and 0.8% agar,  in petri plates wrapped with parafilm that was pierced to allow gas exchange; Light: 16 h long day, from fluorescent bulbs at ~80umole/m2/second;Temperature:22oC

extract_protocol: The aerial part of the seedlings were flooded in liquid nitrogen and scrapped off from the medium.  Polysome gradient and RNA purification were carried out essentially as described in Kim et al., (2007)Genome Biology 8:R60 with a modified gradient of 30% to 50% sucrose.   The top 4 fractions were pooled as non-polysomal (NP), the next 4 fractions as small polysomal (SP) and the bottom 4 fractions were pooled as large polysomal (LP).  Labeling and hybridization to Affymetrix ATH1 microarrays (platform  GPL198)were performed following standard protocols.

treatment_protocol: At 2 hours after light on, seedlings were submerged in  0.5mM chlorosufuron (5 mM stock was dissolved in 20% Acetone, diluted 1:10,000 in ddH2O)) or solvent only for 1 minute, and the liquid was removed and the seedlings were returned to the growth chamber and incubated for 2 hours.

tag: line

value: Landsberg erecta

value: aerial part

tag: genotype/variation

value: mock

tag: rna type

value: total RNA


title: CMML_108_BM

description: Hybridized to Cytoscan_HD


title: Mouse 8 HF KO

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Total RNA isolated from gastrocnemius muscle from FoxO1,3,4 knockdown mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 8.

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MoGene 2.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented within the R statistical software environment using the 'oligo' package (Bioconductor project).

organism: Mus musculus

source_name: Gastrocnemius muscle, FoxO1,3,4 knockdown

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

growth_protocol: From 7-8 weeks of age, male FVB/n mice were fed a high-fat diet containing 58% fat, 25.5% carbohydrate and 16.4% protein for 8 weeks. All animals were maintained under pathogen-free condition at the York University vivarium on a 12/12h light-dark cycle with food and water available ad libitum.

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

treatment_protocol: n=8 mice harbouring an endothelial directed deletion of FoxO1/3/4 (Mx1-Cre+);FoxO1,3,4L/L) were contrasted to n=8 MxCre-;FoxO1,3,4L/L littermates. At 4-5 weeks of age, these mice received a series of three polyinosine:cytidine (pI:pC) injections to induce transient activation of the Mx1 promoter resulting in Cre expression and subsequent deletion of floxed FoxO alleles. Animals were sacrificed at 16 weeks of age and total RNA was isolated from gastrocnemius muscle.

tag: strain/background

value: FVB/n

value: FoxO1,3,4 knockdown

tag: Sex

value: male

tag: age

value: 16 weeks

value: skeletal muscle (gastrocnemius)

value: high-fat diet

tag: treatment duration

value: 8 weeks

tag: subject

value: biological replicate 8


title: CMML_106_BM

description: Hybridized to Cytoscan_HD

value: chronic myelomonocytic leukemia


title: Replicate3_gcn2_herbicide treated_total

description: total RNA

value: 0.5mM chlorosufuron


title: CMML_105_BM

description: Hybridized to Cytoscan_HD


title: Nodal_Marginal_Zone_Lymphoma_4672

description:
1T
Hybridized to Cytoscan HD array Affymetrix

source_name: genomic DNA extracted from lymphonode cells of patient 4672 affected by NMZL sampled at diagnosis

value: NMZL

value: patient 4672


title: Mouse 7 HF KO

description: Total RNA isolated from gastrocnemius muscle from FoxO1,3,4 knockdown mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 7.

value: biological replicate 7


title: Replicate3_wild type_mock treated_total

description: total RNA

value: Landsberg erecta

value: wild type


title: Replicate3_wild type_herbicide treated_total

description: total RNA

value: aerial part


title: Mouse 6 HF KO

description: Total RNA isolated from gastrocnemius muscle from FoxO1,3,4 knockdown mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 6.

value: biological replicate 6


title: CMML_100_BM

description: Hybridized to Cytoscan_HD


title: CMML_98_BM

description: Hybridized to Cytoscan_HD


title: CMML_96_BM

description: Hybridized to Cytoscan_HD


title: Mouse 5 HF KO

description: Total RNA isolated from gastrocnemius muscle from FoxO1,3,4 knockdown mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 5.

value: FVB/n

value: biological replicate 5


title: CMML_83_BM

description: Hybridized to Cytoscan_HD


title: CMML_104_BM

description: Hybridized to Cytoscan_HD


title: CMML_74_BM

description: Hybridized to Cytoscan_HD


title: CMML_107_BM

description: Hybridized to Cytoscan_HD


title: Replicate2_gcn2_mock treated_total

description: total RNA

value: mock

value: total RNA


title: CMML_91_BM

description: Hybridized to Cytoscan_HD


title: Mouse 4 HF KO

description: Total RNA isolated from gastrocnemius muscle from FoxO1,3,4 knockdown mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 4.

value: FoxO1,3,4 knockdown

value: male

value: 16 weeks

value: skeletal muscle (gastrocnemius)

value: biological replicate 4


title: CMML_79_BM

description: Hybridized to Cytoscan_HD

value: chronic myelomonocytic leukemia


title: CMML_95_BM

description: Hybridized to Cytoscan_HD


title: CMML_75_BM

description: Hybridized to Cytoscan_HD


title: CMML_93_BM

description: Hybridized to Cytoscan_HD


title: CMML_73_BM

description: Hybridized to Cytoscan_HD


title: CMML_71_BM

description: Hybridized to Cytoscan_HD


title: CMML_77_BM

description: Hybridized to Cytoscan_HD


title: CMML_84_BM

description: Hybridized to Cytoscan_HD


title: CMML_99_BM

description: Hybridized to Cytoscan_HD


title: CMML_70_BM

description: Hybridized to Cytoscan_HD


title: CMML_82_BM

description: Hybridized to Cytoscan_HD


title: Mouse 1 HF KO

description: Total RNA isolated from gastrocnemius muscle from FoxO1,3,4 knockdown mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 1.

value: high-fat diet

value: 8 weeks

value: biological replicate 1


title: CMML_69_BM

description: Hybridized to Cytoscan_HD


title: CMML_103_BM

description: Hybridized to Cytoscan_HD


title: CMML_80_BM

description: Hybridized to Cytoscan_HD


title: CMML_86_BM

description: Hybridized to Cytoscan_HD


title: Mouse 2 HF KO

description: Total RNA isolated from gastrocnemius muscle from FoxO1,3,4 knockdown mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 2.

value: biological replicate 2


title: Mouse 3 HF KO

description: Total RNA isolated from gastrocnemius muscle from FoxO1,3,4 knockdown mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 3.

value: biological replicate 3


title: Replicate2_gcn2_herbicide treated_total

description: total RNA

value: Landsberg erecta

value: aerial part

value: 0.5mM chlorosufuron


title: Replicate1_gcn2_herbicide treated_total

description: total RNA


title: Replicate2_wild type_mock treated_total

description: total RNA

value: wild type


title: Replicate1_gcn2_mock treated_total

description: total RNA

value: mock


title: Replicate2_wild type_herbicide treated_total

description: total RNA

value: total RNA


title: Mouse 7 HF WT

description: Total RNA isolated from gastrocnemius muscle from wild type mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 7.

source_name: Gastrocnemius muscle, wild type

value: FVB/n

value: biological replicate 7


title: Mouse 5 HF WT

description: Total RNA isolated from gastrocnemius muscle from wild type mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 5.

value: male

value: 16 weeks

value: biological replicate 5


title: Replicate1_wild type_herbicide treated_total

description: total RNA


title: Mouse 8 HF WT

description: Total RNA isolated from gastrocnemius muscle from wild type mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 8.

value: skeletal muscle (gastrocnemius)

value: biological replicate 8


title: Mouse 6 HF WT

description: Total RNA isolated from gastrocnemius muscle from wild type mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 6.

value: high-fat diet

value: 8 weeks

value: biological replicate 6


title: Replicate1_wild type_mock treated_total

description: total RNA


title: Replicate3_gcn2_mock treated_SP fraction

description: small polysome fraction

value: small polysome fraction


title: Replicate3_gcn2_mock treated_LP fraction

description: large polysome fraction

value: Landsberg erecta

value: large polysome fraction


title: Mouse 4 HF WT

description: Total RNA isolated from gastrocnemius muscle from wild type mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 4.

value: biological replicate 4


title: CMML_65_BM

description: Hybridized to Cytoscan_HD

value: chronic myelomonocytic leukemia


title: Mouse 1 HF WT

description: Total RNA isolated from gastrocnemius muscle from wild type mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 1.

value: wild type

value: biological replicate 1


title: Mouse 3 HF WT

description: Total RNA isolated from gastrocnemius muscle from wild type mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 3.

value: FVB/n

value: biological replicate 3


title: Replicate3_gcn2_mock treated_NP fraction

description: non-polysome fraction

value: aerial part

value: mock

value: non-polysome fraction


title: Mouse 2 HF WT

description: Total RNA isolated from gastrocnemius muscle from wild type mouse at 16 weeks of age after 8 weeks of high-fat diet. Biological replicate 2.

value: male

value: 16 weeks

value: skeletal muscle (gastrocnemius)

value: biological replicate 2


title: CMML_67_BM

description: Hybridized to Cytoscan_HD


title: CMML_64_PB

description: Hybridized to Cytoscan_HD

source_name: Peripheral blood


title: Replicate3_gcn2_herbicide treated_LP fraction

description: large polysome fraction

value: 0.5mM chlorosufuron


title: Replicate3_gcn2_herbicide treated_SP fraction

description: small polysome fraction

value: small polysome fraction


title: DopCells_3

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

country: Germany

institute: MPI for Biology of Ageing

description: Sample 3

hyb_protocol: 200 pmol of the labelled samples (corresponding to approx. 2-3 µg cRNA) in hybridization buffer containing salmon testes DNA and yeast tRNA were hybridized to the array at 42°C overnight. After hybridization, slides were washed twice with 1 × SSC at RT for 1 h; 1 × SSC, 0.1% Triton-X- 100 at 60°C for 30 minutes and with 0.1 × SSC, 0.1% Tri- ton-X-100 at 37°C for 30 min. Subsequently, they were washed with 0.1 × SSC for 30 seconds at RT and rinsed with water before dried.

scan_protocol: The slides were scanned with the GenePixTM4000B scanner (Axon Instruments, Molecular Devices, Munich, Germany). For spot finding and generating preliminary result files the raw scanned image files were analyzed using GenePixPro version 6.0 (Axon Instruments) whereas data normalization and further data filtering were performed with Acuity 4.1 (Axon Instruments).

data_processing: Ratio-based normalization using default settings in Acuity. Criteria for inclusion of data in further analysis: Signal-to noise-ratio for at least one of the wavelengths > 3; -10 > log2 ratio ch2/ch1> 10; features is not flagged bad or absent in previous GenePix analysis.

label: Alexa 555

organism: Drosophila melanogaster

source_name: dopaminergic cells_control

label_protocol: In brief, cDNA synthesis from RNA isolated from dopaminergic cells was performed with Prime Script RT (Takara) using the following primers: OdT T7 I (5’-GAG AGA GGA TCC AAG TAC TAA TAC GAC TCA CTA TAG GGA GAT TTT TTT TTT TTT TTT TTT TTT T G/A/C-3’) and CapFinder Sp6rG (5’-CAG CGG CCG CAG ATT TAG GTG ACA CTA TAG A rGrGrG-3’). cDNA was amplified with OdT T7 II (5’-GAG AGA GGA TCC AAG TAC TAA TAC GAC TCA CTA TAG G-3’) and Adaptor Sp6rG (5’-GAC GCC TGC AGG CGA TGA ATT TAG G-3’) and LA Taq polymerase. cDNA was transcribed with MEGAscript® T7 (Ambion) including aminoallyl-UTP (Ambion) and subsequently labeled with Alexa Fluor 555 or 647 (Invitrogen) for control or experimental sample, respectively.

growth_protocol: TH-Gal4 (Bloomington Drosophila Stock Center, USA) were crossed to virgin females of 20XUAS-IVSmCD8::GFP (Bloomington Drosophila Stock Center, USA) to generate flies overexpressing GFP in dopaminergic neurons.

extract_protocol: Seventy heads of F1 generation male adult flies from the crossings between TH-Gal4 and 20XUAS-IVSmCD8::GFP were dissected in pre-chilled HL3 buffer. Dopaminergic neurons were sorted by magnetic Dynabeads MyOne Streptavidin T1 (Invitrogen, Oslo, Norway)  The tissue sample was vortexed for 1 sec, the supernatant was discarded and the procedure was repeated 3-4 times until the supernatant became clear. The heads were transferred to a pre-chilled 7 ml Kontes tissue grinder (Fisher Scientific, Leicestershire, UK), which was rinsed with 1% BSA in HL3 buffer in order to avoid prevent the cells from sticking to the glass surface. About 4 ml of HL3 buffer were added to the tissue grinder and gently using a pestle, the tissues were given 30-32 douncing strokes. The solution was then triturated 5 times using the fire-polished glass pipette narrowed to approximately 50 % of the standard tip diameter. The level of dissociation was assessed by the fluorescent microscope with a GFP filter (Axiovert S. 100, Zeiss). Then the solution was filtered through a 30µm cell filter (Miltenyi Biotec, Bergisch Gladbach, Germany). The Dynabeads coupled to undiluted biotinylated rat anti-mouse CD8a antibody (eBioscience, Frankfurt, Germany), was then added to the filtrate and incubated for 1 hour on ice. Following this, the tubes were placed on a MagnaRack (Invitrogen, Karlsuhe, Germany) for 2 min to pellet the beads along with GFP positive cells. The supernatant was removed and discarded. Then the cells were washed three times with ice cold HL3 buffer by putting the tubes on the magnet to remove non-specific cell binding. Cells bound to the coupled beads were resuspended in 30 µl of HL3 buffer and their purity and yield were controlled by taking 5 µl and observe it under the fluorescent microscope. Approximately, 8-10 GFP-positive cells were counted at one time point. Total RNA (from approx. 200 DA neurons) was isolated using the RNA NucleoSpin Tissue Kit (Macherey & Nagel, Düren, Germany). The RNA pellet was resolved in 10 µl RNase-free H2O and stored at -80ºC until analyses.

treatment_protocol: 3-day- old male flies from the crossing mentioned above were exposed to 0.5mM rotenone in 10% glucose on blotting paper at 25 ºC. A volume of 300µl rotenone/glucose solution was added every 48 h to avoid desiccation. For the control group the same volume of 10 % glucose only was added.

tag: cell type

value: dopaminergic cell

value: 10 % glucose

label: Alexa 647

source_name: dopaminergic cells_rotenone

value: 0.5 mM rotenone in 10 % glucose


title: DopCells_2

description: Sample 2


title: DopCells_1

description: Sample 1


title: Replicate3_gcn2_herbicide treated_NP fraction

description: non-polysome fraction

value: Landsberg erecta

tag: tissue


title: Replicate3_wild type_mock treated_LP fraction

description: large polysome fraction

value: wild type

value: large polysome fraction


title: CMML_66_BM

description: Hybridized to Cytoscan_HD

value: chronic myelomonocytic leukemia


title: Replicate3_wild type_herbicide treated_LP fraction

description: large polysome fraction


title: CMML_63_BM

description: Hybridized to Cytoscan_HD


title: Replicate3_wild type_mock treated_NP fraction

description: non-polysome fraction


title: Replicate3_wild type_herbicide treated_SP fraction

description: small polysome fraction


title: Replicate3_wild type_mock treated_SP fraction

description: small polysome fraction


title: Replicate3_wild type_herbicide treated_NP fraction

description: non-polysome fraction


title: Replicate2_gcn2_mock treated_SP fraction

description: small polysome fraction


title: Replicate2_gcn2_mock treated_NP fraction

description: non-polysome fraction


title: Replicate2_gcn2_herbicide treated_LP fraction

description: large polysome fraction


title: Replicate2_gcn2_herbicide treated_SP fraction

description: small polysome fraction


title: Replicate2_gcn2_mock treated_LP fraction

description: large polysome fraction


title: Replicate2_gcn2_herbicide treated_NP fraction

description: non-polysome fraction


title: Replicate2_wild type_mock treated_SP fraction

description: small polysome fraction


title: Replicate2_wild type_mock treated_LP fraction

description: large polysome fraction


title: CMML_60_BM

description: Hybridized to Cytoscan_HD


title: CMML_53_BM

description: Hybridized to Cytoscan_HD


title: CMML_49_BM

description: Hybridized to Cytoscan_HD


title: CMML_52_BM

description: Hybridized to Cytoscan_HD


title: CMML_62_BM

description: Hybridized to Cytoscan_HD


title: CMML_46_BM

description: Hybridized to Cytoscan_HD


title: CMML_50_BM

description: Hybridized to Cytoscan_HD


title: CMML_61_BM

description: Hybridized to Cytoscan_HD


title: Replicate2_wild type_herbicide treated_NP fraction

description: non-polysome fraction


title: Replicate2_wild type_herbicide treated_LP fraction

description: large polysome fraction


title: CMML_45_BM

description: Hybridized to Cytoscan_HD


title: Replicate2_wild type_herbicide treated_SP fraction

description: small polysome fraction


title: Replicate2_wild type_mock treated_NP fraction

description: non-polysome fraction


title: CMML_44_BM

description: Hybridized to Cytoscan_HD


title: Replicate1_gcn2_mock treated_SP fraction

description: small polysome fraction


title: CMML_38_BM

description: Hybridized to Cytoscan_HD


title: CMML_43_BM

description: Hybridized to Cytoscan_HD


title: Replicate1_gcn2_mock treated_LP fraction

description: large polysome fraction


title: CMML_48_BM

description: Hybridized to Cytoscan_HD


title: Replicate1_gcn2_herbicide treated_LP fraction

description: large polysome fraction


title: CMML_39_BM

description: Hybridized to Cytoscan_HD


title: CMML_34_BM

description: Hybridized to Cytoscan_HD


title: CMML_41_BM

description: Hybridized to Cytoscan_HD


title: CMML_35_BM

description: Hybridized to Cytoscan_HD


title: Replicate1_gcn2_herbicide treated_SP fraction

description: small polysome fraction


title: Replicate1_gcn2_herbicide treated_NP fraction

description: non-polysome fraction


title: CMML_29_BM

description: Hybridized to Cytoscan_HD


title: Replicate1_gcn2_mock treated_NP fraction

description: non-polysome fraction


title: CMML_36_BM

description: Hybridized to Cytoscan_HD


title: CMML_28_BM

description: Hybridized to Cytoscan_HD


title: CMML_31_BM

description: Hybridized to Cytoscan_HD


title: CMML_37_BM

description: Hybridized to Cytoscan_HD


title: CMML_33_BM

description: Hybridized to Cytoscan_HD


title: Replicate1_wild type_mock treated_SP fraction

description: small polysome fraction


title: Replicate1_wild type_mock treated_NP fraction

description: non-polysome fraction


title: Replicate1_wild type_herbicide treated_LP fraction

description: large polysome fraction


title: Replicate1_wild type_mock treated_LP fraction

description: large polysome fraction


title: Replicate1_wild type_herbicide treated_SP fraction

description: small polysome fraction


title: replicate 3_gcn2_total RNA

description: total RNA

extract_protocol: under room light, flood seedlings with liquid Nitrogen and scrape off into liquid nitrogen with spatula; Timing: 4 hours after light on.  Polysome gradient and RNA purification were carried out essentially as described in Kim et al., (2007)Genome Biology 8:R60.   The top 6 fractions were pooled as non-polysomal (NP) and the bottom 6 fractions were pooled as polysomal (PL)

value: total RNA


title: replicate 3_wild type_total RNA

description: total RNA

value: aerial part


title: CMML_30_BM

description: Hybridized to Cytoscan_HD


title: Mast cell progenitors, subject 3

city: Solna

first: Joakim

middle: S

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

hyb_protocol: GeneChip® Human Gene 2.0 ST Arrays were hybridized for 40 hours in a 45°C incubator during rotation at 60 rpm according to the standard protocols from Nugen Technologies Inc. (Ovation® One-Direct System M01312 v1 and Encore Biotin Module M01111 v5). The arrays were washed and stained using the Fluidics Station 450 according to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G according to standard protocol from Affymetrix Inc. (GeneChip® Expression Wash, Stain and Scan Manual, PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA).

data_processing: The raw data were normalized using the robust multi-array average (RMA) method. An empirical Bayes moderated t-test was used to test for differentially expressed genes using the computing language R (http://www.r-project.org) and the limma package available from the Bioconductor project (www.bioconductor.org). All analyses were performed according to the limma: Linear Models for Microarray Data User’s Guide (The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia).

source_name: Mast cell progenitors from human blood

label_protocol: Biotinylated and amplified sense transcript cDNA was generated from the entire expressed genome according to the standard protocols from Nugen Technologies Inc. (Ovation® One-Direct System  M01312 v1 and Encore Biotin Module M01111 v5).

growth_protocol: Cells were isolated from human peripheral blood using Ficoll-Paque Premium (ρ = 1.077 g/ml) (GE Healthcare)

extract_protocol: 91-100 cells of each population were sorted into 12 μl lysis buffer, provided with the Ovation® One-Direct System (Nugen Technologies Inc.).

treatment_protocol: The cells were stained with fluorescently labeled antibodies and doubly sorted using a FACS Aria III (BD Biosciences, Franklin Lakes, NJ). The gene expression microarray analyses were performed similarly to the method described in GSE63507 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63507)

tag: tisse

value: Peripheral blood

tag: subject id

value: subject 3

value: Sorted as CD4 negative, CD8 negative, CD19 negative, CD14 negative, CD34 high, CD117 intermediate/high, FcεRI positive blood cells


title: Basophils, subject 3

source_name: Basophils from human blood

value: Sorted as CD4 negative, CD8 negative, CD19 negative, CD14 negative, CRTH2 positive, FcεRI positive blood cells


title: CMML_32_BM

description: Hybridized to Cytoscan_HD


title: replicate 2_wild type_total RNA

description: total RNA


title: Basophils, subject 2

value: subject 2


title: replicate 1_wild type_total RNA

description: total RNA


title: CMML_27_BM

description: Hybridized to Cytoscan_HD


title: HT-29, carnosic acid, rep3

city: Madrid

first: Alberto

last: Valdés

state: Madrid

address: C\Nicolás Cabrera, 9

department: Bioactividad y Análisis de Alimentos

institute: Instituto de Investigación en Ciencias de la Alimentación

description: RMA signal intensity derived from package oligo in R (Bioconductor)

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix GeneChip Human Gene 2.0 ST array(Affymetrix, Santa Clara, CA)  for 16 hours in a GeneChip Hybridization oven 640 at 45C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix Fluidics Station 450, using the standard format and protocols as described by Affymetrix.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: Background subtraction, quantile normalization and summarization were done using the RMA method contained in the oligo package for R/Bioconductor.

source_name: HT29 colon cancer cells treated with carnosic acid for 24 hours

label_protocol: Samples were prepared according to Affymetrix protocols (Affymetrix, Inc). RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc) respectively. Per RNA labeling, 250 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 2.0 ST chips

growth_protocol: HT-29 cells were cultured in McCoy's 5A with 10% heat-inactivated fetal calf serum and allowed to adhere overnight at 37 ºC.

extract_protocol: Cells were trypsinized after the treatment and total RNA was extracted with Trizol according to the manufacturer's instructions.

treatment_protocol: Cells were treated with vehicle (control), rosemary extract or carnosic acid and microparray was performed after 24 hours.

tag: treatment

value: carnosic acid

tag: cell line


title: CMML_26_BM

description: Hybridized to Cytoscan_HD

tag: disease


title: Replicate1_wild type_herbicide treated_NP fraction

description: non-polysome fraction

value: 0.5mM chlorosufuron

value: non-polysome fraction


title: Mast cell progenitors, subject 2


title: replicate 1_gcn2_total RNA

description: total RNA


title: CMML_21_BM

description: Hybridized to Cytoscan_HD


title: replicate 2_gcn2_total RNA

description: total RNA


title: replicate 3_gcn2_polysome fraction

description: polysome fraction

value: polysome fraction


title: Basophils, subject 1

value: subject 1


title: CMML_25_BM

description: Hybridized to Cytoscan_HD


title: replicate 2_gcn2_non polysome fraction

description: non polysome fraction

value: non polysome fraction


title: replicate 1_gcn2_non polysome fraction

description: non polysome fraction

value: Landsberg erecta


title: replicate 3_gcn2_non polysome fraction

description: non polysome fraction


title: replicate 2_gcn2_polysome fraction

description: polysome fraction


title: HT-29, carnosic acid, rep2


title: replicate 2_wild type_non polysome fraction

description: non polysome fraction

value: wild type


title: HT-29, carnosic acid, rep1


title: replicate 1_gcn2_polysome fraction

description: polysome fraction


title: replicate 1_wild type_non polysome fraction

description: non polysome fraction


title: replicate 3_wild type_non polysome fraction

description: non polysome fraction


title: Mast cell progenitors, subject 1


title: HT-29, rosemary extract, rep3

source_name: HT29 colon cancer cells treated with rosemary extract for 24 hours

value: rosemary extract


title: replicate 2_wild type_polysome fraction

description: polysome fraction


title: replicate 1_wild type_polysome fraction

description: polysome fraction


title: HT-29, rosemary extract, rep1


title: replicate 3_wild type_polysome fraction

description: polysome fraction


title: HT-29, rosemary extract, rep2


title: HT-29, untreated, rep2

source_name: HT29 colon cancer cells untreated for 24 hours

value: untreated


title: HT-29, untreated, rep3


title: HT-29, untreated, rep1


title: CMML_18_BM

description: Hybridized to Cytoscan_HD

value: chronic myelomonocytic leukemia


title: CMML_17_BM

description: Hybridized to Cytoscan_HD


title: CMML_13_PB

description: Hybridized to Cytoscan_HD


title: CMML_15_BM

description: Hybridized to Cytoscan_HD


title: CMML_9_BM

description: Hybridized to Cytoscan_HD


title: patient 34 IDC

city: New Lambton Heights

first: Kelly

last: Kiejda

state: NSW

address: HMRI

country: Australia

institute: University of Newcastle

description: Gene expression data from TNBC patients grade 3

hyb_protocol: 100ng total RNA of all FFPE samples was amplified (Ovation FFPE WTA kit) and biotinylated (Encore Biotin module) according to the manufacturers’ instructions (Nugen, San Carlos, California, United States). The samples were hybridised to HuGene 2.0 arrays (Affymetrix, Santa Clara, California, United States) and 17 hours later washed and stained.

scan_protocol: The Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The HumanGene 2.0 arrays (Affymetrix) contain probe features representing 11,000 lncRNAs, 24,000 genes, and 30,000 coding transcripts. The data was imported to Genomic Suite 6.6 (Partek) and a robust multi-array analysis (RMA) was performed, which included log2 transformation, background correction, quantile normalisation and summarisation of the probe features resulting in a set of expression signal intensities.

source_name: FFPE tissue specimen

label_protocol: standard affymetrix protocol

extract_protocol: Total RNA was extracted from 2mm punch biopsies of FFPE tissue using the RNeasy FFPE kit (Qiagen, Doncaster, VIC, Australia).

tag: patient id

value: patient 34

tag: patient status

value: triple negative breast cancer (TNBC)

tag: tumor grade

value: grade 3

tag: tissue type

value: invasive ductal carcinomas (IDC)


title: CMML_8_BM

description: Hybridized to Cytoscan_HD

source_name: Bone marrow


title: CMML_19_BM

description: Hybridized to Cytoscan_HD


title: Liver_TAA_6 week_rep2

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

source_name: Total Liver,TAA treated, 6 weeks

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

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

tag: strain

tag: gender

value: Female

value: gender


title: patient 33 IDC

value: patient 33


title: patient 33 NAT

value: matched normal adjacent tissues from the tumour specimen (NAT)


title: CMML_7_PB

description: Hybridized to Cytoscan_HD


title: patient 33 LN

value: lymph node metastases (LN)


title: Liver_TAA_1 week_rep3

scan_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

source_name: Total Liver,TAA treated,1 week


title: patient 32 NAT

value: patient 32


title: CMML_16_BM

description: Hybridized to Cytoscan_HD


title: Liver_TAA_4 week_rep3

source_name: Total Liver,TAA treated, 4 weeks


title: patient 32 IDC


title: patient 31 LN

value: patient 31


title: Liver_TAA_4 week_rep1


title: CMML_3_BM

description: Hybridized to Cytoscan_HD


title: Liver_TAA_4 week_rep2


title: CMML_1_PB

description: Hybridized to Cytoscan_HD


title: Liver_TAA_1 week_rep1


title: Liver_TAA_4 week_rep4


title: Liver_TAA_1 week_rep2


title: Liver_TAA_6 week_rep3


title: Liver_Naive_rep2

source_name: Total Liver, untreated


title: patient 32 LN


title: patient 30 NAT

value: patient 30


title: patient 30 IDC


title: patient 30 LN


title: patient 29 IDC

value: patient 29


title: Liver_TAA_6 week_rep1


title: patient 28 NAT

value: patient 28


title: Liver_Naive_rep3


title: patient 26 IDC

value: patient 26


title: patient 28 IDC


title: CMML_10_BM

description: Hybridized to Cytoscan_HD


title: CMML_6_BM

description: Hybridized to Cytoscan_HD


title: patient 27 IDC

value: patient 27


title: CMML_4_PB

description: Hybridized to Cytoscan_HD

value: chronic myelomonocytic leukemia


title: patient 25 LN

value: patient 25


title: first visit [11045]

city: Decatur

first: Aliza

middle: P.

last: Wingo

state: GA

address: 1670 Clairmont Rd

department: Psychiatry

institute: Atlanta VAMC/Emory University

hyb_protocol: Illumina BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and GenomeStudio (Gene expression module)

data_processing: The raw log2 transformed probes were normalized by ANOVA fitting technical effects of date of hybridization and RIN score. The reason why there are so many missing probes in the normalized dataset is because they are below the expression threshold and so not included in the normalization process.

source_name: whole peripheral blood

label_protocol: Illumina BeadArray protocol

extract_protocol: Total RNA was extracted from whole peripheral blood using Norgen protocol and kits. Quality control was performed using Agilent's Bioanalyzer

tag: Sex

value: female

tag: comorbid ptsd and depression status

tag: rin

tag: hybridization batch

value: Z

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: principal component 5

value: whole peripheral blood


title: first visit [11119]

tag: age

value: Y

tag: tissue


title: first visit [11294]


title: first visit [11109]

value: male


title: patient 35 LN

tag: patient id

value: patient 35

value: triple negative breast cancer (TNBC)

value: grade 3


title: first visit [11073]


title: patient 21 IDC

value: patient 21

tag: patient status

value: invasive ductal carcinomas (IDC)


title: patient 23 NAT

value: patient 23

tag: tumor grade

value: matched normal adjacent tissues from the tumour specimen (NAT)


title: patient 26 NAT

tag: tissue type


title: first visit [10992]


title: patient 24 IDC

value: patient 24


title: patient 20 LN

value: patient 20

value: lymph node metastases (LN)


title: first visit [10969]


title: patient 23 IDC


title: patient 22 IDC

value: patient 22


title: patient 25 IDC

value: patient 25


title: first visit [10923]

value: female


title: first visit [10653]

value: Z


title: patient 18 LN

value: patient 18


title: patient 20 IDC


title: patient 19 NAT

value: patient 19


title: first visit [10411]

value: male

value: whole peripheral blood


title: first visit [10361]


title: first visit [10585]


title: first visit [10482]

value: Y


title: patient 17 IDC

value: pateint 17

value: triple negative breast cancer (TNBC)

value: grade 3


title: Liver_Naive_rep1

tag: strain

value: Female

value: gender


title: patient 19 IDC

value: invasive ductal carcinomas (IDC)


title: patient 18 IDC


title: first visit [10858]


title: patient 16 LN

value: patient 16


title: first visit [10493]


title: patient 18 NAT

value: matched normal adjacent tissues from the tumour specimen (NAT)


title: Mock_121812

city: Research Triangle Park

first: Georgette

middle: Mona

last: Charles

state: NC

address: 111 T.W. Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: National Institutes of Environmental Health Sciences

description: Mock_1; Control, replicate 1

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor (http://www.bioconductor.org). Gene-specific probesets were constructed using the Entrez Gene – centric custom CDF, version 13 (Dai et al. (2005); Nucl Acids Res 33: e175). Log-scale data was further normalized by 1) setting the per-sample median to 6.5 and 2) subtracting the per-gene median.

source_name: mESCs_mock control

label_protocol: Affymetrix Whole Mouse Genome oligo arrays using the Affymetrix 1-color microarray-based gene expression analysis protocol.

growth_protocol: ESCs were cultured in gelatin-coated plates in M15 medium.

extract_protocol: Cells were harvested for RNA extraction on day 4, post-transfection. For quality assessment, extracts were checked using qRT-PCR for Fip1 expression as well as appropriate expression markers

treatment_protocol: Lipofectamine 2000-mediated transfections were performed as previously described (PMID 22367759). Mock transfections were performed using lipofectamine but without siRNAs.

tag: cell line

tag: cell type

value: mouse embryonic stem cells (mESCs)

tag: transfected with

value: lipofectamine but without siRNAs (control)


title: siFip1-3_122212

description: Fip1L1_3_2; Fip1L1 siRNA3, replicate 2

source_name: mESCs_Fip1 depletion

value: Fip1L1 siRNA


title: first visit [10222]

tag: Sex

tag: comorbid ptsd and depression status

tag: rin


title: first visit [10175]

value: female

tag: hybridization batch

value: Z

tag: principal component 1

tag: principal component 2


title: first visit [10306]

tag: principal component 3

tag: principal component 4

tag: principal component 5


title: siFip1-2_122212

description: Fip1L1_2_2; Fip1L1 siRNA2, replicate 2


title: Mock_122212

description: Mock_2; Control, replicate 2


title: first visit [10244]

tag: age

tag: tissue


title: patient 15 IDC

tag: patient id

value: patient 15

tag: patient status

tag: tumor grade


title: patient 13 IDC

value: patient 13

tag: tissue type


title: siFip1-2_121812

description: Fip1L1_2_1; Fip1L1 siRNA2, replicate 1

tag: cell line

tag: cell type


title: siFip1-3_121812

description: Fip1L1_3_1; Fip1L1 siRNA3, replicate 1

tag: transfected with


title: first visit [10101]

tag: Sex

value: male

tag: comorbid ptsd and depression status

value: whole peripheral blood


title: first visit [10333]

tag: rin

tag: hybridization batch


title: UhiPS-S127R-2

city: Nantes

first: Karim

last: Si-Tayeb

address: 8,quai Moncousu

country: France

institute: l'institut du thorax, UMR INSERM1087 / CNRS6291, IRS-UN

description: US82400123_252800418271_S01_GE2_107_Sep09_2_3.txt

hyb_protocol: 0.3 ug of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug cRNA) pooled with 0.3 µg of Cy5-labelled cRNA (specific activity > 8 pmol Cy5/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent GEx hybridization buffer Hi-RPM was added to the fragmentation mixture and hybridized to Agilent Sure Print G3  Human   8x 60K Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with Acetonitrile anhydrous 99.8% at room temperature and 1 minute with Stabilization and Drying solution (Agilent) at room temperature. Then, Microarrays were dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using two colors scan setting for 8x60k array slides (Scan Area HD 61x21.6 mm, Scan resolution 3 µm, Dye channels are set to Green and Red) and PMT is setup on autoscale.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 028004_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Urine cells reprogrammed

label_protocol: Cyanine-3 (Cy3) labeled cRNA and Cyanine-5 (Cy5) labeled cRNA were prepared from 0.1 ug RNA using the Low Input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Gene expression in 4%O2 and 5%CO2 culture condition

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

tag: gender

tag: individual

value: Patient carrying the PCSK9-S127R mutation

value: hiPS cells reprogrammed from urine-derived cells


title: patient 14 IDC

value: patient 14

value: triple negative breast cancer (TNBC)

value: grade 3


title: patient 12 IDC

value: patient 12

value: invasive ductal carcinomas (IDC)


title: UhiPS-S127R-3

description: US82400123_252800418271_S01_GE2_107_Sep09_1_2.txt

value: Female


title: patient 14 LN

value: lymph node metastases (LN)


title: patient 11 NAT

value: patient 11

value: matched normal adjacent tissues from the tumour specimen (NAT)


title: first visit [10170]

value: Y

tag: principal component 1

tag: principal component 2

tag: principal component 3

tag: principal component 4


title: first visit [10036]

value: female

tag: age

tag: principal component 5

tag: tissue


title: patient 16 IDC

tag: patient id

value: pateint 16

tag: patient status

tag: tumor grade

tag: tissue type


title: first visit [10073]

tag: Sex


title: first visit [10030]

tag: comorbid ptsd and depression status


title: patient 11 LN


title: UhiPS-ct-3

description: US82400123_252800418271_S01_GE2_107_Sep09_2_4.txt

value: Healthy donor

tag: cell type


title: patient 11 IDC


title: first visit [9709]

tag: rin

tag: hybridization batch

value: X


title: first visit [9757]

value: whole peripheral blood


title: UhiPS-S127R-1

tag: gender

tag: individual

value: Patient carrying the PCSK9-S127R mutation


title: patient 10 IDC

value: pateint 10


title: UhiPS-ct-1

description: US82400123_252800418270_S01_GE2_107_Sep09_1_1.txt

value: hiPS cells reprogrammed from urine-derived cells


title: UhiPS-ct-2

description: US82400123_252800418270_S01_GE2_107_Sep09_1_2.txt


title: patient 10 NAT

value: patient 10

value: triple negative breast cancer (TNBC)


title: Ucell-S127R-1

source_name: Urine sample

growth_protocol: Gene expression in atmospheric O2 and 5%CO2 culture condition

value: Progenitor cells isolated from urines samples


title: first visit [9688]

tag: principal component 1

tag: principal component 2


title: patient 9 NAT

value: patient 9

value: grade 3


title: CMML_59_BM

description: Hybridized to Genome-Wide Human SNP Array 6.0

tag: disease

value: chronic myelomonocytic leukemia


title: Ucell-S127R-2

value: Female


title: patient 9 IDC

value: invasive ductal carcinomas (IDC)


title: first visit [9599]

tag: age

tag: principal component 3

tag: principal component 4


title: Ucell-ct-1


title: first visit [9704]

tag: principal component 5

tag: tissue


title: patient 8 IDC

tag: patient id

value: patient 8

tag: patient status

tag: tumor grade


title: first visit [9603]

tag: Sex

value: female

tag: comorbid ptsd and depression status


title: patient 9 LN

tag: tissue type

value: lymph node metastases (LN)


title: patient 7 NAT

value: pateint 7

value: matched normal adjacent tissues from the tumour specimen (NAT)


title: first visit [9646]

value: male

tag: rin

tag: hybridization batch

value: X

value: whole peripheral blood


title: Mixture rep 4 vs. Oleate rep 4

first: Anna

middle: Maria

last: Gómez Foix

address: Diagonal 643

department: Bioquímica i Biologia Molecular

institute: Universitat de Barcelona

description: Zhu, C. H et al. 2007. Cellular senescence in human myoblasts is overcome by human telomerase reverse transcriptase and cyclin-dependent kinase 4: consequences in aging muscle and therapeutic strategies for muscular dystrophies. Aging Cell 6: 515-523.

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

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: LHCN-M2 mytoubes

label_protocol: Low Input Quick Amp Labeling Protocol v 6.5 (Agilent)

growth_protocol: Myoblasts were grown in DMEM/MEM199 (4:1) added with 15% fetal bovine serum (FBS), 16 mM Hepes, 0.03 μg/ml zinc sulfate, 1.4 μg/ml vitamin B12, 0.055 µg/ml dexamethasone , 0.025 μg/ml human hepatocyte growth factor and 2.5 ng/ml fibroblast growth factor. In confluent cultures, myoblast fusion was stimulated by incubating cells in the DMEM/MEM199 media supplemented with 0.005% FBS, 20 mM Hepes, 10 µg/ml insulin, 0.1 mg/ml apotransferrin and 0.055 µg/ml dexamethasone during 2 days. To further induce cell differentiation, media was then switched to DMEM/MEM199 supplemented with 0.005% FBS, 20 mM Hepes and 0.055 µg/ml dexamethasone, and the culture was continued for 8 additional days.

extract_protocol: Total RNA was extracted from cultured LHCN-M2 myotubes with RNeasy kit (Qiagen, Valencia, CA, USA), with the same DNase treatment than in the RNeasy fibrous tissue kit, and homogenized with a Polytron.

treatment_protocol: Sodium salts of palmitic and oleic acids were prepared in deionized water containing 1.2 equivalents of NaOH at 70ºC, until an optically clear dispersion was obtained. The fatty acid salt solution was added to cell culture media containing fatty acid-free bovine serum albumin (BSA) with continuous agitation. The fatty acid: BSA molar ratio were 5:1.

tag: treatment

value: 0.25 mM Palmitate and 0.25 mM Oleate

tag: cell line

tag: differentiation

value: 10 days post-differentiation induction

value: skeletal muscle

value: 0.5 mM Oleate


title: CMML_56_BM

tag: disease


title: patient 12 NAT

value: patient 12

value: triple negative breast cancer (TNBC)


title: CMML_58_BM

value: chronic myelomonocytic leukemia


title: CMML_57_BM


title: Control rep 3 vs. Mixture rep 2

value: Control


title: CMML_55_BM


title: Mixtture rep 1 vs. Control rep 4

value: 10days post-differentiation induction


title: first visit [10230]

tag: age

value: Y

tag: principal component 1

tag: principal component 2


title: first visit [9552]

value: female

tag: principal component 3

tag: principal component 4

tag: principal component 5


title: first visit [9589]

tag: tissue


title: patient 7 LN

tag: patient id

value: patient 7

tag: patient status

tag: tumor grade

value: grade 3

value: lymph node metastases (LN)


title: first visit [9403]

tag: Sex

tag: comorbid ptsd and depression status


title: Oleate rep 3 vs. Mixture rep 3


title: patient 6 NAT

value: patient 6

tag: tissue type

value: matched normal adjacent tissues from the tumour specimen (NAT)


title: patient 6 IDC

value: invasive ductal carcinomas (IDC)


title: first visit [9377]

value: male

tag: rin

tag: hybridization batch

value: X

value: whole peripheral blood


title: patient 8 NAT

value: patient 8


title: patient 7 IDC


title: first visit [9483]


title: first visit [9372]


title: first visit [9367]


title: Palmitate rep 3 vs. Oleate rep2

tag: treatment

value: 0.5 mM Palmitate

tag: cell line

tag: differentiation

value: 10 days post-differentiation induction

value: skeletal muscle

value: 0.5 mM Oleate


title: patient 5 NAT

value: patient 5

value: triple negative breast cancer (TNBC)


title: Oleate rep 1 vs. Palmitate rep 4


title: patient 5 LN


title: Palmitate rep1 vs. Control rep1

value: Control


title: patient 4 LN

value: patient 4


title: Subset 4_rep2

city: London

first: Paul

middle: Leo

last: Ryan

address: 4 Newark Street

department: Centre for Immunobiology

institute: Queen MAry University of London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation using Genome Studio

source_name: Subset 4=Cell sorted peripheral blood CD28-CD27-CD16+ Vg9Vd2 T cells

label_protocol: Ambion WT expression kit® (Life Technologies) was used to Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with commercial kit as per standard protocol RNeasy Micro Kit (Qiagen), purity tested with NanoDrop TM8000 Spectrophotometer, RIN scores all >7 (Quality control) was performed with Agilent Bioanalyser.

treatment_protocol: Peripheral blood mononuclear cells were isolated using Ficoll-Paque density gradient cell separation, positively enriched by magnetic bead separation and then cell sorted on Aria II cell sorter to isolate the four Vg9Vd2 subsets  (Subset 1=CD28+CD27+, Subset 2=CD28-CD27+, Subset 3=CD28-CD7-CD16-, Subset 4 = CD28-CD27-CD16+)

value: blood

tag: cell type


title: Control rep 2 vs. Palmitate rep 2


title: first visit [9301]

value: female

tag: age

tag: principal component 1

tag: principal component 2


title: patient 4 IDC

value: grade 3


title: Subset 4_rep3


title: first visit [9350]

tag: principal component 3

tag: principal component 4

tag: principal component 5


title: patient 3 NAT

tag: patient id

value: patient 3

tag: patient status

value: matched normal adjacent tissues from the tumour specimen (NAT)


title: Subset 1_rep3

source_name: Subset 1=Cell sorted peripheral blood CD28+CD27+ Vg9Vd2 T cells

tag: tissue


title: patient 5 IDC

tag: tumor grade

value: invasive ductal carcinomas (IDC)


title: Subset 3

source_name: Subset 3=Cell sorted peripheral blood CD28-CD27-CD16- Vg9Vd2 T cells


title: first visit [9300]

tag: Sex

value: male

tag: comorbid ptsd and depression status

value: X


title: first visit [9304]

tag: rin

tag: hybridization batch

value: whole peripheral blood


title: Subset 4_rep1


title: first visit [9270]


title: patient 1 IDC

value: patient 1

tag: tissue type


title: Subset 1_rep2


title: first visit [9257]


title: Subset 1_rep1


title: patient 3 IDC


title: first visit [9251]


title: first visit [9204]


title: Subset 2_rep3

source_name: Subset 2=Cell sorted peripheral blood CD28-CD27+ Vg9Vd2 T cells


title: patient 2 IDC

value: patient 2


title: Subset 2_rep1


title: first visit [9215]


title: first visit [9295]


title: con/veh_4

city: Leiden

first: Marcel

last: Schaaf

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

description:
Biological replicate 4 of 4: con/veh
5.1/1

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

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

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

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

extract_protocol: Twenty larvae per treatment group were collected in 1 ml of TRIZOL® Reagent (Invitrogen) and stored at -80°C. Larvae were homogenized in TRIZOL® and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Tail fins were amputated from zebrafish larvae (3dpf) under anaesthesia using a sapphire blade. Amputated and control larvae were treated with 25 microM beclomethasone or vehicle (0.05 % DMSO) for 2 hours before and 4 hours after the amputation. Four hours after the amputation, 20 larvae per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent. Four individual experiments were performed, yielding quadruplicate samples per treatment group.

tag: reference type

value: The CR (common reference) was a mixture of all RNA samples from this microarray study.

tag: treatment

value: Control-treated, vehicle-treated 3dpf larvae. RNA isolated from 20 larvae.

value: whole larvae


title: con/beclo_4

description:
Biological replicate 4 of 4: con/beclo
4.3/36

value: Control-treated, beclomethasone-treated 3dpf larvae. RNA isolated from 20 larvae.


title: amp/beclo_4

description:
Biological replicate 4 of 4: amp/beclo
4.4/38

value: Tail fin-amputated, beclomethasone-treated 3dpf larvae. RNA isolated from 20 larvae.


title: first visit [9167]

tag: age


title: amp/veh_4

description:
Biological replicate 4 of 4: amp/veh
5.2/2

value: Tail fin-amputated, vehicle-treated 3dpf larvae. RNA isolated from 20 larvae.


title: amp/veh_3

description:
Biological replicate 3 of 4: amp/veh
3.2/33


title: first visit [9157]

tag: principal component 1


title: BR16-2(100)

city: Zhunan Miaoli County

first: Cheng Ta

last: Chung

address: 35, Keyan Rd.

department: Institute of Biotechnology and Pharmaceutical Research

country: Taiwan

institute: National Health Research Institutes

description: Afatinib-resistant BR16-2 subline generated by in vivo selection, treated with afatinib at 100 nM for 48 hr.

hyb_protocol: Standard Hybridization protocol of Illumina Human HT-12 Beadchips

scan_protocol: Standard Illumina Scanning protocol

data_processing: Data analysis was performed with GeneSpring GX software (Agilent Technologies). Quantile normalisation was performed.

source_name: BR16-2 resistant cell_100

label_protocol: 500ng total RNA was converted into cDNA using biotinylated random nonamers, oligodeoxythymidine 18 primers and Illumina-supplied reagents, according to Illumina manufacturer's instructions.

growth_protocol: RPMI 1640, 10% FBS, culture at 37 ℃, 5% CO2

extract_protocol: Qiagen RNEasy mini kit, following standard protocol culture cells

treatment_protocol: Afatinib-resistant cells were treated with afatinib at 0, 10, 100, and 1000 nM in 10-cm culture dishs for 48 hr. Parental HCC827 cells were not treated with afatinib.

value: xenograft tumors isolated from nude mice

tag: cell line origin

value: Adenocarcinoma from lung of 38 year-old caucasian female


title: Ucell-ct-2

description: US82400123_252800418270_S01_GE2_107_Sep09_1_3.txt

tag: gender

value: Female

tag: individual

value: Healthy donor

tag: cell type

value: Progenitor cells isolated from urines samples


title: BR16-2(10)

description: Afatinib-resistant BR16-2 subline generated by in vivo selection, treated with afatinib at 10 nM for 48 hr.

source_name: BR16-2 resistant cell_10


title: BR16-2(1000)

description: Afatinib-resistant BR16-2 subline generated by in vivo selection, treated with afatinib at 1000 nM for 48 hr.

source_name: BR16-2 resistant cell_1000


title: Subset 2_rep2

value: blood


title: con/beclo_3

description:
Biological replicate 3 of 4: con/beclo
3.3/35


title: first visit [9083]

value: female

tag: principal component 2

tag: principal component 3

tag: principal component 4

tag: principal component 5


title: first visit [9065]

tag: Sex

value: X

tag: tissue


title: first visit [9048]

tag: comorbid ptsd and depression status

tag: rin

value: whole peripheral blood


title: BR16-2(0)

description: Afatinib-resistant BR16-2 subline generated by in vivo selection, not treated with afatinib.

source_name: BR16-2 resistant cell_0


title: con/veh_3

description:
Biological replicate 3 of 4: con/veh
3.1/31


title: BR16-1(1000)

description: Afatinib-resistant BR16-1 subline generated by in vivo selection, treated with afatinib at 1000 nM for 48 hr.

source_name: BR16-1 resistant cell_1000


title: BR16-1(100)

description: Afatinib-resistant BR16-1 subline generated by in vivo selection, treated with afatinib at 100 nM for 48 hr.

source_name: BR16-1 resistant cell_100


title: BR16-1(10)

description: Afatinib-resistant BR16-1 subline generated by in vivo selection, treated with afatinib at 10 nM for 48 hr.

source_name: BR16-1 resistant cell_10


title: BR16-2

description: generated by in vivo selection in nude mice

hyb_protocol: Standard Illumina Hybridization protocol of Illumina Human HT-12 Beadchips

source_name: afatinib resistant

label_protocol: 500 ng total RNA was converted into cDNA using biotinylated random nonamers, oligodeoxythymidine 18 primers and Illumina-supplied reagents, according to Illumina manufacturer's instructions.

extract_protocol: Qiagen RNEasy mini kit (Qiagen, Valencia, CA), following standard protocol.

treatment_protocol: HCC827 cells were subcutaneously implanted into nude mouse at 5×10 6 cells per mouse.When the tumor volumes reached 800-1200 mm 3, the tumor-bearing mice were orally administered with afatinib at an initial dose of 10 mg/kg followed by a series of incremental doses of 5, 10, 20, 40, 60, and 100 mg/kg given at different doing intervals to maintain the tumor volumes around 500-1500 mm3. Tumors with afatinib-resistant phenotype established were surgically harvested, minced with a pair of sterile surgical blades, and re-implanted subcutaneously into nude mice. The mice with a tumor of approximate 500 mm3 were orally gavaged with afatinib of high doses (40, 60, and 100 mg/kg) to confirm the maintenance of the drug resistance phenotype.


title: amp/beclo_3

description:
Biological replicate 3 of 4: amp/beclo
3.4/37


title: first visit [9116]

source_name: whole peripheral blood

value: male

tag: hybridization batch


title: first visit [8993]


title: BR16-1


title: first visit [8897]


title: BR16-1(0)

description: Afatinib-resistant BR16-1 subline generated by in vivo selection , not treated with afatinib.

source_name: BR16-1 resistant cell_0


title: con/veh_2

description:
Biological replicate 2 of 4: con/beclo
2.1/I1

tag: reference type


title: first visit [8985]


title: first visit [8857]


title: BR42


title: amp/beclo_2

description:
Biological replicate 2 of 4: amp/beclo
2.4/IV1

tag: treatment


title: amp/veh_2

description:
Biological replicate 2 of 4: amp/veh
2.2/III1


title: con/beclo_2

description:
Biological replicate 2 of 4: con/beclo
2.3/II1


title: first visit [8855]

tag: age


title: amp/veh_1

description:
Biological replicate 1 of 4: amp/veh
1.2/D


title: amp/beclo_1

description:
Biological replicate 1 of 4: amp/beclo
1.4/E1


title: Parental HCC827

description: without in vivo selection, not treated with afatinib.

source_name: parental cell

value: parental HCC827 NSCLC cell line


title: Parental HCC827

description: without in vivo selection


title: first visit [8798]

tag: principal component 1


title: first visit [8777]


title: first visit [8697]


title: con/veh_1

description:
Biological replicate 1 of 4: con/veh
1.1/A

value: The CR (common reference) was a mixture of all RNA samples from this microarray study.


title: first visit [8586]


title: first visit [8502]

value: W


title: first visit [8597]


title: HCC1395_γKlotho knockdown (siKLG-134)_rep2

city: Ljubljana

first: Nusa

last: Trost

address: Vrazov trg 2

country: Slovenia

institute: Institute of Biochemistry

description: Gene expression profiling of HCC1395 cells transfected with a pool of γKlotho siRNAs (siKLG-134), replicate 2

hyb_protocol: Standard Illumina procedure.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Microarrays were background-corrected and summarized with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008) and then quantile-normalized and log2-transformed. Normalized data contains the quantile normalized, log2-transformed intensity values. The normalized data are available within the sample tables and on the series record. The Non-normalized data contain the raw data, non-normalized average signal intensity and are available on the series record.  Both the Non-normalized and normalized data sets includes the Detection P-value, which is the p value computed from the background model characterizing the chance that the target sequence signal was distinguishable from the negative controls.

source_name: HCC1395 cells, transfected with a pool of γKlotho siRNAs (siKLG-134)

label_protocol: Standard Illumina procedure.

growth_protocol: Human breast cancer cells HCC1395 were maintained in RPMI-1640 medium supplemented with 10% FBS. Cells were grown in a humidified incubator at 37°C with 5% CO2.

extract_protocol: RNA was extracted using RNAStat60 (TelTest) according to the manufacturer’s directions.

treatment_protocol: Cells were transfected with siRevL1 or siKLG-134. siRNA transfections were performed with Lipofectamine RNAiMAX  according to the manufacture’s protocol.

tag: cell line

value: Epithelial breast cancer cells

tag: disease model

value: Triple negative breast cancer


title: HCC1395_γKlotho knockdown (siKLG-134)_rep1

description: Gene expression profiling of HCC1395 cells transfected with a pool of γKlotho siRNAs (siKLG-134), replicate 1


title: con/beclo_1

description:
Biological replicate 1 of 4: con/beclo
1.3/B1

value: Control-treated, beclomethasone-treated 3dpf larvae. RNA isolated from 20 larvae.

value: whole larvae


title: Treated 1-b

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: Replicate 1

data_processing: The data were normalised using quantile normalisation with GeneSpring Gx v 12.0

source_name: WERI RB1_FASN_siRNA

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

growth_protocol: WERI RB1 is a suspension cell line, suplemmented with RPMI 1640, 10%FBS and antibiotic solution containing penecillin and streptomycin. It was grown under 37°C incubator with 5% Co2.

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

treatment_protocol: WERI RB1 cells were treated with optimised FASN siRNA concentration complexed with lipoifectamine using manufacturer's protocol. After 48 hours incubation in  37°C incubator with 5% Co2, the cells were removed and washed with 1xPBS.

value: WERI RB1

tag: transfection line

value: Cell transfection line P-5


title: first visit [8622]


title: RERF-LC-Sq

city: Macclesfield

first: Molly

middle: Ann

last: Taylor

address: 33F83 Mereside, Alderley Park

institute: AstraZeneca

description: microRNA expression

hyb_protocol: labeled RNA was hybridized to the array using the miRNA complete labeling and hyb kit from Agilent

scan_protocol: AgilentG3_miRNA protocol was selected for scanning using Agilent Feature Extraction Software version 10.7.3.1

data_processing: The data was imported into R and RMA normalized using the package AgiMicroRNA, then summarized to the log 2 scale and returned for further association analysis as a gene by sample matrix.

source_name: Cell Line

label_protocol: 100ng of RNA was labeled

extract_protocol: Total RNA was purified using the miRNeasy kit (Qiagen)

value: RERF-LC

value: Lung Squamous Cell Carcinoma


title: NCI-H1703

description: microRNA expression


title: SK-MES-1

description: microRNA expression

value: SK-MES


title: NCI-H647

description: microRNA expression


title: first visit [8593]


title: NCI-H520

description: microRNA expression


title: Treated 3-2

description: Replicate 2

value: Cell transfection line P-6


title: first visit [8383]

value: female


title: NCI-H226_2

description: microRNA expression


title: Treated 1-a

description: Replicate 1


title: Treated 3-1

description: Replicate 2


title: LUDULU-1

description: microRNA expression


title: first visit [8357]


title: Control 3-2

description: Replicate 2

source_name: WERI RB1_control


title: HCC1395_Control siRNA (siRevL1)_rep1

description: Gene expression profiling of HCC1395 cells transfected with control siRNA (siRevL1), replicate 1

source_name: HCC1395 cells, transfected with control siRNA (siRevL1)

tag: cell type


title: Control 1-b

description: Replicate 1


title: first visit [8178]

value: X

tag: principal component 2


title: HCC15

description: microRNA expression


title: HCC1395_Control siRNA (siRevL1)_rep2

description: Gene expression profiling of HCC1395 cells transfected with control siRNA (siRevL1), replicate 2


title: first visit [8369]

tag: principal component 3

value: whole peripheral blood


title: NCIH-1869

description: microRNA expression


title: first visit [7733]

tag: principal component 4


title: HARA

description: microRNA expression

value: HARA


title: first visit [8158]

value: male

tag: principal component 5


title: Control 3-1

description: Replicate 2


title: NCI-H2286

description: microRNA expression


title: first visit [7536]

tag: Sex

value: V


title: LK-2

description: microRNA expression

tag: tissue


title: Control 1-a

description: Replicate 1


title: first visit [7858]

tag: comorbid ptsd and depression status


title: EBC-1

description: microRNA expression


title: QD705_48hr-1

city: Miaoli County

first: Chieh Hua

last: Lin

address: 35, Keyan Road, Zhunan Town

department: Division of Biostatistics and Bioinformatics

hyb_protocol: The labeled cDNA was hybridized to Human 46K cDNA array at 42°C for 12-16 hrs in 0.25 ml formamide, 20X SSC, 10% SDS and 10 mg/ml salmon sperm DNA. The array chip was washed once in 2× SSC with 0.1% SDS for 5 min at 42°C and once in 0.1X SSC with 0.1% SDS for 10 min at room temperature. Finally, the array was washed four times (1 min each time) in 0.1X SSC.

scan_protocol: The arrays were scanned on a GenePix 4000B scanner and analyzed with the GenePix software (Axon Instruments)

data_processing: The signal intensity was corrected by subtracted the background median from foreground mean. Then, the genes were kept with fluorescence signal intensities greater than intensity 250. After that, the raw data of fluorescence ratios (Cy5:Cy3) was adjusted by log transformation (base 2).

source_name: HepG2 cell line with QD705 treatment at 48hr

label_protocol: cRNA was prepared by Roche cDNA Synthesis kit and Microarray RNA Target Synthesis kit from 1 μg total RNA. 1 μg cRNA from QD-treated cell and Universal Human Reference RNA (Stratagene, La Jolla, CA), was reverse transcribed to Cy3- or Cy5-labeled cDNA, respectively, with CyScribe Post-Labeling Kit (Amersham Biosciences, Piscataway, NJ)

growth_protocol: Human hepatoblastoma HepG2 cells were cultured in Dulbecco Minimum Essential Media (DMEM) supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA were extracted using the RNeasy kit (Qiagen)

treatment_protocol: The cultured cells were treated with 50 nM QD655 and QD705 separately. Total cellular RNA were harvested from 4, 8, 12, 24 and 48 hr QD-treated and untreated cells.

tag: time point

tag: agent

source_name: Stratagene’s Universal Human Reference RNA

tag: sample type

value: pooled from 10 humal cell lines


title: NCI-H226_1

description: microRNA expression


title: QD705_24hr-2

source_name: HepG2 cell line with QD705 treatment at 24hr


title: first visit [7620]

tag: rin

tag: hybridization batch


title: QD705_24hr-1


title: SW900

description: microRNA expression


title: QD705_48hr-2


title: QD705_12hr-1

source_name: HepG2 cell line with QD705 treatment at 12hr


title: first visit [8293]

tag: age

value: W

tag: principal component 1


title: first visit [7528]


title: QD705_12hr-2

tag: cell line


title: QD705_8hr-1

source_name: HepG2 cell line with QD705 treatment at 8hr


title: first visit [7470]


title: QD705_8hr-2


title: first visit [7463]


title: first visit [7465]


title: first visit [7462]


title: QD705_4hr-2

source_name: HepG2 cell line with QD705 treatment at 4hr


title: DLBCL_DS-41_Specimen 9

city: Rutherford

first: Jane

last: Houldsworth

state: NJ

address: 201 Route 17 North

institute: Cancer Genetics, Inc.

description: DLBCL_DS-41_Specimen 9 as test DNA and Promega normal DNA as reference

hyb_protocol: Oligoarray hybridization buffer, block (both from Agilent In Situ Hybridization Kit Plus), and Cot-1 DNA (Life Technologies) were added to each sample prior to application to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization for 24 hours, slides were washed sequentially as described by the manufacturer.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B.

data_processing: Data extraction was performed using Feature Extraction Version 10.7.3.1 (Agilent Technologies).

source_name: Human DLBCL specimen

label_protocol: Genomic DNA samples were labeled using the Agilent Genomic DNA Enzymatic Labeling Kit, according to the manufacturer's protocol, except that 1μg of DNA was used per 25μl labeling reaction mix.

extract_protocol: Extraction of genomic DNA was performed using Qiagen DNeasy Blood and Tissue kit according to the manufacturer's instructions.

tag: disease state

value: diffuse large B-cell lymphoma

tag: treatment

value: R-CHOP or R-CHOP like immuno-chemo therapy

source_name: Reference human genome DNA equimixture of normal male and normal female (Promega).

value: reference


title: DLBCL_DS-41_Specimen 8

description: DLBCL_DS-41_Specimen 8 as test DNA and Promega normal DNA as reference


title: first visit [7458]

tag: principal component 2


title: QD705_4hr-1


title: DLBCL_DS-41_Specimen 6

description: DLBCL_DS-41_Specimen 6 as test DNA and Promega normal DNA as reference


title: HT29 3D cell culture replicate 3

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

description: Biological replicate 3 of 3. HT29 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3 (2D cell culture) or Cy5 (3D cell culture). For differential gene expression analysis cell grown under 2D conditions served as a control.

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Human Gene Expression (v2) 4x44k Oligonucleotide Microarrays (Agilent) for 17 hours at 65°C  using HS 400 hybridization station (Tecan).

scan_protocol: Microarrays were scanned  using Tecan LS Reloaded scanner

data_processing: Image analysis was performed performed Imagene v9.0 software (BioDiscovery). Raw probe signal values were LOWES normalized

source_name: Control HT29 cell line cultivated in 2D cell culture

label_protocol: 1µg of total RNA was used for cDNA synthesis and amplification using MessageTMAmp aRNA kit (Ambion).  cRNA labeled with Cy3/Cy5 dyes using Arcturus® TURBO labelingTM CyTM3/CyTM5 Kit (Applied Biosystems).

growth_protocol: For 2D cell culture, cells were cultured in DMEM (HT29 cell line) or RPMI-1640 (DLD1 cell line) cell culture medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2nM glutamine (Gibco), 100 UI/ml penicillin (ROTH) and 0.1 mg/ml streptomycin (ROTH) at 37°C in a humidified atmosphere containing 5% CO2. For 3D cell culture, cells were plated in 0.5 mg/ml laminin rich extracellular matrix (GeltrexTM, Gibco) and cell culture medium upon a layer of agarose ir a 24-well cell culture plates.

extract_protocol: Total RNA was isolated from harvested cells using GeneJET RNA Purification Kit (ThermoFisher Scientific) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

value: Control

tag: growth condition

source_name: HT29 cell line cultivated in 3D cell culture

value: Experimental


title: DLBCL_DS-41_Specimen 7

description: DLBCL_DS-41_Specimen 7 as test DNA and Promega normal DNA as reference


title: first visit [7411]

source_name: whole peripheral blood

tag: principal component 3

tag: principal component 4


title: DLBCL_DS-41_Specimen 46

description: DLBCL_DS-41_Specimen 46 as test DNA and Promega normal DNA as reference


title: QD655_48hr-2

source_name: HepG2 cell line with QD655 treatment at 48hr


title: DLBCL_DS-41_Specimen 4

description: DLBCL_DS-41_Specimen 4 as test DNA and Promega normal DNA as reference


title: first visit [7427]

tag: Sex

tag: principal component 5


title: first visit [9050]

tag: comorbid ptsd and depression status

tag: tissue


title: first visit [7395]


title: DLBCL_DS-41_Specimen 5

description: DLBCL_DS-41_Specimen 5 as test DNA and Promega normal DNA as reference


title: QD655_48hr-1

tag: time point

tag: agent


title: DLD1 3D cell culture replicate 3

description: Biological replicate 3 of 3. DLD1 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3 (2D cell culture) or Cy5 (3D cell culture). For differential gene expression analysis cell grown under 2D conditions served as a control.

source_name: Control DLD1 cell line cultivated in 2D cell culture

tag: sample type

source_name: DLD1 cell line cultivated in 3D cell culture


title: HT29 3D cell culture replicate 2

description: Biological replicate 2 of 3. HT29 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3 (2D cell culture) or Cy5 (3D cell culture). For differential gene expression analysis cell grown under 2D conditions served as a control.


title: QD655_8hr-2

source_name: HepG2 cell line with QD655 treatment at 8hr


title: HT29 3D cell culture replicate 1

description: Biological replicate 1 of 3. HT29 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3 (2D cell culture) or Cy5 (3D cell culture). For differential gene expression analysis cell grown under 2D conditions served as a control.


title: first visit [7372]

tag: rin

tag: hybridization batch


title: DLD1 3D cell culture replicate 2

description: Biological replicate 2 of 3. DLD1 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3 (2D cell culture) or Cy5 (3D cell culture). For differential gene expression analysis cell grown under 2D conditions served as a control.


title: first visit [7406]

tag: age

tag: principal component 1


title: QD655_12hr-1

source_name: HepG2 cell line with QD655 treatment at 12hr

tag: cell line


title: QD655_12hr-2


title: QD655_8hr-1


title: DLBCL_DS-41_Specimen 43

description: DLBCL_DS-41_Specimen 43 as test DNA and Promega normal DNA as reference

tag: disease state

tag: treatment


title: DLD1 3D cell culture replicate 1

description: Biological replicate 1 of 3. DLD1 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3 (2D cell culture) or Cy5 (3D cell culture). For differential gene expression analysis cell grown under 2D conditions served as a control.

tag: growth condition