title: rep.3rd grade of malignancy no.72

status: Public on May 31 2013

type: RNA

city: Warsaw

first: Magdalena

last: Król

address: Nowoursynowska 159

department: Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences

description: rep. 3rd grade of malignancy no. 72

hyb_protocol: For each slide, the RNA of cells from a different passage was used.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using microarray scanner ScanArray HT and ScanExpress software (PerkinElmer, USA).

data_processing:
Different types of values were obtained for quantification of the dot intensity. Due to experimental variations in specific activity of oligo-nucleotide target preparations or exposure time that might alter the signal intensity, hybridization data were automatically normalized (LOWESS method) (Oshlack et al. 2007) by ScanExpress software.
The statistical analysis of gene expression was performed using linear methods for microarrays (limma package in Bioconductor software). The method tests the null hypothesis of no differential expression between the groups of samples compared using the moderated t-statistic, which has similar interpretation as the ordinary t-test statistic. The expression of genes with the Benjamini-Hochberg (FDR) multiple-testing corrected p-value below 0.05 were qualified as significantly changed. The groups of samples compared in the analysis of differential expression were identified using hierarchical clustering (unsupervised analysis) and visually illustrated in the space of differentially expressed genes using a dendrogram.

label: Alexa 555

molecule: total RNA

organism: Canis lupus familiaris

source_name: pooled RNA from all tumours

label_protocol: For each microarray slide, total RNA (10 μg) of each tumour and pooled RNA from all the tumours was reverse-transcribed using the SuperScript Plus Direct cDNA Labeling System (Invitrogen, USA) according to the manufacturer's protocol. Single-strand cDNA were stained with Alexa 647 and Alexa 555 (Invitrogen). The efficiency of dye incorporation was measured using NanoDrop (NanoDrop Technologies, USA).

extract_protocol: The total RNA from the samples was isolated using a Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer's protocol.

tag: tissue

value: mammary tumors

tag: malignancy grade

value: 1st, 2nd, 3rd

tag: sample type

value: reference

label: Alexa 647

source_name: tumour no.72

value: mammary tumor

tag: tumor no.


title: rep.2nd grade of malignancy no.26

description: rep. 2nd grade of malignancy no. 26

source_name: tumour no.26


title: rep.2nd grade of malignancy no.82

description: rep. 2nd grade of malignancy no. 82

source_name: tumour no.82


title: rep.3rd grade of malignancy no.51

description: rep. 3rd grade of malignancy no. 51

source_name: tumour no.51


title: rep.3rd grade of malignancy no.67

description: rep. 3rd grade of malignancy no. 67

source_name: tumour no.67


title: rep.3rd grade of malignancy no.36

description: rep. 3rd grade of malignancy no. 36

source_name: tumour no.36


title: rep.1st grade of malignancy no.40

description: rep. 1st grade of malignancy no. 40

source_name: tumour no.40


title: rep.2nd grade of malignancy no.21

description: rep. 2nd grade of malignancy no. 21

source_name: tumour no.21


title: rep.2nd grade of malignancy no.71

description: rep. 2nd grade of malignancy no. 71

source_name: tumour no.71


title: rep.1st grade of malignancy no.84

description: rep. 1st grade of malignancy no. 84

source_name: tumour no.84


title: 3rd grade of malignancy no.67

description: 3rd grade of malignancy no.67


title: 2nd grade of malignancy no.26

description: 2nd grade of malignancy no.26


title: rep.1st grade of malignancy no.32

description: rep. 1st grade of malignancy no. 32

source_name: tumour no.32


title: rep.1st grade of malignancy no.28

description: rep. 1st grade of malignancy no. 28

source_name: tumour no.28


title: rep.3rd grade of malignancy no.12

description: rep. 3rd grade of malignancy no. 12

source_name: tumour no.12


title: 1st grade of malignancy no.84

description: 1st grade of malignancy no.84


title: rep.2nd grade of malignancy no.9

description: rep. 2nd grade of malignancy no. 9

source_name: tumour no.9


title: rep.2nd grade of malignancy no.37

description: rep. 2nd grade of malignancy no. 37

source_name: tumour no.37


title: 3rd grade of malignancy no.89

description: 3rd grade of malignancy no.89

source_name: tumour no.89


title: 2nd grade of malignancy no.37

description: 2nd grade of malignancy no.37

source_name: pooled RNA from all tumours


title: 3rd grade of malignancy no.72

description: 3rd grade of malignancy no.72

source_name: tumour no.72


title: rep.1st grade of malignancy no.27

description: rep. 1st grade of malignancy no. 27

source_name: tumour no.27


title: 3rd grade of malignancy no.36

description: 3rd grade of malignancy no.36


title: 2nd grade of malignancy no.82

description: 2nd grade of malignancy no.82

source_name: tumour no.82


title: 1st grade of malignancy no.40

description: 1st grade of malignancy no.40


title: 1st grade of malignancy no.27

description: 1st grade of malignancy no.27


title: 1st grade of malignancy no.88

description: 1st grade of malignancy no.88

source_name: tumour no.88


title: 2nd grade of malignancy no.71

description: 2nd grade of malignancy no.71


title: 1st grade of malignancy no.28

description: 1st grade of malignancy no.28


title: 1st grade of malignancy no.32

description: 1st grade of malignancy no.32


title: 3rd grade of malignancy no.12

description: 3rd grade of malignancy no.12


title: 2nd grade of malignancy no.9

description: 2nd grade of malignancy no.9


title: rep.3rd grade of malignancy no.89

description: rep. 3rd grade of malignancy no. 89


title: rep.1st grade of malignancy no.88

description: rep. 1st grade of malignancy no. 88


title: 3rd grade of malignancy no.51

description: 3rd grade of malignancy no.51

source_name: tumour no.51


title: LMS_3

city: Stanford

first: Craig

middle: Patrick

last: Giacomini

state: CA

address: 269 Campus Drive (CCSR 3245A)

department: Pathology

country: USA

institute: Stanford University

description: Sarcoma sample 7, no known gene fusions

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: Microarrays were imaged using Agilent's High-Resolution C Scanner.

data_processing: LOWESS normalized fluorescence ratios were extracted using Agilent Feature Extraction Software.

organism: Homo sapiens

source_name: Leiomyosarcoma clinical specimen

label_protocol: Sample labeling was performed using the Fairplay III Microarray Labeling Kit (Agilent).  Briefly, 10ug of sample total RNA and 1ug of reference mRNA were differentially labeled with Cy5 and Cy3, respectively, and co-hybridized to the microarray.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen).

tag: cancer subtype

value: Leiomyosarcoma

tag: cell line or clinical sample

value: clinical specimen

molecule: polyA RNA

source_name: Common mRNA reference (pooled from 11 diverse cell lines)

tag: reference


title: LMS_4

description: Sarcoma sample 8, no known gene fusions

value: Common mRNA reference (pooled from 11 diverse cell lines)


title: 2nd grade of malignancy no.21

description: 2nd grade of malignancy no.21

source_name: tumour no.21


title: Angiosarcoma_1

description: Sarcoma sample 1, no known gene fusions

source_name: Angiosarcoma clinical specimen

value: Angiosarcoma


title: LMS_1

description: Sarcoma sample 5, no known gene fusions


title: DTF_2

description: Sarcoma sample 4, no known gene fusions

source_name: Desmoid type fibromatosis clinical specimen

value: Desmoid type fibromatosis


title: DTF_1

description: Sarcoma sample 3, no known gene fusions


title: EwingSarcoma_EWSR1/FLI1

description: Positive control sample 5, harbors the known gene fusion EWSR1/FLI1, Untreated

source_name: Ewing's sarcoma cell line harboring EWSR1/FLI1

value: Ewing's sarcoma

value: cell line


title: Angiosarcoma_2

description: Sarcoma sample 2, no known gene fusions


title: LMS_2

description: Sarcoma sample 6, no known gene fusions


title: ProstateCancer_ETV1

description: Positive control sample 3, harbors a suspected gene fusion of ETV1, Untreated

source_name: Prostate cancer clinical specimen harboring suspected ETV1 rearrangement

value: Prostate cancer


title: ProstateCancer_ETV4

description: Positive control sample 4, harbors a suspected gene fusion of ETV4, Untreated

source_name: Prostate cancer clinical specimen harboring suspected ETV4 rearrangement


title: ProstateCancer_TMPRSS2/ERG

description: Positive control sample 8, harbors the known gene fusion TMPRSS2/ERG, Untreated

source_name: Prostate cancer cell line harboring TMPRSS2/ERG


title: CML_BCR/ABL1

description: Positive control sample 2, harbors the known gene fusion BCR/ABL1, Untreated

source_name: CML cell line harboring BCR/ABL1

value: Chronic myelogenous leukemia


title: wild type under aerobic conditions, biological replicate 2

city: Tübingen

first: Diana

last: Mader

address: Morgenstelle 28

country: Germany

institute: University of Tübingen

description: Gene expression data of aerobic S. aureus cultures in exponential phase of growth

hyb_protocol: Hybridization of cDNA and following washing and staining of GeneChips were carried out according to standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, Chapter 6 Prokaryotic; 702232, Rev.3).

scan_protocol: GeneChips were scanned using a GeneChip® Scanner 3000 (Affymetrix; P/N 00-00212)

data_processing: The data were analyzed with GCOS version 2.1 using Affymetrix default analysis settings.

label: biotin

organism: Staphylococcus aureus subsp. aureus RN4220

source_name: wildtype under aerobic conditions in exponential growth phase

label_protocol: cDNA were prepared according to the standard Affymetrix protocol from 10 µg total RNA (GeneChip Expression Analysis Technical Manual, Chapter 4 Prokaryotic; 702232, Rev.3). cDNA were labeled with GeneChip® DNA Labeling Reagent (Affymetrix P/N 900542).

growth_protocol: Basic media (BM composed of 1% casein peptone, 0.5% yeast extract, 0.5% NaCl, 0.1% K2HPO4 x H2O, and 0.1% glucose) were inoculated with bacterial over-night cultures in BM at an OD578 of 0.08 and cultivated either aerobically (notched flasks on shaker) or anaerobically (completely filled, sealed tubes) at 37°C.

extract_protocol: Cells were thawed on ice and resuspended with 1 ml Trizol (Invitrogen) and bacteria were disrupted with 0.5 ml glass bead suspension in a homogenizer. Supernatants of the lysates were mixed with chloroform for 60 s and incubated for another three minutes . After centrifugation the upper phase was collected and pipetted into isopropanole. After 10 minutes incubation and centrifugation for 30 minutes to collect supernatants. 70 % ethanole was added and samples were centrifuged for 5 minutes. After removing supernatants pellets were dried, dissolved in sodium citrate buffer and purified with a Microcon filter catridge (Millipore) and stored at -80°C

treatment_protocol: Strains were harvested by centrifugation at an OD578 1.0 (aerobe cultures) or OD578 0.5 (anaerobe cultures) and immediately frozen at -80°C.

tag: genotype

value: wild type parental strain

tag: treatment

value: aerobic


title: ThyroidCancer_CCDC6/RET

description: Positive control sample 7, harbors the known gene fusion CCDC6/RET, Untreated

source_name: Thyroid cancer cell line harboring CCDC6/RET

value: Papillary thyroid cancer


title: fmt mutant under aerobic conditions, biological replicate 2

source_name: fmt mutant under aerobic conditions in exponential growth phase

value: formyltransferase lacking strain


title: ALCL_NPM1/ALK

description: Positive control sample 6, harbors the known gene fusion NPM1/ALK, Untreated

source_name: Anaplastic large cell lymphoma cell line harboring NPM1/ALK

value: Anaplastic large cell lymphoma


title: fmt mutant under aerobic condition, biological replicate 1


title: fmt mutant under anaerobic condition, biological replicate 2

source_name: fmt mutant under anaerobic conditions in exponential growth phase

value: anaerobic


title: wild type under anaerobic conditions, biological replicate 1

source_name: wildtype under anaerobic conditions in exponential growth phase


title: wild type under anaerobic conditions, biological replicate 2


title: fmt mutant under anaerobic condition, biological replicate 1


title: wild type under aerobic conditions, biological replicate 1


title: EosinophilicLeukemia_FIP1L1/PDGFRA

description: Positive control sample 1, harbors the known gene fusion FIP1L1/PDGFRA, Untreated

source_name: Eosinophilic leukemia cell line harboring FIP1L1/PDGFRA

value: Eosinophilic leukemia


title: d5 pre BI cell clone PC5B7 on DLL4 , biological replicate 2

city: Basel

first: Nadine

last: Gehre

department: Biomedicine

country: Switzerland

institute: University Basel

description:
PC5B7 on DLL4 S2
Gene expression data from Pax5-deficent preBI cells cultured with IL7 and SCF on 2ug/ml plastic bound DLL4-Fc, cells were sorted for CD93-/c-Kit+

hyb_protocol: Per Chip 80 μl of the hybridization cocktail, containing fragmented 22 biotin-labeled target DNA at a final concentration of 25 ng/μl was used. After addition Arrays were incubated at 45 °C on a rotator in a hybridization oven 640 for 17 h at 60 rpm.

scan_protocol: The Gene Chips were processed by the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: The raw data was then analyzed with Agilent GeneSpringGX 9.0 or Partek genomics suite.

organism: Mus musculus

source_name: Cell line (isolated from BM of Pax5 deficicent mice)

label_protocol: For preparation of labeled cDNA fragments an average of 15 μg cRNA (starting with a concentration of 200 ng RNA) was used for preparation using WT Target Labeling and Control Reagents (Affymetrix). All steps were carried out according to the GeneChip Whole Transcript Sense Target Labeling Assay Manual, Version 4 provided by Affimetrix.

growth_protocol: PC5B7 were cultured on irradiated OP9 stroma cells in the presence of IL7 in medium.

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

treatment_protocol: For differentiation cells were collected and cultured on 2ug/ml plate bound DLL4-Fc or without. The experiment was performed in medium supplemented with 100ng/ml stem cell factor (SCF) and 4 % IL-7. Cells were collected and analyzed by FACS and RNA was isolated for gene expression analysis on day 5.

tag: cell line

tag: sorted for

value: CD93lo, c-Kit hi cells

value: Pax5 deficient preBI, Bcl2 transduced


title: d5 pre BI cell clone PC5B7, biological replicate 2

description:
PC5B7 control 2
Gene expression data from Pax5-deficent preBI cells cultured with IL7 and SCF as control

value: CD93+, c-Kit lo cells


title: d5 pre BI cell clone PC5B7 on DLL4, biological replicate 1

description:
PC5B7 on DLL4 S1
Gene expression data from Pax5-deficent preBI cells cultured with IL7 and SCF on 2ug/ml plastic bound DLL4-Fc, cells were sorted for CD93-/c-Kit+


title: Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Knockout 1

city: new haven

first: qingle

last: li

state: ct

address: 10 Amistad st

institute: yale universtiy

description:
FBN+/-.TGFBRIIko_10
Gene expression data from fibrillin-1 mutant with Tgfbr2 knockout mice

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C (GeneChip® WT Terminal Labeling and Hybridization User Manual, P/N 702808 Rev.5, Affymetrix). GeneChips were washed and stained according to the standard Affymetrix protocol(GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays,P/N 702731 Rev.3,Affymetrix).

scan_protocol: The stained chips were read and analyzed with GeneChip Scanner 3000 (Affymetrix).

data_processing: Expression intensities were quantified and compared using Partek Genomics Suite v6.4 (Partek Inc.) with Robust Multi-Array Average for normalization and fold-change calculations. Comparisons between groups were by unpaired Student t-test on log2 transformed data. The results of fold changes and the expression values are shown as anti-logged data.

source_name: aorta of Tgfbr2 knockout and fibrillin-1 mutant mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® WT Terminal Labeling and Hybridization User Manual, P/N 702808 Rev.5, Affymetrix).

extract_protocol: Total RNA was isolated using RNeasy mini kits(QIAGEN) according to the manufacturer’s protocol.

treatment_protocol: At 4 weeks of age, we injected vehicle (corn oil) i.p. x5 days in Myh11-CreERT2.Tgfbr2f/f Control and Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Control mice or we injected tamoxifen 1 mg i.p. x5 days for Myh11-CreERT2.Tgfbr2f/f Knockout and Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Knockout  mice. The animals were euthanized at 6 weeks of age and their ascending aorta was analyzed.

tag: genotype/variation

value: Fbn1C1039G mutant

tag: tgfbr2 status

value: conditional disruption of Tgfbr2

value: ascending aorta

tag: age

value: 6 weeks


title: Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Control 3

description:
FBN+/-_9
Gene expression data from fibrillin-1 mutant mice

source_name: aorta of fibrillin-1 mutant mice

value: intact TGF-β signaling


title: Myh11-CreERT2.Tgfbr2f/f Knockout 1

description:
FBN+/+.TGFBRIIko_4
Gene expression data from Tgfbr2 knockout mice

source_name: aorta of Tgfbr2 knockout mice

value: Fbn1 wild-type


title: Myh11-CreERT2.Tgfbr2f/f Control 3

description:
FBN+/+_3
Gene expression data from wildtype mice

source_name: aorta of wildtype mice


title: Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Knockout 3

description:
FBN+/-.TGFBRIIko_12
Gene expression data from fibrillin-1 mutant with Tgfbr4 knockout mice


title: Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Control 1

description:
FBN+/-_7
Gene expression data from fibrillin-1 mutant mice


title: Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Knockout 2

description:
FBN+/-.TGFBRIIko_11
Gene expression data from fibrillin-1 mutant with Tgfbr3 knockout mice


title: Fbn1C1039G/+.Myh11-CreERT2.Tgfbr2f/f Control 2

description:
FBN+/-_8
Gene expression data from fibrillin-1 mutant mice


title: Myh11-CreERT2.Tgfbr2f/f Control 2

description:
FBN+/+_2
Gene expression data from wildtype mice


title: d5 pre BI cell clone PC5B7, biological replicate 1

description:
PC5B7 control 1
Gene expression data from Pax5-deficent preBI cells cultured with IL7 and SCF as control


title: slt2_ Tunicamycin_3h

city: Suzuka

first: Hironobu

last: Nakayama

state: Mie

address: 3500-3 Minami-Tamagaki Cho

department: Phamaceutical Science

country: Japan

institute: Suzuka University of Medical Science

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., following their standard operating protocol. See www.nimblegen.com.

scan_protocol: The arrays were scanned in a NimbleGen MS 200 Microarray Scanner by NimbleGen Systems Inc., following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249-64, 2003), quantile normalization (Bolstad et al. Bioinformatics 19(2):185-93, 2003), and background correction as implemented in the NimbleScan v2.6 Software (Roche NimbleGen, Inc.).

organism: Nakaseomyces glabratus

label_protocol: The cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA Labeling Kit by NimbleGen Systems Inc., following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Candida glabrata was grown to mid-log phase (O.D.600nm 0.7) in synthetic media at 30°C.

extract_protocol: Total RNA was extracted using the FastRNA Red Kit (Qbiogene, Carlsbad, CA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer by NimbleGen Systems Inc., Tokyo, Japan.

treatment_protocol: Candida glabrata was grown in synthetic media containing tunicamycin (1.5 mg/L) for 0.5 or 3 h at 30°C.

value: slt2::HIS3, trp1

tag: drug exposure

value: tunicamycine for 3h


title: ire1_Tunicamycin_0.5h

value: ire1::HIS3, trp1

value: tunicamycine for 0.5h


title: crz1_ Tunicamycin_3h

value: crz1::HIS3, trp1


title: cnb1_ Tunicamycin_3h

value: cnb1::HIS3, trp1


title: slt2_ Tunicamycin_0.5h


title: WT_ Tunicamycin_3h

source_name: WT

value: wild-type control (trp1)


title: ire1_Tunicamycin_3h


title: WT_ Tunicamycin_0.5h


title: crz1_ no drug_0h

value: No drug


title: slt2_ no drug_0h


title: crz1_ Tunicamycin_0.5h


title: Myh11-CreERT2.Tgfbr2f/f Knockout 3

description:
FBN+/+.TGFBRIIko_6
Gene expression data from Tgfbr4 knockout mice


title: Myh11-CreERT2.Tgfbr2f/f Knockout 2

description:
FBN+/+.TGFBRIIko_5
Gene expression data from Tgfbr3 knockout mice


title: ire1_ no drug_0h


title: WT_ no drug_0h


title: cnb1_ Tunicamycin_0.5h


title: cnb1_ no drug_0h


title: Day 7 after NK cell differentiation compare with 24h after NK cell differentiation

city: Cheongwon-gun

first: Su Ui

last: Lee

address: Ochang-eup

country: South Korea

institute: Korea Research institute of Bioscience & Biotechnology

description: Harvested 1 day and 7day after differentiation induction

hyb_protocol: After checking labeling efficiency, each 750 ng of cyanine 3-labeled and cyanine 5-labeled cRNA target were mixed and the fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 °C for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent Whole Human Genome Oligo Microarray. The arrays hybridized at 65 °C for 17 h with 10 rpm rotating in Agilent Hybridization Oven. The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: NK cells_24h

label_protocol: Each 0.5 μg total RNA was mixed with the diluted Spike mix and T7 promoter primer mix and incubated at 65 °C for 10 min. cDNA master mix (5X First strand buffer, 0.1 M DTT, 10 mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40 °C for 2 h and then the RT and dsDNA synthesis was terminated by incubating at 65 °C for 15 min.

growth_protocol: In vitro differentiated mNK were generated and differentiated from a starting population of purified CD34+ cells isolated from human umbilical cord blood (UCB)(Spanholtz et al. ; Lee et al. 2009; Park et al. 2009).  Cells were maintained at 37°C in humidified air (5% CO2) and grown in RPMI 1640 medium (Gibco BRL) supplemented with 10% fetal bovine serum (Hyclone), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: Total RNA from each sample was extracted using TRIZOL reagent (GibcoBRL, Rockville, MD, USA) according to the protocol of the manufacturer.

treatment_protocol: The purified HSCs were cultured in MyeloCult H5100 supplemented with stem cell factor (SCF, 30 ng/ml) and flt-3 ligand (FL, 50 ng/ml) for 14 days at 37 ◦C, 5% CO2. The culture medium was refreshed every 3 days. Then, the medium was changed to differentiation medium containing human IL-15 (30 ng/ml, R&D Systems) and cultured for 14 days. Every 3-4 days, half of the medium was discarded and replenished by fresh medium containing freshly added cytokines. The population of CD56+CD3−NK cells was determined via flow cytometric analysis.

tag: tissue source

value: human umbilical cord blood (UCB)

tag: cell type

value: Human Natural killer cells

tag: developmental stage

value: 24 hr after differentiation induction

source_name: total RNA

value: 7 day after differentiation induction


title: MC3T3-E1 Cells Treated 7 Day

city: Augusta

first: James

last: Cray Jr.

state: GA

institute: Georgia Regents University

description: Gene Expression data

hyb_protocol: Following labeling, cDNAs were hybridized for 16 hr at 45C on Mouse Gene 1.0 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: Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6).  Differential expressions were calculated using ANOVA of Partek package.

source_name: MC3T3-E1 Cells Treated 7 Day

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

growth_protocol: MC3T3-E1 cells purchased from ATCC (Manassas, VA), were reconstituted and grown in a T-75 flask until transfer into T-175 flask. Cells were cultured in alpha minimum Eagles medium (αMEM) supplemented with penicillin/streptomycin (pen/strep) and 1% fetal bovine serum (FBS).

treatment_protocol: The experiment was set up in a 6 well plates with 3 wells as control untreated cells, and 3 well thyroxine treated cells. Seeding density was 50,000 cells per well. treatments were set up as follows 1) proliferation medium: control cells fed proliferation medium or 2) Thyroxine 1x10-6 mM. Cultures were treated for 3 or 7 days feeding every other day.

tag: strain

tag: tissue

value: Murine Calvarial derived Pre-Osteoblasts


title: Myh11-CreERT2.Tgfbr2f/f Control 1

description:
FBN+/+_1
Gene expression data from wildtype mice

value: ascending aorta


title: MC3T3-E1 Cells Control 7 Day

description: Gene Expression data

source_name: MC3T3-E1 Cells Control 7 Day


title: female 69.41820671y #880

city: ROTTERDAM

first: Marjolein

middle: J.

last: Peters

address: Wytemaweg 80

department: Internal Medicine

country: Netherlands

institute: Erasmus MC

hyb_protocol: RNA was hybridized to the Illumina Whole-Genome Expression Beadchips (HT12-v4), using the standard Illumina Hybridization Protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Missing intensities were not imputed but deleted. Background values were not substracted. Raw intensities were quantile normalized, log2-transformed, and centered. Samples were standardized. We used the software-pipeline AssociationGG (www.genenetwork.nl/associationgg).

label_protocol: The isolated RNAs were amplified and labelled using the Ambion TotalPrep RNA Protocol.

extract_protocol: RNA was stabilized using PAXgene Tubes (Becton Dickinson) and RNA was isolated using the Qiagen PAXgene Blood RNA kit. Quality Control was performed with the Caliper Life Sciences LabChip GX system.

tag: gender

value: female

tag: age (y)

value: blood


title: MC3T3-E1 Cells Control 3 Day

description: Gene Expression data

source_name: MC3T3-E1 Cells Control 3 Day


title: female 81.47570157y #878


title: MC3T3-E1 Cells Treated 3 Day

description: Gene Expression data

source_name: MC3T3-E1 Cells Treated 3 Day


title: Day 14 after NK cell differentiation compare with 24h after NK cell differentiation

description: Harvested 1 day and 14day after differentiation induction

value: 14 day after differentiation induction


title: female 54.48870637y #881


title: male 48.96646133y #872

value: male


title: male 55.77002053y #879


title: male 67.95893224y #876


title: female 63.43052704y #868


title: male 84.11498973y #864


title: female 57.9247091y #867


title: male 59.96167009y #877


title: male 57.64271047y #874


title: female 49.18548939y #865


title: female 52.15879535y #866


title: female 56.64613279y #873


title: male 60.93360712y #869


title: female 54.02327173y #875


title: male 50.34907598y #863


title: male 48.26557153y #871


title: male 52.06297057y #870


title: male 79.34017796y #856


title: female 86.85284052y #858


title: female 83.90691307y #857


title: male 61.93566051y #861


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title: female 55.53182752y #511


title: male 56.58042437y #500


title: Adenocarcinoma #2340

city: Roterdam

first: Maikel

last: Wouters

address: Dr. Molewaterplein 50

department: Genetics

institute: Erasmus Medical Center

hyb_protocol: Labeled RNA were hybridized to Custom Exiqon LNA probes for 16 hours at 60°C, subsequently washed and scanned

scan_protocol: After hybridization, samples were scanned using the ScanArray Express HT (Tecan). Image generation and feature extraction were performed using Imagene 6.0.

data_processing: The raw microRNA data, median signal minus median background, were normalized using quantile normalization. Duplicate spots on the array were averaged and human miRNAs were analyzed for differentially expressed microRNAs using Significant Analysis of Micro-arrays (SAM)(MeV; v4.4). Only microRNAs above background were further analyzed.

source_name: Adenocarcinoma #2340

label_protocol: 1ug of total RNA was labeled using the Createch Cy3 label kit (Createch).

extract_protocol: Lung tumors and (if possible) adjacent healthy lung tissue was isolated from patients by surgery. Afterwards, tumors or healthy tissue were frozen in liquid nitrogen and stored at -80 0C. Total RNA was isolated using RNA Bee (BioConnect, the Netherlands) according to the manufacturer’s instructions. All samples passed RNA quality control using Nanodrop 2000. MicroRNA profiling was performed as previously described (Pothof et al. 2009).

value: Adenocarcinoma

tag: paired samples

value: Adjacent to Normal sample #2309


title: Adenocarcinoma #2308

source_name: Adenocarcinoma #2308


title: Adenocarcinoma #2254

source_name: Adenocarcinoma #2254


title: Adenosquamous #2248

source_name: Adenosquamous #2248

value: Adenosquamous carcinoma

value: Adjacent to Normal sample #2247


title: male 60.91444216y #484


title: female 56.64339493y #485


title: male 58.84188912y #479


title: female 60.6844627y #482


title: Adenocarcinoma #2316

source_name: Adenocarcinoma #2316

value: Adjacent to Normal sample #2315


title: female 53.50034223y #480


title: female 50.58726899y #481


title: female 47.99178645y #478


title: female 63.23887748y #477


title: Adenocarcinoma #2224

source_name: Adenocarcinoma #2224


title: Large cell #2286

source_name: Large cell #2286

value: Large cell carcinoma


title: Large cell #2304

source_name: Large cell #2304

value: Adjacent to Normal sample #2303


title: male 77.32511978y #476


title: female 52.30390144y #483


title: Large cell #2250

source_name: Large cell #2250


title: Adenocarcinoma #2212

source_name: Adenocarcinoma #2212


title: Large cell #2228

source_name: Large cell #2228

value: Adjacent to Normal sample #2227


title: Large cell #2282

source_name: Large cell #2282


title: Large cell #2234

source_name: Large cell #2234

value: Adjacent to Normal sample #2233


title: Squamous #2214

source_name: Squamous #2214

value: Squamous carcinoma


title: Squamous #2222

source_name: Squamous #2222


title: Squamous #2300

source_name: Squamous #2300


title: male 69.16906229y #508


title: Squamous #2252

source_name: Squamous #2252

value: Adjacent to Normal sample #2251


title: female 58.73785079y #472


title: female 70.74332649y #470


title: Squamous #2302

source_name: Squamous #2302

value: Adjacent to Normal sample #2301


title: Normal sample #2247

source_name: Normal sample #2247

value: Healthy lung tissue

value: Adjacent to Adenosquamous #2248


title: female 53.65913758y #475

value: female

value: blood


title: Normal sample #2303

source_name: Normal sample #2303

value: Adjacent to Large cell #2304


title: Normal sample #2309

source_name: Normal sample #2309

value: Adjacent to Adenocarcinoma #2340


title: Normal sample #2227

source_name: Normal sample #2227

value: Adjacent to Large cell #2228


title: male 77.44284736y #474

value: male


title: male 58.26146475y #471


title: Normal sample #2249

source_name: Normal sample #2249


title: male 69.70294319y #466


title: male 53.30321697y #464


title: Normal sample #2211

source_name: Normal sample #2211


title: male 57.68925394y #469


title: female 59.37577002y #473


title: male 57.84531143y #465


title: male 73.61259411y #468


title: female 59.45516769y #467


title: female 54.95687885y #462


title: male 57.60985626y #460


title: female 60.39151266y #461


title: male 50.55167693y #463


title: female 70.38193018y #458


title: male 62.35181383y #459


title: Normal sample #2315

source_name: Normal sample #2315

value: Adjacent to Adenocarcinoma #2316


title: male 47.31279945y #457


title: Normal sample #2223

source_name: Normal sample #2223


title: Normal sample #2233

source_name: Normal sample #2233

value: Adjacent to Large cell #2234


title: Normal sample #2209

source_name: Normal sample #2209


title: Normal sample #2393

source_name: Normal sample #2393


title: Normal sample #2251

source_name: Normal sample #2251

value: Adjacent to Squamous #2252


title: Normal sample #2301

source_name: Normal sample #2301

value: Adjacent to Squamous #2302


title: Normal sample #2305

source_name: Normal sample #2305


title: male 54.65845311y #452


title: SW1573

data_processing: The raw microRNA data, median signal minus median background, were normalized using quantile normalization. Obvious outliers were removed and human miRNAs were selected with an average expression above background. Duplicate spots on the array were averaged and the normalized values were analyzed for differentially expressed microRNAs using Significant Analysis of Micro-arrays (SAM)(MeV; v4.4).

growth_protocol: Lung cancer cell lines were cultured in RPMI1640 Glutamax, supplemented with 10% FBS and Penicillin/Streptomycin. The cells were cultured at 37 0C, 5% CO2 in a humidified incubator

extract_protocol: Total RNA was isolated using RNA Bee (BioConnect, the Netherlands) according to the manufacturer’s instructions. All samples passed RNA quality control using Nanodrop 2000. MicroRNA profiling was performed as previously described (Pothof et al. 2009).


title: female 64.61054073y #455


title: female 50.55441478y #454


title: female 60.47091034y #451


title: H460


title: H522


title: H292


title: male 66.50239562y #449


title: female 53.97125257y #456


title: male 60.53935661y #453


title: H226


title: H322


title: H1975


title: H1703


title: H3255


title: female 55.87679671y #448


title: male 57.67556468y #450


title: GLC-34


title: female 61.25393566y #447


title: GLC-4


title: female 76.56947296y #444


title: female 78.02053388y #443


title: female 57.00752909y #446


title: A549


title: female 64.26283368y #440


title: HSAEpC high IR 12h #6

source_name: Human Small Airway Epithelial primary Cells

growth_protocol: HMEpC and HSAEpC were grown untill 10 cell doublings according to supplier protocol.

treatment_protocol: Cells were treated with a indicated continuous dose of cisplatin (Pharmachemie, the Netherlands) or one pulse treatment of the indicated IR dose using a Cs137 source.

value: ionizing radiation

tag: dose

tag: time point


title: male 67.00616016y #438


title: female 85.83436003y #445


title: HSAEpC high cpt 24h #4

tag: treatment

value: cisplatin

value: Human Small Airway Epithelial primary Cells


title: male 51.42231348y #441


title: male 61.63175907y #439


title: HSAEpC control 6h #6

value: mock


title: male 48.55030801y #442


title: HSAEpC low IR 24h #6


title: HSAEpC low cpt 24h #3


title: female 49.7467488y #436


title: HSAEpC low cpt 12h #3


title: HSAEpC control 0h #6


title: male 71.94250513y #437


title: HSAEpC high IR 6h #1


title: HSAEpC low IR 6h #5


title: male 53.19096509y #435


title: male 64.97467488y #433


title: HSAEpC high IR 6h #6


title: female 81.76865161y #429


title: HSAEpC high cpt 12h #3


title: HSAEpC high cpt 6h #4


title: female 63.67693361y #428


title: female 59.6440794y #432


title: HSAEpC control 12h #2


title: HSAEpC low IR 24h #2


title: HSAEpC low IR 12h #2


title: HSAEpC control 24h #3


title: HSAEpC high IR 24h #1


title: female 48.89801506y #431


title: female 56.36960986y #424


title: female 61.34976044y #427


title: female 53.3798768y #430


title: female 54.50787132y #423


title: HSAEpC low cpt 12h #5


title: HSAEpC high cpt 6h #3


title: male 52.6954141y #422


title: female 55.44969199y #434


title: HSAEpC low cpt 24h #4


title: female 62.71321013y #425


title: HSAEpC low IR 12h #6


title: HSAEpC high IR 6h #2


title: HSAEpC high cpt 12h #1


title: HSAEpC control 12h #6


title: HSAEpC control 6h #5


title: HSAEpC control 0h #5


title: male 50.35728953y #426


title: HSAEpC control 24h #1


title: female 63.6440794y #415


title: male 54.11635866y #416


title: male 58.13552361y #421


title: male 64.96646133y #419


title: female 49.12251882y #413


title: HSAEpC high IR 12h #5


title: male 74.10540726y #418


title: female 66.30800821y #420


title: male 61.97672827y #417


title: HSAEpC control 6h #4


title: male 48.18617385y #412


title: HSAEpC high IR 12h #3


title: female 79.18412047y #414


title: female 59.46064339y #411


title: female 67.93429158y #410


title: HSAEpC control 0h #4


title: male 60.91991786y #409


title: HSAEpC high cpt 24h #6


title: HSAEpC high cpt 6h #6


title: HSAEpC high cpt 6h #1


title: HSAEpC low cpt 6h #1


title: HSAEpC control 12h #5


title: HSAEpC low IR 6h #4


title: HSAEpC control 6h #1


title: male 61.99589322y #408


title: HSAEpC high cpt 24h #1


title: male 55.41683778y #404


title: female 54.69404517y #403


title: female 54.33538672y #407


title: HSAEpC low IR 12h #5


title: female 49.33333333y #400


title: male 54.4476386y #405


title: male 60.29021218y #396


title: female 57.7303217y #406


title: female 62.70225873y #401


title: female 61.18275154y #399


title: HSAEpC control 0h #3


title: HSAEpC low cpt 12h #1


title: HSAEpC high IR 12h #1


title: male 59.52361396y #395


title: male 69.08692676y #402


title: HSAEpC low cpt 6h #6


title: HSAEpC low IR 24h #3


title: female 51.86858316y #398


title: HSAEpC low IR 6h #6


title: HSAEpC high cpt 12h #2


title: HSAEpC high cpt 24h #5


title: female 72.24914442y #397


title: female 55.08281999y #394


title: HSAEpC low IR 12h #1


title: HSAEpC low cpt 6h #5


title: male 61.64544832y #391


title: female 68.85968515y #389


title: HSAEpC control 24h #4


title: HSAEpC control 24h #2


title: HSAEpC low cpt 24h #1


title: HSAEpC high IR 24h #2


title: HSAEpC control 0h #2


title: HSAEpC low cpt 24h #2


title: HSAEpC high IR 6h #5


title: female 89.36892539y #392


title: female 50.54346338y #393


title: female 69.00752909y #390


title: male 63.76180698y #386


title: female 53.5633128y #388


title: HSAEpC low IR 24h #5


title: HSAEpC low IR 6h #1


title: HSAEpC high IR 24h #6


title: female 52.12320329y #387


title: HSAEpC low cpt 12h #6


title: female 53.5742642y #384


title: male 67.14031485y #383


title: female 73.48939083y #385


title: male 60.08761123y #381


title: male 54.91854894y #379


title: HSAEpC high IR 24h #3


title: male 50.78986995y #378


title: HSAEpC high cpt 12h #5


title: HSAEpC low cpt 6h #3


title: female 74.76249144y #382


title: HSAEpC control 0h #1


title: HSAEpC control 12h #3


title: male 48.62149213y #380


title: HMEpC high cpt 24h 10

source_name: Human Mammary Epithelial primary Cells

value: Human Mammary Epithelial primary Cells


title: HMEpC high IR 24h 4


title: HMEpC low IR 24h 1


title: male 51.70431211y #375


title: female 52.47364819y #373


title: female 61.61806982y #377


title: HMEpC control 6h 1


title: male 55.87953457y #374


title: HMEpC high cpt 6h #5


title: HMEpC high cpt 6h #2


title: male 58.6091718y #369


title: female 61.25393566y #376


title: female 51.38945927y #370


title: female 72.39151266y #366


title: HMEpC low IR 12h #1


title: HMEpC high cpt 12h #3


title: female 67.04996578y #371


title: female 67.03080082y #372


title: female 63.38398357y #368


title: HMEpC high IR 24h 1


title: female 48.00273785y #365


title: male 56.53661875y #363


title: HMEpC 0h 6


title: female 61.53593429y #367


title: HMEpC low IR 6h #3


title: HMEpC high IR 24h #3


title: HMEpC control 12h #6


title: male 63.34565366y #361


title: male 52.55030801y #358


title: HMEpC high IR 6h #2


title: HMEpC control 6h #6


title: HMEpC high IR 6h #1


title: HMEpC 0h #5


title: female 67.75085558y #364


title: HMEpC low cpt 12h #3


title: HMEpC high IR 12h #3


title: HMEpC low IR 24h #3


title: male 52.37782341y #362


title: male 59.84941821y #359


title: HMEpC high cpt 12h #1


title: HMEpC low cpt 6h #2


title: female 47.69609856y #353


title: male 60.3504449y #357


title: male 61.80150582y #351


title: male 48.59137577y #348


title: female 53.87268994y #354


title: female 76.61054073y #360


title: HMEpC high IR 6h #5


title: HMEpC control 24h #4


title: HMEpC low cpt 12h #6


title: HMEpC low IR 12h #2


title: HMEpC low IR 12h #5


title: HMEpC control 12h #5


title: HMEpC 0h #3


title: HMEpC low IR 6h #5


title: HMEpC 0h #4


title: female 47.43326489y #350


title: HMEpC low IR 6h #2


title: HMEpC low cpt 24h #3


title: HMEpC low cpt 24h #6


title: female 64.03559206y #356


title: female 66.48049281y #355


title: HMEpC control 24h #3


title: HMEpC high IR 12h #6


title: HMEpC low IR 24h #6


title: female 70.2642026y #352


title: HMEpC control 6h #5


title: HMEpC control 24h #5


title: HMEpC high IR 6h #6


title: HMEpC control 12h #1


title: female 59.94798084y #340


title: male 48.41341547y #349


title: female 72.92539357y #346


title: female 61.08692676y #338


title: male 62.51334702y #347


title: male 54.1026694y #335


title: male 49.25667351y #341


title: male 62.23408624y #344


title: male 60.93634497y #330


title: male 66.47227926y #339


title: male 70.81724846y #333


title: male 58.54072553y #331


title: female 60.97193703y #336


title: male 59.60027379y #337


title: female 51.27720739y #343


title: HMEpC low cpt 24h #1


title: male 52.14784394y #342


title: male 58.97330595y #329


title: male 61.98767967y #332


title: female 51.00889802y #345


title: male 72.90896646y #328


title: female 57.51950719y #334


title: HMEpC high IR 12h #2


title: HMEpC high cpt 24h #9


title: HMEpC low cpt 6h #4


title: HMEpC low cpt 6h #6


title: HMEpC low cpt 12h #2


title: HMEpC low cpt 24h #2


title: HMEpC high cpt 24h #3


title: female 60.41615332y #323


title: HMEpC 0h #2


title: HMEpC control 6h #2


title: HMEpC high cpt 12h #6


title: HMEpC low IR 12h #4


title: HMEpC high cpt 6h #6


title: male 60.25735797y #327


title: HMEpC high cpt 6h #3


title: HMEpC high IR 24h #5


title: male 62.26146475y #326


title: female 53.31416838y #325


title: male 48.25188227y #319


title: HMEpC control 24h #1


title: male 60.76386037y #322


title: female 82.94592745y #321


title: HMEpC low cpt 6h #5


title: female 61.5578371y #318


title: male 57.43189596y #317


title: female 81.26488706y #320


title: male 71.137577y #324


title: male 59.84941821y #316


title: HMEpC high cpt 12h #5


title: HMEpC 0h #1


title: HMEpC high cpt 24h #5


title: HMEpC low IR 24h #4


title: male 56.81861739y #315


title: HMEpC high IR 12h #5


title: female 51.47433265y #314


title: HMEpC low IR 6h #4


title: female 58.13826146y #310


title: HMEpC low cpt 12h #5


title: female 56.32854209y #313


title: HMEpC control 12h #2


title: male 69.41273101y #312


title: female 60.85147159y #309


title: female 59.50718686y #307


title: sera control 1

type: protein

city: Shanghai

first: Qian-qian

last: Yin

state: Shanghai

address: No280, Chongqing South Road

country: China

institute: Shanghai Jiao Tong University School of Medicine

hyb_protocol: protocol see manufacturer's website http://www.raybiotech.com/antibody-array.html

scan_protocol: Expose to x-ray film and detect signal using film developer or detect signal directly from membrane using chemiluminescene imaging system.

data_processing: By comparing the signal intensities, relative expression levels of cytokines can be made. The intensities of signals can be quantified by densitometry. Positive control can be used to normalize the results from different membranes being compared

molecule: protein

source_name: sera of control mice

extract_protocol: 1.Collect blood in eppendorf tubes.  2.Leave them at r.t. for 20 min. 3. Spin the tubes at 5,000 rpm x 1 min. 4. Transfer all liquid part into 15 ml conical tubes. 5. Spin the tubes at 3,000 rpm x 10 min. 6. Transfer the serum into one tube (15 or 50 ml tube). Be careful not to contaminate erythrocytes.

value: sera


title: sera control 2

label_protocol: protocol see manufacturer's website http://www.raybiotech.com/antibody-array.html


title: sera EAE 2

source_name: sera of experimental autoimmune encephalomyelitis (EAE) mice


title: sera EAE 1


title: female 51.8275154y #311


title: female 55.87405886y #305


title: female 58.6255989y #303


title: female 56.1615332y #304


title: male 53.44284736y #306


title: male 61.81793292y #308


title: female 57.09787817y #298


title: female 66.14373717y #301


title: male 50.70499658y #302


title: GFP-KLF2 transduced CTL, biological rep. 3

city: Dundee

first: Gavin

middle: Charles

last: Preston

address: 4 Old Hawkhill

department: Cell Signaling & Immunology

country: United Kingdom

institute: University of Dundee

description: Gene expression data from CTL with enforced KLF2 expression

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

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

data_processing: The data were normalized and expression measures computed using the Robust Multiarray Average (RMA) method (Irizarry et. al. 2003).  A linear model was fitted to the normalised intensity data with fixed constants for each replicate group using the R package 'limma' (Smyth 2004)

source_name: In vitro differentiated CTL, day 4

label_protocol: Biotinylated cRNA were prepared using the Affymetrix GeneChip 3’ IVT Express Kit from 250ng total RNA

growth_protocol: Splenocytes were activated for 48 hours with gp33-41 peptide, then washed out and cultured a further 48 hours in IL-2

extract_protocol: RNA was extracted using RNeasy Minikit (Qiagen) according to manufacturers instructions

treatment_protocol: Retroviral transduction of isolated T cells was performed at 18 hours after peptide stimulation

value: In vitro cell culture

tag: genotype

value: P14 LCMV TCR transgenic

value: 8-12 week old


title: GFP-KLF2 transduced CTL, biological rep. 2


title: female 62.18480493y #300

value: female

value: blood


title: male 54.69404517y #295


title: female 68.52019165y #299


title: NeckCells_adult

city: Houston.

first: Jason

middle: C

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

hyb_protocol: Biotinylated cRNA probes were hybridized to the GeneChips. Post hybridization staining/washing using Affymetrix (manufacturer?s) protocols using the Fluidics Station 450 instrument.

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner.

data_processing: The seeting for modeling on dChip was Model-based expression and background subtraction was by PM/MM difference, which are the default settings.

source_name: gastric epithelial mucous neck cells

label_protocol: total RNA pooled from multiple dissections and multiple mice to make ~100 ng RNA, which was then amplirifed, labeled, and fragmented (by Arctureus RiboAmp HS kit followed by the RNA Amplification and Labeling Kit from Enzo Life Sciences).

extract_protocol: RNA was purified by PicoPure kit, RNA integrity verified on Agilent Bioanalyzer.

value: wild-type

value: 6-8 weeks


title: evGFP transduced CTL, biological rep. 1

description: Gene expression data from control CTL


title: female 61.02121834y #296


title: evGFP transduced CTL, biological rep. 2

description: Gene expression data from control CTL


title: male 58.88295688y #294

value: male


title: male 53.66735113y #297


title: evGFP transduced CTL, biological rep. 3

description: Gene expression data from control CTL


title: female 53.5687885y #291


title: female 55.74811773y #292


title: male 60.14510609y #289


title: female 70.31348392y #293


title: male 59.91512663y #290


title: DF-1, biological rep3

city: East Lansing

first: sugalesini

last: Subramaniam

state: MI

address: 3606 E Mount Hope Rd

department: CMIB

institute: Michigan State University

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix chips (GeneChip Chicken Genome Array). GeneChips were then washed and stained in the Affymetrix Fluidics Station

scan_protocol: Genechips were scanned and the resultant intensities analyzed for levels of transcripts of interest

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

organism: Gallus gallus

source_name: DF-1 cells

label_protocol: High quality RNA was labeled using Affymetrix (Santa Clara, CA) One-Cycle Target Labeling and Control Reagents

growth_protocol: Cells were cultured in Lebowitz's L-15 and McCoy 5A media with 15% inactivated fetal bovine serum, 100 U of penicillin per ml, and maintained at 37 °C.

extract_protocol: Total RNA was extracted using the Absolutely RNA Miniprep Kit (Stratagene, Santa Clara, CA)

value: DF-1 cells


title: male 57.76865161y #288


title: male 60.08213552y #284


title: female 61.63997262y #285


title: Meq-DF-1, biological rep3

source_name: Meq-DF-1 cells

value: Meq-DF-1 cells


title: DF-1, biological rep2


title: female 72.88158795y #287


title: male 61.5578371y #283


title: Meq-DF-1, biological rep2


title: male 55.24161533y #286


title: male 61.5687885y #281


title: Meq-DF-1, biological rep1


title: male 67.78918549y #280


title: male 71.91238877y #279


title: WT8S

city: Kanazawa

first: Awad

last: Shamma

state: Ishikawa

address: Kakuma-machi

department: Cancer Research Institute

institute: Kanazawa Uiniversity

description: 163 cells reconstituted with vector expressing ATM, selected with 4μg/ml puromycin for 3 days, grown under normal culture conditions for another 4 days and analysed.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >7.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Whole Genome Microarray 4x44K (G4122F) 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried by raise it slowly from buffer 2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20100617) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary mouse embryonic fibroblasts (MEFs) from E10.0 embryo obtained from Rb-ATM double knockout C57BL/6J mouse

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions with some changes. 3rd Spike mix was made by diluted 2nd Spike-Mix 10 times, and 1.8 ul of 3rd Spike-Mix was added to samples. Cy3 labeled cRNA was synthesized at 40°C for 20 hours and purified by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Primary MEFs were grown in MEM-α supplemented with 10% FBS under normal culture conditions.

extract_protocol: RNA isolation RNA was quantified and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary MEFs were transduced with empty vector or vector expressing ATM or vector expressing DNMT1 shRNA, selected with 4μg/ml puromycin for 3 days, grown under normal culture conditions for another 4 days and analysed.

tag: background strain

tag: transfection

value: vector expressing ATM

value: Rb-/-;ATM-/-;ATM-reconstituted


title: RNA_R.equi Day1-RNA_Requi Week8-rep5

city: College Station

first: Priyanka

last: Kachroo

address: University Drive

institute: Texas A&M University

description: Amplified RNA from blood leukocytes from foal-5 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and stimulated leukocytes from foal-5 (week-8) labeled with Cy5

hyb_protocol: Hybridizations were performed with 6 biological replicates at each experimental time-point: day 1 (D-1) and weeks 2 (W-2), 4 (W-4), and 8 (W-8). In order to compare the stimulated blood leukocytes with the unstimulated ones, we performed direct co-hybridization of cDNA from unstimulated samples and the corresponding stimulated samples at each experimental time-point. Dye-swap was embedded in the biological replicates at each time point such that if the 3 samples of stimulated leukocytes were labeled with Cy3 and hybridized to 3 samples of unstimulated leukocytes labeled with Cy5; the opposite was done with the other 3 stimulated samples and unstimulated samples. Additionally, in order to obtain the temporal expression changes in the in vitro R. equi stimulated leukocytes, we utilized the common reference design for microarray hybridizations

scan_protocol: Arrays were scanned with GenePix 4000B scanner at 5-micron resolution

data_processing: GenePix Pro 6.1 software was used for acquisition, spot finding and quantification of array images

organism: Equus caballus

source_name: blood leukocytes_foal-5 stimulated with R equi

label_protocol: For each sample, cDNA was generated from amplified RNA using Superscript II Reverse Transcription kit and labeled with Cy3 or Cy5 dye with the 3DNA Array 900 MPX expression array detection kit

growth_protocol: 60 mL of blood was collected at day 1 and  week 2, 4, 6 and 8 weeks post birth

extract_protocol: RNA was extracted using LeukoLock Total RNA isolation system. 500ng of RNA from each sample was used for RNA amplification using RampUp commercially available kit.

treatment_protocol: Blood leukocytes spilt into two parts, part 1 from foal-5 stimulated with Rhodococcus equi at MOI 10

tag: foal id

value: day 1 of birth

value: peripheral blood leukocytes

tag: stimulated with

value: Live virulent Rhodococcus equi at MOI 10

tag: sample type

value: common reference

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-5 stimulated with Rhodococcus equi at MOI 10

value: 8 wks after birth


title: RNA_R.equi Day1-RNA_Requi Week8-rep3

description: Amplified RNA from blood leukocytes from foal-3 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and stimulated leukocytes from foal-3 (week-8) labeled with Cy3

source_name: blood leukocytes_foal-3 stimulated with R equi

treatment_protocol: Blood leukocytes spilt into two parts, part 1 from foal-3 stimulated with Rhodococcus equi at MOI 10

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-3 stimulated with Rhodococcus equi at MOI 10


title: female 59.22518823y #282


title: RNA_R.equi Day1-RNA_Requi Week8-rep4

description: Amplified RNA from blood leukocytes from foal-4 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and stimultaed leukocytes from foal-4 (week-8) labeled with Cy5

source_name: blood leukocytes_foal-4 stimulated with R equi

treatment_protocol: Blood leukocytes spilt into two parts, part 1 from foal-4 stimulated with Rhodococcus equi at MOI 10

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-4 stimulated with Rhodococcus equi at MOI 10


title: GFP-KLF2 transduced CTL, biological rep. 1

value: In vitro cell culture

tag: age


title: female 50.57631759y #276


title: DF-1, biological rep1

tag: cell type


title: female 52.86516085y #278


title: D4

description: 163 cells depleted of DNMT1, selected with 4μg/ml puromycin for 3 days, grown under normal culture conditions for another 4 days and analysed.

value: primary mouse embryonic fibroblasts (MEFs)

value: vector expressing DNMT1 shRNA

tag: genotype/variation


title: male 61.32511978y #277


title: RNA_R.equi Day1-RNA_Requi Week8-rep2

description: Amplified RNA from blood leukocytes from foal-2 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and stimulated leukocytes from foal-2 (week-8) labeled with Cy3

source_name: blood leukocytes_foal-2 stimulated with R equi

treatment_protocol: Blood leukocytes spilt into two parts, part 1 from foal-2 stimulated with Rhodococcus equi at MOI 10

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-2 stimulated with Rhodococcus equi at MOI 10


title: 163

description: Rb-/-;ATM-/- MEFs transfected with empty vector are selected with 4μg/ml puromycin for 3 days, grown under normal culture conditions for another 4 days and analyzed.

value: empty vector


title: RNA_R.equi Day1-RNA_Requi Week8-rep1

description: Amplified RNA from blood leukocytes from foal-1 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and stimulated leukocytes from foal-1 (week-8) labeled with Cy3

source_name: blood leukocytes_foal-1 stimulated with R equi

treatment_protocol: Blood leukocytes spilt into two parts, part 1 from foal-1 stimulated with Rhodococcus equi at MOI 10

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-1 stimulated with Rhodococcus equi at MOI 10


title: female 61.27583847y #275

value: female

value: blood


title: RNA_R.equi Day1-RNA_Requi Week4-rep3

description: Amplified RNA from blood leukocytes from foal-3 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and stimulated leukocytes from foal-3 (week-4) labeled with Cy3

value: 4 wks after birth


title: RNA_R.equi Day1-RNA_Requi Week4-rep4

description: Amplified RNA from blood leukocytes from foal-4 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and stimulated leukocytes from foal-4 (week-4) labeled with Cy5


title: RNA_R.equi Day1-RNA_Requi Week4-rep5

description: Amplified RNA from blood leukocytes from foal-5 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and stimulated leukocytes from foal-5 (week-4) labeled with Cy5


title: female 55.9890486y #270


title: male 69.31416838y #271

value: male


title: RNA_R.equi Day1-RNA_Requi Week4-rep2

description: Amplified RNA from blood leukocytes from foal-2 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and stimulated leukocytes from foal-2 (week-4) labeled with Cy3


title: female 47.32375086y #273


title: RNA_R.equi Day1-RNA_Requi Week4-rep6

description: Amplified RNA from blood leukocytes from foal-6 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and stimulated leukocytes from foal-6 (week-4) labeled with Cy5

source_name: blood leukocytes_foal-6 stimulated with R equi

treatment_protocol: Blood leukocytes spilt into two parts, part 1 from foal-6 stimulated with Rhodococcus equi at MOI 10

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-6 stimulated with Rhodococcus equi at MOI 10


title: male 60.70362765y #272


title: female 47.64134155y #274


title: male 53.15537303y #268


title: female 84.38329911y #269


title: RNA_R.equi Day1-RNA_Requi Week2-rep5

description: Amplified RNA from blood leukocytes from foal-5 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and stimulated leukocytes from foal-5 (week-2) labeled with Cy5

value: 2 wks after birth


title: male 53.42094456y #266


title: RNA_R.equi Day1-RNA_Requi Week4-rep1

description: Amplified RNA from blood leukocytes from foal-1 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and stimulated leukocytes from foal-1 (week-4) labeled with Cy3


title: RNA_R.equi Day1-RNA_Requi Week2-rep3

description: Amplified RNA from blood leukocytes from foal-3 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and stimulated leukocytes from foal-3 (week-2) labeled with Cy3


title: RNA_R.equi Day1-RNA_Requi Week2-rep4

description: Amplified RNA from blood leukocytes from foal-4 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and stimulated leukocytes from foal-1 (week-2) labeled with Cy5


title: male 48.02190281y #267


title: RNA_R.equi Day1-RNA_Requi Week2-rep6

description: Amplified RNA from blood leukocytes from foal-6 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and stimulated leukocytes from foal-6 (week-2) labeled with Cy5


title: RNA_R.equi Day1-RNA_Requi Week2-rep1

description: Amplified RNA from blood leukocytes from foal-1 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and stimulated leukocytes from foal-1 (week-2) labeled with Cy3


title: female 70.13278576y #265


title: RNA_R.equi Day1-RNA_Requi Week2-rep2

description: Amplified RNA from blood leukocytes from foal-2 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and stimulated leukocytes from foal-2 (week-2) labeled with Cy3


title: male 62.01505818y #261


title: male 60.43805613y #263


title: RNA_R.equi-RNA_Control Week8-rep3

description: Amplified RNA from blood leukocytes from foal-3 (week-8) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-3 (week-8)  labeled with Cy3

source_name: blood leukocytes_unstimulated with PBS as control

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-3 unstimulated with PBS as control

value: PBS (unstimulated control)


title: male 77.80971937y #259


title: male 49.70841889y #264


title: RNA_R.equi-RNA_Control Week8-rep5

description: Amplified RNA from blood leukocytes from foal-5 (week-8) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-5 (week-8) labeled with Cy5

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-5 unstimulated with PBS as control


title: RNA_R.equi Day1-RNA_Requi Week8-rep6

description: Amplified RNA from blood leukocytes from foal-6 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and stimulated leukocytes from foal-6 (week-8)  labeled with Cy5


title: RNA_R.equi-RNA_Control Week8-rep4

description: Amplified RNA from blood leukocytes from foal-4 (week-8) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-4 (week-8)  labeled with Cy5

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-4 unstimulated with PBS as control


title: male 74.40657084y #258


title: male 65.59890486y #260


title: female 59.02806297y #257


title: female 51.24709103y #262


title: RNA_R.equi-RNA_Control Week8-rep6

description: Amplified RNA from blood leukocytes from foal-6 (week-8) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-6 (week-8) labeled with Cy5

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-6 unstimulated with PBS as control


title: RNA_R.equi-RNA_Control Week8-rep2

description: Amplified RNA from blood leukocytes from foal-2 (week-8) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-2 (week-8)  labeled with Cy3

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-2 unstimulated with PBS as control


title: RNA_R.equi-RNA_Control Week4-rep5

description: Amplified RNA from blood leukocytes from foal-5 (week-4) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-5 (week-4) labeled with Cy5

treatment_protocol: Blood leukocytes spilt into two parts, part 1 from foal-5 stimulated with Rhodococcus equi at MOI 10


title: female 67.20602327y #255


title: RNA_R.equi-RNA_Control Week8-rep1

description: Amplified RNA from blood leukocytes from foal-1 (week-8) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-1 (week-8) labeled with Cy3

treatment_protocol: Blood leukocytes spilt into two parts, part 2 from foal-1 unstimulated with PBS as control


title: RNA_R.equi-RNA_Control Week4-rep3

description: Amplified RNA from blood leukocytes from foal-3 (week-4) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-3 (week-4)  labeled with Cy3

treatment_protocol: Blood leukocytes spilt into two parts, part 1 from foal-3 stimulated with Rhodococcus equi at MOI 10


title: female 60.64887064y #256


title: RNA_R.equi-RNA_Control Week4-rep2

description: Amplified RNA from blood leukocytes from foal-2 (week-4) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-2 (week-4) labeled with Cy3


title: RNA_R.equi-RNA_Control Week4-rep6

description: Amplified RNA from blood leukocytes from foal-6 (week-4) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-6 (week-4)  labeled with Cy5


title: RNA_R.equi-RNA_Control Week4-rep4

description: Amplified RNA from blood leukocytes from foal-4 (week-4) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-4 (week-4) labeled with Cy5


title: RNA_R.equi-RNA_Control Week4-rep1

description: Amplified RNA from blood leukocytes from foal-1 (week-4) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-1 (week-4) labeled with Cy3


title: female 59.52361396y #254


title: RNA_R.equi-RNA_Control Week2-rep5

description: Amplified RNA from blood leukocytes from foal-5 (week-2) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-5 (week-2)labeled with Cy5


title: male 54.14373717y #252


title: male 51.20328542y #251


title: RNA_R.equi-RNA_Control Week2-rep4

description: Amplified RNA from blood leukocytes from foal-4 (week-2) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-4 (week-2) labeled with Cy5


title: female 66.85831622y #247


title: RNA_R.equi-RNA_Control Week2-rep3

description: Amplified RNA from blood leukocytes from foal-3 (week-2) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-3 (week-2) labeled with Cy3


title: male 48.66803559y #253


title: female 66.05886379y #249


title: male 63.49623546y #250


title: male 48.18617385y #245


title: female 62.93497604y #246


title: RNA_R.equi-RNA_Control Week2-rep6

description: Amplified RNA from blood leukocytes from foal-6 (week-2) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-6 (week-2) labeled with Cy5


title: RNA_R.equi-RNA_Control Week2-rep2

description: Amplified RNA from blood leukocytes from foal-2 (week-2) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-2 (week-2) labeled with Cy3


title: RNA_R.equi-RNA_Control Week2-rep1

description: Amplified RNA from blood leukocytes from foal-1 (week-2) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-1 (week-2) labeled with Cy3


title: female 59.03627652y #248


title: female 61.63449692y #243


title: RNA_R.equi-RNA_Control Day1-rep6

description: Amplified RNA from blood leukocytes from foal-6 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-6 (day-1) labeled with Cy5


title: RNA_R.equi-RNA_Control Day1-rep4

description: Amplified RNA from blood leukocytes from foal-4 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-4 (day-1) labeled with Cy5


title: RNA_R.equi-RNA_Control Day1-rep3

description: Amplified RNA from blood leukocytes from foal-3 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-3 (day-1) labeled with Cy3


title: female 62.28336756y #244


title: male 49.76317591y #242


title: male 60.46817248y #240


title: male 61.54140999y #241


title: RNA_R.equi-RNA_Control Day1-rep2

description: Amplified RNA from blood leukocytes from foal-2 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-2 (day-1) labeled with Cy3


title: female 60.28473648y #239


title: male 53.12525667y #238


title: RNA_R.equi-RNA_Control Day1-rep5

description: Amplified RNA from blood leukocytes from foal-5 (day-1) stimulated with Rhodococcus equi labeled with Cy3 and unstimulated leukocytes from foal-5 (day-1) labeled with Cy5


title: male 62.03148528y #237


title: female 55.29089665y #236


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(2)_24.2]

city: Maastricht

first: Lize

last: Deferme

state: Limburg

address: Universiteitssingel 50

department: TGX

institute: Maastricht University

hyb_protocol: 12.5µg of cRNA was used. The GeneTitan arrays were hybridized, washed and stained using the GeneTitan hybridization, wash and stain kit for 3’ IVT Arrays and GeneTitan Operating Software and scanned by means of an Affymetrix GeneTitan scanner

scan_protocol: Arrays were scanned with the GeneTitan scanner

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/entrezg.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008).

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Qiazol extraction was performed using the miRNAeasy kit from Qiagen according to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing, or fresh medium containing either 100µM menadione, 200µM TBH or 50µM H2O2

tag: cell line

tag: compound, dose

value: Control

tag: time (h)


title: female 52.8843258y #232

tag: gender

tag: age (y)

tag: tissue


title: RNA_R.equi-RNA_Control Day1-rep1

description: Amplified RNA from blood leukocytes from foal-1 (day-1) stimulated with Rhodococcus equi labeled with Cy5 and unstimulated leukocytes from foal-1 (day-1) labeled with Cy3

tag: time point


title: male 66.86652977y #235


title: male 49.10335387y #234


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(1)_24.1]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(3)-24.7]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(2)_24.6]

value: 50µM H2O2


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2-50(3)-8.8]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(2)_8.6]


title: female 49.47022587y #230


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(1)_24.5]


title: female 56.41341547y #229


title: female 65.39904175y #231


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(3)-8.7]


title: male 57.00752909y #228


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(1)_8.1]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(1)_8.5]


title: female 57.55509925y #227


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(2)_6.6]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2-50(3)-6.8]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(1)_6.5]


title: female 62.17659138y #224


title: female 52.14236824y #225


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(3)-6.7]


title: female 55.52908966y #226


title: male 59.6659822y #217


title: male 53.81519507y #222


title: male 55.05817933y #223


title: female 49.12525667y #221


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2-50(3)-4.8]


title: male 56.6954141y #220


title: female 62.20670773y #218


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(3)-4.7]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(1)_6.1]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(1)_4.1]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(2)_4.6]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(1)_4.5]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(2)_6.2]


title: male 51.60301164y #215


title: male 62.4312115y #214


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(2)_4.2]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(3)-2.7]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2-50(3)-24.8]


title: female 64.5065024y #216


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(2)_2.6]


title: female 71.40862423y #212


title: female 59.45242984y #211


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(1)_2.5]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2-50(3)-2.8]


title: female 58.67761807y #210


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2-50(3)-1.8]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(2)_1.6]


title: male 58.16563997y #213


title: female 56.64887064y #209


title: female 54.11362081y #206


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(2)_2.2]


title: female 53.81519507y #219


title: female 52.37508556y #203


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2contr(3)-1.7]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(1)_2.1]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(1)_1.5]


title: female 53.78507871y #205


title: female 57.33880903y #204


title: male 55.45516769y #208


title: female 56.82135524y #207


title: male 59.39219713y #202


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2contr(2)_1.2]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2contr(3)-30.7]


title: male 53.9137577y #201


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2contr(1)_1.1]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2-50(3)-30.8]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(1)_30.5]


title: female 57.94387406y #198


title: male 62.39561944y #199


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2contr(1)_30.1]


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(3)-24.8]

value: 200µM TBH


title: female 56.0109514y #200


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_50(2)_30.6]


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2contr(2)_30.2]


title: female 60.10403833y #233


title: female 64.19986311y #196


title: male 51.321013y #197


title: Effect of H2O2/FeSO4 on mRNA levels in HepG2 cells [H2O2_contr(2)_8.2]


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(1)-24.5]


title: female 54.15195072y #194


title: female 58.6091718y #191


title: male 57.24024641y #195


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(2)-24.6]


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(3)-24.7]


title: female 53.13620808y #190


title: male 59.52361396y #193


title: male 51.17043121y #186


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(2)-24.2]


title: male 58.06160164y #189


title: male 76.83778234y #187


title: male 73.17727584y #183


title: female 50.74606434y #192


title: male 52.94182067y #184


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(1)-24.1]


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(2)-8.6]


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(3)-8.8]


title: female 58.58726899y #185


title: male 58.03148528y #188


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(3)-8.7]


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(1)-8.5]


title: male 67.52361396y #182


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(2)-8.2]


title: male 53.28678987y #176


title: male 64.27926078y #181


title: male 75.62217659y #178


title: male 58.98151951y #173


title: male 60.09582478y #179


title: male 69.55509925y #175


title: female 60.23545517y #177


title: female 66.0698152y #169


title: female 54.16563997y #180


title: male 51.80561259y #170


title: female 56.41341547y #171


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(1)-8.1]


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(2)-6.6]


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(3)-6.7]


title: female 54.93223819y #174


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(1)-6.5]


title: male 51.52908966y #172


title: male 78.92128679y #164


title: female 67.34017796y #162


title: male 58.22039699y #166


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(2)-6.2]


title: female 67.24982888y #165


title: female 79.56468172y #163


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(3)-6.8]


title: male 52.88706366y #168


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(1)-6.1]


title: male 73.46748802y #157


title: male 49.34702259y #152


title: line12, subline -D, biological rep2

city: Vigo

first: Humberto

last: Quesada

state: Galicia

address: Facultad de Biologia. Campus Lagoas-Marcosende

department: Bioquimica, Genetica e Inmunologia

country: Spain

institute: Universidad de Vigo

hyb_protocol: 15 mg of each biotinylated cRNA sample were fragmented and mixed with hybridization buffer (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20) using Affymetrix fluidic station

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

data_processing:
The robust multichip average (RMA) method was used for background adjustment, quantile normalization, and probe-level summarization of the microarray samples. RMA expression summary was computed using Partek Genomics Suite v. 7.3.3 (Partek) and the affy package in Bioconductor (v.1.18.2).
Normalized  data for Drosophila expression patterns including  inbred lines (N = 24) and the outbred controls  (N = 3) are provided in the sample data table.
Normalized data matrix of Drosophila expression patterns including only inbred lines (N = 24) is provided as Series supplementary file (inbred_only_data.txt)

organism: Drosophila melanogaster

source_name: line12_least depressed subline

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol  (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Flies were reared in a culture medium composed of 1 liter water, 100 g brewer’s yeast, 100 g sucrose, 12 g agar, 2.5 g NaCl, and 5 ml propionic acid and were handled at room temperature under CO2 anesthesia. All cultures were incubated in a chamber at 25 6 1_, 65 6 5% relative humidity, and maintained under continuous lighting. Virgin males and females were used for mating across the entire experiment.

extract_protocol: Total RNA was performed  with RNeasy Mini kit (QIAGEN, Valencia, CA)

treatment_protocol: From a large outbred base population we sampled four couples to found four inbred lines. From each initial couple, 55 inbred sublines were established and maintained for 8 generations of sib mating with the objective of fixing in different sublines the genetic variation segregating in the initial couple. Single pair mating was carried out until generation 4, but two males and two females were mated per vial thereafter, to avoid further subline losses. The final average inbreeding coefficient was about 0.7.

tag: origin

value: Vigo (NW Spain)

tag: line

value: least depressed inbred subline from line 12

tag: age/gender

value: adult male

value: whole body


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(2)-4.6]


title: line12, subline -D, biological rep1

value: least depressed inbred subline  from line 12


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(3)-4.8]


title: line7, subline -D, biological rep1

source_name: line7_least depressed subline

value: least depressed inbred subline from line 7


title: female 65.78781656y #158


title: female 52.12594114y #160


title: line15, subline -D, biological rep1

source_name: line15_least depressed subline

value: least depressed inbred subline  from line 15


title: female 50.67214237y #155


title: female 57.45927447y #154


title: male 60.183436y #161


title: outbred control, biological rep3

source_name: outbred control

value: outbred control


title: male 63.39219713y #156


title: line5, subline -D, biological rep1

source_name: line5_least depressed subline

value: least depressed inbred subline from line 5


title: male 53.59616701y #167

value: blood


title: outbred control, biological rep2


title: female 48.30390144y #149

value: female


title: female 69.47022587y #153


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(1)-4.5]


title: male 83.94524298y #159

value: male


title: line7, subline -D, biological rep2


title: male 56.96919918y #150


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(1)-4.1]


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(3)-4.7]


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(2)-4.2]


title: outbred control, biological rep1


title: male 53.48391513y #148


title: male 72.89527721y #151


title: male 52.25462012y #147


title: female 62.33264887y #145


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(2)-2.6]


title: line15, subline -D, biological rep2

value: least depressed inbred subline from line 15


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(3)-2.8]


title: female 61.43463381y #144


title: line15, subline -D, biological rep3


title: line15, subline +D, biological rep1

source_name: line15_most depressed subline

value: most depressed inbred subline from line 15


title: female 53.28952772y #146


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(1)-2.5]


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(2)-2.2]

value: Control


title: female 69.89185489y #141


title: female 56.97741273y #140


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(3)-2.7]


title: female 54.12183436y #142


title: line12, subline -D, biological rep3


title: line15, subline +D, biological rep2


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(2)-1.6]


title: male 53.38809035y #143


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(3)-1.8]


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(1)-2.1]


title: line12, subline +D, biological rep3

source_name: line12_most depressed subline

value: most depressed inbred subline from line 12


title: female 63.85215606y #135


title: female 60.74743326y #137


title: line12, subline +D, biological rep1


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(1)-1.1]


title: line12, subline +D, biological rep2


title: female 62.84188912y #129


title: line15, subline +D, biological rep3


title: female 52.58590007y #136


title: male 54.29979466y #138


title: male 54.84462697y #131


title: male 61.58795346y #128


title: male 62.04243669y #139


title: line7, subline +D, biological rep3

source_name: line7_most depressed subline

value: most depressed inbred subline from line 7


title: male 70.02600958y #133


title: male 77.30047912y #127


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(1)-1.5]

value: 200µM TBH


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(2)-1.2]


title: female 61.02669405y #134


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(3)-1.7]


title: male 56.52019165y #125


title: male 47.12936345y #126


title: line7, subline -D, biological rep3

value: Vigo (NW Spain)


title: female 74.41752225y #132


title: female 61.46201232y #130


title: female 58.03422313y #123


title: line7, subline +D, biological rep2

value: adult male


title: line7, subline +D, biological rep1

value: whole body


title: male 76.38056126y #124


title: line5, subline -D, biological rep3


title: line5, subline +D, biological rep3

source_name: line5_most depressed subline

value: most depressed inbred subline from line 5


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(3)-30.8]


title: female 54.03422313y #119


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(2)-30.2]


title: line5, subline +D, biological rep2


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200()-30.5]


title: Effect of TBH on mRNA levels in HepG2 cells [TBH200(2)-30.6]


title: female 64.40793977y #122


title: line5, subline +D, biological rep1


title: female 48.32580424y #117


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(1)-30.1]


title: Effect of TBH on mRNA levels in HepG2 cells [TBHcontr(3)-30.7]


title: male 54.85010267y #116


title: female 55.12936345y #114


title: female 64.77207392y #111


title: female 53.58795346y #118


title: male 72.45995893y #120


title: male 62.07802875y #121


title: female 74.69678303y #112


title: female 64.63791923y #113


title: line5, subline -D, biological rep2


title: female 59.46885695y #115


title: female 51.71252567y #110


title: Effect of menadione on mRNA levels in HepG2 cells [men100(3)-24.8]

value: 100µM Men


title: Effect of menadione on mRNA levels in HepG2 cells [men100(2)-24.6]


title: female 58.26146475y #105


title: male 55.96167009y #107


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(3)-24.7]


title: female 60.10403833y #109