title: U251-park2, biological rep3

city: Los Angeles

first: DECHEN

last: LIN

address: 8700 Beverly Boulevard

institute: Cedars-Sinai Medical Center

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

source_name: U251 cells with PARK2 overexpression

label_protocol: Affymetrix standard protocol

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin/streptomycin, at 37℃, 5% CO2 in a humidified atmosphere.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: For generation of stable lines, the cells were infected with viral particles in the presence of 8 μg/mL polybrene followed by puromycin selection.

value: Glioma

value: PARK2 overexpression


title: trh3cmyc_1_2

status: Public on Oct 03 2014

type: genomic

city: Seattle

first: Christopher

middle: L

last: Plaisier

state: Washington

address: 401 Terry Avenue North

country: USA

institute: Institute for Systems Biology

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh3 cMyc-tagged and sampled at late growth, biological replicate 1.

hyb_protocol: According to Agilent protocol.

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software.

data_processing:
Agilent Feature Extraction for spotfinding/quantitation.
Normalized log10 intensity of X_INT/Y_INT (IP/WCE) averaged over dye flip between IP and WCE DNA. Second raw data file contains Agilent Feature Extraction file for the dye flip experiment.

label: Cy3, Cy5

molecule: genomic DNA

organism: Halobacterium salinarum NRC-1

source_name: Halobacterium sp. NRC-1 Trh3 cMyc-tagged strain IP fraction

label_protocol: See Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35.

growth_protocol: Halobacterium salinarum NRC-1 strains were batch cultured in complete defined media (CDM) with 19 amino acids in flasks at 37°C with constant shaking (125 rpm).

extract_protocol: Chromatin immunoprecipitation (IP) was conducted as described in Facciotti, MT, Reiss, DJ, Pan, M, Kaur, A, Vuthoori, M, Bonneau, R, Shannon, P, Srivastava, A, Donohoe, SM, Hood, LE and Baliga, NS. General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 2007;104: 4630-4635. Optimizations of the ChIP protocol are described in Schmid AK, Pan M, Sharma K, Baliga NS.2011. Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res.39(7):2519-33. Primary antibody is the Covance 9E10 monoclonal antibody (anti-c-myc) from mouse, cat #MMS-150P, and secondary antibody is ECL mouse IgG HRP-linked whole antibody from sheep, Amersham cat #NA931.

treatment_protocol: Over-expression of c-Myc-tagged FFRPs allowed enrichment of genomic regions bound by each FFRP in either early or late growth in CDM.

tag: strain

tag: condition

value: late

tag: replicate

value: over-expression

tag: chip antibody

value: anti-c-myc (9E10) monoclonal antibody

label: Cy5, Cy3

source_name: Halobacterium sp. NRC-1 Trh3 cMyc-tagged strain whole cell extract (WCE) fraction


title: BPDCN_31

type: RNA

city: Bologna

first: Fabio

last: Fuligni

address: Via Massarenti 9

department: Department of Experimental, Diagnostic, and Specialty Medicine Bologna University Medical School

country: Italy

institute: University of Bologna

hyb_protocol: Standard 29K Whole-Genome DASL HT Assay hybridization protocol (WGDASL HT Assay Guide (15018210 D)

scan_protocol: Standard 29K Whole-Genome DASL HT Assay scan protocol (WGDASL HT Assay Guide (15018210 D)

data_processing: Gene expression analysis was carried according to MIAME guidelines.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: BPDCN Patient

label_protocol: Standard 29K Whole-Genome DASL HT Assay label protocol (WGDASL HT Assay Guide (15018210 D)

extract_protocol: total RNA from cryopreserved and FFPE samples was extracted using TRIzol reagent (Invitrogen) and the RecoverAll Total Nucleic Acid Isolation Kit (Ambion, Austin, TX), respectively, following the manufacturer's protocols

treatment_protocol: Treatment with imatinib mesylate (0 and 1 microM) for 6 hours

tag: tumor type

value: BPDCN

tag: phenotype

value: BPDCN Patient


title: trh3cmyc_1_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh3 cMyc-tagged and sampled at early growth, biological replicate 1.

value: early


title: BPDCN_3


title: U251-park2, biological rep1

tag: cell line

tag: cell type

tag: genotype/variation


title: U251-park2, biological rep2


title: BPDCN_29


title: BPDCN_26


title: trh2cmyc_1_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh2 cMyc-tagged and sampled at late growth, biological replicate 1.

source_name: Halobacterium sp. NRC-1 Trh2 cMyc-tagged strain IP fraction

source_name: Halobacterium sp. NRC-1 Trh2 cMyc-tagged strain whole cell extract (WCE) fraction


title: U251-control, biological rep3

source_name: U251 cells with GFP overexpression

value: GFP overexpression


title: BPDCN_24


title: U251-control, biological rep1


title: BPDCN_23


title: trh2cmyc_1_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh2 cMyc-tagged and sampled at early growth, biological replicate 1.


title: trh2cmyc_2_2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh2 cMyc-tagged and sampled at late growth, biological replicate 2.


title: trh2cmyc_2_1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Trh2 cMyc-tagged and sampled at early growth, biological replicate 2.


title: BPDCN_25


title: BPDCN_22


title: asnCcmyc_2-1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
AsnC cMyc-tagged and sampled at early growth, biological replicate 2.

source_name: Halobacterium sp. NRC-1 AsnC cMyc-tagged strain IP fraction

value: AsnC

source_name: Halobacterium sp. NRC-1 AsnC cMyc-tagged strain whole cell extract (WCE) fraction


title: BPDCN_20


title: asnCcmyc_2-2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
AsnC cMyc-tagged and sampled at late growth, biological replicate 1.


title: U251-control, biological rep2


title: pMTFcmyc_2-2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Empty vector control cMyc-tagged and sampled at late growth, biological replicate 2.

source_name: Halobacterium sp. NRC-1 Empty Vector Control cMyc-tagged strain IP fraction

value: empty vector control

value: no regulator

source_name: Halobacterium sp. NRC-1 Empty Vector Control cMyc-tagged strain whole cell extract (WCE) fraction


title: ET1-CM, experiment2

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: Gene expression data from ET-1 stimulated hiPSC-CMs from experiment 2

hyb_protocol: Samples were hybridized following affymetrix GeneChip® 3’IVT express array protocol

scan_protocol: Samples were scanned following affymetrix GeneChip® 3’IVT express array protocol

data_processing: mRNA expression arrays were analyzed using the limma and affy packages in R/Bioconductor. The limma and affy packages were used with their default methods and a contrast matrix constituted of the differences between the three ET1-CM and three control-CM experiments. Annotation to the probe sets was generated using the hgu133plus2.db package in R/Bioconductor.

source_name: hiPSC-CM from experiment2 after ET-1 stimulation

label_protocol: Samples were labeled following affymetrix GeneChip® 3’IVT express array protocol

growth_protocol: iCell Cardiomyocytes were plated at 2.0 × 105 cells/well in a 96-well plate precoated with 0.1% gelatin solution.

extract_protocol: 18 h post ET-1 stimulation, cells were harvested with Total RNA Purification 96-Well Kit (Norgen Biotek Corp.).  Total RNA was extracted per manufacturer’s recommendations, resuspended in nuclease-free water, and quantified by UV spectrophotometry (NanoDrop™ 2000, Thermo Scientific).

treatment_protocol: After two days of recovery, the cells were cultured in William’s E medium supplemented with Cocktail B (1:25) from the Hepatocyte Maintenance Supplement Pack (Life Technologies). After an additional 11 days of recovery, cells were stimulated for 18 h with ET-1 at 10-8M

value: hiPSC-derived cardiomyocyte


title: BPDCN_21


title: BPDCN_2


title: ET1-CM, experiment3

description: Gene expression data from ET-1 stimulated hiPSC-CMs from experiment 3

source_name: hiPSC-CM from experiment3 after ET-1 stimulation


title: control-CM, experiment3

description: Gene expression data from unstimulated hiPSC-CMs from experiment 3

source_name: hiPSC-CM from experiment3 before ET-1 stimulation


title: pMTFcmyc_2-1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Empty vector control cMyc-tagged and sampled at early growth, biological replicate 2.


title: BPDCN_17


title: ET1-CM, experiment1

description: Gene expression data from ET-1 stimulated hiPSC-CMs from experiment 1

source_name: hiPSC-CM from experiment1 after ET-1 stimulation


title: control-CM, experiment2

description: Gene expression data from unstimulated hiPSC-CMs from experiment 2

source_name: hiPSC-CM from experiment2 before ET-1 stimulation


title: control-CM, experiment1

description: Gene expression data from unstimulated hiPSC-CMs from experiment 1

source_name: hiPSC-CM from experiment1 before ET-1 stimulation


title: BPDCN_18


title: BPDCN_19


title: Idh-R195H hemocytes, biological replicate 2

city: Durham

first: Zachary

middle: J.

last: Reitman

state: NC

address: 159 MSRB1

department: Pathology

institute: Duke Univ. Medical Ctr.

description: Gene expression data from total hemocytes

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Drosophila Genome 2.0 Arrays (18,880 probe sets, >18,500 transcripts)

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

data_processing: Data were processed using the Ambion MessageAmp Premier Package and Partek Genomics Suite v6.0 at the Duke Institute for Genome Sciences and Policy Microarray Facility.

organism: Drosophila melanogaster

source_name: hemocytes from wandering 3rd instar larvae

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

growth_protocol: 24-hour egg lays were set up with 10 male and 10 female adults at 29°C.  Wandering 3rd instar larvae were harvested on day 7.

extract_protocol: RNA was extracted with the RNeasy kit with DNase treatment (Qiagen, Hilden, Germany).

treatment_protocol: Hemocytes from 400 larvae, collected 10 at a time in 100ul droplets of ice-cold Hank’s medium on paraffin on ice, were obtained by carefully piercing and opening the rear dorsal aspect of segments 11-13 with No. 5 forceps and gently shaking circulating hemocytes into the droplet without disturbing the lymph gland, spun down gently (300xg 5min), washed, and pooled.

tag: genotype

value: hml-Gal4, UAS-2xEGFP; UAS-Idh-R195H


title: HaCaT_M1 stimulated_biological rep 2

city: Lund

first: Sandra

middle: Therese

last: Persson

address: Tornavägen 10

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

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

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

data_processing: The data were analyzed using expression console software version 1.1.2 using default analysis settings and RMA as normalization method. In the supplemental data file (GSE61993_SAM_T-test_C_vs_M_q(0)_pvalue(0_0001).txt.gz) your get the complete list of data that were used for further analysis and conclusions, based on SAM and a T-test p-value below 0.0001.

label: Biotin

source_name: Keratinocyte cell line, HaCaT, M1 stimulated

growth_protocol: HaCaT cells were cultured in serum-free media, without calcium, in 37°C, 5% CO2, until 80% confluency.

extract_protocol: Sigma's GeneElute Mammalian total RNA kit were used for RNA extraction according to manufaturer's protocol.

treatment_protocol: Cells were either treated or left untreated with 5μg/ml M1 protein for 6 hours before RNA extraction.

tag: tissue

value: Skin

value: HaCat


title: HaCaT_M1 stimulated_biological rep 3


title: control hemocytes, biological replicate 3

value: hml-Gal4, UAS-2xEGFP


title: Idh-R195H hemocytes, biological replicate 1


title: BPDCN_16


title: pMTFcmyc_1-2

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Empty vector control cMyc-tagged and sampled at late growth, biological replicate 1.


title: 2013-07-04_VF_CD8+

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

description: mRNA expression profiles from primary cells

hyb_protocol: according to the manufacturers guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Sample data was processed using AGCC (Affymetrix default settings) and normalized using RMA

source_name: blood

extract_protocol: RNA extracted using miRVana (Ambion) according to the manufacturers guidelines

treatment_protocol: PBMCs were isolated by density gradient and subsequently sorted by employing anti CD4 and anti-CD8 antibodies using FACSAria

tag: diagnosis

value: healthy control

value: primary t-cells

tag: facs


title: asnCcmyc_1-1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
AsnC cMyc-tagged and sampled at early growth, biological replicate 1.


title: 2013-07-04_VF_CD4+

label_protocol: according to the manufacturers guidelines (Affymetrix)


title: Idh-R195H hemocytes, biological replicate 3


title: pMTFcmyc_1-1

description:
*Sep09_2*.txt Agilent FES file: Cy3=IP, Cy5=WCE.
*Sep09_1*.txt Agilent FES file: Cy3=WCE, Cy5=IP (dye flip).
Empty vector control cMyc-tagged and sampled at early growth, biological replicate 1.


title: control hemocytes, biological replicate 2


title: BPDCN_14

source_name: BPDCN Patient


title: control hemocytes, biological replicate 1


title: HaCaT_control_biological rep 1

source_name: Keratinocyte cell line, HaCaT, unstimulated


title: 2013-07-04_VF_CD4+CD8+


title: HaCaT_M1 stimulated_biological rep 1


title: BPDCN_13


title: Manganese excess, biological replicate 1

city: Kgs. Lyngby

first: Lars

last: Poulsen

address: Soltofts Plads 1

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

description: SAMPLE 7

hyb_protocol: hybridized to the 3AspergDTU GeneChip (PMID: 18332432 )

scan_protocol: A GeneChip Fluidics Station FS-400 was applied for hybridization followed by scanning using a GeneChip Scanner 3000. The scanned probe array images (.DAT files) were converted into .CEL files using the GeneChip Operating Software

data_processing:
The analysis of the affymetrix CEL-data files was carried out accordingly to the protocol described in PMID: 19409083
probe group file: 3AspergDTU GeneChip (PMID: 18332432 )

organism: Aspergillus niger

source_name: Biomass from pseudo steady state

label_protocol: Biotin-labeled cRNA was prepared from total RNA according to the Affymetrix GeneChip Expression Analysis Technical Manual

growth_protocol: Nine one-liter baffled-flasks containing 250 ml of citric acid production media with 10 ppb Mn2+ were used. Each flask was inoculated with 1 × 10^6 spores/ml and incubated for thirty hours at 30C and 220 rpm to obtain large-amount biomass in pelleted  morphology, then 1000 ppb Mn2+ was added to three of the flasks to induce filamentous growth and the same amount of H2O was added into another three flasks for control.

extract_protocol: Total RNA was isolated from the above A. niger biomasses according to the modified acid-guanidinium isothiocyanate phenol-chloroform extraction method previously described (Chomczynski and Sacchi 1987, Dai et al 2000), and the total RNA concentration was quantified spectrophotometrically. Polyadenylated RNA was isolated from the total RNA with the Oligotex kit (QIAGEN, Valencia, CA, USA).

treatment_protocol: The growth of fungal cultures was rapidly terminated by cooling in an ice-water bath. The biomass was immediately separated from the culture supernatant by centrifugation in 500 ml centrifuge bottles for 10 minutes at 4oC and 10,000 g. The biomass was ransferred from the centrifugation bottles to Corning 50 ml polypropylene centrifugation tubes, washed with 50 ml ice-cold 50mM phosphate buffer once, and centrifuged again at 9,000 g and 4oC for 5 min. The biomass was immediately frozen in liquid N2 and then stored at -80oC until use.

tag: experimental condition

value: Manganese excess


title: 2013-07-04_SU_CD8+


title: Manganese depleted, biological replicate 3

description: SAMPLE 6

value: Manganese depleted


title: Manganese excess, biological replicate 2

description: SAMPLE 8


title: HaCaT_control_biological rep 2


title: BPDCN_10


title: BPDCN_1


title: 2013-07-04_IR_CD8+


title: BPDCN_12


title: 2013-07-04_SU_CD4+


title: Manganese depleted, biological replicate 1

description: SAMPLE 4


title: Manganese depleted, biological replicate 2

description: SAMPLE 5


title: Manganese excess, biological replicate 3

description: SAMPLE 9


title: 2013-07-04_IR_CD4+


title: ob/ob hypothalamus, rep5

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: A hybridization mixture containing 15 µg of biotinylated cRNA, adjusted for possible carryover of residual total RNA, was prepared and hybridized to the arrays

data_processing: Intensity values were quantified by using MAS 5.0 software (Affymetrix)

organism: Mus musculus

source_name: ob/ob hypothalamus

label_protocol: Double-stranded cDNA synthesis was reverse-transcribed from 10 µg of isolated RNA from each hypothalamus by using the SuperScript (Invitrogen) with an oligo(dT) primer containing a T7 RNA polymerase promoter site. Double-stranded cDNA was purified with Phase Lock Gel (Eppendorf). Biotin-labeled cRNA was transcribed by using a BioArray RNA transcript labeling kit (Enzo).

extract_protocol: RNA was isolated using an RNeasy kit (Qiagen)

treatment_protocol: For STZ-induced diabetes experiments, mice were treated with a single intraperitoneal (i.p.) injection (200 µg/g body weight) of STZ (Sigma). Control mice were injected with the same volume of vehicle.

value: ob/ob

tag: gender

value: male

tag: age

value: 9 weeks old

value: brain hypothalamus


title: hIAPP-INS1E_b [gene-level]

city: Barcelona

first: Gema

last: Alcarraz-Vizán

address: Rossello 149

department: Diabetes & Obesity Laboratory

country: Spain

institute: IDIBAPS

description:
hIAPP-INS1E_b.CEL
INS1E clone stably transfected with hIAPP

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing:
The data were analyzed with Expression Console Software using default analysis settings and RMA as normalization method.
RaGene-2_0-st.pgf
RaGene-2_0-st.mps

organism: Rattus norvegicus

source_name: pancreatic b-cell line

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

growth_protocol: INS1E cells stably transfected with human or rat IAPP were grown in RPMI at 11.1 mM glucose and supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 100 U/mL penicillin, 100 microg/mL streptomycin, 200 microg/mL geneticin and 50 microM beta-mercaptoethanol at 37°C with 5% CO2

extract_protocol: Cells were collected after 3 days of culture.  All samples contained 5microg of carrier glycogen and were prepared using Trizol reagent.

treatment_protocol: not applicable

tag: transcript transfected

value: hIAPP


title: rIAPP-INS1E_a [gene-level]

description:
rIAPP-INS1E_a.CEL
INS1E clone stably transfected with rIAPP

value: rIAPP


title: HaCaT_control_biological rep 3


title: hIAPP-INS1E_a [gene-level]

description:
hIAPP-INS1E_a.CEL
INS1E clone stably transfected with hIAPP


title: rIAPP-INS1E_b [gene-level]

description:
rIAPP-INS1E_b.CEL
INS1E clone stably transfected with rIAPP


title: ob/ob hypothalamus, rep4

tag: strain


title: 2013-07-04_IR_CD4+CD8+


title: 2013-07-04_GPA4_CD8+

value: granulomatotis with polyangiitis (GPA)


title: ob/ob hypothalamus, rep3


title: INS1E_b [gene-level]

description:
INS1E_b.CEL
INS1E clone stably transfected with pcDNA3 (control)


title: MCF7_cell line

city: Singapore

first: Min

last: FENG

address: 60 Biopolis Street,

department: Cancer Therapeutics & Stratified Oncology

country: Singapore

institute: Genome Institute of Singapore

description: luminal BC cell line

hyb_protocol: The labeled RNAs were hybridized to Agilent human miRNA microarray slide for 22 hours

scan_protocol: the arrays were scanned with Agilent microarray scanner

data_processing:
raw value above 1 in at least one of the 4 samples. the raw intensity data were further analyzed using GeneSpring GX software (Agilent Technologies).  GeneSpring (2009 version) normalization methods:
1) threshold signals to 1.0
2) Use 75% percentile shift
3) no baseline transformation

source_name: BC cell line

label_protocol: labeled with pCp-Cy3 using T4 RNA ligase

growth_protocol: exponentially growing cell lines

extract_protocol: RNA including small RNAs from both human breast cancer tissue as well as the cell lines were isolated using miRNeasy Mini Kit (Qiagen, cat. 217004) according manual

value: female

tag: group

value: luminal


title: H2O control, biological rep 3

description: SAMPLE 3

value: H2O control


title: H2O control, biological rep 2

description: SAMPLE 2


title: BT549_cell line

description: TNBC cell line

value: TNBC


title: ob/ob hypothalamus, rep2


title: MB231_cell line

description: TNBC cell line


title: BT474_cell line

description: luminal BC cell line


title: ob/ob hypothalamus, rep1


title: H2O control, biological rep 1

description: SAMPLE 1


title: 2013-07-04_GPA2_CD8+


title: 2013-07-04_GPA2_CD4+


title: 2013-07-04_GPA4_CD4+CD8+


title: 2013-07-04_GPA1_CD8+


title: Streptozotocin-induced diabetic hypothalamus, rep2

value: wildtype


title: Streptozotocin-induced diabetic hypothalamus, rep1


title: Streptozotocin-induced diabetic hypothalamus, rep4


title: INS1E_a [gene-level]

description:
INS1E_a.CEL
INS1E clone stably transfected with pcDNA3 (control)


title: 2013-07-04_GPA2_CD4+CD8+


title: 2013-07-04_GPA4_CD4+


title: Streptozotocin-induced diabetic hypothalamus, rep5


title: Streptozotocin-induced diabetic hypothalamus, rep6


title: Streptozotocin-induced diabetic hypothalamus, rep3


title: 2013-07-04_GPA1_CD4+CD8+


title: Control hypothalamus, rep5

source_name: Control hypothalamus


title: Control hypothalamus, rep4


title: 2013-07-04_SU_CD4+CD8+


title: Control hypothalamus, rep6


title: ∆ptpB_CASAvsGlucose_4h_B

city: Ribeirão Preto

first: Leandro

middle: Jose

last: Assis

state: São pAULO

address: Av. do Cafe S/N

department: FCFRP

country: Brazil

institute: USP

description: Biological rep 2 of 3

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SEB-treated samples) for 2 hours at 40 oC.

growth_protocol: All A. nidulans strains were grown in minimal media plus casaminoacids for 24h

extract_protocol: Total RNA was extracted with RNeasy® Plant Mini Kit  (Qiagen) following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

treatment_protocol: Wash one time dH2O and tranfer to minimal media plus 1% glucose for 4 hours

value: ∆ptpB


title: ∆ptpB_CASAvsGlucose_4h_A

description: Biological rep 1 of 3


title: rIAPP-INS1E_b [exon-level]


title: ∆ptpB_CASAvsGlucose_4h_C

description: Biological rep 3 of 3


title: hIAPP-INS1E_b [exon-level]


title: rIAPP-INS1E_a [exon-level]


title: hIAPP-INS1E_a [exon-level]


title: TNO_CASAvsGlucose_4h_A

description: Biological rep 1 of 3


title: Control hypothalamus, rep1


title: Root_CK_72 h

status: Public on Oct 02 2014

city: Guangzhou

first: Qiaoying

last: Zeng

address: Chi Gang

country: China

institute: Guangzhou Sugarcane Industry Research Institute

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

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

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Saccharum

source_name: Root of non-tangentic sugarcane at 72 h after exposure to low-K stress

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

growth_protocol: Seedlings with four leaves were cultured hydroponically in greenhouse under natural lighting. The temperature in greenhouse was controlled within 30°C. The nutrient solution was the modified Magnavaca’s solution. Six seedlings were planted in 10 L plastic basin. The nutrient solution was replaced every week.

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

treatment_protocol: After pre-plant two weeks, all plants were transferred to low K nutrient solution (containing 0.1 mM KCl). Roots and shoots of three seedlings were separately collected at 0 h (CK), 8 h, 24 h, 72 h and 7d after initiating low-K treatment.

tag: species

value: Saccharum species hybrid L.

tag: cultivar

value: non-transgenic

tag: treated with

value: low-K hydroponic (containing 0.1 mmol.L-1 K+)

tag: developmental stage

value: seedling

value: root

tag: time after low-k exposure


title: INS1E_a [exon-level]


title: TNO_CASAvsGlucose_4h_B

description: Biological rep 2 of 3


title: INS1E_b [exon-level]


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1377_p0-PQ_d0-4_0mM_dt-160m_id-001

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
AsnC knock-out (delta-AsnC) at 160 minute post-addition of sub-lethal 4mM paraquat, replicate 1.

hyb_protocol: see http://www.chem.agilent.com/Scripts/PDS.asp?lPage=34519 for details

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing:
Agilent FeatureExtraction for spotfinding/quantitation. See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details
Normalized log10 intensity of X_INT/Y_INT (sample/reference) averaged over dye flip between sample and reference RNA. Second raw data file contains Agilent Feature Extraction file for the dye flip experiment.

source_name: paraquat 4mM Dura3 D1377 160min rep 1

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

growth_protocol: Halobacterium salinarum NRC-1 strains were batch cultured in rich media (CM) in flasks at 37°C with constant shaking (125 rpm)

extract_protocol: Total RNA was prepared from the cell pellets using the mirVANA RNA isolation kit

treatment_protocol: Two genetic knock-outs (delta-AsnC and delta-VNG1237C) were compared to wildtype (delta-ura3) in two different conditions:  1) intact and knock-out of AsnC were tested in sub-lethal 4mM paraquat, and 2) intact and knock-out VNG1237C was tested across a batch culture growth curve.

value: delta-ura3 delta-AsnC

tag: condition

tag: replicate

tag: condition specifics

value: 4 mM

tag: experiment

value: paraquat

value: AsnC

value: knock-out

source_name: Halobacterium NRC-1 Reference sample

tag: sample type

value: reference


title: Control hypothalamus, rep2

tag: genotype

value: male

value: 9 weeks old

tag: tissue

value: brain hypothalamus


title: Root_CK_8 h

source_name: Root of non-tangentic sugarcane at 8 h after exposure to low-K stress

tag: genotype/variation


title: Root_CK_0 h

source_name: Root of sugarcane at 0 h after exposure to low-K stress


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1377_p0-PQ_d0-4_0mM_dt-160m_id-003

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
AsnC knock-out (delta-AsnC) at 160 minute post-addition of sub-lethal 4mM paraquat, replicate 3.

source_name: paraquat 4mM Dura3 D1377 160min rep 3


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1377_p0-PQ_d0-4_0mM_dt--1m_id-003

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
AsnC knock-out (delta-AsnC) at 1 minute post-addition of sub-lethal 4mM paraquat, replicate 3.

source_name: paraquat 4mM Dura3 D1377 1min rep 3


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1377_p0-PQ_d0-4_0mM_dt-160m_id-002

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
AsnC knock-out (delta-AsnC) at 160 minute post-addition of sub-lethal 4mM paraquat, replicate 2.

source_name: paraquat 4mM Dura3 D1377 160min rep 2


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1377_p0-PQ_d0-4_0mM_dt--1m_id-002

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
AsnC knock-out (delta-AsnC) at 1 minute post-addition of sub-lethal 4mM paraquat, replicate 2.

source_name: paraquat 4mM Dura3 D1377 1min rep 2


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-PQ_d0-4_0mM_dt-160m_id-003

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) at 160 minute post-addition of sub-lethal 4mM paraquat, replicate 3.

source_name: paraquat 4mM Dura3 160min rep 3

value: inactive


title: Control hypothalamus, rep3

value: wildtype

tag: gender

tag: age


title: Root_CK_24 h

source_name: Root of non-tangentic sugarcane at 24 h after exposure to low-K stress


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-PQ_d0-4_0mM_dt--1m_id-002

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) at 1 minute post-addition of sub-lethal 4mM paraquat, replicate 2.

source_name: paraquat 4mM Dura3 1min rep 2

tag: strain

value: active


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-PQ_d0-4_0mM_dt--1m_id-003

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) at 1 minute post-addition of sub-lethal 4mM paraquat, replicate 3.

source_name: paraquat 4mM Dura3 1min rep 3


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-PQ_d0-4_0mM_dt-160m_id-001

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) at 160 minute post-addition of sub-lethal 4mM paraquat, replicate 1.

source_name: paraquat 4mM Dura3 160min rep 1


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-PQ_d0-4_0mM_dt-160m_id-002

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) at 160 minute post-addition of sub-lethal 4mM paraquat, replicate 2.

source_name: paraquat 4mM Dura3 160min rep 2


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1377_p0-PQ_d0-4_0mM_dt--1m_id-001

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
AsnC knock-out (delta-AsnC) at 1 minute post-addition of sub-lethal 4mM paraquat, replicate 1.

source_name: paraquat 4mM Dura3 D1377 1min rep 1


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-PQ_d0-4_0mM_dt--1m_id-001

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) at 1 minute post-addition of sub-lethal 4mM paraquat, replicate 1.

source_name: paraquat 4mM Dura3 1min rep 1


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1237_p0-NULL_d0-NULL_cd-1_1679od_id-003

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
VNG1237C knock-out (delta-VNG1237C) for late growth sampled at OD=1.1679 from VNG1237C deletion (DVNG1237C), biological replicate 3.

source_name: growth OD=1.1679 Dura3 D1237 late rep 3

value: delta-ura3 delta-VNG1237C

value: late

value: growth


title: NF54 vs. 3D7

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

description: Comparative Genomic Hybridizaion of strain NF54 compared to referance strain 3D7.

hyb_protocol: Used the standard NimbleGen CGH protocol (Selzer etl. 2005)

scan_protocol: Arrays were scanned with the NimbleGen MS 200 Microarray Scanner (NimbleGen Systems, Inc.) at a 5 µm resolution with autogain per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html)

data_processing: Cy3 and Cy5 signal intensities were normalized according to standard Nimblegen CGH protocol (http://www.nimblegen.com/products/lit/cgh_userguide_v6p0.pdf). The normalized values were used for calculation of Log2ratio values

organism: Plasmodium falciparum NF54

source_name: Plasmodium falciparum NF54 Genomic DNA

growth_protocol: NF54 were cultured in human O+ erythrocytes at 4% haematocrit in RPMI 1640 supplemented with 0.5% albumax (Invitrogen) and 0.25% sodium bicarbonate, using standard procedures (Trager & Jenson, 1978).

extract_protocol: Genomic DNA was extracted using the DNA Blood Mini Kit (Qiagen)

organism: Plasmodium falciparum 3D7

source_name: Genomic DNA from Plasmodium falciparum 3D7


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1237_p0-NULL_d0-NULL_cd-0_1572od_id-002

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
VNG1237C knock-out (delta-VNG1237C) for early growth sampled at OD=0.1572 from VNG1237C deletion (DVNG1237C), biological replicate 2.

source_name: growth OD=0.1572 Dura3 D1237 early rep 2

value: early

source_name: Halobacterium NRC-1 Reference sample


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1237_p0-NULL_d0-NULL_cd-1_1754od_id-001

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
VNG1237C knock-out (delta-VNG1237C) for late growth sampled at OD=1.1754 from VNG1237C deletion (DVNG1237C), biological replicate 1.

source_name: growth OD=1.1754 Dura3 D1237 late rep 1


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1237_p0-NULL_d0-NULL_cd-0_1479od_id-001

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
VNG1237C knock-out (delta-VNG1237C) for early growth sampled at OD=0.1479 from VNG1237C deletion (DVNG1237C), biological replicate 1.

source_name: growth OD=0.1479 Dura3 D1237 early rep 1


title: 2013-07-04_GPA1_CD4+

description: mRNA expression profiles from primary cells

source_name: blood

tag: diagnosis

value: granulomatotis with polyangiitis (GPA)

tag: cell type

value: primary t-cells

tag: facs


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-NULL_d0-NULL_cd-1_1207od_id-003

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) for late growth sampled at OD=1.207 from wild-type (Dura3), biological replicate 3.

source_name: growth OD=1.1207 Dura3 late rep 3


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-NULL_d0-NULL_cd-0_1789od_id-002

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) for early growth sampled at OD=0.1789 from wild-type (Dura3), biological replicate 2.

source_name: growth OD=0.1789 Dura3 early rep 2


title: 3D7∆PfSir2a vs. 3D7

description: Comparative Genomic Hybridizaion of 3D7∆PfSir2a compared to referance strain 3D7.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum 3D7∆PfSir2a Genomic DNA

label_protocol: Used the standard NimbleGen CGH protocol (Selzer etl. 2005)

growth_protocol: 3D7∆PfSir2a were cultured in human O+ erythrocytes at 4% haematocrit in RPMI 1640 supplemented with 0.5% albumax (Invitrogen) and 0.25% sodium bicarbonate, using standard procedures (Trager & Jenson, 1978).


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-NULL_d0-NULL_cd-1_1709od_id-002

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) for late growth sampled at OD=1.1709 from wild-type (Dura3), biological replicate 2.

source_name: growth OD=1.1709 Dura3 late rep 2


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-NULL_d0-NULL_cd-0_1783od_id-001

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) for early growth sampled at OD=0.1783 from wild-type (Dura3), biological replicate 1.

source_name: growth OD=0.1783 Dura3 early rep 1


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-NULL_d0-NULL_cd-1_1723od_id-001

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) for late growth sampled at OD=1.1723 from wild-type (Dura3), biological replicate 1.

source_name: growth OD=1.1723 Dura3 late rep 1


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1237_p0-NULL_d0-NULL_cd-0_1437od_id-003

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
VNG1237C knock-out (delta-VNG1237C) for early growth sampled at OD=0.1437 from VNG1237C deletion (DVNG1237C), biological replicate 3.

source_name: growth OD=0.1437 Dura3 D1237 early rep 3


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3_p0-NULL_d0-NULL_cd-0_1905od_id-003

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
Wildtype control (delta-ura3) for early growth sampled at OD=0.1905 from wild-type (Dura3), biological replicate 3.

source_name: growth OD=0.1905 Dura3 early rep 3


title: NRC_1h2_v_sp-hal_st-NRC1_gt-Dura3D1237_p0-NULL_d0-NULL_cd-1_1683od_id-002

description:
*Sep09_2*.txt Agilent FES file: Cy3=sample, Cy5=reference.
*Sep09_1*.txt Agilent FES file: Cy3=reference, Cy5=sample (dye flip)
VNG1237C knock-out (delta-VNG1237C) for late growth sampled at OD=1.1683 from VNG1237C deletion (DVNG1237C), biological replicate 2.

source_name: growth OD=1.1683 Dura3 D1237 late rep 2


title: FSW 1hr #6_FW-->SW+As 1hr #6

city: Bloomington

first: Richard

middle: Nathan

last: Keith

department: School of Public and Environmental Affairs

institute: Indiana University

description: gill

hyb_protocol: Hybridizations were conducted in a Roche multi-chambered hybridization unit. Hybridization and post hybridization washing were performed using Hybridization Kit and Wash Buffer Kit per manufacturers recommendations (Roche Nimblegen). Hybridization reactions for subarrays 1 through 6 were loaded with displacement pipette, with overflow being removed. Hybrization commenced at  42°C for 17 hours, then washed with four SSC and SDS was buffers, then dried at 2000 x g for 1 minute.

scan_protocol: Arrays were scanned using Axon GenePix 4200A Professional Scanner

data_processing: Quantile normalization was perfomed on all samples. Following normalization, the Log2 (Cy3/Cy5) ratio of intensities was computed for each dual hybridization.

molecule: polyA RNA

organism: Fundulus heteroclitus

source_name: FSW 1hr #6

label_protocol: ds cDNA was labeled with NimbleGen Dual Color Labeling Kit per manufacturers recommendations to produce enough labeled product for a 12 x 135k microarray chip.

extract_protocol: RNAeasy kits were used for RNA extraction (Qiagen, Valencia, CA). Tissue samples were homogenized on ice with guanidine isothyocyanate with a Tissue-Tearor (Biospec Products, Barlesville, OK), with RNA being preciptated with equal parts ethanol. After washing and elution with nuclease free water on a glass fiber column, samples were treated with DNase

value: gills

tag: exposure type

value: Freshwater to seawater for 1 hour

source_name: FW-->SW+As 1hr #6

value: Freshwater to seawater for 1 hour with arsenic


title: FW-->SW+As 1hr #4a&b_FSW 1hr #2

description: gill

source_name: FW-->SW+As 1hr #4a&b

source_name: FSW 1hr #2


title: TNO_CASAvsGlucose_4h_C

description: Biological rep 3 of 3


title: FW-->SW+As 1hr #5b_FSW 1hr #8

description: gill

source_name: FW-->SW+As 1hr #5b

source_name: FSW 1hr #8


title: FSW 24hr #5_FW-->SW+As 24hr #7b

description: gill

source_name: FSW 24hr #5

value: Freshwater to seawater for 24 hours

source_name: FW-->SW+As 24hr #7b

value: Freshwater to seawater for 24 hours with arsenic


title: FW-->SW+As 24hr #5_FSW 24hr #3

description: gill

source_name: FW-->SW+As 24hr #5

source_name: FSW 24hr #3


title: FSW 1hr #1_FW-->SW+As 1hr #3

description: gill

source_name: FSW 1hr #1

source_name: FW-->SW+As 1hr #3


title: FSW 24hr #2_FW-->SW+As 24hr #3

description: gill

source_name: FSW 24hr #2

source_name: FW-->SW+As 24hr #3


title: FW+As 48hr #10c_FW-->SW+As 24hr #8b

description: gill

source_name: FW+As 48hr #10c

value: Freshwater with arsenic for 48 hours

source_name: FW-->SW+As 24hr #8b


title: FW-->SW+As 24hr #5_FW-->SW+As 1hr #4a&b

description: gill


title: FSW 24hr #7b_FSW 1hr #8

description: gill

source_name: FSW 24hr #7b


title: FW-->SW+As 1hr #6_FW-->SW+As 24hr #7b

description: gill


title: FW+As 48hr #6_FW #5

description: gill

source_name: FW+As 48hr #6

source_name: FW #5

value: Freshwater Exposure


title: FW+As 48hr #10c_FW #7b

description: gill

source_name: FW #7b


title: FW #4_FW+As 48hr #4

description: gill

source_name: FW #4

value: Freshwater exposure

source_name: FW+As 48hr #4


title: FW-->SW+As 1hr #3_FW-->SW+As 24hr #3

description: gill


title: FW-->SW+As 24hr #3_FW+As 48hr #4

description: gill


title: FW-->SW+As 24hr #8b_FSW 24hr #7b

description: gill


title: FW-->SW+As 24hr #7b_FW+As 48hr #8b

description: gill

source_name: FW+As 48hr #8b


title: FW+As 48hr #6_FW-->SW+As 24hr #5

description: gill


title: FW+As 48hr #8b_FW-->SW+As 1hr #6

description: gill

source_name: FW-->SW+As 1hr #6


title: FW-->SW+As 1hr #4a&b_FW+As 48hr #6

description: gill

source_name: FW-->SW+As 1hr #4a&b


title: FSW 24hr #3_FSW 1hr #2

description: gill

source_name: FSW 1hr #2


title: FW #6_FW+As 48hr #8b

description: gill

source_name: FW #6


title: FW+As 48hr #4_FW-->SW+As 1hr #3

description: gill


title: FW-->SW+As 24hr #8b_FW-->SW+As 1hr #5b

description: gill

source_name: FW-->SW+As 1hr #5b


title: FSW 1hr #1_FSW 24hr #2

description: gill

source_name: FSW 1hr #1


title: FW #7b_FSW 24hr #7b

description: gill


title: MS_52.1 EtOH 30 min rep1

city: Fayetteville

first: Jeffrey

middle: A.

last: Lewis

state: AR

address: 850 W. Dickson St.

institute: University of Arkansas

hyb_protocol: Hybridized for 16 hours on a Maui hybridization machine as per Nimblegen protocol.

scan_protocol: Arrays were scanned using GenePix (4000B from Axon Instruments)

data_processing: Data were extracted and background subtracted using Nimblescan version 2.6.0.0. Probe data from the entire data set were quantile normalized together using the bioconductor affy package. Gene expression changes were calculated as the median log2 ratio for all of the probes that completely encompassed the open reading frame of interest. Probes with mismatches against either the YPS163 or M22 genome sequences were excluded from the analysis.

label: Oyster 550 cyanine dye

organism: Saccharomyces cerevisiae

source_name: MS_52.1  grown 4 generations and collected 30 min rep1

label_protocol: Cyanine dyes (Flownamics, Madison, WI) were used; otherwise, as in Gasch, Methods in Enzymology, 2002

growth_protocol: Cells were grown in YPD (2% peptone, 2% dextrose, 1% yeast extract) for 4 generations to an OD600 of 0.3.  A sample of unstressed cells was collected directly prior to ethanol treatment.

extract_protocol: Hot phenol extraction as in Gasch, Methods in Enzymology, 2002

treatment_protocol: Ethanol was added to a final concentration of 5% (v/v) for 30 min

tag: treatment

label: Oyster cyanine 650 dye


title: MS_52.1 EtOH 30 min rep2

source_name: MS_52.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_51.2 EtOH 30 min rep2

source_name: MS_51.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: FSW 1hr #6_FSW 24hr #5

description: gill

source_name: FSW 1hr #6

source_name: FSW 24hr #5


title: MS_51.2 EtOH 30 min rep1

source_name: MS_51.2  grown 4 generations and collected 30 min rep1


title: MS_50.1 EtOH 30 min rep1

source_name: MS_50.1  grown 4 generations and collected 30 min rep1


title: MS_50.1 EtOH 30 min rep2

source_name: MS_50.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_49.2 EtOH 30 min rep2

source_name: MS_49.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_49.2 EtOH 30 min rep1

source_name: MS_49.2  grown 4 generations and collected 30 min rep1


title: MS_47.1 EtOH 30 min rep2

source_name: MS_47.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_47.1 EtOH 30 min rep1

source_name: MS_47.1  grown 4 generations and collected 30 min rep1


title: MS_48.1 EtOH 30 min rep1

source_name: MS_48.1  grown 4 generations and collected 30 min rep1


title: MS_46.3 EtOH 30 min rep1

source_name: MS_46.3  grown 4 generations and collected 30 min rep1


title: MS_48.2 EtOH 30 min rep2

source_name: MS_48.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: FSW 24hr #2_FW #4

description: gill

source_name: FSW 24hr #2

source_name: FW #4


title: FSW 1hr #8_FW #7b

description: gill

source_name: FSW 1hr #8

source_name: FW #7b


title: FSW 1hr #2_FW #5

description: gill

source_name: FSW 1hr #2

source_name: FW #5


title: FW #6_FSW 1hr #6

description: gill

source_name: FW #6

source_name: FSW 1hr #6


title: MS_44.1 EtOH 30 min rep1

source_name: MS_44.1  grown 4 generations and collected 30 min rep1


title: MS_44.1 EtOH 30 min rep2

source_name: MS_44.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_45.2 EtOH 30 min rep1

source_name: MS_45.2  grown 4 generations and collected 30 min rep1


title: MS_45.2 EtOH 30 min rep2

source_name: MS_45.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_40.2 EtOH 30 min rep1

source_name: MS_40.2  grown 4 generations and collected 30 min rep1


title: MS_41.3 EtOH 30 min rep1

source_name: MS_41.3  grown 4 generations and collected 30 min rep1


title: MS_38.3 EtOH 30 min rep2

source_name: MS_38.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_42.1 EtOH 30 min rep2

source_name: MS_42.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: FW #4_FSW 1hr #1

description: gill

source_name: FSW 1hr #1


title: MS_38.3 EtOH 30 min rep1

source_name: MS_38.3  grown 4 generations and collected 30 min rep1


title: MS_42.1 EtOH 30 min rep1

source_name: MS_42.1  grown 4 generations and collected 30 min rep1


title: MS_40.2 EtOH 30 min rep2

source_name: MS_40.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_37.2 EtOH 30 min rep2

source_name: MS_37.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_41.3 EtOH 30 min rep2

source_name: MS_41.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_46.3 EtOH 30 min rep2

source_name: MS_46.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_37.2 EtOH 30 min rep1

source_name: MS_37.2  grown 4 generations and collected 30 min rep1


title: MS_35.3 EtOH 30 min rep2

source_name: MS_35.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_36.1 EtOH 30 min rep1

source_name: MS_36.1  grown 4 generations and collected 30 min rep1


title: MS_36.1 EtOH 30 min rep2

source_name: MS_36.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_32.3 EtOH 30 min rep2

source_name: MS_32.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_33.1 EtOH 30 min rep1

source_name: MS_33.1  grown 4 generations and collected 30 min rep1


title: MS_33.1 EtOH 30 min rep2

source_name: MS_33.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_34.2 EtOH 30 min rep2

source_name: MS_34.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_32.2 EtOH 30 min rep1

source_name: MS_32.2  grown 4 generations and collected 30 min rep1


title: MS_31.2 EtOH 30 min rep2

source_name: MS_31.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: FW #5_FSW 24hr #3

description: gill

source_name: FW #5

source_name: FSW 24hr #3


title: MS_35.3 EtOH 30 min rep1

source_name: MS_35.3  grown 4 generations and collected 30 min rep1


title: MS_28.2 EtOH 30 min rep1

source_name: MS_28.2  grown 4 generations and collected 30 min rep1


title: MS_31.2 EtOH 30 min rep1

source_name: MS_31.2  grown 4 generations and collected 30 min rep1


title: MS_28.2 EtOH 30 min rep2

source_name: MS_28.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: FSW 24hr #5_FW #6

description: gill

source_name: FSW 24hr #5

source_name: FW #6


title: MS_26.1 EtOH 30 min rep1

source_name: MS_26.1  grown 4 generations and collected 30 min rep1


title: MS_25.3 EtOH 30 min rep2

source_name: MS_25.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_26.1 EtOH 30 min rep2

source_name: MS_26.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_34.2 EtOH 30 min rep1

source_name: MS_34.2  grown 4 generations and collected 30 min rep1


title: MS_30.1 EtOH 30 min rep2

source_name: MS_30.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_30.1 EtOH 30 min rep1

source_name: MS_30.1  grown 4 generations and collected 30 min rep1


title: MS_17.1 EtOH 30 min rep1

source_name: MS_17.1  grown 4 generations and collected 30 min rep1


title: MS_17.1 EtOH 30 min rep2

source_name: MS_17.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_25.3 EtOH 30 min rep1

source_name: MS_25.3  grown 4 generations and collected 30 min rep1


title: FW-->SW+As 1hr #5b_FW+As 48hr #10c

description: gill

source_name: FW-->SW+As 1hr #5b

source_name: FW+As 48hr #10c


title: MS_18.2 EtOH 30 min rep1

source_name: MS_18.2  grown 4 generations and collected 30 min rep1


title: MS_18.2 EtOH 30 min rep2

source_name: MS_18.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_16.2 EtOH 30 min rep2

source_name: MS_16.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_24.2 EtOH 30 min rep1

source_name: MS_24.2  grown 4 generations and collected 30 min rep1


title: MS_16.2 EtOH 30 min rep1

source_name: MS_16.2  grown 4 generations and collected 30 min rep1


title: MS_24.2 EtOH 30 min rep2

source_name: MS_24.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_13.1 EtOH 30 min rep2

source_name: MS_13.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_15.3 EtOH 30 min rep2

source_name: MS_15.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_13.1 EtOH 30 min rep1

source_name: MS_13.1  grown 4 generations and collected 30 min rep1


title: MS_14.2 EtOH 30 min rep2

source_name: MS_14.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_19.2 EtOH 30 min rep2

source_name: MS_19.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_20.1 EtOH 30 min rep1

source_name: MS_20.1  grown 4 generations and collected 30 min rep1


title: MS_11.2 EtOH 30 min rep2

source_name: MS_11.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_20.1 EtOH 30 min rep2

source_name: MS_20.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_12.4 EtOH 30 min rep1

source_name: MS_12.4  grown 4 generations and collected 30 min rep1


title: MS_11.2 EtOH 30 min rep1

source_name: MS_11.2  grown 4 generations and collected 30 min rep1


title: MS_12.4 EtOH 30 min rep2

source_name: MS_12.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_19.2 EtOH 30 min rep1

source_name: MS_19.2  grown 4 generations and collected 30 min rep1


title: MS_10.2 EtOH 30 min rep2

source_name: MS_10.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_10.2 EtOH 30 min rep1

source_name: MS_10.2  grown 4 generations and collected 30 min rep1


title: MS_15.3 EtOH 30 min rep1

source_name: MS_15.3  grown 4 generations and collected 30 min rep1


title: MS_9.3 EtOH 30 min rep2

source_name: MS_9.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_14.2 EtOH 30 min rep1

source_name: MS_14.2  grown 4 generations and collected 30 min rep1


title: MS_9.3 EtOH 30 min rep1

source_name: MS_9.3  grown 4 generations and collected 30 min rep1


title: MS_6.4 EtOH 30 min rep2

source_name: MS_6.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_8.2 EtOH 30 min rep2

source_name: MS_8.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_7.4 EtOH 30 min rep2

source_name: MS_7.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_7.4 EtOH 30 min rep1

source_name: MS_7.4  grown 4 generations and collected 30 min rep1


title: MS_8.2 EtOH 30 min rep1

source_name: MS_8.2  grown 4 generations and collected 30 min rep1


title: MS_5.4 EtOH 30 min rep2

source_name: MS_5.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_3.2 EtOH 30 min rep1

source_name: MS_3.2  grown 4 generations and collected 30 min rep1


title: MS_5.4 EtOH 30 min rep1

source_name: MS_5.4  grown 4 generations and collected 30 min rep1


title: MS_6.4 EtOH 30 min rep1

source_name: MS_6.4  grown 4 generations and collected 30 min rep1


title: YS_58.3 EtOH 30 min rep1

source_name: YS_58.3  grown 4 generations and collected 30 min rep1


title: MS_1.3 EtOH 30 min rep2

source_name: MS_1.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_48.4 EtOH 30 min rep2

source_name: YS_48.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_1.3 EtOH 30 min rep1

source_name: MS_1.3  grown 4 generations and collected 30 min rep1


title: YS_48.4 EtOH 30 min rep1

source_name: YS_48.4  grown 4 generations and collected 30 min rep1


title: MS_4.2 EtOH 30 min rep1

source_name: MS_4.2  grown 4 generations and collected 30 min rep1


title: YS_59.1 EtOH 30 min rep1

source_name: YS_59.1  grown 4 generations and collected 30 min rep1


title: YS_47.2 EtOH 30 min rep2

source_name: YS_47.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_58.3 EtOH 30 min rep2

source_name: YS_58.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_47.2 EtOH 30 min rep1

source_name: YS_47.2  grown 4 generations and collected 30 min rep1


title: MS_3.2 EtOH 30 min rep2

source_name: MS_3.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_45.3 EtOH 30 min rep1

source_name: YS_45.3  grown 4 generations and collected 30 min rep1


title: YS_44.2 EtOH 30 min rep1

source_name: YS_44.2  grown 4 generations and collected 30 min rep1


title: YS_44.2 EtOH 30 min rep2

source_name: YS_44.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_2.1 EtOH 30 min rep1

source_name: MS_2.1  grown 4 generations and collected 30 min rep1


title: YS_45.3 EtOH 30 min rep2

source_name: YS_45.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_2.1 EtOH 30 min rep2

source_name: MS_2.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: MS_4.3 EtOH 30 min rep2

source_name: MS_4.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_59.1 EtOH 30 min rep2

source_name: YS_59.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_46.3 EtOH 30 min rep1

source_name: YS_46.3  grown 4 generations and collected 30 min rep1


title: YS_46.3 EtOH 30 min rep2

source_name: YS_46.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_38.3 EtOH 30 min rep1

source_name: YS_38.3  grown 4 generations and collected 30 min rep1


title: YS_38.3 EtOH 30 min rep2

source_name: YS_38.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_39.4 EtOH 30 min rep1

source_name: YS_39.4  grown 4 generations and collected 30 min rep1


title: YS_37.2 EtOH 30 min rep2

source_name: YS_37.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_41.1 EtOH 30 min rep2

source_name: YS_41.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_34.3 EtOH 30 min rep2

source_name: YS_34.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_37.2 EtOH 30 min rep1

source_name: YS_37.2  grown 4 generations and collected 30 min rep1


title: YS_41.1 EtOH 30 min rep1

source_name: YS_41.1  grown 4 generations and collected 30 min rep1


title: YS_34.2 EtOH 30 min rep1

source_name: YS_34.2  grown 4 generations and collected 30 min rep1


title: YS_31.4 EtOH 30 min rep1

source_name: YS_31.4  grown 4 generations and collected 30 min rep1


title: YS_33.1 EtOH 30 min rep2

source_name: YS_33.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_31.4 EtOH 30 min rep2

source_name: YS_31.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_29.2 EtOH 30 min rep1

source_name: YS_29.2  grown 4 generations and collected 30 min rep1


title: YS_24.4 EtOH 30 min rep2

source_name: YS_24.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_25.3 EtOH 30 min rep2

source_name: YS_25.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_39.4 EtOH 30 min rep2

source_name: YS_39.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_24.4 EtOH 30 min rep1

source_name: YS_24.4  grown 4 generations and collected 30 min rep1


title: YS_23.3 EtOH 30 min rep2

source_name: YS_23.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_30.3 EtOH 30 min rep2

source_name: YS_30.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_30.3 EtOH 30 min rep1

source_name: YS_30.3  grown 4 generations and collected 30 min rep1


title: YS_29.2 EtOH 30 min rep2

source_name: YS_29.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_28.2 EtOH 30 min rep1

source_name: YS_28.2  grown 4 generations and collected 30 min rep1


title: YS_33.1 EtOH 30 min rep1

source_name: YS_33.1  grown 4 generations and collected 30 min rep1


title: YS_27.1 EtOH 30 min rep2

source_name: YS_27.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_27.1 EtOH 30 min rep1

source_name: YS_27.1  grown 4 generations and collected 30 min rep1


title: YS_26.4 EtOH 30 min rep2

source_name: YS_26.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_26.4 EtOH 30 min rep1

source_name: YS_26.4  grown 4 generations and collected 30 min rep1


title: YS_28.2 EtOH 30 min rep2

source_name: YS_28.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_25.3 EtOH 30 min rep1

source_name: YS_25.3  grown 4 generations and collected 30 min rep1


title: YS_22.2 EtOH 30 min rep1

source_name: YS_22.2  grown 4 generations and collected 30 min rep1


title: YS_22.2 EtOH 30 min rep2

source_name: YS_22.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_23.3 EtOH 30 min rep1

source_name: YS_23.3  grown 4 generations and collected 30 min rep1


title: YS_21.1 EtOH 30 min rep2

source_name: YS_21.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_20.1 EtOH 30 min rep2

source_name: YS_20.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_20.1 EtOH 30 min rep1

source_name: YS_20.1  grown 4 generations and collected 30 min rep1


title: YS_19.1 EtOH 30 min rep1

source_name: YS_19.1  grown 4 generations and collected 30 min rep1


title: YS_19.1 EtOH 30 min rep2

source_name: YS_19.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_18.4 EtOH 30 min rep2

source_name: YS_18.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_18.4 EtOH 30 min rep1

source_name: YS_18.4  grown 4 generations and collected 30 min rep1


title: YS_17.4 EtOH 30 min rep2

source_name: YS_17.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_16.3 EtOH 30 min rep2

source_name: YS_16.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_13.1 EtOH 30 min rep2

source_name: YS_13.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_15.2 EtOH 30 min rep2

source_name: YS_15.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_15.2 EtOH 30 min rep1

source_name: YS_15.2  grown 4 generations and collected 30 min rep1


title: YS_16.3 EtOH 30 min rep1

source_name: YS_16.3  grown 4 generations and collected 30 min rep1


title: YS_13.1 EtOH 30 min rep1

source_name: YS_13.1  grown 4 generations and collected 30 min rep1


title: YS_14.2 EtOH 30 min rep1

source_name: YS_14.2  grown 4 generations and collected 30 min rep1


title: YS_14.2 EtOH 30 min rep2

source_name: YS_14.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_12.1 EtOH 30 min rep2

source_name: YS_12.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_21.1 EtOH 30 min rep1

source_name: YS_21.1  grown 4 generations and collected 30 min rep1


title: YS_8.2 EtOH 30 min rep2

source_name: YS_8.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_11.4 EtOH 30 min rep2

source_name: YS_11.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_7.3 EtOH 30 min rep2

source_name: YS_7.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_7.3 EtOH 30 min rep1

source_name: YS_7.3  grown 4 generations and collected 30 min rep1


title: YS_9.3 EtOH 30 min rep1

source_name: YS_9.3  grown 4 generations and collected 30 min rep1


title: YS_12.1 EtOH 30 min rep1

source_name: YS_12.1  grown 4 generations and collected 30 min rep1


title: YS_8.2 EtOH 30 min rep1

source_name: YS_8.2  grown 4 generations and collected 30 min rep1


title: YS_10.3 EtOH 30 min rep2

source_name: YS_10.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_17.4 EtOH 30 min rep1

source_name: YS_17.4  grown 4 generations and collected 30 min rep1


title: YS_10.3 EtOH 30 min rep1

source_name: YS_10.3  grown 4 generations and collected 30 min rep1


title: YS_9.3 EtOH 30 min rep2

source_name: YS_9.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_6.1 EtOH 30 min rep2

source_name: YS_6.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_6.1 EtOH 30 min rep1

source_name: YS_6.1  grown 4 generations and collected 30 min rep1


title: YS_5.1 EtOH 30 min rep1

source_name: YS_5.1  grown 4 generations and collected 30 min rep1


title: YS_3.3 EtOH 30 min rep1

source_name: YS_3.3  grown 4 generations and collected 30 min rep1


title: YS_5.1 EtOH 30 min rep2

source_name: YS_5.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_4.4 EtOH 30 min rep1

source_name: YS_4.4  grown 4 generations and collected 30 min rep1


title: YS_4.4 EtOH 30 min rep2

source_name: YS_4.4 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_11.4 EtOH 30 min rep1

source_name: YS_11.4  grown 4 generations and collected 30 min rep1


title: YS_3.3 EtOH 30 min rep2

source_name: YS_3.3 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_2.2 EtOH 30 min rep2

source_name: YS_2.2 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: YS_1.1 EtOH 30 min rep2

source_name: YS_1.1 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected 30 min rep2


title: M22 EtOH 30 min rep3

source_name: M22 grown 4 generations and collected

value: grown 4 generations and collected

source_name: M22 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected


title: YS_2.2 EtOH 30 min rep1

source_name: YS_2.2  grown 4 generations and collected 30 min rep1


title: M22 EtOH 30 min rep4

value: grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected


title: M22 EtOH 30 min rep2


title: YS_1.1 EtOH 30 min rep1

source_name: YS_1.1  grown 4 generations and collected 30 min rep1


title: M22 EtOH 30 min rep5


title: M22 EtOH 30 min rep6


title: M22 EtOH 30 min rep1


title: DBY8268 EtOH 30 min rep6

source_name: DBY8268 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected

source_name: DBY8268 grown 4 generations and collected


title: DBY8268 EtOH 30 min rep5


title: DBY8268 EtOH 30 min rep4


title: YPS163 EtOH 30 min rep 5

source_name: YPS163 grown 4 generations and collected

source_name: YPS163 grown 4 generations, exposed to 5% EtOH (v/v) for 30 min, and collected


title: YPS163 EtOH 30 min rep 6


title: YPS163 EtOH 30 min rep 4


title: YPS163 EtOH 30 min rep 2 (2)


title: YPS163 EtOH 30 min rep 3 (2)


title: DBY8268 EtOH 30 min rep1


title: DBY8268 EtOH 30 min rep3


title: DBY8268 EtOH 30 min rep2


title: YPS163 EtOH 30 min rep 1 (2)


title: Post-operative serum from the CRC patient 10

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Post-operative serum from the patient 10 with colorectal cancer (CRC)

hyb_protocol: Refer to Agilent miRNA hybridization protocol. Probes were hybridized at 55°C for 20 hours with rotation. Then the slides were washed by Gene expression wash buffer 1 at room temperature for 5 minutes and by Gene expression wash buffer 2 at 37°C for 5 minutes.

scan_protocol: After hybridization and washing, the slides were scanned using an Agilent scanner (G2505C). Images were extracted using Agilent Feature Extraction software (ver. 10.7.3.1) and Agilent GeneSpring GX software (ver. 10.0.2).

data_processing: Differences in miRNA expressions between the 10 pairs was determined if the fold change of cel-miR-39 normalized expression values was >2.0 and the p value was <0.05 using paired t test for further analysis.

label_protocol: Total RNA was dephosphorylated with calf intestine alkaline phosphatase, denatured with dimethyl sulfoxide, and labeled with pCp-Cy3 using T4 RNA ligase using the miRNA Labeling Reagent and Hybridization Kit.

extract_protocol: Small RNA was enriched from all serum samples using the mirVana PARIS RNA isolation kit (Ambion, Austin, TX), following the manufacture’s Briefly, 400 uL of serum was thawed on ice and centrifuged at 15,000 rpm for 15 min to remove cell debris. Next, 300 L of supernatant was lysed with an equal volume of 2x denaturing solution. For normalization of sample-to-sample variation during the RNA isolation procedures, 20 fmol of synthetic C. elegans miRNA cel-miR-39 was added to each denatured sample. Small RNAs were then enriched and purified following manufacturer’s protocol. The concentration of all RNA samples were quantified by NanoDrop ND-1000 (Nanodrop, DE, USA).

treatment_protocol: no treatment

tag: rna concentration (ng/ul)

tag: Stage

value: Ⅲa

tag: t

value: MP

tag: n


title: Pre-operative serum from the CRC patient 10

description: Pre-operative serum from the patient 10 with colorectal cancer (CRC)


title: Pre-operative serum from the CRC patient 07

description: Pre-operative serum from the patient 07 with colorectal cancer (CRC)

value: Ⅲb


title: Pre-operative serum from the CRC patient 02

description: Pre-operative serum from the patient 02 with colorectal cancer (CRC)

value: Ⅱ

value: SS


title: Post-operative serum from the CRC patient 09

description: Post-operative serum from the patient 09 with colorectal cancer (CRC)

value: SM


title: Pre-operative serum from the CRC patient 04

description: Pre-operative serum from the patient 04 with colorectal cancer (CRC)


title: Post-operative serum from the CRC patient 08

description: Post-operative serum from the patient 08 with colorectal cancer (CRC)

value: SE


title: Pre-operative serum from the CRC patient 09

description: Pre-operative serum from the patient 09 with colorectal cancer (CRC)


title: Pre-operative serum from the CRC patient 03

description: Pre-operative serum from the patient 03 with colorectal cancer (CRC)


title: Post-operative serum from the CRC patient 03

description: Post-operative serum from the patient 03 with colorectal cancer (CRC)


title: Post-operative serum from the CRC patient 02

description: Post-operative serum from the patient 02 with colorectal cancer (CRC)


title: Post-operative serum from the CRC patient 07

description: Post-operative serum from the patient 07 with colorectal cancer (CRC)


title: Pre-operative serum from the CRC patient 06

description: Pre-operative serum from the patient 06 with colorectal cancer (CRC)


title: Pre-operative serum from the CRC patient 05

description: Pre-operative serum from the patient 05 with colorectal cancer (CRC)


title: Post-operative serum from the CRC patient 04

description: Post-operative serum from the patient 04 with colorectal cancer (CRC)


title: Post-operative serum from the CRC patient 05

description: Post-operative serum from the patient 05 with colorectal cancer (CRC)


title: Pre-operative serum from the CRC patient 08

description: Pre-operative serum from the patient 08 with colorectal cancer (CRC)


title: Post-operative serum from the CRC patient 01

description: Post-operative serum from the patient 01 with colorectal cancer (CRC)


title: Post-operative serum from the CRC patient 06

description: Post-operative serum from the patient 06 with colorectal cancer (CRC)


title: Pre-operative serum from the CRC patient 01

description: Pre-operative serum from the patient 01 with colorectal cancer (CRC)


title: 4165638020F patient after chemotherapy with Chinese herbal Rikkunshito (CT+R group)

city: Kaohsiung

first: yungche

last: chen

address: 123, Ta-Pei Rd. Niao-Sung Dist.

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: PBMC

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

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

treatment_protocol: All the cancer patients received first line chemotherapy with CDDP (mean dose 70 mg/m2) on day 1 plus GEM (GEMZAR®; EliLilly and Company, Indianapolis, IN; mean dose 1000 mg/m2) on day 1, 8, and 15 of a 28-day cycle plus dry power placebo 30 gram P.O. daily (CT group), or combination chemotherapy plus Rikkunshito 30 gram P.O. daily (CT+R group). Treatment was planned for a maximum of six cycles (median 4, range 1-6) unless discontinued because of progressive disease, stable disease, unacceptable toxicity, or death.

tag: tumor stage

tag: Sex

value: M

tag: treatment group

value: CT+R


title: 4200270050D patient after chemotherapy alone (CT group)

value: CT


title: 4165638020B patient after chemotherapy with Chinese herbal Rikkunshito (CT+R group)


title: 4200270050E patient after chemotherapy with Chinese herbal Rikkunshito (CT+R group)

value: F


title: 4165638020A patient after chemotherapy with Chinese herbal Rikkunshito (CT+R group)


title: 4200270040H patient after chemotherapy with Chinese herbal Rikkunshito (CT+R group)


title: 4200270050H patient after chemotherapy alone (CT group)


title: 4200270050F patient after chemotherapy alone (CT group)


title: 4165638020G patient after chemotherapy with Chinese herbal Rikkunshito (CT+R group)


title: 4200270040G patient after chemotherapy with Chinese herbal Rikkunshito (CT+R group)


title: 4200270050G patient after chemotherapy with Chinese herbal Rikkunshito (CT+R group)


title: 4165638020C patient after chemotherapy with Chinese herbal Rikkunshito (CT+R group)


title: 4200270040F patient after chemotherapy alone (CT group)


title: 7days cold acclimation and subsequent 10hours deacclimation-treated plants, biological rep1

city: Yokohama

first: Motoaki

last: Seki

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

institute: RIKEN CSRS

description: Gene expression data from 7d cold acclimation- and subsequent 10h deacclimation-treated Col-0 plants

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed and dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with GeneSpring (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Arabidopsis thaliana

source_name: 7days cold acclimation and subsequent 10hours deacclimation-treated Arabidopsis Col-0 plants

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown on MS plate for 2 weeks under 16-h-light/8-h-dark.

extract_protocol: The total RNA was extracted from whole seedling of plants before or after cold acclimation and deacclimation treatment using Plant RNA Purification Reagent (Invitrogen) according to manufacture’s instruction.

treatment_protocol: The plants were treated with cold for 7days, followed by 4, 10, 24 hours of deacclimation treatment.

tag: cultivar/ecotype

tag: tissue

value: Whole seedling


title: 7days cold acclimation and subsequent 10hours deacclimation-treated plants, biological rep3


title: 4200270040E patient after chemotherapy alone (CT group)


title: 4165638020E patient after chemotherapy alone (CT group)


title: 7days cold acclimation and subsequent 24hours deacclimation-treated plants, biological rep2

description: Gene expression data from 7d cold acclimation- and subsequent 24h deacclimation-treated Col-0 plants

source_name: 7days cold acclimation and subsequent 24hours deacclimation-treated Arabidopsis Col-0 plants


title: 7days cold acclimation and subsequent 4hours deacclimation-treated plants, biological rep2

description: Gene expression data from 7d cold acclimation- and subsequent 4h deacclimation-treated Col-0 plants

source_name: 7days cold acclimation and subsequent 4hours deacclimation-treated Arabidopsis Col-0 plants


title: 4200270050C patient after chemotherapy alone (CT group)


title: Untreated plants, biological rep3

description: Gene expression data from untreated Col-0 plants

source_name: Untreated Arabidopsis Col-0 plants


title: 7days cold acclimation and subsequent 10hours deacclimation-treated plants, biological rep2


title: 7days cold acclimation and subsequent 4hours deacclimation-treated plants, biological rep1


title: 7days cold acclimation and subsequent 24hours deacclimation-treated plants, biological rep1


title: 7days cold acclimation-treated plants, biological rep1

description: Gene expression data from 7d cold acclimation-treated Col-0 plants

source_name: 7days cold acclimation-treated Arabidopsis Col-0 plants


title: 4165638020D patient after chemotherapy alone (CT group)


title: 7days cold acclimation and subsequent 24hours deacclimation-treated plants, biological rep3


title: 7days cold acclimation-treated plants, biological rep2


title: 7days cold acclimation and subsequent 4hours deacclimation-treated plants, biological rep3


title: Untreated plants, biological rep1


title: TRS-HGPS2

city: Bethesda

first: Patricia

last: Fernandez Ferri

state: MD

address: 41 Library Drive, B513

institute: NCI/NIH

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files from Affymetrix were imported into Partek Genomics Suite (Partek Incorporated) and RMA normalized. Analysis of variance (ANOVA) with false discovery correction (FDR) was performed and differentially expressed genes (DEG) were defined as genes having ≥ 2-fold change of expression in pair-wise comparisons, with an FDR-corrected P value <0.05, unless otherwise stated (unadjusted p value).

source_name: HGPS dermal fibroblasts from patient 2 transformed by retroviral introduction of TERT, HRAS and SV40 T antigens (Hahn et al 1999)

label_protocol: standard Affymetrix protocol

growth_protocol: Not applicable

extract_protocol: RNA was extracted using the RNAeasy kit (Qiagen)

treatment_protocol: Not applicable


title: TERT-HGPS1

source_name: HGPS dermal fibroblasts from patient 1 immortalized by retroviral introduction of TERT


title: TERT-HGPS2

source_name: HGPS dermal fibroblasts from patient 2 immortalized by retroviral introduction of TERT


title: TRS-HGPS1

source_name: HGPS dermal fibroblasts from patient 1 transformed by retroviral introduction of TERT, HRAS and SV40 T antigens (Hahn et al 1999)


title: TERT-WT2

source_name: WT dermal fibroblasts from individual 2 immortalized by retroviral introduction of TERT


title: TERT-WT1

source_name: WT dermal fibroblasts from individual 1 immortalized by retroviral introduction of TERT


title: Untreated plants, biological rep2


title: 7days cold acclimation-treated plants, biological rep3


title: Human primary keratinocytes, interleukin-6 treated, biological replicate 1

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

description: Gene expression data from IL-6 treated-cultured human epidermal primary keratinocytes for 24 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays. GeneChips were hybridized and washed using the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Affymetrix Expression Console software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Cultured human primary epidermal keratinocytes, IL-6 treated, 24 hours

growth_protocol: Normal human keratinocytes (NHK) from neonatal foreskin were purchased from Lonza (Basel, Switzerland) and cultured in KBM medium with KGM2 growth supplements according to the manufacturer's instuction

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

treatment_protocol: At passge 2, when NHKs were confluent in culture, cytokines were treated. After 24 hours in culture, NHKs were harvested for total RNA isolation.

tag: cell

value: human epidermal keratinocytes


title: Human primary keratinocytes, interleukin-22 treated, biological replicate 2

description: Gene expression data from IL-22 treated-cultured human epidermal primary keratinocytes for 24 hours

source_name: Cultured human primary epidermal keratinocytes, IL-22 treated, 24 hours


title: Human primary keratinocytes, interleukin-17A treated, biological replicate 2

description: Gene expression data from IL-17A treated-cultured human epidermal primary keratinocytes for 24 hours

source_name: Cultured human primary epidermal keratinocytes, IL-17A treated, 24 hours


title: Human primary keratinocytes, interleukin-6 treated, biological replicate 2


title: TRS-WT1

source_name: WT dermal fibroblasts from individual 1 transformed by retroviral introduction of TERT, HRAS and SV40 T antigens (Hahn et al 1999)


title: TRS-WT2

source_name: WT dermal fibroblasts from individual 2 transformed by retroviral introduction of TERT, HRAS and SV40 T antigens (Hahn et al 1999)


title: Human primary keratinocytes, interleukin-22 treated, biological replicate 1


title: Human primary keratinocytes, interleukin-4 treated, biological replicate 1

description: Gene expression data from IL-4 treated-cultured human epidermal primary keratinocytes for 24 hours

source_name: Cultured human primary epidermal keratinocytes, IL-4 treated, 24 hours


title: CaOv3:PTX_3

city: Andover

first: Zoltan

last: Dezso

address: 4 Corporate dr

institute: Eisai Inc

description: drug

hyb_protocol: We used manufacture recommened protocol (Affymetrix). Arrays were washed and stained using Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000

data_processing: Gene chips were analyzed using Affymetrix Microarray Analysis Suite (MAS) version 5. RMA normalization was performed using Affymetrix Power Tools version 1.12.0.

source_name: CaOv3 Paclitaxel 24h

label_protocol: Biotinylated fragmenetd cRNA was used.

growth_protocol: Cell lines were growing in growth media recommanded by ATCC.

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

treatment_protocol: Treated with eribulin and paclitaxel at 10xIC50 conc. for 24 hours. IC50 determinded in growth inhibitation assay for cell line separately.

tag: cell line

value: ovarian cancer


title: CaOv3:PTX_2

description: drug


title: Human primary keratinocytes, interleukin-4 treated, biological replicate 2

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


title: CaOv3:PTX_1

description: drug


title: CaOv3:Ctrl_3

description: vehicle

source_name: CaOv3 Control


title: Human primary keratinocytes, interferon gamma treated, biological replicate 2

description: Gene expression data from IFNgamma treated-cultured human epidermal primary keratinocytes for 24 hours

source_name: Cultured human primary epidermal keratinocytes, IFNgamma treated, 24 hours


title: COV434:ERI_3

description: drug

source_name: COV434 Eribulin 24h


title: Human primary keratinocytes, interferon gamma treated, biological replicate 1


title: Human primary keratinocytes, interleukin-17A treated, biological replicate 1


title: CaOv3:ERI_1

description: drug

source_name: CaOv3 Eribulin 24h


title: COV434:ERI_2

description: drug


title: COV434:PTX_1

description: drug

source_name: COV434 Paclitaxel 24h


title: COV434:Ctrl_2

description: vehicle

source_name: COV434 Control


title: COV434:PTX_3

description: drug


title: CaOv3:ERI_2

description: drug


title: CaOv3:Ctrl_1

description: vehicle


title: CaOv3:ERI_3

description: drug


title: COV434:PTX_2

description: drug


title: EFO-21:PTX_3

description: drug

source_name: EFO-21 Paclitaxel 24h


title: CaOv3:Ctrl_2

description: vehicle


title: EFO-21:ERI_2

description: drug

source_name: EFO-21 Eribulin 24h


title: EFO-21:ERI_3

description: drug


title: COV434:Ctrl_1

description: vehicle


title: COV434:Ctrl_3

description: vehicle


title: EFO-21:PTX_2

description: drug


title: EFO-21:PTX_1

description: drug


title: EFO-21:Ctrl_3

description: vehicle

source_name: EFO-21 Control


title: COV434:ERI_1

description: drug


title: EFO-21:ERI_1

description: drug


title: OVSAHO:PTX_3

description: drug

source_name: OVSAHO Paclitaxel 24h

value: OVSAHO


title: EFO-21:Ctrl_2

description: vehicle


title: EFO-21:Ctrl_1

description: vehicle


title: OVSAHO:Ctrl_1

description: vehicle

source_name: OVSAHO Control


title: OVSAHO:Ctrl_3

description: vehicle


title: OVSAHO:ERI_1

description: drug

source_name: OVSAHO Eribulin 24h


title: OVCAR-4:PTX_2

description: drug

source_name: OVCAR-4 Paclitaxel 24h


title: OVSAHO:ERI_2

description: drug


title: OVCAR-4:PTX_1

description: drug


title: OVCAR-4:PTX_3

description: drug


title: OVCAR-4:ERI_2

description: drug

source_name: OVCAR-4 Eribulin 24h


title: OVSAHO:ERI_3

description: drug


title: OVSAHO:PTX_1

description: drug


title: OVSAHO:Ctrl_2

description: vehicle


title: OVSAHO:PTX_2

description: drug


title: OVCAR-4:Ctrl_3

description: vehicle

source_name: OVCAR-4 Control


title: OVCAR-4:Ctrl_1

description: vehicle


title: OVCAR-4:Ctrl_2

description: vehicle


title: OVCAR-4:ERI_3

description: drug


title: OVCAR-4:ERI_1

description: drug


title: OVTOKO:PTX_3

description: drug

source_name: OVTOKO Paclitaxel 24h

value: OVTOKO


title: OVTOKO:PTX_1

description: drug


title: OVTOKO:PTX_2

description: drug


title: OVTOKO:ERI_1

description: drug

source_name: OVTOKO Eribulin 24h


title: OVTOKO:ERI_2

description: drug


title: OVTOKO:ERI_3

description: drug


title: OVTOKO:Ctrl_3

description: vehicle

source_name: OVTOKO Control


title: KURAMOCHI:PTX_3

description: drug

source_name: KURAMOCHI Paclitaxel 24h

value: KURAMOCHI


title: OVTOKO:Ctrl_1

description: vehicle


title: KURAMOCHI:ERI_3

description: drug

source_name: KURAMOCHI Eribulin 24h


title: KURAMOCHI:ERI_1

description: drug


title: KURAMOCHI:ERI_2

description: drug


title: OV-90:PTX_2

description: drug

source_name: OV-90 Paclitaxel 24h


title: OVTOKO:Ctrl_2

description: vehicle


title: KURAMOCHI:PTX_1

description: drug


title: KURAMOCHI:Ctrl_1

description: vehicle

source_name: KURAMOCHI Control


title: OV-90:PTX_1

description: drug


title: OV-90:Ctrl_2

description: vehicle

source_name: OV-90 Control


title: KURAMOCHI:Ctrl_2

description: vehicle


title: KURAMOCHI:Ctrl_3

description: vehicle


title: KURAMOCHI:PTX_2

description: drug


title: OV-90:PTX_3

description: drug


title: OV-90:ERI_2

description: drug

source_name: OV-90 Eribulin 24h


title: OV-90:Ctrl_3

description: vehicle


title: OVCAR-3:PTX_1

description: drug

source_name: OVCAR-3 Paclitaxel 24h


title: OV-90:ERI_3

description: drug


title: OV-90:ERI_1

description: drug


title: OVCAR-3:PTX_2

description: drug


title: OVCAR-3:PTX_3

description: drug


title: OVCAR-3:ERI_2

description: drug

source_name: OVCAR-3 Eribulin 24h


title: OV-90:Ctrl_1

description: vehicle


title: OVCAR-3:Ctrl_2

description: vehicle

source_name: OVCAR-3 Control


title: OVCAR-3:ERI_3

description: drug


title: OVCAR-3:Ctrl_1

description: vehicle


title: OVCAR-3:Ctrl_3

description: vehicle


title: EFO-27:PTX_3

description: drug

source_name: EFO-27 Paclitaxel 24h


title: OVCAR-3:ERI_1

description: drug


title: EFO-27:PTX_1

description: drug


title: EFO-27:Ctrl_2

description: vehicle

source_name: EFO-27 Control


title: COV644:PTX_1

description: drug

source_name: COV644 Paclitaxel 24h


title: COV644:PTX_3

description: drug


title: EFO-27:ERI_2

description: drug

source_name: EFO-27 Eribulin 24h


title: EFO-27:ERI_3

description: drug


title: EFO-27:PTX_2

description: drug


title: COV644:Ctrl_2

description: vehicle

source_name: COV644 Control


title: COV644:Ctrl_3

description: vehicle


title: COV644:ERI_1

description: drug

source_name: COV644 Eribulin 24h


title: A2780:PTX_3

description: drug

source_name: A2780 Paclitaxel 24h


title: COV644:PTX_2

description: drug


title: COV644:Ctrl_1

description: vehicle


title: EFO-27:Ctrl_3

description: vehicle


title: EFO-27:ERI_1

description: drug


title: A2780:ERI_2

description: drug

source_name: A2780 Eribulin 24h


title: A2780:ERI_1

description: drug


title: COV644:ERI_2

description: drug


title: COV644:ERI_3

description: drug


title: A2780:ERI_3

description: drug


title: COLO 720E:PTX_1

description: drug

source_name: COLO 720E Paclitaxel 24h

value: COLO 720E


title: A2780:Ctrl_2

description: vehicle

source_name: A2780 Control


title: A2780:Ctrl_3

description: vehicle


title: A2780:PTX_1

description: drug


title: A2780:PTX_2

description: drug


title: A2780:Ctrl_1

description: vehicle


title: COLO 720E:PTX_2

description: drug


title: COLO 720E:PTX_3

description: drug


title: COLO 720E:Ctrl_1

description: vehicle

source_name: COLO 720E Control


title: COLO-704:ERI_1

description: drug

source_name: COLO-704 Eribulin 24h


title: COLO 720E:ERI_2

description: drug

source_name: COLO 720E Eribulin 24h


title: COLO 720E:ERI_1

description: drug


title: COLO 720E:Ctrl_3

description: vehicle


title: COLO 720E:Ctrl_2

description: vehicle


title: COLO-704:PTX_3

description: drug

source_name: COLO-704 Paclitaxel 24h


title: COLO-704:ERI_2

description: drug


title: COV504:PTX_3

description: drug

source_name: COV504 Paclitaxel 24h


title: COLO-704:Ctrl_3

description: vehicle

source_name: COLO-704 Control


title: COV504:PTX_2

description: drug


title: COLO-704:Ctrl_1

description: vehicle


title: COLO-704:Ctrl_2

description: vehicle


title: COLO-704:PTX_2

description: drug


title: COV504:PTX_1

description: drug


title: COV504:ERI_1

description: drug

source_name: COV504 Eribulin 24h


title: COLO-704:PTX_1

description: drug


title: COLO-704:ERI_3

description: drug


title: COV504:ERI_3

description: drug


title: COV362:ERI_3

description: drug

source_name: COV362 Eribulin 24h


title: COV504:Ctrl_1

description: vehicle

source_name: COV504 Control


title: COV362:PTX_2

description: drug

source_name: COV362 Paclitaxel 24h


title: COV504:ERI_2

description: drug


title: COV362:ERI_2

description: drug


title: COV362:PTX_1

description: drug


title: COV504:Ctrl_2

description: vehicle


title: COV362:PTX_3

description: drug


title: HT29 cell treated by 5-FU

city: Xi'an

first: Ni

last: Hou

state: Shaanxi Province

address: 76 Western Yanta Road

department: Department of Genetics and Molecular Biology

institute: Xi'an Jiaotong University

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Four replicated spots of each miRNA probe were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering (>=2).

source_name: HT-29 cell

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: HT29 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere of 5% CO2/ 95% air with medium changes every two days. Cells in mid-log phase were used in this study.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: For 5-FU treatment, HT29s were treated with 5 μM of 5-FU for 24 h. For nutrient starvation, HT29s were incubated in Krebs-Ringer buffer (120 mM NaCl, 5 mM KCl, , 24 mM NaHCO3, 5.6 mM glucose, 2mM CaCl2, pH 7.6) at 37 °C for 7 h.

value: colorectal carcinoma cells


title: HT29 cell treated by nutrient starvation

description: Starvation


title: HT29 cell treated by control for 5-FU treatment


title: COV362:ERI_1

description: drug


title: OV56:PTX_1

description: drug

source_name: OV56 Paclitaxel 24h


title: OV56:ERI_3

description: drug

source_name: OV56 Eribulin 24h


title: COV362:Ctrl_3

description: vehicle

source_name: COV362 Control