title: MCF7, siRNA targeting GSN, 48hr transfection, biological rep1


title: Con B (4)

status: Public on Dec 27 2013

type: RNA

city: New York

first: Vivek

middle: Kumar

last: Arora

state: NY

address: 1275 York Avenue

department: HOPP

country: USA

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: LnCaP/AR Mouse Xenograft

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

extract_protocol: Total RNA was harvested from xenografts with Triazole and then further purified using the RNAeasy (Qiagen) Kit.

value: LnCaP/AR

tag: tissue

value: prostate cancer

tag: treatment

value: Vehicle


title: MCF7, siRNA targeting MAP2K4, 48hr transfection, biological rep2

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St

department: Medicine

institute: Indiana University

description: Gene expression profiling of MCF7 after 48hr incubation with siRNA tranfection mix (RNAi+ Lypofectamine RNAiMAX Reagent)

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on the Affymetrix HG-U133 Plus2.0 GeneChip according to the protocols provided by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: MCF7 cells after transfection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)..The cDNA was prepared from 1 µg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthesizing the cRNA using the IVT labeling kit (Affymetrix). The synthesized cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: MCF7 cells were growth in Dulbecco’s Modified Eagle Medium supplemented with 10%FBS, under humidified 37°C incubator at 5% CO2.

extract_protocol: siRNA-MSG transfected MCF7 cells were collected at 48 h and 96 h using TRIzol Reagent method (Invitrogen). RNA was extracted using RNeasy® miny Kit (Qiagen, Valencia, CA) and DNase I (Qiagen) following the manufacturer’s instructions.  The RNA concentration was assessed using the Nanodrop ND-1000 spectrophotometer (ThermoScientific, Wilmington, DE). RNA quality was measured by calculating the RNA integrity number on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). To assess the MSG-knockdown efficiency in each sample, real-time quantitative RT-PCR (qRT-PCR) analysis was performed.

treatment_protocol: MCF7 cells were transfection with small RNA interference (siRNA; Qiagen) using LipofectamineTM RNAiMax (Invitrogen) according to the manufacturer’s protocol. Briefly, 30 nM siRNAs and 30 µl Lipofectamine RNAiMax were diluted in 2 ml Opti-MEM I Medium and added to 100mm-plate. After 20 min incubation at room temperature, either 1x106 (end time point: 96 h) or 2x106 (end time point: 48 h) cells were diluted in 9 ml DMEM, added to the dishes and incubated for either 48 h or 96 h at 37°C.

tag: tissue of origin

value: breast tumor cell line

tag: sirna transfection time

value: Cells were collected 48hr after siRNA transfection

tag: cell line

value: siRNA targeting MAP2K4

tag: time

value: 48hr transfection


title: MCF7, siRNA targeting MAP2K4, 96hr transfection, biological rep2

description: Gene expression profiling of MCF7 after 96hr incubation with siRNA tranfection mix (RNAi+ Lypofectamine RNAiMAX Reagent)

value: Cells were collected 96hr after siRNA transfection

value: 96hr transfection


title: Con B (3)


title: MCF7, siRNA targeting CDH11, 96hr transfection, biological rep2

value: siRNA targeting CDH11


title: MCF7, siRNA targeting MAP2K4, 96hr transfection, biological rep1


title: Con B (13)


title: MCF7, siRNA targeting GSN, 48hr transfection, biological rep2

value: siRNA targeting GSN


title: MCF7, siRNA targeting MAP2K4, 48hr transfection, biological rep1


title: LREX' (10)

source_name: LREX' Mouse Xenograft

value: LREX'

value: Enzalutamide


title: LREX' (9)


title: Con B (2)


title: MCF7, siRNA targeting CDH11, 48hr transfection, biological rep1


title: MCF7, siRNA targeting CDH11, 96hr transfection, biological rep1


title: Con B (1)


title: MCF7, siRNA targeting CDH11, 48hr transfection, biological rep2


title: Res - top 75th percentile of GR expressers (900_35)


title: Res - top 75th percentile of GR expressers (900_34)


title: Res - top 50th percentile of GR expressers (900_32)


title: Res - top 50th percentile of GR expressers (900_36)


title: MCF7, siRNA targeting CDH2, 96hr transfection, biological rep1

value: siRNA targeting CDH2


title: Res - top 75th percentile of GR expressers (900_33)


title: MCF7, siRNA targeting CDH2, 48hr transfection, biological rep1


title: MCF7, siRNA targeting CDH1, 96hr transfection, biological rep1

value: siRNA targeting CDH1


title: 4 day (900_29)


title: MCF7, siRNA targeting CDH2, 96hr transfection, biological rep2


title: Con A (900_27)


title: Res - top 50th percentile of GR expressers (900_3)


title: MCF7, siRNA targeting CDH1, 48hr transfection, biological rep1


title: MCF7, siRNA targeting CASP8, 96hr transfection, biological rep1

value: siRNA targeting CASP8


title: MCF7, siRNA targeting CDH1, 48hr transfection, biological rep2


title: MCF7, siRNA targeting CASP8, 96hr transfection, biological rep2


title: Con A (909L)


title: MCF7, siRNA targeting NME1, 48hr transfection, biological rep2

value: siRNA targeting NME1


title: 4 day (900_28)

value: LnCaP/AR


title: MCF7, siRNA targeting NME1, 96hr transfection, biological rep2


title: Res - Low GR (920L)

value: prostate cancer


title: MCF7, siRNA targeting NME1, 48hr transfection, biological rep1


title: MCF7, siRNA targeting CASP8, 48hr transfection, biological rep1


title: Con A (900_25)

value: Vehicle


title: MCF7, siRNA targeting NME1, 96hr transfection, biological rep1

value: breast tumor cell line


title: Res - Low GR (929R)


title: Res - Low GR (927R)


title: Res - Low GR (926R)


title: Res - top 75th percentile of GR expressers (929L)


title: MCF7, siRNA targeting CD82, 48hr transfection, biological rep1

value: Cells were collected 48hr after siRNA transfection

value: siRNA targeting CD82


title: MCF7, siRNA targeting CD82, 96hr transfection, biological rep1


title: Con A (900_26)


title: Res - top 50th percentile of GR expressers (927L)


title: Res - top 50th percentile of GR expressers (919R)


title: Res - top 50th percentile of GR expressers (918R)


title: Res - top 50th percentile of GR expressers (915R)


title: MCF7, siRNA targeting CD82, 48hr transfection, biological rep2

value: 48hr transfection


title: Res - top 50th percentile of GR expressers (917L)


title: 4 day (914L)


title: oocyte_pool_43_embryo_blastocyst_slide_2

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

hyb_protocol: Three micrograms of oocyte labeled RNA was combined with 3ug of reference labeled RNA in a final volume of 40ul, containing 10 µg of bovine Cot1 DNA. Solution was denatured for 3 minutes at 94oC and added to 40ul of hybridization buffer (50% formamide, 10x SSC, 02% SDS). Solution was as hybridized to the microarray for 40 hours at 45oC. Microarrays were subjected to sequential washes to remove non-hybridized RNAs (1xSSC/0.2% SDS, 0.1xSSC/0.2% SDS, 0.1xSSC)

scan_protocol: Slides were scanned with GenePix 4000B scanner and images were analyzed using GenePix Pro 6.0

data_processing: Foreground was subtracted from Background. Print-tip-lowess normalized data within microarray and quantile normalization was used within microarrays.

organism: Bos taurus

label_protocol: Three micrograms of aRNA were subjected to integration of either Cy3-ester and Cy5-ester (Amershan, Piscataway-NJ,USA), followed by a cleanup with Rneasy mini kit.

growth_protocol: Oocytes were aspirated from follicles 3-8mm of diameter and subjected to in vitro maturation. Oocytes were micro-manipulated and approximately 30% of the cytoplasm was aspirated, collected in micro drop (PBS 1x, PVA 1%) containing RNAse inhibitor 1U/ul and snap frozen in Trizol reagent. In vitro matured oocytes were chemically activated and presumptive zygotes were in in vitro cultured in individual medium micro drops.

extract_protocol: Each cytoplasm fraction was considered a biological replicate. Five cytoplasm fractions from the same group were pooled for RNA extraction. Total RNA was extracted using Trizol reagent (Invitrogen). The entire RNA was subjected to amplification using TargetAmpTM 2-Round Aminoallyl-aRNA Amplification kit 1.0 (Epicentre® Biotechnology, Madison-WI, USA).  One nanogram of reference RNA was also amplified using the same procedure. For statistical purposes, the each pool was considered biological replicate.

value: good quality oocyte

value: B

tag: cell stage

value: embryo blastocyst

value: reference RNA


title: 4 day (913L)


title: oocyte_pool_27_embryo_blastocyst_slide_2

value: A


title: oocyte_pool_22_embryo_blastocyst_slide_2


title: oocyte_pool_25_embryo_blastocyst_slide_2


title: oocyte_pool_42_embryo_blastocyst_slide_2


title: oocyte_pool_41_embryo_blastocyst_slide_2


title: 4 day (912L)


title: oocyte_pool_21_embryo_blastocyst_slide_2


title: 4 day (910L)


title: Con A (907L)


title: oocyte_pool_26_embryo_blastocyst_slide_2


title: 4 day (911L)


title: 4 day (913R)


title: Smc5-3V5 ChIP in spo11 delete cells replicate 1

type: genomic

first: Andreas

last: Hochwagen

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description: biological replicate 1 of 2 of Smc5-3V5 ChIP log ratios from spo11 delete cells

hyb_protocol: Half of the immunoprecipitated DNA or one tenth of the input DNA was labeled with Cy3- or Cy5-dUTP (GE Healthcare) by random priming using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

scan_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65 degrees for 16 hours. Samples were washed according to manufacturer's instructions. Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser).

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).
Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the sma package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: meiotic budding yeast cells, 3 hours in SPO-medium

label_protocol: 25 ml of cells were harvested after 3 hours in sporulation media. Chromatin immunoprecipitation was performed as described (Aparicio et al., 1997). One tenth of the lysate was removed as an input sample. Proteins were immunoprecipitated with the indicated antibodies in combination with 20 µl GammaBind-Sepharose (GE Healthcare) for 16 hours at 4°C.

growth_protocol: Cells were pre-grown in presporulation medium (BYTA) and transferred into sporulation medium (SPO) at 0 hours.

extract_protocol: Genomic DNA

tag: ip or input dna

value: IP

tag: ip conditions

value: 20 µl anti-V5 beads (Serotec)

tag: chip antibody

tag: chip antibody manufacturer

value: Serotec

source_name: meiotic budding yeast cells

tag: strain

value: input


title: oocyte_pool_44_embryo_blastocyst_slide_2


title: Con A (903L)


title: Con A (907R)


title: Con A (902L)


title: oocyte_pool_23_embryo_blastocyst_slide_2


title: oocyte_pool_28_embryo_blastocyst_slide_2


title: Enzalutamide 10 micromolar + Dexamethasone 100 nM - exp1091_3_7

source_name: VCaP

extract_protocol: Total RNA was harvested from cells using the RNAeasy (Qiagen) Kit.

tag: cell type

value: VCaP


title: Smc5-3V5 ChIP in wild-type cells replicate 2

description: biological replicate 2 of 2 of Smc5-3V5 ChIP log ratios from wild-type cells


title: DHT 0.1 nM - exp1091_3_2

value: DHT 0.1 nM


title: Con A (900R)

value: LnCaP/AR

value: prostate cancer


title: Con A (900L)

value: Vehicle


title: Veh (DMSO) - exp1091_3_1

value: Veh (DMSO)


title: Smc5-3V5 ChIP in spo11 delete cells replicate 2

description: biological replicate 2 of 2 of Smc5-3V5 ChIP log ratios from spo11 delete cells


title: Enzalutamide 10 micromolar - exp1091_3_5

value: Enzalutamide 10 micromolar


title: Smc5-13myc ChIP in wild-type cells replicate 2

description: biological replicate 2 of 2 of Smc5-13myc ChIP log ratios from wild-type cells

value: 2 µg Myc antibody (9E11, Abcam)

value: Myc 9E11

value: Abcam


title: oocyte_pool_12_embryo-18/16-cells_slide_2

value: bad qualtiy oocyte

value: embryo 18/16 cells


title: Smc5-13myc ChIP in wild-type cells replicate 1

description: biological replicate 1 of 2 of Smc5-13myc ChIP log ratios from wild-type cells


title: Smc5-3V5  ChIP in wild-type cells replicate 1

description: biological replicate 1 of 2 of Smc5-3V5 ChIP log ratios from wild-type cells


title: Enzalutamide 10 micromolar + Dexamethasone 100 nM - exp1091_2_7


title: oocyte_pool_33_embryo-18/16-cells_slide_2

value: B

value: reference RNA


title: oocyte_pool_13_embryo-18/16-cells_slide_2

value: A


title: oocyte_pool_32_embryo-18/16-cells_slide_2


title: oocyte_pool_11_embryo-18/16-cells_slide_2


title: Enzalutamide 10 micromolar - exp1091_2_5


title: DHT 0.1 nM - exp1091_2_2


title: oocyte_pool_32_embryo-18/16-cells_slide_1


title: oocyte_pool_33_embryo-18/16-cells_slide_1


title: oocyte_pool_13_embryo-18/16-cells_slide_1


title: Veh (DMSO) - exp1091_2_1


title: Enzalutamide 10 micromolar - exp1091_1_5


title: DHT 0.1 nM - exp1091_1_2


title: oocyte_pool_11_embryo-18/16-cells_slide_1


title: Enzalutamide 10 micromolar + Dexamethasone 100 nM - exp1091_1_7


title: MCF7, siRNA targeting CASP8, 48hr transfection, biological rep2

value: breast tumor cell line

value: Cells were collected 48hr after siRNA transfection

value: siRNA targeting CASP8

value: 48hr transfection


title: Veh (DMSO) - exp1091_1_1

value: VCaP


title: Enzalutamide  + Dex 100nM (ECS195_30)

source_name: LREX' cells in charcoal-stripped media

value: prostate cancer

value: Enzalutamide  + Dex 100nM

value: LREX'


title: Enzalutamide  + Dex 10nM (ECS195_29)

value: Enzalutamide  + Dex 10nM


title: Enzalutamide 10 micromolar (ECS195_26)

value: Enzalutamide 10 micromolar


title: DHT 1nM (ECS195_22)

value: DHT 1nM


title: Enzalutamide  + DHT 1nM (ECS195_27)

value: Enzalutamide  + DHT 1nM


title: Enzalutamide  + DHT 1nM (ECS195_17)


title: oocyte_pool_12_embryo-18/16-cells_slide_1

value: bad qualtiy oocyte


title: Dex 10 nM (ECS195_24)

value: Dex 10 nM


title: Enzalutamide  + Dex 100nM (ECS195_20)


title: Vehicle (DMSO) (ECS195_21)

value: Vehicle (DMSO)


title: oocyte_pool_43_embryo_blastocyst_slide_1

value: good quality oocyte

value: B

value: embryo blastocyst

value: reference RNA


title: Enzalutamide 10 micromolar (ECS195_16)


title: MCF7, siRNA targeting CD82, 96hr transfection, biological rep2

value: breast tumor cell line

value: Cells were collected 96hr after siRNA transfection

value: siRNA targeting CD82

value: 96hr transfection


title: Enzalutamide  + Dex 10nM (ECS195_19)

value: prostate cancer


title: Dex 100 nM (ECS195_25)

value: Dex 100 nM

value: LREX'


title: Namalwa_3d_rep3

city: Bengbu

first: yiwen

last: zhang

state: Anhui

address: 287 Chang Huai Road

department: Hematology

country: China

institute: The First Affiliated Hospital of Bengbu Medical College

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to the 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. Replicated miRNAs were averaged and miRNAs that intensities >=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering.

source_name: human Burkitt lymphoma cells, untreated, 3d

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: Cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum in 5% CO2-95% air humidified atmosphere at 37℃.

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 were measured by using Nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Cells were cultured in the presence or absence of 5-aza for 3 days.

value: Namalwa

value: Burkitt lymphoma cell line


title: oocyte_pool_27_embryo_blastocyst_slide_1

value: A


title: oocyte_pool_42_embryo_blastocyst_slide_1


title: oocyte_pool_25_embryo_blastocyst_slide_1


title: oocyte_pool_23_embryo_blastocyst_slide_1


title: Dex 10 nM (ECS195_14)


title: Namalwa_3d_rep1


title: Namalwa_3d_rep2


title: DHT 1nM (ECS195_12)

value: DHT 1nM


title: Enzalutamide  + DHT 1nM (ECS195_7)

value: Enzalutamide  + DHT 1nM


title: Dex 100 nM (ECS195_15)


title: Namalwa_5-aza_3d_rep3

source_name: human Burkitt lymphoma cells, 5-aza, 3d

tag: treatment duration

value: 3 days


title: oocyte_pool_22_embryo_blastocyst_slide_1

value: good quality oocyte


title: oocyte_pool_41_embryo_blastocyst_slide_1

value: B


title: Vehicle (DMSO) (ECS195_11)

value: Vehicle (DMSO)


title: 17-siCHOP

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

country: Japan

institute: Tokyo Medical University

description: The myxoid liposarcoma-derived cell lines, 1955/91 and 2645/94, were kindly provided from Prof. David Ron (University of Cambridge Institute of Metabolic Science, Cambridge, UK).

hyb_protocol: Labeled RNA was hybridized to the microarray and washed with iAmplify cRNA Preparation and Hybridization Reagents Kit (GE Healthcare) according to Expression Bioarray System USER GUIDE (Rev.2006-9 ver2.0).

scan_protocol: Hybridization signals were detected with a DNA microarray scanner G2505A (Agilent Technologies).

data_processing: The scanned images were analyzed and median-normalized using CodeLink Expression Analysis Version 4.0.

source_name: myxoid liposarcoma cell-line

label_protocol: One ug of total RNA was labeled with CodeLink iExpress Expression Assay Reagent Kit No. 6760200 (GE Healthcare) according to Expression Bioarray System USER GUIDE (Rev.2006-9 ver2.0).

growth_protocol: The myxoid liposarcoma-derived cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma, St. Louis, MO) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted from liposarcoma cell-line with ISOGEN (NIPPONGENE) following the manufacture's protocol.

treatment_protocol: For siRNA trasnfection, myxoid liposarcoma-derived cells were trasnfected with 1uM of chemically-synthesized siRNAs in DMEM without serum using Oligofectamine Reagent (Invitrogen Japan, Tokyo, Japan) and Opti-MEM I (Invitrogen Japan).

value: siRNA


title: 16-Nega

value: Randomized sequence oligo


title: Namalwa_5-aza_3d_rep2


title: Namalwa_5-aza_3d_rep1


title: oocyte_pool_21_embryo_blastocyst_slide_1

value: embryo blastocyst

value: reference RNA


title: oocyte_pool_28_embryo_blastocyst_slide_1


title: oocyte_pool_44_embryo_blastocyst_slide_1


title: 17-Nega


title: oocyte_pool_26_embryo_blastocyst_slide_1


title: Enzalutamide  + Dex 100nM (ECS195_10)

value: Enzalutamide  + Dex 100nM


title: Dex 10 nM (ECS195_4)

value: prostate cancer

value: Dex 10 nM


title: Enzalutamide  + Dex 10nM (ECS195_9)

value: Enzalutamide  + Dex 10nM

value: LREX'


title: Enzalutamide 10 micromolar (ECS195_6)

value: Enzalutamide 10 micromolar


title: 16-siCHOP


title: Dex 100 nM (ECS195_5)

value: Dex 100 nM


title: DHT 1nM (ECS195_2)

value: DHT 1nM


title: HCC1954 Cell Treated 1

status: Public on Dec 26 2013

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

country: Canada

institute: University Health Network

description:
T1
replicate 1

hyb_protocol: Illumina HumanHT-12 V4.0 expression beadchip experiment were performed by the Microarray Centre (University Health Network, Toronto)

data_processing: The data were normalized using quantile normalization with lumi package in R

source_name: Breast Cancer Cell Line

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: HCC1954 cells

tag: subtype

value: HER2 Positive

tag: treatment type

value: TBK1 inhibitor II

tag: treatment time

value: 3 Days


title: Vehicle (DMSO) (ECS195_1)

value: Vehicle (DMSO)


title: HCC1954 Cell Treated 3

description:
T3
replicate 3

scan_protocol: Illumina HumanHT-12 V4.0 expression beadchip experiment were performed by the Microarray Centre (University Health Network, Toronto)


title: HCC1954 Cell Treated 2

description:
T2
replicate 2

label_protocol: Illumina HumanHT-12 V4.0 expression beadchip experiment were performed by the Microarray Centre (University Health Network, Toronto)


title: Yellow nosed Hanwoo

city: Anseong

first: Sang Hwan

last: Kim

state: Kyonggi-do

address: Chungang-no

department: Institute of Genetic Engineering

country: South Korea

institute: Hankyong national university

description:
Differentially expression of genes in yellow nose vs. black nose HanWoo
YH

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >5.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Bovine Genome Oligo Microarrays (G2519F-023647) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 023647_D_20100914) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: YH-nose tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Animal collection protocol: Pigment deposition in the nostril was categorized as either strong black, medium black, weak black, and yellow, according to the system developed by Lee et al. (2012).

extract_protocol: Total RNA was extracted from the Bovine tissue using the TRI REAGENT (MRC, OH) according to the manufacturer’s instructions. The total RNA quality and quantity was assessed by Agilent bioanalyzer 2100 analysis.

value: Hanwoo

tag: tissue

value: nose

tag: tissue color

value: Yellow

tag: gender

value: female

tag: age

value: 30 month


title: HCC1954 Cell Control 3

description:
C3
replicate 3

tag: cell line

value: Vehicle Only


title: Ov_Tumor_Ref_Mix vs. CS-OV-169

city: Santa Monica

first: Judy

last: Dering

state: CA

address: 2825 Santa Monica Blvd. Suite 200

institute: UCLA School of Medicine

hyb_protocol: Slides were incubated for 16-17 hr at 60°C and washed using the SSPE method described in the Agilent 60-mer Oligo Microarray Processing Protocol, Version 2.1. Slides were treated with Agilent Stabilization and Drying Solution, a wash was used to protect the dyes from ozone degradation.

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing:
Agilent Feature Extraction Software (v7.5.1) was used for local background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, ratio error model=hybrid, dye normalization select method = Rank Consistency Filter, no spatial detrend method applied.
Agilent Feature Extraced data was imported into Rosetta Resolver version 7.1.1  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.

source_name: 106 pooled ovarian samples

label_protocol: Total  RNA (750ng) was labeled with cyanine 5-CTP or cyanine 3-CTP using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies)

extract_protocol: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA),quantitated using a Nanodrop Spectrophotometer (Agilent Technolies, Canta Clara, CA), and purified on RNeasy Mini columns (Qiagen Inc.)

value: ovarian

tag: sample type

value: reference pool

tag: sample included in reference pool

value: YES

tag: sample rin

tag: age at surgery

tag: histology

value: Serous

tag: Stage

value: IIIC

tag: grade

tag: tissue status

value: Primary

tag: tcga id

tag: follow up months

tag: disease status

value: Not Free

tag: patient status

value: Dead

tag: disease state

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-168

tag: tissue

value: NO

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-172

value: IV

value: Recurrence


title: HCC1954 Cell Control 2

description:
C2
replicate 2

value: HCC1954 cells

tag: subtype

value: HER2 Positive

tag: treatment type

tag: treatment time

value: 3 Days


title: Ov_Tumor_Ref_Mix vs. CS-OV-170

tag: sample type


title: Black nosed Hanwoo

description:
Differentially expression of genes in yellow nose vs. black nose HanWoo
BH

source_name: BH-nose tissue

tag: strain

value: Hanwoo

value: nose

tag: tissue color

value: Black

tag: gender

value: female

tag: age

value: 30 month


title: HCC1954 Cell Control 1

description:
C1
replicate 1

tag: cell line

value: Vehicle Only


title: Ov_Tumor_Ref_Mix vs. CS-OV-171

value: ovarian

value: reference pool

tag: sample included in reference pool

value: YES

tag: sample rin

tag: age at surgery

tag: histology

value: Serous

tag: Stage

value: IIIC

tag: grade

value: Primary


title: Ov_Tumor_Ref_Mix vs. CS-OV-167

value: Mucinous

value: IA

tag: tissue status

tag: follow up months

tag: disease status

value: Free

tag: patient status

value: Alive

tag: disease state

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-164

tag: tissue

tag: sample type

value: NO


title: Ov_Tumor_Ref_Mix vs. CS-OV-163

value: MMMT

value: Not Free

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-165

value: Normal

value: Benign

value: Normal ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-161

value: ovarian

value: reference pool


title: Ov_Tumor_Ref_Mix vs. CS-OV-159

value: YES

value: Serous


title: Ov_Tumor_Ref_Mix vs. CS-OV-154

value: IIIC

value: Primary

tag: tcga id


title: Ov_Tumor_Ref_Mix vs. CS-OV-162

value: Endometrioid

value: IC


title: Ov_Tumor_Ref_Mix vs. CS-OV-157


title: Ov_Tumor_Ref_Mix vs. CS-OV-158

value: Benign ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-155


title: Ov_Tumor_Ref_Mix vs. CS-OV-166

value: Adenocarcinoma

value: Recurrence

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-160

value: NO

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-156

value: IV

value: Unknown

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-146

value: ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-153

value: reference pool

value: IIIB


title: Ov_Tumor_Ref_Mix vs. CS-OV-145

value: Mucinous

value: IA

value: Free

value: Alive

value: Borderline ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-141

value: YES

value: Serous

value: IIC

value: Primary


title: Ov_Tumor_Ref_Mix vs. CS-OV-150

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-148

value: NO

value: IIB

value: Recurrence

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-149

value: ovarian

value: IIIC

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-138

value: reference pool


title: Ov_Tumor_Ref_Mix vs. CS-OV-144


title: Ov_Tumor_Ref_Mix vs. CS-OV-147

value: IIIB


title: Ov_Tumor_Ref_Mix vs. CS-OV-151


title: Ov_Tumor_Ref_Mix vs. CS-OV-152

value: IV


title: Ov_Tumor_Ref_Mix vs. CS-OV-140


title: Ov_Tumor_Ref_Mix vs. CS-OV-139


title: Ov_Tumor_Ref_Mix vs. CS-OV-142

value: Benign

value: Benign ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-143

value: YES

value: IIIA


title: Ov_Tumor_Ref_Mix vs. CS-OV-134

value: Serous

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-135

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-137

value: Primary


title: Ov_Tumor_Ref_Mix vs. CS-OV-128

value: NO


title: Ov_Tumor_Ref_Mix vs. CS-OV-133

value: Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-129

value: III

value: Recurrence

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-136

value: ovarian

value: Normal

value: Normal ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-122

value: reference pool


title: Ov_Tumor_Ref_Mix vs. CS-OV-126

value: IIIC

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-127

value: Benign


title: Ov_Tumor_Ref_Mix vs. CS-OV-130

value: YES


title: Ov_Tumor_Ref_Mix vs. CS-OV-125

value: Serous

value: IC


title: Ov_Tumor_Ref_Mix vs. CS-OV-123

value: Benign ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-119

value: Primary

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-132

value: IIIB


title: Ov_Tumor_Ref_Mix vs. CS-OV-115

value: NO

value: MMMT

value: IIC

value: Free

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-113

value: ovarian

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-131

value: reference pool


title: Ov_Tumor_Ref_Mix vs. CS-OV-112

value: IIIC

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-121

value: Normal

value: Benign

value: Normal ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-116

value: YES

value: Serous

value: Recurrence


title: Ov_Tumor_Ref_Mix vs. CS-OV-118

value: IV

value: Primary

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-114

value: Clear Cell

value: IC


title: Ov_Tumor_Ref_Mix vs. CS-OV-124

value: NO

value: IIIB


title: Ov_Tumor_Ref_Mix vs. CS-OV-120

value: ovarian

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-109

value: reference pool

value: IIIC


title: Ov_Tumor_Ref_Mix vs. CS-OV-111

value: Transitional Cell

value: IIB

value: Free

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-108

value: YES

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-107

value: Serous


title: Ov_Tumor_Ref_Mix vs. CS-OV-117

value: Primary


title: Ov_Tumor_Ref_Mix vs. CS-OV-106

value: MMMT

value: Recurrence

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-104

value: Normal

value: Benign

value: Normal ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-105

value: ovarian

value: NO

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-103

value: reference pool


title: Ov_Tumor_Ref_Mix vs. CS-OV-110


title: Ov_Tumor_Ref_Mix vs. CS-OV-100

value: Mucinous

value: IIIB


title: Ov_Tumor_Ref_Mix vs. CS-OV-099

value: IIIC


title: Ov_Tumor_Ref_Mix vs. CS-OV-093

value: YES


title: Ov_Tumor_Ref_Mix vs. CS-OV-101

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-097

value: Serous


title: Ov_Tumor_Ref_Mix vs. CS-OV-092

value: IIIA

value: Primary


title: Ov_Tumor_Ref_Mix vs. CS-OV-094

value: Transitional Cell

value: IIA

value: Free

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-102

value: IB

value: Borderline ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-098

value: ovarian

value: NO

value: MMMT

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-096

value: reference pool

value: Endometrioid

value: IA

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-091

value: YES

value: Serous

value: IIIC


title: Ov_Tumor_Ref_Mix vs. CS-OV-086

value: IIC

value: Primary

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-095

value: Mucinous


title: Ov_Tumor_Ref_Mix vs. CS-OV-084

value: Free

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-087

value: ovarian

value: IIIC/IB


title: Ov_Tumor_Ref_Mix vs. CS-OV-079

value: NO


title: Ov_Tumor_Ref_Mix vs. CS-OV-089

value: Borderline ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-080

value: reference pool

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-077


title: Ov_Tumor_Ref_Mix vs. CS-OV-090

value: Endometrioid

value: IA


title: Ov_Tumor_Ref_Mix vs. CS-OV-088

value: IIIB

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-081

value: Serous

value: IIIC


title: Ov_Tumor_Ref_Mix vs. CS-OV-073

value: Primary


title: Ov_Tumor_Ref_Mix vs. CS-OV-075

value: IC

value: Unknown

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-068

value: Benign

value: Free

value: Alive

value: Benign ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-072

value: ovarian

value: NO


title: Ov_Tumor_Ref_Mix vs. CS-OV-074

value: reference pool

value: YES


title: Ov_Tumor_Ref_Mix vs. CS-OV-067

value: IB

value: Borderline ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-070

value: Clear Cell

value: IA

value: Not Free

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-065

value: Serous

value: IV

value: Primary


title: Ov_Tumor_Ref_Mix vs. CS-OV-066

value: unknown

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-082

value: IIIC

value: Recurrence


title: Ov_Tumor_Ref_Mix vs. CS-OV-083

value: ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-085

value: NO


title: Ov_Tumor_Ref_Mix vs. CS-OV-076

value: reference pool


title: Ov_Tumor_Ref_Mix vs. CS-OV-069

value: Free

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-078

value: YES


title: Ov_Tumor_Ref_Mix vs. CS-OV-071


title: Ov_Tumor_Ref_Mix vs. CS-OV-064

value: IIIC/IA


title: Ov_Tumor_Ref_Mix vs. CS-OV-061

value: Borderline ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-060

value: Endometrioid

value: IIIB

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-063

value: Serous

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-059

value: IA


title: Ov_Tumor_Ref_Mix vs. CS-OV-053

value: Primary

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-051

value: IIIC


title: Ov_Tumor_Ref_Mix vs. CS-OV-046

value: ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-044

value: NO


title: Ov_Tumor_Ref_Mix vs. CS-OV-062

value: reference pool

value: IV


title: Ov_Tumor_Ref_Mix vs. CS-OV-057

value: IIIA

value: Unknown

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-058

value: YES

value: MMMT

value: IC


title: Ov_Tumor_Ref_Mix vs. CS-OV-055

value: Recurrence

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-043

value: Normal

value: Benign

value: Normal ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-050

value: Endometrioid

value: Primary

value: Dead

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-039

value: ovarian

value: reference pool

value: NO

value: Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-054

value: Mucinous

value: IA

value: Alive

value: Borderline ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-040

value: YES

value: Serous

value: IIIB


title: Ov_Tumor_Ref_Mix vs. CS-OV-041

value: Normal

value: Benign


title: Ov_Tumor_Ref_Mix vs. CS-OV-052

value: IV

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-045

value: IIIC

value: Primary

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-047

value: ovarian

value: reference pool


title: Ov_Tumor_Ref_Mix vs. CS-OV-038

value: NO

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-037

value: Recurrence


title: Ov_Tumor_Ref_Mix vs. CS-OV-056


title: Ov_Tumor_Ref_Mix vs. CS-OV-048


title: Ov_Tumor_Ref_Mix vs. CS-OV-034

value: Mucinous

value: IA

value: Free

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-031

value: YES

value: Serous


title: Ov_Tumor_Ref_Mix vs. CS-OV-042


title: Ov_Tumor_Ref_Mix vs. CS-OV-036

value: IC


title: Ov_Tumor_Ref_Mix vs. CS-OV-035

value: IIIA


title: Ov_Tumor_Ref_Mix vs. CS-OV-033

value: Normal

value: Benign

value: Normal ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-029

value: IIIC

value: Primary

value: Not Free

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-032

value: ovarian

value: reference pool

value: NO

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-027

value: IV

value: Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-025

value: YES


title: Ov_Tumor_Ref_Mix vs. CS-OV-018

value: Serous


title: Ov_Tumor_Ref_Mix vs. CS-OV-026


title: Ov_Tumor_Ref_Mix vs. CS-OV-049


title: Ov_Tumor_Ref_Mix vs. CS-OV-024


title: Ov_Tumor_Ref_Mix vs. CS-OV-019

value: IIC


title: Ov_Tumor_Ref_Mix vs. CS-OV-030


title: Ov_Tumor_Ref_Mix vs. CS-OV-028

value: Borderline ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-022

value: Recurrence


title: Ov_Tumor_Ref_Mix vs. CS-OV-021

value: IIIB


title: Ov_Tumor_Ref_Mix vs. CS-OV-023


title: Ov_Tumor_Ref_Mix vs. CS-OV-016

value: unknown

value: Unknown


title: Ov_Tumor_Ref_Mix vs. CS-OV-012

value: IIIC

value: Primary


title: Ov_Tumor_Ref_Mix vs. CS-OV-020

value: IC

value: Alive


title: Ov_Tumor_Ref_Mix vs. CS-OV-011

value: ovarian

value: reference pool

value: Mucinous

value: IA


title: Ov_Tumor_Ref_Mix vs. CS-OV-014

value: Not Free

value: Dead

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-017

value: YES

value: Serous

value: IV


title: Ov_Tumor_Ref_Mix vs. CS-OV-015

value: NO


title: Ov_Tumor_Ref_Mix vs. CS-OV-010


title: Ov_Tumor_Ref_Mix vs. CS-OV-008

value: MMMT

value: IIB


title: Ov_Tumor_Ref_Mix vs. CS-OV-007

value: IIIB


title: Ov_Tumor_Ref_Mix vs. CS-OV-009

value: IIIC

value: Primary


title: Ov_Tumor_Ref_Mix vs. CS-OV-006

value: Adenocarcinoma


title: Ov_Tumor_Ref_Mix vs. CS-OV-013

value: ovarian

value: Normal

value: Benign

value: Normal ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-005

value: reference pool

value: Not Free


title: Ov_Tumor_Ref_Mix vs. CS-OV-003

value: Unknown

value: Alive

value: Malignant ovarian


title: Ov_Tumor_Ref_Mix vs. CS-OV-004

value: YES

value: Serous

value: Dead


title: Ov_Tumor_Ref_Mix vs. CS-OV-001

value: MMMT


title: Ov_Tumor_Ref_Mix vs. CS-OV-002

value: NO


title: PrEC LH cells NKX3.1 10h rep1

status: Public on Dec 25 2013

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description:
replicate 1
1705168246_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were filtered for p> 0.01 and normalised using quantile normalisation with GeneSpring

source_name: Human prostate epithelium

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.

value: prostate epithelium

tag: expression construct

tag: expression time hours


title: PrEC LH cells NKX3.1 7h rep2

description:
replicate 2
1705168246_B


title: PrEC LH cells NKX3.1 7h rep1

description:
replicate 1
1705168246_A


title: Nasopharyngeal carcinoma cell 5-8F transfected with empty vector, experimental repeat 1

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description: Gene expression data from nasopharyngeal carcinoma cell 5-8F which stably expressed PIRES empty vector.

hyb_protocol: Following fragmentation, 15 μg of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Gene U133 plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 μg total RNA.

growth_protocol: Nasopharyngeal carcinoma cell line 5-8F was transfected with either PIRES empty vector (Clontech) or PITRS-LTF vector, and stable cell lines were generated by selection with G418.

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

treatment_protocol: Cells were grown in RPMI1640 medium supplemented with 10% fetal bovine serum and G418 (400 μg/mL).

tag: cell line

tag: transfection

value: empty vector control


title: Nasopharyngeal carcinoma cell 5-8F transfected with LTF, experimental repeat 1

description: Gene expression data from nasopharyngeal carcinoma cell 5-8F which stably expressed PIRES-LTF vector.

value: LTF


title: PrEC LH cells NKX3.1 10h rep2

description:
replicate 2
1705168246_D


title: PrEC LH cells GFP 7h rep2

description:
replicate 2
1705168210_B

value: Ad-GFP (control)


title: PrEC LH cells GFP 10h rep1

description:
replicate 1
1705168210_C


title: Nasopharyngeal carcinoma cell 5-8F transfected with LTF, experimental repeat 2


title: PrEC LH cells GFP 10h rep2

description:
replicate 2
1705168210_D


title: MEFdBA_KOSM, day7, biological rep3

city: Bunkyo-ku

first: Naoko

last: Yokota

address: 1-1-1 yayoi

department: Department of Cell and Molecular Biology

institute: The University of Tokyo

description: Th2a/Th2b-deficient MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc, day 7, rep3

hyb_protocol: Hybridization was performed according to standard Affymetrix procedure.

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

data_processing: The data were analyzed with RMA using R-Bioconductor xps package.

organism: Mus musculus

source_name: Th2a-/-Th2b-/- MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc, day 7, rep3

label_protocol: All samples were processed with the GeneChip WT terminal labeling in conjunction with the Ambion WT expression kit according the manufacturers instructions.

growth_protocol: ES cells and iPS cells were maintained in ES cell media. MEFs were cultured in DMEM containing 10% FBS and antibiotics. ES cell media were used for MEFs from 4 days postinfection.

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

treatment_protocol: MEFs were infected with retrovirus vectors expressing indicated genes or empty vector and harvested on day 7 postinfection.

tag: cell type

value: MEF

tag: genotype

value: Th2a-/-Th2b-/-; Nanog-GFP transgenc

tag: induced genes

value: Klf4, Oct4, Sox2, c-Myc


title: MEF_KOSMBAN, day7, biological rep3

description: MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc/Th2a/Th2b/pNpm, day 7, rep3

value: Th2a+/+Th2b+/+; Nanog-GFP transgenc

value: Klf4, Oct4, Sox2, c-Myc, Th2a, Th2b, p-Npm


title: MEF_KOSM, day7, biological rep3

description: MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc, day 7, rep3


title: MEF_vec, day7, biological rep3

description: MEF infected with empty retrovirus vector, day 7, rep3

value: Nanog-GFP transgenc


title: MEF_KOSMBAN, day7, biological rep2

description: MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc/Th2a/Th2b/pNpm, day 7, rep2


title: Nasopharyngeal carcinoma cell 5-8F transfected with empty vector, experimental repeat 2


title: PrEC LH cells GFP 7h rep1

description:
replicate 1
1705168210_A


title: MEFdBA_KOSM, day7, biological rep1

description: Th2a/Th2b-deficient MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc, day 7, rep1

source_name: Th2a-/-Th2b-/- MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc, day 7, rep1


title: MEF_vec, day7, biological rep2

description: MEF infected with empty retrovirus vector, day 7, rep2


title: MEFdBA_KOSM, day7, biological rep2

description: Th2a/Th2b-deficient MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc, day 7, rep2

source_name: Th2a-/-Th2b-/- MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc, day 7, rep2


title: MEF_KOSM, day7, biological rep2

description: MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc, day 7, rep2


title: MEF_KOSM, day7, biological rep1

description: MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc, day 7, rep1


title: iPSC_KOSM, clone #3

description: iPS cell induced by Klf4/Oct4/Sox2/c-Myc, clone #3

source_name: iPSC induced by Klf4/Oct4/Sox2/c-Myc, clone #3

value: iPS cells


title: iPSC_KOBAN, clone #3

description: iPS cell induced by Klf4/Oct4/Th2a/Th2b/p-Npm, clone #3

source_name: iPSC induced by Klf4/Oct4/Th2a/Th2b/p-Npm, clone #3

value: Klf4, Oct4, Th2a, Th2b, p-Npm


title: iPSC_KOBAN, clone #7

description: iPS cell induced by Klf4/Oct4/Th2a/Th2b/p-Npm, clone #7

source_name: iPSC induced by Klf4/Oct4/Th2a/Th2b/p-Npm, clone #7


title: MEF_KOSMBAN, day7, biological rep1

description: MEF infected with retrovirus expressing Klf4/Oct4/Sox2/c-Myc/Th2a/Th2b/pNpm, day 7, rep1


title: MEF_vec, day7, biological rep1

description: MEF infected with empty retrovirus vector, day 7, rep1


title: iPSC_KOBAN, clone #6

description: iPS cell induced by Klf4/Oct4/Th2a/Th2b/p-Npm, clone #6

source_name: iPSC induced by Klf4/Oct4/Th2a/Th2b/p-Npm, clone #6


title: Patient_CTRL2

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 HG-U133 2.0 Plus microarrays (Affymetrix, Inc.) Hybridization protocol

scan_protocol: Standard HG-U133 2.0 Plus microarrays (Affymetrix, Inc.) scan protocol

data_processing: The gene expression values were determined by MAS 5 algorithm in Expression Console (Affymetrix) and normalization was performed by scaling to a target intensity of 500. Normalization quality control was performed by box-plot and MA plot consistency.

source_name: PTCL/NOS Patient_control

label_protocol: Standard HG-U133 2.0 Plus microarrays (Affymetrix, Inc.) label protocol

extract_protocol: total RNA was extracted using the TRIzol reagent (Invitrogen and Life Technologies), purified using the RNeasy Kit (QIAGEN)

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

value: primary PTCL/NOS cells

tag: tumor type

value: Peripheral T-cell lymphoma/not otherwise specified (PTCL/NOS)

tag: treated with

value: none (control)


title: DP rep2

city: basel

first: maria alessandra

last: vigano

department: department of biomedicine

country: Switzerland

institute: university of basel

description: Gene expression data from double positive T cells

hyb_protocol: According to Affymetrix protocol

scan_protocol: GeneChips were scanned according to Affymetrix protocol

data_processing: The data were analyzed with Partek genomic suite software with standard settings (RMA upload)

source_name: double positive thymocytes derived from in vitro expanded bone marrow cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

extract_protocol: Trizol total RNA extraction followed by Rnaesy clean up according to manufacturers' Instructions

value: double positive T cells

tag: treatment

value: transduced with Nup98-HoxB4, grown with IL7 and DLL4 (Notch signaling) and injected into Rag2-/- mouse


title: ESC, TT2

description: ES cell line TT2

source_name: ES cell line TT2

value: ES cells

value: Wild type


title: contralateral breast recurrence PTCL_CL_10

status: Public on Dec 24 2013

city: Paris

first: Matahi

last: MOARII

address: 70 Rue Mouffetard

country: France

institute: Mines Paristech

description: cancerous breast tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: breast tissue 75

label_protocol: Standard Illumina Protocol

extract_protocol: Total genomic DNA was extracted from tissue samples using a variation of the standard phenol : chloroform protocol . Genomic DNA was quantified by spectrophotometry using a ND-1000 Spectrophotometer (NanoDrop, Wilmington, DE), and quality was assessed by 0.8% agarose gel electrophoresis.

tag: gender

value: Female

value: breast tissue

value: cancerous

value: contralateral breast recurrence


title: HSC rep1

description: Gene expression data from hematopoietic stem cells

source_name: in vitro expanded bone marrow cells

value: hematopoietic stem cells

value: transduced with Nup98-HoxB4


title: iPSC_KOSM, clone #2

description: iPS cell induced by Klf4/Oct4/Sox2/c-Myc, clone #2

source_name: iPSC induced by Klf4/Oct4/Sox2/c-Myc, clone #2

value: Klf4, Oct4, Sox2, c-Myc


title: iPSC_KOSM, clone #1

description: iPS cell induced by Klf4/Oct4/Sox2/c-Myc, clone #1

source_name: iPSC induced by Klf4/Oct4/Sox2/c-Myc, clone #1

value: Nanog-GFP transgenc


title: ESC, R1

description: ES cell line R1

source_name: ES cell line R1


title: EOL1_CTRL3

source_name: EOL1 Cell line_control

value: eosinophilic leukemia cells


title: ESC, E14

description: ES cell line E14

source_name: ES cell line E14


title: EOL1_CTRL4


title: Patient_IMA1

source_name: PTCL/NOS Patient_IMA

value: 1 microM imatinib mesylate for 6 hrs


title: EOL1_IMA1

source_name: EOL1 Cell line_IMA


title: Patient_CTRL1

value: primary PTCL/NOS cells


title: DP rep1


title: HSC rep2


title: contralateral breast recurrence PTCL_CL_8

description: cancerous breast tissue

source_name: breast tissue 73


title: Patient_IMA2

value: Peripheral T-cell lymphoma/not otherwise specified (PTCL/NOS)


title: contralateral breast recurrence PTCL_CL_6

description: cancerous breast tissue

source_name: breast tissue 71


title: contralateral breast recurrence PTCL_CL_11

description: cancerous breast tissue

source_name: breast tissue 76


title: EOL1_IMA2


title: contralateral breast recurrence PTCL_CL_5

description: cancerous breast tissue

source_name: breast tissue 70


title: contralateral breast recurrence PTC_CL_4

description: cancerous breast tissue

source_name: breast tissue 69


title: contralateral breast recurrence PTCL_CL_7

description: cancerous breast tissue

source_name: breast tissue 72


title: ProT rep1

description: Gene expression data from committed T cells

value: committed T cells

value: transduced with Nup98-HoxB4 and grown with IL7 and DLL4 (Notch signaling)


title: ProT rep2


title: contralateral breast recurrence PTCL_CL_3

description: cancerous breast tissue

source_name: breast tissue 68


title: primary breast tumor PTCL_PT_10

description: cancerous breast tissue

source_name: breast tissue 64

value: primary breast tumor


title: primary breast tumor PTCL_PT_5

description: cancerous breast tissue

source_name: breast tissue 59


title: contralateral breast recurrence PTCL_CL_2

description: cancerous breast tissue

source_name: breast tissue 67


title: primary breast tumor PTCL_PT_3

description: cancerous breast tissue

source_name: breast tissue 57


title: contralateral breast recurrence PTCL_CL_1

description: cancerous breast tissue

source_name: breast tissue 66


title: primary breast tumor PTCL_PT_11

description: cancerous breast tissue

source_name: breast tissue 65


title: primary breast tumor PTCL_PT_1

description: cancerous breast tissue

source_name: breast tissue 55


title: primary breast tumor PTCL_PT_9

description: cancerous breast tissue

source_name: breast tissue 63


title: local recurrence PTLR_LR_16

description: cancerous breast tissue

source_name: breast tissue 53

value: local recurrence


title: primary breast tumor PTCL_PT_7

description: cancerous breast tissue

source_name: breast tissue 61


title: primary breast tumor PTCL_PT_2

description: cancerous breast tissue

source_name: breast tissue 56


title: local recurrence PTLR_LR_17

description: cancerous breast tissue

source_name: breast tissue 54


title: primary breast tumor PTCL_PT_8

description: cancerous breast tissue

source_name: breast tissue 62


title: local recurrence PTLR_LR_15

description: cancerous breast tissue

source_name: breast tissue 52


title: primary breast tumor PTCL_PT_4

description: cancerous breast tissue

source_name: breast tissue 58


title: local recurrence PTLR_LR_10

description: cancerous breast tissue

source_name: breast tissue 47


title: local recurrence PTLR_LR_11

description: cancerous breast tissue

source_name: breast tissue 48


title: contralateral breast recurrence PTCL_CL_9

description: cancerous breast tissue

source_name: breast tissue 74


title: local recurrence PTLR_LR_12

description: cancerous breast tissue

source_name: breast tissue 49


title: primary breast tumor PTCL_PT_6

description: cancerous breast tissue

source_name: breast tissue 60


title: local recurrence PTLR_LR_8

description: cancerous breast tissue

source_name: breast tissue 45


title: local recurrence PTLR_LR_9

description: cancerous breast tissue

source_name: breast tissue 46


title: local recurrence PTLR_LR_13

description: cancerous breast tissue

source_name: breast tissue 50


title: local recurrence PTLR_LR_3

description: cancerous breast tissue

source_name: breast tissue 40


title: local recurrence PTLR_LR_7

description: cancerous breast tissue

source_name: breast tissue 44


title: local recurrence PTLR_LR_5

description: cancerous breast tissue

source_name: breast tissue 42


title: local recurrence PTLR_LR_2

description: cancerous breast tissue

source_name: breast tissue 39


title: local recurrence PTLR_LR_14

description: cancerous breast tissue

source_name: breast tissue 51


title: local recurrence PTLR_LR_6

description: cancerous breast tissue

source_name: breast tissue 43


title: primary breast tumor PTLR_PT_15

description: cancerous breast tissue

source_name: breast tissue 35


title: primary breast tumor PTLR_PT_16

description: cancerous breast tissue

source_name: breast tissue 36


title: primary breast tumor PTLR_PT_8

description: cancerous breast tissue

source_name: breast tissue 28


title: primary breast tumor PTLR_PT_12

description: cancerous breast tissue

source_name: breast tissue 32


title: primary breast tumor PTLR_PT_4

description: cancerous breast tissue

source_name: breast tissue 24


title: local recurrence PTLR_LR_4

description: cancerous breast tissue

source_name: breast tissue 41


title: primary breast tumor PTLR_PT_6

description: cancerous breast tissue

source_name: breast tissue 26


title: primary breast tumor PTLR_PT_11

description: cancerous breast tissue

source_name: breast tissue 31


title: primary breast tumor PTLR_PT_14

description: cancerous breast tissue

source_name: breast tissue 34


title: primary breast tumor PTLR_PT_3

description: cancerous breast tissue

source_name: breast tissue 23


title: primary breast tumor PTLR_PT_17

description: cancerous breast tissue

source_name: breast tissue 37


title: primary breast tumor PTLR_PT_5

description: cancerous breast tissue

source_name: breast tissue 25


title: primary breast tumor PTLR_PT_9

description: cancerous breast tissue

source_name: breast tissue 29


title: primary breast tumor PTLR_PT_1

description: cancerous breast tissue

source_name: breast tissue 21


title: primary breast tumor PTLR_PT_7

description: cancerous breast tissue

source_name: breast tissue 27


title: primary breast tumor PTLR_PT_2

description: cancerous breast tissue

source_name: breast tissue 22


title: primary breast tumor PTLR_PT_13

description: cancerous breast tissue

source_name: breast tissue 33


title: axillary metastasis PTAM_AM_20

description: cancerous lymph node

source_name: lymph node 20

value: lymph node

value: axillary metastasis


title: axillary metastasis PTAM_AM_16

description: cancerous lymph node

source_name: lymph node 16

value: Female


title: local recurrence PTLR_LR_1

description: cancerous breast tissue

source_name: breast tissue 38

value: breast tissue

value: cancerous


title: axillary metastasis PTAM_AM_17

description: cancerous lymph node

source_name: lymph node 17


title: axillary metastasis PTAM_AM_13

description: cancerous lymph node

source_name: lymph node 13


title: axillary metastasis PTAM_AM_15

description: cancerous lymph node

source_name: lymph node 15


title: axillary metastasis PTAM_AM_9

description: cancerous lymph node

source_name: lymph node 9


title: axillary metastasis PTAM_AM_5

description: cancerous lymph node

source_name: lymph node 5


title: axillary metastasis PTAM_AM_2

description: cancerous lymph node

source_name: lymph node 2


title: axillary metastasis PTAM_AM_6

description: cancerous lymph node

source_name: lymph node 6


title: axillary metastasis PTAM_AM_19

description: cancerous lymph node

source_name: lymph node 19


title: axillary metastasis PTAM_AM_3

description: cancerous lymph node

source_name: lymph node 3


title: axillary metastasis PTAM_AM_10

description: cancerous lymph node

source_name: lymph node 10


title: primary breast tumor PTLR_PT_10

description: cancerous breast tissue

source_name: breast tissue 30


title: primary breast tumor PTAM_PT_20

description: cancerous breast tissue

source_name: breast tissue 20


title: axillary metastasis PTAM_AM_14

description: cancerous lymph node

source_name: lymph node 14


title: axillary metastasis PTAM_AM_12

description: cancerous lymph node

source_name: lymph node 12


title: primary breast tumor PTAM_PT_19

description: cancerous breast tissue

source_name: breast tissue 19


title: axillary metastasis PTAM_AM_7

description: cancerous lymph node

source_name: lymph node 7


title: axillary metastasis PTAM_AM_11

description: cancerous lymph node

source_name: lymph node 11


title: primary breast tumor PTAM_PT_18

description: cancerous breast tissue

source_name: breast tissue 18


title: primary breast tumor PTAM_PT_14

description: cancerous breast tissue

source_name: breast tissue 14


title: axillary metastasis PTAM_AM_8

description: cancerous lymph node

source_name: lymph node 8


title: primary breast tumor PTAM_PT_15

description: cancerous breast tissue

source_name: breast tissue 15


title: primary breast tumor PTAM_PT_17

description: cancerous breast tissue

source_name: breast tissue 17


title: primary breast tumor PTAM_PT_12

description: cancerous breast tissue

source_name: breast tissue 12


title: primary breast tumor PTAM_PT_13

description: cancerous breast tissue

source_name: breast tissue 13


title: primary breast tumor PTAM_PT_11

description: cancerous breast tissue

source_name: breast tissue 11


title: primary breast tumor PTAM_PT_16

description: cancerous breast tissue

source_name: breast tissue 16


title: axillary metastasis PTAM_AM_1

description: cancerous lymph node

source_name: lymph node 1


title: axillary metastasis PTAM_AM_4

description: cancerous lymph node

source_name: lymph node 4


title: primary breast tumor PTAM_PT_10

description: cancerous breast tissue

source_name: breast tissue 10


title: primary breast tumor PTAM_PT_9

description: cancerous breast tissue

source_name: breast tissue 9


title: primary breast tumor PTAM_PT_7

description: cancerous breast tissue

source_name: breast tissue 7


title: primary breast tumor PTAM_PT_8

description: cancerous breast tissue

source_name: breast tissue 8


title: primary breast tumor PTAM_PT_2

description: cancerous breast tissue

source_name: breast tissue 2


title: primary breast tumor PTAM_PT_3

description: cancerous breast tissue

source_name: breast tissue 3


title: axillary metastasis PTAM_AM_18

description: cancerous lymph node

source_name: lymph node 18


title: primary breast tumor PTAM_PT_5

description: cancerous breast tissue

source_name: breast tissue 5


title: EA WT compound 9 rep1

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1210 Gregory Dr.

department: Crop Sciences

institute: University of Illinois

hyb_protocol: 1. Add 20 μl water to dissolve the dried labeled-cDNA (600ng). 2. Add 5 μl 10 × Blocking Agent 3. Add 25 μl 2 × GE × Hybridization Buffer H1-RPM. Mix well by pipetting to reduce bubble formation. Spin for 1 min and place on ice. Prepare the hybridization assembly 1. Load a clean gasket slide into the Agilent Suretlyb chamber base with the label facing up. 2. Slowly dispense 40 μl hybridization samples onto the gasket well. To minimize bubble formation. 3. Slowly place an array “active side (Agilent facing down)” onto the gasket slide. 4. Place the SureHyb chamber clamp cover on the sandwiched slides and slide the clamp assembly onto both pieces. 5. Hand-tighten the clamp on to the chamber. Rotate the gasket slide when tightening. 6. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. 7. Place assembled slide chamber in a hybridization oven set to 65°C, 15 rpm. 8. Hybridize at 65°C for 17 h. Washing This step is performed under dark conditions. 1. Add triton into the X-102 to Gene Expression washing buffer 1 and 2. 2. Pre-warm gene expression wash buffer 2 in a 37°C water bath O/N 3. Dessemble the hybridization chamber, put gaskets and slide into Washing Buffer 1. Use a tweezer to separate the slide from the cover slide. 4. Put the slide into the washing container and array side facing out. Wash for 1 min 5. Transfer the slide into another container containing Washing Buffet 2 and wash for another min. 6. Remove the slide slowly to minimize the attachment of water. Put the slide into a 50 ml tubes in dark places.

scan_protocol: Slides were scanned using an Agilent Scanner (Agilent technologies, Santa Clara, CA, USA) at 5-µm resolution. All slides were scanned using 100% laser power; PMT voltages were automatically adjusted using the Genepix Pro 6.0 software acquisition system to obtain maximal signal intensities with <0.02% probe saturation. The resulting 16 bit images were processed using the GenePix Pro 6.0 image analysis software (v6.0.1.26).

data_processing: Microarray data normalization Microarray normalization is carried out using maanova function in R program version 2.2.1. Eight arrays in one slide were globally normalized using glowess method. 1. library(maanova) go to the directory: setwd(C:\\Documents and Settings\\Wang\\Desktop\\Erwinia in vivo\\rcsC MBMA) 2. Read data: Data = read.madata(NormInput.txt, designfile=Designfile1.txt, header=TRUE, spotflag=TRUE, metarow=1, metacol=2, row=3, col=4, geneID=5, pmt=6) 3. Log transformation: LogData = createData(Data, n.rep=1, log.trans=TRUE) 4. Normalization by Glowess method: NormalData=transform.madata(LogData, method=c(glowess)) 5. Save the plot files postscript(file=PlotRawData.ps) riplot(LogData, onScreen=FALSE) postscript(file=PlotGLOWESS.ps) riplot(NormalData, onScreen=FALSE) 6. close the graph: graphics.off() norm.temp<-cbind(NormalData$metarow, NormalData$metacol,NormalData$row, NormalData$col, NormalData$geneID, NormalData$data) 7. output: write.table(norm.temp, file=Normal_Data.csv, sep=,, row.names=FALSE, col.names=TRUE, quote=FALSE) Data selection Statistical comparisons were performed using multiple testing procedures to evaluate statistical significance for differentially expressed genes. A modified t-test (p-value) was computed to measure the significance associated with each differential expression value. A gene expression value was decided to be significantly different in the mutant and over-expression strains when the p-value was less than 0.05 (except otherwise mentioned) and the expression ratio was ≥ 2.0or ≤ 0.5.

label: Fluor dye 555

organism: Erwinia amylovora

source_name: compound 9 rep1

label_protocol: cDNA labeling was carried out using the FairPlay III Microarray Labeling Kit from Agilent. Reverse transcription 10 μ g total RNA was used to generate cDNA. Add 1 μl of 500 ng/ μl random primers into the 10 μg total RNA which is dissolved in 12 μl RNase free water. Incubate at 70°C for 10 min in a PCR machine. Cool samples immediately on ice until ready for use. Combine the following components in a sterile, RNase and DNase free tube: 2 μl 10 × AffinityScript RT Buffer; 1 μl 20 × dNTP mix; 1.5 μl 0.1 M DTT; 0.5 μl 40 U/ul RNase Block. Add the annealed primers and RNA into the mixture. Add 3 μl of AffinityScript RT and incubate at 42°C for 60 min. Add 10 μl of 1 M NaOH and incubate at 70°C for 10 min to hydrolyzed RNA. Cool to room temperature and add 10 μl 1 M HCL to neutralize the solution. cDNA purification Add 4 μl of 3 M sodium acetate pH 5.5 to the reaction. Add 1 μl of 20 mg/ml glycogen to the reaction. Add 100 μl ice cold 100% ethanol and incubate at -20°C overnight. Spin the reaction at 13.2 rpm for 15 min at 4°C and decant the supernatant (You should see some white pellet at the bottom of the tube). Wash with 200 μl ice cold 70% ethanol and spin 5 min. Decant supernatant carefully and allow for air dry for about 30 min to eliminate ethanol. cDNA labeling with a reaction fluorescence dye Prepare the amine-modified cDNA. Thoroughly dissolve the amine-modified DNA in 5 μl of nuclease-free water, warm in a 42°C water bath for 5 min. Prepare labeling buffer: 2.5 g sodium bicarbonate in 100 ml water. Add 3 μl labeling buffer to the amine-labeled cDNA. Dissolve one vial of dye in 2 μl of high quality DMSO, vortex for 10 s. Add the 8 ul amine-modified cDNA into the dissolved dye. Incubate the reaction in dark for 1 h. Purification of dye-labeled cDNA using QIAquick PCR Purification column Add 8 μl of nuclease-free water and 2 μl 3 M sodium acetate pH 5.5 to the reaction mixture. Add 100 μl buffer PB to the mixture. Apply the sample to the QIAquick column and centrifuge for 60 s. Discard flow-through and place the QIAquick column back into the same tube. To wash, add 0.75 ml buffer PE to the column and centrifuge for 60 s. Centrifuge in a 2 ml collection tube for 1 min. Place QIAquick column in a clean 1.5 ml tube. Add 50 μl buffer EB and centrifuge for 1 min.

growth_protocol: Bacterial strains were grown in Hrp-inducing minimal medium (HMM) (1g [NH4]2SO4, 0.346 g MgCl2.6H2O, 0.099 g NaCl, 8.708 g K2HPO4, 6.804 g KH2PO4)

extract_protocol: Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C.

treatment_protocol: Wild type Ea273 was grown overnight in LB broth at 28 °C. Cells were washed and re-inoculated in HMM after washing twice by PBS. 2 ml cells were seeded into 12-well tissue-culture plates at a density of OD600 = 0.3 cells/well. Compounds were added into each well at a final concentration of 50 µmol, and equal volume of DMSO was used as control. The plates were incubated at 18 °C for 18 h with shaking. 1.5 ml cultures were stabilized using 3 ml of RNA protect reagent (Qiagen, Hilden, Germany).

tag: strain

tag: agent

value: compound 9


title: EA WT DMSO rep2

source_name: WT DMSO rep2

value: DMSO


title: EA WT compound 9 rep3

source_name: compound 9 rep3


title: EA WT compound 9 rep2

source_name: compound 9 rep2


title: DBA1_F1

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

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

source_name: anti-GBM sensitive strain

value: Mouse

tag: age

value: 2 months

value: Kidney cortex


title: primary breast tumor PTAM_PT_4

description: cancerous breast tissue

source_name: breast tissue 4

tag: disease state


title: BALB/C_F4

description: BALB/C_F1 replicate

source_name: anti-GBM resistant strain

tag: tissue

value: BALB/C


title: 129/svj_F3


title: DBA1_F4

description: DBA1_F1 replicate


title: DBA1_F3


title: EA WT compound 3 rep3

source_name: compound 3 rep3

value: compound 3


title: primary breast tumor PTAM_PT_1

description: cancerous breast tissue

source_name: breast tissue 1

tag: sample type


title: EA WT compound 3 rep2

source_name: compound 3 rep2


title: EA WT compound 3 rep1

source_name: Compound 3 rep1


title: BALB/C_F3


title: 129/svj_F1


title: BALB/C_F2


title: DBA1_F2


title: EA WT DMSO rep1

source_name: WT DMSO rep1


title: 129/svj_F2


title: BALB/C_F1


title: hypoNP_rep1

city: New Haven

first: Dejian

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

description: biological replicate 1 of 6

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Following instructions of GenePix 4000B Array Scanner; extract intensity information using GenePix Pro 6

data_processing: Background corrected and LOWESS normalized; R plus limma package

organism: Locusta migratoria

source_name: NP locusts in normoxia

label_protocol: 40 µg of total RNA were primed with 2.5 µl of 2 µg/µl oligo(dT) at 68°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dCTP, dGTP, with 25 µM dTTP, 25 µM aa-dUTP

growth_protocol: 30 centidegree, light:dark=14h:10h, wheat bran as food

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Simulated 4km altitude hypoxia

value: thoratic flight muscle

tag: population

value: lab

source_name: NP locusts in hypoxia


title: HEK293-EGFP-ZFP36_ZFP36_Rep5

city: Aurora

first: Neelanjan

last: Mukherjee

state: CO

department: BMG/RBI

institute: University of Colorado School of Medicine

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45° C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1)

data_processing: Data was normalized using gcrma and then filtered for retaining only unambiguously mapping probes and minimal expression level (mean log hybridization value for replicates within a group > 4.5).

source_name: FlpIn T-Rex Human embryonic kidney 293 stable cell line

label_protocol: 1.5 μg of RNA from each sample was provided to the NIEHS Microarray Core Facility for analysis, using Affymetrix Human Genome U133 Plus 2.0 gene chip  (Affymetrix, Santa Clara, CA). One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.

growth_protocol: Doxycycline-inducible epitope-tagged ZFP36 HEK293 cell lines were produced utilizing the Flp-In™ T-REx™ 293 Cell Line system (Life Technologies). Flp-In™ T-REx™ HEK293 cells were generated that contained a FLAG/HA-tagged human ZFP36 or an EGFP-tagged human ZFP36. Both cell lines were cultured in DMEM supplemented with 10% tet-reduced FBS and appropriate selection antibiotics. For induction of FLAG/HA-tagged or EGFP-tagged ZFP36 protein, cells were treated for 16 hrs with 1 μg/ml doxycycline (Sigma).

extract_protocol: Total or immunoprecipitated RNA was extracted by phenol-chloroform, followed by ethanol precipitation. Rneasy Mini Kit (Invitrogen) was used according to manufacturer's instructions as a final step.

treatment_protocol: Expression of stable transgenes were induced by incubation with 1 µg/ml doxycyline for 16 h.

tag: cell

value: Doxycline


title: field_rep5

description: biological replicate 5 of 6

source_name: NP locusts

value: field

source_name: TP locusts


title: field_rep6

description: biological replicate 6 of 6


title: hypoTP_rep4

description: biological replicate 4 of 6

source_name: TP locusts in hypoxia

source_name: TP locusts in normoxia


title: field_rep4

description: biological replicate 4 of 6


title: HEK293-Parental_Vehicle_Rep4

source_name: FlpIn T-Rex Human embryonic kidney 293 parental cell line

tag: cell line

value: Parental

value: Water


title: hypoTP_rep3

description: biological replicate 3 of 6


title: field_rep3

description: biological replicate 3 of 6


title: HEK293-Parental_Vehicle_Rep5


title: hypoTP_rep2

description: biological replicate 2 of 6


title: hypoTP_rep6

description: biological replicate 6 of 6


title: HEK293-Parental_Vehicle_Rep1


title: hypoTP_rep5

description: biological replicate 5 of 6


title: field_rep2

description: biological replicate 2 of 6


title: hypoTP_rep1

description: biological replicate 1 of 6


title: HEK293-Parental_Vehicle_Rep3


title: HEK293-EGFP-ZFP36_Mock_Rep5


title: HEK293-EGFP-ZFP36_ZFP36_Rep4


title: HEK293-Parental_Vehicle_Rep2


title: hypoNP_rep6

description: biological replicate 6 of 6


title: HEK293-EGFP-ZFP36_ZFP36_Rep3


title: hypoNP_rep5

description: biological replicate 5 of 6


title: HEK293-EGFP-ZFP36_ZFP36_Rep2


title: hypoNP_rep2

description: biological replicate 2 of 6


title: HEK293-EGFP-ZFP36_Mock_Rep4


title: HEK293-EGFP-ZFP36_ZFP36_Rep1


title: hypoNP_rep3

description: biological replicate 3 of 6


title: HEK293-EGFP-ZFP36_Mock_Rep3


title: field_rep1

description: biological replicate 1 of 6


title: hypoNP_rep4

description: biological replicate 4 of 6


title: HEK293-Parental_Dox_Rep3


title: HEK293-EGFP-ZFP36_Mock_Rep2


title: HEK293-Parental_Dox_Rep5


title: HEK293-Parental_Dox_Rep2


title: HEK293-Parental_Dox_Rep4


title: HEK293-EGFP-ZFP36_Mock_Rep1


title: primary breast tumor PTAM_PT_6

description: cancerous breast tissue

source_name: breast tissue 6

value: primary breast tumor


title: ir-hd20_corolla_rep1

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

country: Germany

institute: Max-Planck-Institute for Chemical Ecology

description: Gene expression in corolla

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL13527 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 75 percentile normalization was performed for all probes including all controls and replicate probes. Controls were removed from the list. All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: ir-hd20 corolla replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds from N. attenuata wild type and ir-lecRK1 plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from corollas using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: Corollas were harvested at 12 pm from flowers of wild type and ir-hd20 N. attenuata plants.

value: corolla

tag: genotype/variation


title: HEK293-Parental_Dox_Rep1


title: 129/svj_F4

description: 129/svj_F1 replicate

source_name: anti-GBM sensitive strain


title: HM67_before

city: Wageningen

first: Milene

last: Catoire

address: Bomenweg 2

department: Human Nutrition

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of Affymetrix GeneChip Human Gene 1.1 ST arrays was carried out according to standard Affymetrix protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner according to standard protocol.

data_processing: Expression estimates were calculated using RMA

source_name: muscle biopsy

label_protocol: One hundred nanogram of  total RNA was labelled using Ambion WT expression kit (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: 18 healthy middle-aged men (age 59±4 years, body weight 95±11 kg, body mass index 30 ± 4) participated in the study.  The study was approved by the medical ethical committee of Maastricht University and all subjects received oral and written information about the experimental procedures and provided written informed consent.

extract_protocol: Percutaneous needle biopsies were taken before and 3 days after the last exercise training bout from the vastus lateralis muscle, using the Bergström technique with suction.  After each biopsy, the collected tissue sample was carefully cleared from visible adipose tissue and directly frozen into liquid nitrogen.

treatment_protocol: All subjects performed a exercise training consisting of 2 endurance exercise session and 1 resistance exercise session per week. Endurance training consisted of cycling, resistance training of exercises training all major muscle groups, intensities were adapted throughout the training.

tag: ethnicity

value: Caucasian

value: male

value: 56 years


title: BE50_before

value: 60 years


title: ir-hd20_corolla_rep3

description: Gene expression in corolla

source_name: ir-hd20 corolla replicate 3


title: HM67_after


title: WT_corolla_rep2

description: Gene expression in corolla

source_name: wild type corolla replicate 2

value: wild type


title: RS59_before

value: 57 years


title: PP58_after

value: 62 years


title: RS59_after


title: WT_corolla_rep3

description: Gene expression in corolla

source_name: wild type corolla replicate 3


title: WT_corolla_rep1

description: Gene expression in corolla

source_name: wild type corolla replicate 1


title: BE50_after


title: DG51_after

value: 52 years


title: PP58_before


title: RN38_before


title: RN38_after


title: ir-hd20_corolla_rep2

description: Gene expression in corolla

source_name: ir-hd20 corolla replicate 2


title: RT1_after


title: irDCL4_1h_Oselicitation_rep3

description: Gene expression after 1hr of elicitation with oral secretions from Manduca sexta larvae

source_name: irDCL4 leaves_1hr after oral secretion elicitation

growth_protocol: Seeds from N. attenuata wild type and irDCL3 and irDCL4 plants were grown in the glasshouse under high-pressure sodium lamps (200-300 µmol s-1 m-2 light) with a day/night cycle of 16 h(26-28°C)/8 h(22-24°C) and 45 to 55% humidity.

extract_protocol: Total RNA was extracted from leaves using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: For elicitation treatment, leaves were wounded by rolling a fabric-pattern wheel three times on each side of the midvein and the wounds were supplemented with 20 microliters of Manduca sexta oral secretions diluted 1/4 (v/v) in water.

value: leaves


title: irDCL4_1h_Oselicitation_rep1


title: irDCL4_1h_Oselicitation_rep2


title: irDCL3_1h_Oselicitation_rep3

source_name: irDCL3  leaves_1hr after oral secretion elicitation


title: irDCL3_1h_Oselicitation_rep1

source_name: irDCL3 leaves_1hr after oral secretion elicitation


title: Wildtype_1h_Oselicitation_rep3

source_name: wild type leaves_1hr after oral secretion elicitation


title: irDCL3_1h_Oselicitation_rep2


title: CT2-MM rep2

city: Farmington

first: Ren-he

last: Xu

address: 263 FARMINGTON AVE MC 6403

department: Genetics and developmental biology

institute: university of Connecticut health center

hyb_protocol: Amplified RNA for hybridization with Illumina Sentrix arrays

data_processing: The analysis is done using the GenomeStudio software

source_name: Human embryonic stem cells

label_protocol: TotalPrep RNA amplification kit from Ambion is used for generating biotinylated

extract_protocol: RNA were extracted by RNAqueous-4PCR Kit (Applied Biosystems) followed DNase I treatment. Quality control was performed with Agilent Bioanalyser.

value: mismatch shRNA


title: DG51_before


title: CT2 rep1


title: CT2 rep2


title: CT2-KD rep2

value: JMJD1C KD


title: whole_CDDP_10mg/kg_1

city: Kyoto

first: Satohiro

last: Masuda

address: Shogoin

department: Pharmacy

institute: Kyoto University Hospital

description: Rat Genome Survey Microarray® (Applied Biosystems)

hyb_protocol: A total of 10 μg of labeled cRNA from each RT-IVT reaction was hybridized onto Rat Genome Survey Microarray at 55°C for 16 h.

scan_protocol: Microarrays were analyzed using the ABI 1700 Chemiluminescent Microarray Analyzer (Applied Biosystems)

data_processing: The array contained 34,656 oligonucleotide probes, including 26,857 individual gene probes and more than 1000 control probes. Microarray signal data were analyzed using Spotfire® software (TIBCO Software Inc. Palo Alto, CA). Expression values were normalized across the experiments with each 50% percentile values. Genes were defined as detectable on the basis of the recommendations from Applied Biosystems; a gene with a signal:noise ratio > 3.0 in 2 or 3 assays, and a FLAG value < 5000 was considered to be detectable. Normalized signal data were analyzed statistically with a one-way ANOVA. Probability values of less than 0.05 were considered statistically significant.

label: Digoxigenin-UTP

organism: Rattus norvegicus

source_name: whole kidneys

label_protocol: Digoxigenin (DIG)-labeled cRNA was generated from total RNA extracted from the proximal tubules or whole kidney using Applied Biosystems Chemiluminescent Reverse Transcription-In Vitro Transcription (RT-IVT) Labeling Kit v2.0 (Applied Biosystems part of Life Technologies, Foster City, CA, USA)

growth_protocol: Male Wistar/ST rats (8 weeks old) were purchased from SLC Animal Research Laboratories (Shizuoka, Japan). The rats were fed normal pellet food ad libitum, and given water freely.

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany)

treatment_protocol: Cisplatin (0.5 mg/mL; Randa®; Nippon Kayaku Co. Ltd., Tokyo, Japan) was administered intraperitoneally; the same volume of saline solution was injected in the sham controls.

value: Wistar/ST

value: 8 weeks old

value: whole kidneys

tag: dose


title: whole_CDDP_10mg/kg_2


title: CT2-KD rep1


title: whole_ctrl_3

value: vehicle

value: control


title: FL37_after

value: 51 years


title: whole_CDDP_10mg/kg_3


title: Wildtype_1h_Oselicitation_rep1


title: CT2-MM rep1


title: H9-MM rep1


title: LC26_after

value: Caucasian


title: whole_ctrl_2

value: male


title: Wildtype_1h_Oselicitation_rep2


title: H9-KD rep2


title: H9-KD rep1


title: FL37_before


title: whole_ctrl_1


title: JS22_after

value: 63 years


title: H9-MM rep2


title: Six1-transfected HKc/DR - Replicate 1

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

hyb_protocol: Labeled cRNA samples were hybridized to Agilent Whole Human Genome Microarrays 4x44K (Agilent, Wilmington, DE) using Agilent’s Gene Expression Hybridization Kit (Agilent, Wilmington, DE). Four HKc/DR-Ctrl samples were hybridized against four HKc/DR-Six1 samples in a dye swap design.

scan_protocol: Arrays were scanned for both the Cy3 and Cy5 channels at 5 μm resolution using a ProScanArray Express HT scanner (Perkin Elmer Life and Analytical Sciences) and the ScanArray Express SP3 software.

data_processing: The scanned TIFF images were quantitated using ImaGene 8.0.1 software (BioDiscovery). Raw backgrounds and foregrounds intensities were uploaded into limmaGUI where features were background corrected using the Normexp method with offset equal to 50.  Subsequently, data was normalized within arrays using the LOESS algorithm and between arrays performing scale normalization and differentially expressed genes were determined.

source_name: Six1-transfected HKc/DR

label_protocol: Total RNA was amplified and labeled using Agilent’s Low Input Quick Amp Labeling Kit (Agilent, Wilmington, DE) according to the manufacturer’s instructions.

growth_protocol: HKc/DR cells were cultured in keratinocyte medium supplemented with epidermal growth factor (EGF), bovine pituitary extract (BPE) (Invitrogen, Carlsbad, CA), 1 mM calcium chloride and 5% fetal bovine serum.

extract_protocol: Total RNA was isolated using the Agilent Total RNA Isolation Mini Kit according to the manufacturer’s protocol. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA Integrity Numbers (RIN) ranged from 9.8 to 10.0.

treatment_protocol: HKc/DR cells were transfected with pcDNA3.1 or pcDNA3.1-Six1 using TransFast (Promega, Madison, WI) and stable transfectants were selected in the presence of 50 µg/ml Zeocin (Invitrogen, Carlsbad, CA).


title: Six1-transfected HKc/DR - Replicate 4


title: tubule_CDDP_10mg/kg_3

source_name: proximal tubules

value: proximal tubules


title: Six1-transfected HKc/DR - Replicate 2


title: H9 rep2


title: LC26_before

value: 60 years


title: H9 rep1


title: JS22_before


title: tubule_CDDP_10mg/kg_2


title: RT1_before


title: Six1-transfected HKc/DR - Replicate 3


title: Control-transfected HKc/DR - Replicate 3

source_name: Control-transfected HKc/DR


title: GS25_after


title: LD21_after


title: LB36_after

value: 66 years


title: Control-transfected HKc/DR - Replicate 4


title: Control-transfected HKc/DR - Replicate 2


title: Control-transfected HKc/DR - Replicate 1


title: tubule_CDDP_10mg/kg_1


title: tubule_CDDP_2mg/kg_3


title: Heart from naïve mice on 7 days post infection_3

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

institute: Kindai University Faculty of Medicine

hyb_protocol: Labeled-cRNA was hybridized with Affymetrix Mouse Gene 1.0 ST Arrays using the GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: We used the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were normalized by Robust Multi-array Average (RMA), using Expression Console (Affymetrix) and applied for bioinformatics analyses using R version 2.15.1.

source_name: Heart_naïve mice_7 dpi

label_protocol: RNA samples were processed according to the instructions of Ambion WT Expression Kit (Life Tecnologies Corporation) and the Affymetrix WT Terminal Labeling Kit (Affymetrix).

growth_protocol: We purchased male C3H/HeN mice (4 week-old)

extract_protocol: We used RNeasy Mini Kit (Qiagen) for RNA isolation.

treatment_protocol: Mice (5 week-old) were infected with Theiler's murine encephalomyelitis virus intraperitoneally and hearvested their hearts on 4, 7, 60 days post infection (n=5).

tag: age (at the timeof infection)

value: 5 weeks

tag: infected with

value: none (naïve control)

tag: time point

value: 7 days post infection

value: heart


title: Heart from naïve mice on 7 days post infection_1


title: LB36_before


title: Heart from naïve mice on 7 days post infection_4


title: Heart from naïve mice on 7 days post infection_5


title: GS25_before


title: tubule_CDDP_2mg/kg_1


title: Heart from TMEV-infected mice on 7 days post infection_3

source_name: Heart_TMEV-infected mice_7 dpi

value: Theiler's murine encephalomyelitis virus (TMEV)


title: tubule_ctrl_3

value: Wistar/ST


title: LD21_before

source_name: muscle biopsy


title: Heart from TMEV-infected mice on 7 days post infection_4


title: JW34_after

value: 59 years


title: tubule_CDDP_2mg/kg_2

value: 8 weeks old


title: Heart from TMEV-infected mice on 7 days post infection_5


title: tubule_ctrl_1

value: vehicle


title: tubule_ctrl_2

value: control


title: Heart from TMEV-infected mice on 7 days post infection_2


title: Heart from naïve mice on 7 days post infection_2


title: HE24_after

value: 62 years


title: Heart from TMEV-infected mice on 7 days post infection_1


title: Heart from naïve mice on 4 days post infection_5

source_name: Heart_naïve mice_4 dpi

value: 4 days post infection


title: Heart from naïve mice on 4 days post infection_4

value: male


title: npr1-1 water, biological replicate 2

city: Lucknow

first: Samir

last: Sawant

state: U.P, India

address: Rana Pratap Marg

department: Centre of Plant Molecular Biology

country: India

institute: National Botanical Research Institute

description: Two week old npr1-1 seedlings, water treated

hyb_protocol: According to affymatrix gene chip instruction manual using Fluidisc station 450.

scan_protocol: GeneChips were scanned using Affymatrix gene chip scanner.

data_processing:
affymetrix-algorithm-name = rma
program-name = Expression Console

organism: Arabidopsis thaliana

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

growth_protocol: Seed sterilization and plant growth conditions were followed as reported earlier (Hardtke and Deng, 2000) for both Arabidopsis thaliana Col-0 and npr1-1 mutant. All seeds were grown in vitro in MS medium by keeping them on a mesh at 4°C for 2 days for stratification before placing them in the growth chamber.  A. thaliana plants were grown under controlled environmental conditions (22±1ºC, 120 mol m-2 sec-1, 16h light/8h dark cycle).

extract_protocol: Total RNA was isolated from complete seedlings using Sigma Spectrum® Plant total RNA  kit (STRN 250)

treatment_protocol: After two weeks of growth, the medium was exchanged with either water or 2mM SA and 24h incubation was given in light at 22±2ºC.

value: Two weeks old

value: npr1-1 mutant

value: complete seedling


title: JW34_before

value: Caucasian


title: Col-0 SA, biological replicate 2

description: Two week old col-0 seedlings, SA treated

value: salicylic acid


title: npr1-1 SA, biological replicate 2

description: Two week old npr1-1 seedlings, SA treated


title: RP12_after

value: 57 years


title: B6_F3

source_name: anti-GBM resistant strain

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.

value: Mouse

value: 2 months

value: Kidney cortex


title: RP12_before


title: Heart from naïve mice on 4 days post infection_1

value: 5 weeks

value: none (naïve control)

value: heart


title: npr1-1 SA, biological replicate 1

source_name: Two week old npr1-1 seedlings, SA treated


title: npr1-1 water, biological replicate 1

description: Two week old npr1-1seedlings, water treated


title: B6_F2


title: Col-0 SA, biological replicate 1

source_name: Two week old col-0 seedlings, SA treated


title: B6_F1


title: Heart from naïve mice on 4 days post infection_2


title: HE24_before


title: NZW_F3

source_name: anti-GBM sensitive strain

value: NZW


title: Heart from naïve mice on 4 days post infection_3


title: Heart from TMEV-infected mice on 4 days post infection_5

source_name: Heart_TMEV-infected mice_4 dpi

value: Theiler's murine encephalomyelitis virus (TMEV)


title: Col-0 water, biological replicate 1

description: Two week old col-0 seedlings, water treated

value: control


title: Heart from TMEV-infected mice on 4 days post infection_2

value: 4 days post infection


title: GL23_after

value: male

value: 59 years


title: NZW_F1


title: Col-0 water, biological replicate 2

source_name: Two week old col-0 seedlings, water treated

value: Two weeks old


title: GL23_before


title: Heart from TMEV-infected mice on 4 days post infection_1


title: RJ28_after

value: 63 years


title: Heart from naïve mice on 60 days post infection_5

source_name: Heart_naïve mice_60 dpi

value: 60 days post infection


title: Specific pathogen free, biological rep2

city: Charlottesville

first: Yong

last: Huang

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: Affymerix protocol

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

data_processing: The data were analyzed with R Bioconductor affy package using Robust Multi-array Average (RMA).

source_name: Specific pathogen free

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

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

treatment_protocol: germ-free, conventionalized or specific pathogen free mice

value: wild type

tag: sample group

value: raised under specific pathogen-free condition

value: liver


title: NZW_F2

hyb_protocol: Standard Illumina hybridization protocol

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

value: Mouse

value: 2 months


title: Specific pathogen free, biological rep1