title: scas_0.8MKCl-40

city: Madison

first: Sushmita

last: Roy

state: WI

address: 330 N. Orchard St.

institute: Wisconsin Institute for Discovery

hyb_protocol: Standard Agilent protocols for Agilent 8x15K and 4x44K Oligo Microarrays

scan_protocol: Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization. Reported expression values for each gene are median log2 ratios across all probes

organism: Naumovozyma castellii

label_protocol: Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.

growth_protocol: All species were grown in the following rich medium chosen to minimize cross-species variation in growth (termed BMW): yeast extract (1.5%), peptone (1%), dextrose (2%), SC amino acid mix (Sunrise Science) 2 g/L, adenine 100 mg/L, tryptophan 100 mg/L, uracil 100 mg/L (Thompson D.A., Roy S., et al., 2012). For each strain, cells were plated onto BMW plates from frozen glycerol stocks. After 2 days, cells were taken from plates and re-suspended into liquid BMW and grown overnight.  Approximately 100-1500ul quantities (depending on the species growth rate and timing constraints for the day’s experiments) of the overnight cultures were used to inoculate pre-warmed, 350 ml BMW cultures in 2L Erlenmeyer flasks in New Brunswick Scientific water bath model C76 shakers. All strains were grown at 180 rpm at 30 °C except for S. castellii, which was grown at 25 °C

extract_protocol: Qiagen Yeast RNA extraction

treatment_protocol: Osmotic Stress: Cultures were grown to mid-log densities (between 5x10^7 and 1x10^8 cells/mL) at 30C and treated with KCl to a final concentration of 0.2M, 0.4M, or 0.8M. Samples were harvested at different time intervals (10, 20, 40, 80 minutes after treatment).  After growth, 150ml of each culture was transferred to each of 100ml BMW (CTRL - defined in the Growth protocol) and 100ml BMW+KCl (EXP).  Both CTRL and EXP media were pre-warmed for 40-60 minutes in the shaker prior to the experiment. EXP media was either BMW + 0.5M KCl, 1M KCl, or 2M KCl, yielding a final concentration of 0.2M KCl, 0.4M KCl, and 0.8M KCl, respectively, upon addition of the culture. In each case, CTRL media was added first, followed by the EXP media, whereupon the shaker was immediately activated to 180 rpm and the timer started simultaneously. Samples (20ml) were collected from the CTRL media + culture immediately upon activation of the shaker (T=0), then at T=10, 20, 40, and 80 minutes from the EXP media + culture.

tag: phase

value: EARLY MID-LOG (OD=0.4)


title: scas_0.4MKCl-40-2

status: Public on Jul 01 2017

type: RNA

country: USA

molecule: total RNA


title: scas_0.8MKCl-80-2


title: Braf mutant mum2c

city: San Francisco

first: Xu

last: Chen

state: CA

address: 1450 3rd street, HD200

department: Dermatology

institute: UCSF

description: Gene expression data from tissue culture cells

hyb_protocol: The labeled cDNA was hybridized to human Transcriptome 2.0 microarrays from Affymetrix according to manufacture’s standard protocol.

scan_protocol: The signal intensity fluorescent images produced during affymetrix GeneChip hybridizations were read using the Affymetrix Model 3000 Scanner and converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).

data_processing: The array data were normalized at gene level with standard RMA method by using Affymetrix expression console software and analyzed by using Affymetrix Transcriptome Analysis Console (TAC) software.

label: biotin

organism: Homo sapiens

source_name: tissue culture cell line

label_protocol: The GeneChip WT PLUS Reagent kit from Affymetrix was used for amplification, fragmentation and biotin-labeling.

growth_protocol: Melanoma cell lines were maintained in RPMI 1640 with 10% FBS.

extract_protocol: Extraction of total RNA was performed using PureLink RNA mini kit from Life technologies according to the manufacturer's instructions.

tag: genotype

value: Braf mutant


title: GNAQ mutant omm1.3

value: GNAQ mutant


title: scas_0.8MKCl-20-2


title: embryos wild-type 25°C 2-3h common reference rep1

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

hyb_protocol: Hybridization was performed in buffer consisting of 1M NaCl, 0.5% SLS, 50mM MES pH 6.5, 33% formamide at 42°C.  Slides were washed once in 6X SSPE and 0.005% SLS, then once for 5 min in 0.06X SSPE.

scan_protocol: Arrays were scanned using an Agilent scanner.

data_processing: Array images were quantified with Imagene software and normalized by the lowess method with R software.  To calculate the log(2)ratio for the common reference experiments, the wild-type log(2)ratio was subtracted from the pum mutant log(2)ratio.

organism: Drosophila melanogaster

source_name: [common reference] oocytes wild-type stage 14

label_protocol: cDNA from total RNA, with incorporated AA-dUTP, was generated by random priming according to the protocol of Kapranov et al (2007) using Superscript II (Invitrogen) and was then labelled with Cy3 and Cy5 dyes (GE Healthcare).  Labelled cDNA was purified on Qiagen PCR purification columns.

growth_protocol: All fly lines were maintained at 25C.

extract_protocol: Total embryonic RNA was extracted using Trizol (Invitrogen), followed by purification on Rneasy columns (Qiagen).

treatment_protocol: pumET7/pumMsc embryos and corresponding wild-type controls were collected on apple juice agar plates for 1 hour at 25°C and allowed to develop to 1-2h, 2-3h, 3-4h or 4-5h after egg laying (AEL) at 25°C.  pum13/pumMsc embryos and corresponding wild-type controls were collected on apple juice agar plates for 1 hour at 25°C, then transferred to 18°C and allowed to develop to 2-3h, 5-6h, 8-9h or 11-12h AEL.

tag: developmental stage

value: oocyte

tag: genotype/variation

value: wild-type

tag: time point

value: stage 14

source_name: embryos wild-type 25°C 2-3h

value: embryo

tag: temperature


title: GNA11 mutant omm-gn11

value: GNA11 mutant


title: GNA11 mutant upmd-1


title: embryos wild-type 18°C 2-3h vs pum13/pumMsc 18°C 2-3h direct comparison

description:
Raw data file: 20080610_251987110006A_S01.datatable.txt
Cy3: wild-type 18°C 2-3h
Cy5: pum13/pumMsc 18°C 2-3h
Raw data file: 20080610_251987110006B_S01.datatable.txt
Cy3: pum13/pumMsc 18°C 2-3h
Cy5: wild-type 18°C 2-3h

source_name: embryos pum13/pumMsc 18°C 2-3h

source_name: embryos wild-type 18°C 2-3h


title: GNAQ mutant 92-1


title: GNAQ mutant mel202


title: scas_0.8MKCl-10-2


title: Nras mutant sk-mel-2

value: Nras mutant


title: scas_0.4MKCl-40-1


title: scas_0.4MKCl-80-2


title: scas_0.8MKCl-0-2


title: scas_0.4MKCl-0


title: scas_0.8MKCl-10-1


title: scas_0.8MKCl-0-1


title: scas_0.4MKCl-Pi-20


title: scas_0.2MKCl-80


title: scas_0.8MKCl-80-1


title: scas_0.4MKCl-10-2


title: scas_0.4MKCl-10-1


title: scas_0.4MKCl-10-3


title: scas_0.4MKCl-80-1


title: scas_0.2MKCl-0


title: scas_0.4MKCl-20


title: scas_0.2MKCl-10


title: scas_0.2MKCl-20


title: scas_0.8MKCl-20-1


title: scas_0.2MKCl-40


title: ECC1 MTDH KO with ES1

city: Iowa city

first: Xiangbing

last: Meng

state: IA

address: 375 Newton Road

department: OB&GYN

institute: University of Iowa

description: replicate 1

hyb_protocol: RNA sample preparation for hybridization and the subsequent hybridization to the Illumina beadchips were performed at the University of Iowa IIHG Genomics Division using the manufacturer’s recommended protocols.  Briefly, 100 nanograms total RNA was converted to amplified biotin-aRNA using the Epicentre TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Illumina, Inc., San Diego, CA, Cat. #TAN07924). The amplified Biotin-aRNA product was purified through a QIAGEN RNeasy MinElute  Cleanup column (QIAGEN Cat #74204) according to modifications from Epicentre.  750ng of this product were mixed with Illumina hybridization buffer, placed onto Illumina-Human H12 v4 BeadChips (Part No. BD-103-0204), and incubated at 58º C for 17h, with rocking, in an Illumina Hybridization Oven.  Following hybridization, the arrays were washed, blocked, then stained with streptavidin-Cy3 (Amersham/GE Healthcare, Piscataway, NJ) according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol.

scan_protocol: Beadchips were scanned with the Illumina iScan System (ID #N0534) and data were collected using the GenomeStudio software v2011.1.

data_processing: Experiments were performed in triplicate and were compared in a factorial design using an one-way analysis of variance (ANOVA). Only gene expression changes with P<0.001 were considered statistically significant

label: Biotin

source_name: ECC1 MTDH KO with ES1

growth_protocol: Human endometrial cancer cell lines ECC1 and ECC1 MTDH KO were cultured in RPMI1640 medium containing 10% fetal bovine serum and 1% penicillin/streptomycin (all from Gibco BRL, Carlsbad, CA) at 37oC in a humidified at mosphere of 5% CO2.

extract_protocol: Total RNA was isolated from cell using the Qiagen RNeasy Mini Kit (QIAGEN),

treatment_protocol: ECC1 cells and ECC1 MTDH KO cells were cultured in RPMI1640 medium containing 5% charcoal stripped fetal bovine serum and 1% penicillin/streptomycin 24 hours before estradiol treatment, then cells were treated with 10nM estradiol (final concentration) for 24 hours.

tag: cell line


title: ECC1 MTDH KO with ES2

description: replicate 2

source_name: ECC1 MTDH KO with ES2

label_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol


title: ECC1 with ES2

description: replicate 2

source_name: ECC1 with ES2


title: ECC1 MTDH KO no ES3

description: replicate 3

source_name: ECC1 MTDH KO no ES3


title: ECC1 MTDH KO no ES2

description: replicate 2

source_name: ECC1 MTDH KO no ES2


title: ECC1 MTDH KO with ES3

description: replicate 3

source_name: ECC1 MTDH KO with ES3


title: ECC1 no ES3

description: replicate 3

source_name: ECC1 no ES3


title: ECC1 with ES1

description: replicate 1

source_name: ECC1 with ES1


title: ECC1 with ES3

description: replicate 3

source_name: ECC1 with ES3


title: ECC1 no ES2

description: replicate 2

source_name: ECC1 no ES2


title: ECC1 MTDH KO no ES1

description: replicate 1

source_name: ECC1 MTDH KO no ES1


title: ECC1 no ES1

description: replicate 1

source_name: ECC1 no ES1


title: Hepa1-6 basal 1h No1

city: Freiburg

first: Clemens

last: Kreutz

address: Habsburger Str. 46

country: Germany

institute: Freiburg University

hyb_protocol: High-throughput quantification of the gene expression induced by TGFβ was performed using Affymetrix Mouse genome 430 2.0 microarrays according to the manufacturer’s instructions

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: For data processing the R statistical computing environment (R Core Team, 2014) was used and the robust multiarray average (RMA) algorithm (Irizarry et al., 2003) was applied as implemented in the simpleaffy package (Wilson and Miller, 2005).

organism: Mus musculus

source_name: Hepa1-6 epithelial liver cell line

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

growth_protocol: The mouse hepatoma cell line Hepa1-6 (ATCC CRL-1830) was cultivatred in Dulbecco's modified Eagle's Medium (DMEM, Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS, Life Technologies), 1% 100x penicillin/streptomycin (Gibco) and 1% 200 mM glutamine (Gibco). 24 hours before the experiment, 1.2e6 cells were seeded. 4 hours before the experiment, the different cell types were washed three times with PBS and kept in growth factor depleted medium supplemented with 1% penicillin/streptomycin (Gibco) and 1% glutamine (Gibco).

extract_protocol: RNA was extracted using the RNeasy Mini Plus Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: 2e6 Hepa1-6 cells were stimulated with 1 ng/ml of TGFβ1 (R&D Systems) for 0, 1, 3, 6 and 10 hours in biological duplicates. As controls, the same time points were evaluated in duplicates without TGFβ treatment.

tag: strain

tag: tissue

value: liver

tag: cell type

value: hepatoma cell line


title: Hepa1-6 TGFbeta treated 10h No1


title: Hepa1-6 basal 10h No2


title: Hepa1-6 basal 6h No2


title: Hepa1-6 TGFbeta treated 6h No1


title: Hepa1-6 TGFbeta treated 6h No2


title: Hepa1-6 TGFbeta treated 3h No1


title: Hepa1-6 TGFbeta treated 1h No2


title: Hepa1-6 basal 10h No1


title: Hepa1-6 basal 3h No1


title: Hepa1-6 basal 0h No1

description: treated 0h is equivalent to untreated 0h


title: Hepa1-6 TGFbeta treated 3h No2


title: Hepa1-6 basal 1h No2


title: Hepa1-6 TGFbeta treated 1h No1


title: Hepa1-6 basal 0h No2


title: Hepa1-6 basal 3h No2


title: Hepa1-6 basal 6h No1


title: Hepa1-6 TGFbeta treated 10h No2


title: scer_0.8MKCl-20

organism: Saccharomyces cerevisiae


title: Hepa1-6 TGFbeta treated 0h No2


title: scer_0.8MKCl-0


title: scer_0.4MKCl-80


title: scer_0.4MKCl-40


title: scer_0.8MKCl-10


title: Hepa1-6 TGFbeta treated 0h No1


title: scer_0.2MKCl-80


title: scer_0.8MKCl-80


title: scer_0.8MKCl-40


title: scer_0.4MKCl-10


title: scer_0.4MKCl-0


title: Si Tyrp1 #2 sample N°27

city: Rennes

first: Nicolas

last: Mouchet

state: Bretagne

address: 2 Av du Professeur Leon Bernard

department: Institut genetique et developpement de Rennes

country: France

institute: CNRS UMR6290

description: 501 Mel transfected with Si Tyrp1 #2

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray 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 DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Using Bioconductor, data were background corrected (normexp, offset=50). A normalization between arrays was done (method= quantile) and data were log2 transformed. Batch effect removal was done using sva package.

source_name: 501Mel_Si Tyrp1 #2 sample N°27

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 501Mel cells were grown in humidified air (37°C, 10% CO2), and in RPMI-1640 medium (Gibco BRL, Invitrogen, Paisley, UK) supplemented with 10% Fetal Bovine Serum (PAA cell culture company, Pasching, Austria) and 1% Penicillin-Streptomycin antibiotics (Gibco BRL, Invitrogen, Paisley, UK).  Cells were mycoplasm free according to the MycoAlert reagent (lonza).

extract_protocol: RNA extraction was performed using the Nucleospin® RNA kit following manufacturer's recommendations (Macherey Nagel). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: siRNA were transfected in 1.5 10(exp6) 501Mel cells during 6h30 using lipofectamine reagent (Lifetechnologies) diluted in optiMEM (25µL/dish of 100mm)(Gibco BRL) to reached a final concentration of 50nM of siRNA. Next cells were cultivated as described below. Cells were collected 3 days after the transfection by trypsination and centrifugation.

tag: replicate type

value: Si Typ1 #2 Biological replicate

tag: batch number

tag: sirna

value: Si Tyrp1 #2


title: scer_0.4MKCl-20


title: scer_0.2MKCl-10


title: Si Tyrp1 #2 sample N°7

description: 501 Mel transfected with Si Tyrp1 #2

source_name: 501Mel_Si Tyrp1 #2 sample N°7


title: scer_0.2MKCl-0


title: Si Tyrp1 #2 sample N°27 technical replicate

description: 501 Mel transfected with Si Tyrp1 #2

value: Si Typ1 #2 technical replicate


title: scer_0.2MKCl-40


title: scer_0.2MKCl-20


title: calb_0.8MKCl-40

organism: Candida albicans


title: calb_0.8MKCl-80


title: Si Tyrp1 #3 sample N°6 technical replicate

description: 501 Mel transfected with Si Tyrp1 #3

source_name: 501Mel_Si Tyrp1 #3 sample N°6

value: Si Typ1 #3 Technical replicate

value: Si Tyrp1 #3


title: Si Tyrp1 #1 sample N°4

description: 501 Mel transfected with Si Tyrp1 #1

source_name: 501Mel_Si Tyrp1 #1 sample N°4

value: Si Typ1 #1 biological replicate

value: Si Tyrp1 #1


title: Si Tyrp1 #3 sample N°6

description: 501 Mel transfected with Si Tyrp1 #3

value: Si Typ1 #3 Biological replicate


title: Si Tyrp1 #3 sample N°26 technical replicate

description: 501 Mel transfected with Si Tyrp1 #3

source_name: 501Mel_Si Tyrp1 #3 sample N°26


title: calb_0.8MKCl-10

value: EARLY MID-LOG (OD=0.4)


title: Si Tyrp1 #2 sample N°7 technical replicate

description: 501 Mel transfected with Si Tyrp1 #2


title: calb_0.8MKCl-0


title: Non targeting Si n°1 sample N°1

description: 501 Mel transfected with non targeting Si Tyrp1 #1

source_name: 501Mel_Non targeting Si n°1 sample N°1

value: NT1 biological replicate


title: Si Tyrp1 #3 sample N°16

description: 501 Mel transfected with Si Tyrp1 #3

source_name: 501Mel_Si Tyrp1 #3 sample N°16


title: calb_0.4MKCl-80


title: Si Tyrp1 #1 sample N°24

description: 501 Mel transfected with Si Tyrp1 #1

source_name: 501Mel_Si Tyrp1 #1 sample N°24


title: calb_0.4MKCl-40


title: calb_0.4MKCl-20-2


title: Non targeting Si n°2 sample N°2

description: 501 Mel transfected with non targeting Si Tyrp1 #2

source_name: 501Mel_Non targeting Si n°2 sample N°2

value: NT2 biological replicate


title: Non targeting Si n°1 sample N°11

source_name: 501Mel_Non targeting Si n°1 sample N°11


title: Si Tyrp1 #3 sample N°26

description: 501 Mel transfected with Si Tyrp1 #3


title: Non targeting Si n°1 sample N°21

source_name: 501Mel_Non targeting Si n°1 sample N°21


title: Non targeting Si n°2 sample N°22

source_name: 501Mel_Non targeting Si n°2 sample N°22


title: Si Tyrp1 #1 sample N°34b

description: 501 Mel transfected with Si Tyrp1 #1


title: Non targeting Si n°2 sample N°32

source_name: 501Mel_Non targeting Si n°2 sample N°32


title: calb_0.8MKCl-20


title: calb_0.4MKCl-0


title: calb_0.4MKCl-10


title: calb_0.2MKCl-80


title: calb_0.2MKCl-40


title: calb_0.2MKCl-20


title: calb_0.4MKCl-20-1


title: calb_0.2MKCl-10


title: klac_0.8MKCl-20

organism: Kluyveromyces lactis


title: calb_0.2MKCl-0


title: klac_0.8MKCl-80


title: klac_0.4MKCl-20-2


title: klac_0.8MKCl-40


title: klac_0.4MKCl-10


title: klac_0.8MKCl-10


title: klac_0.4MKCl-80


title: klac_0.8MKCl-0


title: klac_0.4MKCl-20-1


title: klac_0.4MKCl-0


title: klac_0.4MKCl-40


title: cgla_0.4MKCl-20-2

organism: Nakaseomyces glabratus


title: klac_0.2MKCl-80


title: cgla_0.8MKCl-80


title: klac_0.2MKCl-40


title: klac_0.2MKCl-0


title: klac_0.2MKCl-10


title: klac_0.2MKCl-20


title: cgla_0.8MKCl-40


title: cgla_0.8MKCl-20


title: cgla_0.8MKCl-10


title: cgla_0.4MKCl-20-1


title: cgla_0.4MKCl-80


title: cgla_0.2MKCl-80


title: RM1-MXRA7/RM1-VE, repeat 2

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

country: China

institute: Xi'an Jiaotong-Liverpool University

description: RM1-VE cells

hyb_protocol: Manufacture's protocol.

scan_protocol: Manufacture's protocol with Agilent Scanner G2505C (Agilent Technologies)

data_processing: Scanned images were analyzed with Feature Extraction software (version10.7.1.1, Agilent Technologies), and the raw data was analyzed primarily with Genespring (v12.5, Agilent).

source_name: RM1-MXRA7 cells

label_protocol: RM1-MXRA7 and RM1-VE cells-derived cRNA were labeled with Cyanine-3 (Cy3) and Cy5 respectively.

growth_protocol: All cells were maintained in DMEM supplemented with 10% fetal calf serum (FBS) and 400 μg/mL G418.

extract_protocol: TRIzol reagent lysing, isopropanol precipitation, NucleoSpin RNA clean-up.

treatment_protocol: Cells were split and allowed to grow into exponential phase, usually in two days.

tag: cell typ

value: prostate cancer cell line

tag: day

source_name: RM1-VE cells


title: cgla_0.2MKCl-10


title: cgla_0.8MKCl-0


title: cgla_0.4MKCl-10


title: cgla_0.2MKCl-40


title: RM1-MXRA7/RM1-VE, repeat 3

description: RM1-VE cells


title: RM1-MXRA7/RM1-VE, repeat 1

description: RM1-VE cells


title: 1e-9_Rep5

city: RTP

first: Salil

middle: N

last: Pendse

state: NC

address: 6 Davis Drive

institute: Scitovation

description: SAMPLE 48

hyb_protocol: Samples were loaded onto a HT HG-U133+ PM GeneChip™ array plate and run on the GeneTitan® according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Analysis of gene expression data was performed using Partek software (Partek Inc., St. Louis, MO) utlising GC-RMA normalisation. A 1-way ANOVA with interactions was performed to compare gene expression between the treated and control cells. Probability values were adjusted for multiple comparisons using a false discovery rate of 5%

label_protocol: RNA samples were prepared for microarray hybridization using the GeneAtlas™ 3’ IVT Express Kit according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA).  Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA. The cDNA was then converted into a double-stranded DNA template for transcription. Amplified cRNA (aRNA) was transcribed in vitro, with incorporation of a biotin-congugated nucleotide.  The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate, and samples were fragmented to prepare the biotin-labeled aRNA samples for hybridization onto Affymetrix® GeneChip™

growth_protocol: Ishikawa cells were maintained in phenol red-free 1:1 DMEM/F12 medium supplemented with 1% L-Glutamine (100X), 1% penicillin/streptomycin (10,000 U/ml penicillin, 10,000 µg/ml streptomycin), 1% HEPES (1M), 1% non-essential amino acids (100X), 0.1% ITS Premix (insulin, human transferrin, selenium supplement, 10X), and 10% FBS. Prior to gene analysis Ishikawa cells were passaged into 150 mm cell culture plates at a density of 2x10^6 cells per plate in 10% CSS supplemented media and allowed to grow for 72 hours. Cells were then plated according to assay format requirements in 5% CSS supplemented media for 48 hours prior to treatment

extract_protocol: total RNA was collected from the treated cells using the Qiaxtractor and the Qiagen VX reagent pack according to the manufacturer’s protocol (Qiagen, Valencia, CA).  A DNase 1 incubation was performed on all samples to remove any possible contamination of the RNA samples with cellular DNA (Qiagen)

treatment_protocol: media was replaced with 5% CSS supplemented media containing various concentrations of EE or ethanol (vehicle control), EtOH concentrations in media were 0.1% v/v.  For the remainder of the experiment, half of the treatment media in each well was replaced daily with fresh 5% CSS media containing appropriate treatment.

value: Ishikawa (ECACC cat#99040201)

tag: tissue origin

value: human uterine epithelial adenocarcinoma cells

tag: treated with

value: ethinyl estradiol for 72hrs

tag: ethinyl estradiol conc.

value: 1e-9 moles (M)


title: cgla_0.2MKCl-20

tag: phase


title: cgla_0.4MKCl-0


title: 1e-9_Rep6

description: SAMPLE 49


title: 1e-9_Rep2

description: SAMPLE 45


title: 1e-9_Rep1

description: SAMPLE 44


title: 1e-9_Rep3

description: SAMPLE 46


title: 1e-9_Rep4

description: SAMPLE 47


title: cgla_0.2MKCl-0


title: cgla_0.4MKCl-40


title: 1e-10_Rep6

description: SAMPLE 43

value: 1e-10 moles (M)


title: 1e-10_Rep1

description: SAMPLE 38


title: 1e-10_Rep2

description: SAMPLE 39


title: 1e-10_Rep3

description: SAMPLE 40


title: 1e-10_Rep5

description: SAMPLE 42


title: 1e-11_Rep6

description: SAMPLE 37

value: 1e-11 moles (M)


title: 1e-11_Rep4

description: SAMPLE 35


title: Leaf_CbZIP6-OE2-4ºC_rep3

city: Hangzhou

first: Lu

state: Zhejiang

address: 9th, South Meiling Road

institute: Tea Research Institute, Chinese Academy of Agricultural Sciences

description: Gene expression in leaves of 30d old seedlings grown under 4 ºC for 4 days

hyb_protocol: 1.65 μg 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 55 μl containing 25× Agilent fragmentation buffer and 10× Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 55 μl of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-021169 Arabidopsis Gene 4×44K Expression array,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 DNA Microarray Scanner (G2505C) using one color scan setting for 4×44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

organism: Arabidopsis thaliana

source_name: leaves, CsbZIP6-OE2, 4 ºC 4d, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg 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: Arabidopsis seedlings were germinated, grown on 1/2 MS for 2 weeks and then transferred to soil. When plants (WT, OE-1, OE-2) were 30 days old, they were transferred and cultivated under different growth temperature.Plants were grown in a growth chamber on a 10 hr light/14 hr dark regime at a light intensity of 100 μmol/m2s with daytime temperatures of 22 ºC and nighttime temperatures of 18ºC.

extract_protocol: Total RNA was extracted from leaf samples using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: Seedlings were germinated, grown on 1/2 MS for 2 weeks and then transferred to soil. Thirty-day-old plants (WT, OE-1, OE-2) were grown at 4 ºC (‘cold’) or normal conditions (‘normal’) for 4 days before the leaves were sampled, snap frozen in liquid nitrogen and stored at -80ºC until RNA isolation.

value: Leaves

tag: age

value: 30 days

tag: genotype


title: Leaf_CbZIP6-OE1-22ºC_rep3

description: Gene expression in leaves of 30d old seedlings grown under 22 ºC for 4 days

source_name: leaves, CsbZIP6-OE1, 22 ºC, replicate 3


title: 1e-10_Rep4

description: SAMPLE 41


title: Leaf_CbZIP6-OE1-4ºC_rep3

source_name: leaves, CsbZIP6-OE1, 4 ºC 4d, replicate 3


title: Leaf_CbZIP6-OE2-4ºC_rep2

source_name: leaves, CsbZIP6-OE2, 4 ºC 4d, replicate 2


title: Leaf_Col-0-4 ºC_rep1

source_name: leaves, Col-0, 4 ºC 4d, replicate 1

value: wild type (col-0)


title: Leaf_CbZIP6-OE1-4ºC_rep2

source_name: leaves, CsbZIP6-OE1, 4 ºC 4d, replicate 2


title: Leaf_Col-0-4 ºC_rep2

source_name: leaves, Col-0, 4 ºC 4d, replicate 2


title: 1e-11_Rep5

description: SAMPLE 36


title: Leaf_CbZIP6-OE2-4ºC_rep1

source_name: leaves, CsbZIP6-OE2, 4 ºC 4d, replicate 1


title: Leaf_CbZIP6-OE1-22ºC_rep1

source_name: leaves, CsbZIP6-OE1, 22 ºC, replicate 1


title: Leaf_Col-0-4 ºC_rep3

source_name: leaves, Col-0, 4 ºC 4d, replicate 3


title: 1e-11_Rep1

description: SAMPLE 32


title: 3e-12_Rep4

description: SAMPLE 29

value: 3e-12 moles (M)


title: 1e-11_Rep3

description: SAMPLE 34


title: Leaf_CbZIP6-OE1-22ºC_rep2

source_name: leaves, CsbZIP6-OE1, 22 ºC, replicate 2


title: Leaf_Col-0-22 ºC_rep3

source_name: leaves, Col-0, 22 ºC, replicate 3


title: 1e-11_Rep2

description: SAMPLE 33


title: 3e-12_Rep5

description: SAMPLE 30


title: Leaf_CbZIP6-OE1-4ºC_rep1

source_name: leaves, CsbZIP6-OE1, 4 ºC 4d, replicate 1


title: Leaf_CbZIP6-OE2-22ºC_rep2

source_name: leaves, CsbZIP6-OE2, 22 ºC, replicate 2


title: 3e-12_Rep6

description: SAMPLE 31


title: Leaf_CbZIP6-OE2-22ºC_rep1

source_name: leaves, CsbZIP6-OE2, 22 ºC, replicate 1


title: Leaf_Col-0-22 ºC_rep2

source_name: leaves, Col-0, 22 ºC, replicate 2


title: 3e-12_Rep2

description: SAMPLE 27


title: 3e-12_Rep3

description: SAMPLE 28


title: Patient 02 PROG dabrafenib

city: Macquarie University

first: Helen

last: Rizos

address: 2 Technology Place

country: Australia

institute: Macquarie University

description: total RNA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Gene expression data were normalized using the Lumi R
Raw data was obtained via the GenomeStudio; data have been normalized using the RSN method from R-package lumi.

source_name: Melanoma biospy

label_protocol: Complementary RNA amplification and labelling with biotin were performed using the Illumina. TotalPrep RNA amplification kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions starting with 250 ng total RNA.

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: melanoma


title: 3e-12_Rep1

description: SAMPLE 26


title: Patient 04 PRE dabrafenib

description: total RNA


title: Patient 11 PRE vemurafenib

description: total RNA


title: 1e-12_Rep6

description: SAMPLE 25

value: 1e-12 moles (M)


title: 1e-12_Rep4

description: SAMPLE 23


title: Patient 07 PROG dabrafenib

description: total RNA


title: Patient 04 EDT dabrafenib

description: total RNA


title: Patient 02 PRE dabrafenib

description: total RNA


title: Patient 04 PROG dabrafenib

description: total RNA


title: Patient 16 PRE dabtrafenib+trametinib

description: total RNA


title: Patient 17 EDT dabtrafenib+trametinib

description: total RNA


title: 1e-12_Rep2

description: SAMPLE 21


title: 3e-13_Rep7

description: SAMPLE 19

value: 3e-13 moles (M)


title: Patient 16 EDT dabtrafenib+trametinib

description: total RNA


title: Patient 17 PRE dabtrafenib+trametinib

description: total RNA


title: Patient 07 EDT dabrafenib

description: total RNA


title: 1e-12_Rep3

description: SAMPLE 22


title: Patient 03 PRE dabrafenib

description: total RNA


title: 1e-12_Rep1

description: SAMPLE 20


title: Patient 07 PRE dabrafenib

description: total RNA


title: Patient 01 PRE dabrafenib

description: total RNA


title: Leaf_Col-0-22 ºC_rep1

source_name: leaves, Col-0, 22 ºC, replicate 1


title: 1e-12_Rep5

description: SAMPLE 24


title: Patient 01 EDT dabrafenib

description: total RNA


title: Patient 09 PRE dabrafenib

description: total RNA


title: 3e-13_Rep6

description: SAMPLE 18


title: Patient 03 PROG dabrafenib

description: total RNA


title: Patient 12 EDT vemurafenib

description: total RNA


title: Patient 11 PROG vemurafenib

description: total RNA


title: miR-17 methylated [QH62359]

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: miR-17 methylated oligonuceotides  transfected cells

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: colorectal cancer cell line

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: DICER exon 5-disrupted RKO cells are were maintained in Roswell Park Memorial Institute (RPMI) 1640 Medium supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific) and grown at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from cells by TRIzol (Invitrogen) according to manufacturer’s instructions.

treatment_protocol: Double stranded RNA oligonucleotides are transfected to cells with lipofectamine 3000 (Invitrogen) according to the manufacturer’s protocols. RNA was extracted 48hours after transfection.

value: DICER exon 5-disrupted RKO cells


title: 3e-13_Rep5

description: SAMPLE 17


title: Patient 12 PRE vemurafenib

description: total RNA


title: miR-17 native type [QH62358]

description: miR-17 native type oligonuceotides  transfected cells


title: 3e-13_Rep4

description: SAMPLE 16


title: 3e-13_Rep2

description: SAMPLE 14


title: let7a native type [QH62356]

description: let7a native type oligonuceotides  transfected cells


title: let7a methylated [QH62357]

description: let7a methylated oligonuceotides  transfected cells


title: Patient 06 PROG dabrafenib

description: total RNA


title: Patient 09 PROG dabrafenib

description: total RNA


title: Patient 13 EDT dabtrafenib+trametinib

description: total RNA


title: Patient 06 PRE dabrafenib

description: total RNA


title: Patient 13 PRE dabtrafenib+trametinib

description: total RNA


title: miR-21 methylated [QH62355]

description: miR-21 methylated oligonuceotides  transfected cells


title: 3e-13_Rep3

description: SAMPLE 15


title: Patient 13 PROG dabtrafenib+trametinib

description: total RNA


title: 3e-13_Rep1

description: SAMPLE 13


title: Patient 08 PROG dabrafenib

description: total RNA


title: Patient 08 PRE  dabrafenib

description: total RNA


title: Patient 15 PROG dabtrafenib+trametinib

description: total RNA


title: 1e-13_Rep5

description: SAMPLE 11

value: 1e-13 moles (M)


title: miR-200c native type [QH62350]

description: miR-200c native type oligonuceotides transfected cells


title: Patient 05 PRE dabrafenib

description: total RNA


title: miR-200c methylated [QH62353]

description: miR-200c methylated oligonuceotides  transfected cells


title: 1e-13_Rep6

description: SAMPLE 12


title: miR-21 native type [QH62354]

description: miR-21 native type oligonuceotides  transfected cells


title: Patient 14 PRE dabtrafenib+trametinib

description: total RNA


title: Patient 05 PROG dabrafenib

description: total RNA


title: Negative control [QH62349]

description: Negative control transfected cells


title: Patient 15 PRE dabtrafenib+trametinib

description: total RNA


title: Patient 10 EDT vemurafenib

description: total RNA


title: Patient 10 PROG vemurafenib

description: total RNA


title: Patient 14 PROG dabtrafenib+trametinib

description: total RNA


title: Patient 10 PRE vemurafenib

description: total RNA


title: 1e-13_Rep2

description: SAMPLE 8


title: 1e-13_Rep3

description: SAMPLE 9


title: 1e-13_Rep4

description: SAMPLE 10


title: U2932 AZD5363 6h r1 (b)

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

hyb_protocol: hybridization was performed with HumanHT-12 v4 Expression Bead Chip kit (Illumina) according to manufacturer's protocol

scan_protocol: scanning was performed according to manufacturer's protocol

data_processing: The preprocessing pipeline was implemented in Mathworks MATLAB(R) and works similar to preprocessing Affymetrix CEL files: Measured gene expressions were imported on raw bead level (cf. supplementary TXT files). All microarrays were preprocessed and normalized together. Their intensity distributions for all measured beads were equalized by quantile normalization. The background mode was fitted and removed and a spot filter was applied to exclude too dim beads (< mean background intensity). Intensities were log2-transformed and aggregated by measured sequence to form beadsets. Beadsets with more than 50% of their beads excluded by the spot filter were also excluded. Further analysis was performed on gene level using median aggregation and manufacturer’s annotations. For genes having multiple beadsets the one with the highest expression (in average over all arrays) was selected.

label_protocol: RNA was transcribed and labeled by Illumina TotalPrep RNA Amplification kit according to manufacturer's protocol

growth_protocol: All cell lines were maintained in RPMI medium with 10% FCS at 37°C with 5% CO2 except of OCI-Ly10 that was cultured in IMDM supplemented with 20% human plasma.

extract_protocol: total RNA was extracted using RNeasy kit (Qiagen) according to manufacturer's protocol

treatment_protocol: The cell lines HBL-1, OCI-Ly10 and U2932 were treated with either AZD8835 (0.25 µM for HBL-1 and U2932; 0.1 µM for OCI-Ly10) or with DMSO. The cell lines K422 and U2932 were treated with either AZD5363 (1 µM) or DMSO.

value: DLBCL cell line U2932

tag: treatment

tag: dose

value: 1 µM

tag: duration in hours

tag: replicate


title: miR-200c m6A modified

description: miR-200c m6A modified oligonucleotide transfected cells

tag: cell line

value: RKO

value: colorectal cancer cell line

value: DICER exon 5-disrupted


title: U2932 AZD5363 24h r1 (b)


title: miR-200c m5C modified

description: miR-200c m5C modified oligonucleotide transfected cells

tag: cell type


title: K422 AZD5363 18h r1 (b)

value: DLBCL cell line K422


title: Control_Rep6

description: SAMPLE 6

value: Ishikawa (ECACC cat#99040201)

value: human uterine epithelial adenocarcinoma cells

value: ethanol (vehicle control) for 72hrs


title: K422 AZD5363 24h r1 (b)


title: K422 AZD5363 12h r1 (b)


title: miR-200c native type

description: miR-200c native type oligonucleotide transfected cells


title: U2932 AZD5363 18h r1 (b)


title: Control_Rep5

description: SAMPLE 5


title: 1e-13_Rep1

description: SAMPLE 7

value: ethinyl estradiol for 72hrs


title: U2932 AZD5363 12h r1 (b)


title: Control_Rep4

description: SAMPLE 4


title: Control_Rep3

description: SAMPLE 3


title: Control_Rep2

description: SAMPLE 2


title: spom_0.4MKCl-20-2

organism: Schizosaccharomyces pombe

value: EARLY MID-LOG (OD=0.4)


title: U2932 DMSO 24h r1 (b)

source_name: U2932 DMSO 24h

value: DMSO

value: control


title: K422 AZD5363 6h r1 (b)


title: U2932 AZD8835 24h r1 (a)


title: K422 DMSO 24h r1 (b)

source_name: K422 DMSO 24h


title: spom_0.8MKCl-40


title: spom_0.8MKCl-80


title: U2932 AZD8835 12h r1 (a)


title: U2932 DMSO 18h r1 (b)

source_name: U2932 DMSO 18h


title: K422 DMSO 12h r1 (b)

source_name: K422 DMSO 12h


title: K422 DMSO 18h r1 (b)

source_name: K422 DMSO 18h


title: K422 DMSO 6h r1 (b)

source_name: K422 DMSO 6h


title: Control_Rep1

description: SAMPLE 1


title: U2932 DMSO 12h r1 (b)

source_name: U2932 DMSO 12h


title: U2932 DMSO 6h r1 (b)

source_name: U2932 DMSO 6h


title: Negative control

description: Negative control oligonucleotide transfected cells


title: spom_0.8MKCl-10


title: spom_0.8MKCl-0


title: spom_0.8MKCl-20


title: U2932 AZD8835 18h r1 (a)


title: spom_0.4MKCl-80


title: Ly10 AZD8835 12h r1 (a)

value: DLBCL cell line Ly10


title: Ly10 AZD8835 24h r1 (a)


title: Ly10 AZD8835 18h r1 (a)


title: U2932 AZD8835 6h r1 (a)


title: spom_0.4MKCl-20-1


title: HBL1 AZD8835 18h r1 (a)

source_name: HBL1 AZD8835 18h

value: DLBCL cell line HBL1


title: HBL1 AZD8835 6h r1 (a)

source_name: HBL1 AZD8835 6h


title: HBL1 AZD8835 24h r1 (a)

source_name: HBL1 AZD8835 24h


title: HBL1 AZD8835 12h r1 (a)

source_name: HBL1 AZD8835 12h


title: U2932 DMSO 18h r1 (a)


title: Ly10 AZD8835 6h r1 (a)


title: spom_0.4MKCl-10


title: U2932 DMSO 24h r1 (a)


title: spom_0.4MKCl-40


title: U2932 DMSO 6h r1 (a)


title: spom_0.4MKCl-0


title: spom_0.2MKCl-80


title: spom_0.2MKCl-40


title: Ly10 DMSO 6h r1 (a)

source_name: Ly10 DMSO 6h


title: Ly10 DMSO 18h r1 (a)

source_name: Ly10 DMSO 18h


title: Ly10 DMSO 24h r1 (a)

source_name: Ly10 DMSO 24h


title: spom_0.2MKCl-20


title: U2932 DMSO 12h r1 (a)


title: HBL1 DMSO 18h r1 (a)

source_name: HBL1 DMSO 18h


title: HBL1 DMSO 12h r1 (a)

source_name: HBL1 DMSO 12h


title: HBL1 DMSO 24h r1 (a)

source_name: HBL1 DMSO 24h


title: spom_0.2MKCl-10


title: Subject 30 WK 2

city: New York

first: Joel

middle: M

last: Correa da Rosa

state: New York

address: 1230 York Avenue

department: CTSA

institute: Rockefeller University

description: Subject 30

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

source_name: Skin Tissue Biopsy

label_protocol: Target AMP-Nano labelling kit for Illumina Expression Beadchip

extract_protocol: RNEasy Mini Kit (Qiagen) was used for RNA extraction

tag: timepoint

value: WK 2

value: ADA

tag: tissue

value: Skin Tissue

tag: pasi


title: Subject 30 WK 1

description: Subject 30

value: WK 1


title: Larvae_TRI_5nM_rep3

city: Singapore

first: Siew Hong

last: Lam

address: #02-01, T-Lab Building, 5A Engineering Drive 1

country: Singapore

institute: National University of Singapore

description: Gene expression after 5 days in 5 nM triamcinolone

hyb_protocol: An equal amount of Cy3-labelled cRNA (1.65 µg) was hybridized to G2519F Agilent Zebrafish Whole Genome Oligo Microarray Ver3.0, 4x44K  at 65 °C for 17 h.  The hybridized microarray slides were then washed according to manufacturer’s protocol.

scan_protocol: Slides were scanned using an Agilent G2565BA scanner (Agilent, CA, USA) at 5-µm resolution with green dye channel and a scan region of 61 mm x 21.6 mm.

data_processing: Signal intensity data were then extracted from the scanned Tiff image (20 bit) by Agilent Feature Extraction software version 10.7. Batch normalization of signal intensity was performed using Agilent GeneSpring software version 7.3.1.

organism: Danio rerio

source_name: larvae, 5dpf, 5nM triamcinolone, replicate 3

label_protocol: For each replicate, 200 ng total RNA was diluted using Agilent One-Color RNA Spike-In Kit, followed by amplification and labelling with the Cy3 using Agilent Low Input Quick Amp Labeling Kit  according to the manufacturer’s protocol. The Cy3 labelled cRNA samples were then purified using RNeasy Mini Kit.

growth_protocol: Embryos of wild-type AB strain zebrafish were collected and maintained at 28 ± 0.5 °C in E3 medium [5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2·2H2O, 0.33 mM MgSO4·7H2O, 0.0001% Methylene blue in Milli-Q water, buffered with 1 normal NaOH to pH 7.1–7.2].

extract_protocol: Total RNA of wild-type larvae was extracted TRIzol® Reagentand treated with DNase I, Amplification Grade 100UN according to respective manufacturer’s protocols. Samples with RNA Integrity Numberabove eight as determined by Agilent 2100 Bioanalyzer were used for further experiments.

treatment_protocol: A total of 35-40 embryos aged 3 h post-fertilisation (hpf) were randomly placed into each well of a 6-well plate containing 4 mL of 50 pM, 500 pM, 5 nM or 50 nM of glucocorticoid in 0.05% (v/v) DMSO at final concentration in E3 medium. The control group contained 0.05% (v/v) DMSO in E3 medium only. All media were renewed every 24 h. At 5 dpf, larvae were collected, snap-frozen in liquid nitrogen and stored at -80 °C until RNA extraction.

value: whole larvae

tag: strain

value: AB strain

tag: genotype/variation

value: wild type

value: 5 days


title: Subject 30 LS

description: Subject 30

value: LS


title: spom_0.2MKCl-0


title: Subject 29 WK 1

description: Subject 29

value: MTX


title: Larvae_TRI_5nM_rep5

source_name: larvae, 5dpf, 5nM triamcinolone, replicate 5


title: Ly10 DMSO 12h r1 (a)

source_name: Ly10 DMSO 12h


title: HBL1 DMSO 6h r1 (a)

source_name: HBL1 DMSO 6h


title: Subject 29 NL

description: Subject 29

value: NL


title: Subject 28 WK 4

description: Subject 28

value: WK 4


title: Larvae_TRI_5nM_rep4

source_name: larvae, 5dpf, 5nM triamcinolone, replicate 4


title: Subject 29 LS

description: Subject 29


title: Subject 29 WK 2

description: Subject 29


title: Subject 30 WK 4

description: Subject 30


title: Subject 30 WK 16

description: Subject 30

value: WK 16


title: Subject 29 WK 4

description: Subject 29


title: Subject 28 WK 16

description: Subject 28


title: Subject 29 WK 16

description: Subject 29


title: Subject 28 WK 2

description: Subject 28


title: Subject 30 NL

description: Subject 30


title: Subject 28 WK 1

description: Subject 28


title: Subject 28 WK 1NL

description: Subject 28

value: WK 1NL


title: Larvae_TRI_5nM_rep1

source_name: larvae, 5dpf, 5nM triamcinolone, replicate 1


title: Subject 28 WK 1LS

description: Subject 28

value: WK 1LS


title: Larvae_TRI_5nM_rep2

source_name: larvae, 5dpf, 5nM triamcinolone, replicate 2


title: Larvae_TRI_50nM_rep5

description: Gene expression after 5 days in 50 nM triamcinolone

source_name: larvae, 5dpf, 50nM triamcinolone, replicate 5


title: Subject 27 WK 4

description: Subject 27


title: Larvae_TRI_50nM_rep3

source_name: larvae, 5dpf, 50nM triamcinolone, replicate 3


title: Larvae_TRI_50nM_rep2

source_name: larvae, 5dpf, 50nM triamcinolone, replicate 2


title: Larvae_TRI_50nM_rep4

source_name: larvae, 5dpf, 50nM triamcinolone, replicate 4


title: Subject 27 WK2

description: Subject 27


title: Subject 27 WK16

description: Subject 27


title: Subject 26 WK 16

description: Subject 26


title: Larvae_TRI_50nM_rep1

source_name: larvae, 5dpf, 50nM triamcinolone, replicate 1


title: Subject 25 WK 16

description: Subject 25


title: Subject 26 WK 2

description: Subject 26


title: Larvae_PRE_5nM_rep3

description: Gene expression after 5 days in 5 nM prednisolone

source_name: larvae, 5dpf, 5nM prednisolone, replicate 3


title: Larvae_PRE_5nM_rep4

source_name: larvae, 5dpf, 5nM prednisolone, replicate 4


title: Subject 26 LS

description: Subject 26


title: Subject 27 LS

description: Subject 27


title: Subject 25 LS

description: Subject 25


title: Subject 26 WK 1

description: Subject 26


title: Subject 24 WK 16

description: Subject 24


title: Subject 25 WK 4

description: Subject 25


title: Subject 25 NL

description: Subject 25


title: Subject 25 WK 2

description: Subject 25


title: Subject 26 WK 4

description: Subject 26


title: Larvae_PRE_5nM_rep5

source_name: larvae, 5dpf, 5nM prednisolone, replicate 5


title: Subject 27 WK 1

description: Subject 27


title: Subject 26 NL

description: Subject 26


title: Subject 27 NL

description: Subject 27


title: Larvae_PRE_5nM_rep1

source_name: larvae, 5dpf, 5nM prednisolone, replicate 1


title: Subject 25 WK 1

description: Subject 25

source_name: Skin Tissue Biopsy


title: Larvae_PRE_5nM_rep2

source_name: larvae, 5dpf, 5nM prednisolone, replicate 2


title: Subject 24 WK 4

description: Subject 24


title: Larvae_PRE_50nM_rep5

description: Gene expression after 5 days in 50 nM prednisolone

source_name: larvae, 5dpf, 50nM prednisolone, replicate 5


title: Subject 24 WK 1

description: Subject 24


title: Subject 24 NL

description: Subject 24


title: Subject 24 WK 2

description: Subject 24


title: Larvae_PRE_50nM_rep4

source_name: larvae, 5dpf, 50nM prednisolone, replicate 4


title: Subject 24 LS

description: Subject 24


title: Subject 23 WK 4

description: Subject 23


title: Subject 23 WK 16

description: Subject 23


title: Larvae_PRE_50nM_rep3

source_name: larvae, 5dpf, 50nM prednisolone, replicate 3


title: Larvae_PRE_50nM_rep2

source_name: larvae, 5dpf, 50nM prednisolone, replicate 2


title: Larvae_PRE_50nM_rep1

source_name: larvae, 5dpf, 50nM prednisolone, replicate 1


title: Subject 23 WK 2

description: Subject 23


title: Subject 22 WK 16

description: Subject 22


title: Subject 23 LS

description: Subject 23


title: Larvae_DEX_5nM_rep4

description: Gene expression after 5 days in 5 nM dexamethasone

source_name: larvae, 5dpf, 5nM dexamethasone, replicate 4


title: Larvae_DEX_5nM_rep3

source_name: larvae, 5dpf, 5nM dexamethasone, replicate 3


title: Subject 23 WK 1

description: Subject 23


title: Larvae_DEX_5nM_rep2

source_name: larvae, 5dpf, 5nM dexamethasone, replicate 2


title: Larvae_DEX_5nM_rep5

source_name: larvae, 5dpf, 5nM dexamethasone, replicate 5


title: Subject 22 WK 2

description: Subject 22


title: Subject 23 NL

description: Subject 23


title: Subject 22 LS

description: Subject 22


title: Subject 22 NL

description: Subject 22


title: Subject 22 WK 4

description: Subject 22


title: Subject 21 WK 16

description: Subject 21


title: Subject 21 WK 4

description: Subject 21


title: Subject 21 WK 2

description: Subject 21


title: Larvae_DEX_50nM_rep5

description: Gene expression after 5 days in 50 nM dexamethasone

source_name: larvae, 5dpf, 50nM dexamethasone, replicate 5


title: Subject 22 WK 1

description: Subject 22


title: Subject 21 LS

description: Subject 21


title: Subject 20 WK 16

description: Subject 20


title: Larvae_DEX_50nM_rep4

source_name: larvae, 5dpf, 50nM dexamethasone, replicate 4


title: Subject 21 WK 1

description: Subject 21


title: Subject 21 NL

description: Subject 21


title: Larvae_DEX_5nM_rep1

source_name: larvae, 5dpf, 5nM dexamethasone, replicate 1


title: Larvae_DEX_50nM_rep3

source_name: larvae, 5dpf, 50nM dexamethasone, replicate 3


title: Larvae_DEX_50nM_rep1

source_name: larvae, 5dpf, 50nM dexamethasone, replicate 1


title: Larvae_DEX_50nM_rep2

source_name: larvae, 5dpf, 50nM dexamethasone, replicate 2


title: Larvae_Control_rep3

description: Gene expression after 5 days in 0.05% DMSO

source_name: larvae, 5dpf, 0.05%DMSO, replicate 3


title: Subject 19 WK 1

description: Subject 19

source_name: Skin Tissue Biopsy


title: Subject 19 WK 4

description: Subject 19


title: Subject 20 WK 1

description: Subject 20


title: Subject 19 NL

description: Subject 19


title: Larvae_Control_rep4

source_name: larvae, 5dpf, 0.05%DMSO, replicate 4


title: Subject 18 WK 1

description: Subject 18


title: Subject 18 WK 4

description: Subject 18


title: Larvae_Control_rep2

source_name: larvae, 5dpf, 0.05%DMSO, replicate 2


title: Subject 18 NL

description: Subject 18


title: Subject 20 WK 4

description: Subject 20


title: Subject 20 WK 2

description: Subject 20


title: Huh7 cells with HBeAg, miRNA biological rep1

city: New Delhi

first: Perumal

last: Vivekanandan

state: Delhi

address: Kusuma School of Biological Sciences, IIT Delhi, Hauz Khas, New Delhi-110016

department: Kusuma School of biological Sciences, IIT Delhi

country: India

institute: Indian Institute of technology Delhi

description: miRNA Expression Data from Huh-7 cells transfected with HBeAg-expression vector

hyb_protocol: Hybridization was done for 16 hours at 48°C and 60 rpm using Affymetrix Hybridization Oven

scan_protocol: The gene chips were scanned using Affymetrix Gene chip scanner 3000 7G.

data_processing: The data was analyzed using GeneSpring software

source_name: Human Huh7 cells transfected with HBeAg-expression vector

label_protocol: Biotinlyated miRNAs were prepared according to Flash Tag Biotin HSR labeling kit

growth_protocol: Huh-7 cells were maintained in DMEM supplemented with 10% FBS, 5000U/ml Penicillin and 5000μg/ml Streptomycin at 37°C with 5% carbon-dioxide.

extract_protocol: Total RNA was isolated using Trizol as per the manufacturer's instructions.

treatment_protocol: Huh-7 cells were transfected with HBeAg-expression vector and total RNA was harvested post 48 hours transfection.

value: human hepatocellular carcinoma cell line

tag: transfected with

value: HBeAg-expression vector


title: Larvae_Control_rep1

source_name: larvae, 5dpf, 0.05%DMSO, replicate 1


title: Subject 19 LS

description: Subject 19


title: Subject 18 LS

description: Subject 18


title: Subject 17 WK 16

description: Subject 17


title: Subject 20 NL

description: Subject 20


title: Subject 20 LS

description: Subject 20


title: Huh7 cells control, miRNA biological rep2

description: miRNA Expression Data from Huh-7 cells transfected with Control vector

source_name: Human Huh7 cells transfected with control vector

value: control vector


title: Huh7 cells with HBeAg, miRNA biological rep2


title: Subject 19 WK 16

description: Subject 19

value: ADA


title: Subject 18 WK 16

description: Subject 18

value: Skin Tissue


title: Subject 19 WK 2

description: Subject 19

value: WK 2


title: Subject 17 WK 1

description: Subject 17

value: WK 1


title: Subject 18 WK 2

description: Subject 18


title: Subject 17 WK 4

description: Subject 17


title: Huh7 cells control, miRNA biological rep1


title: Subject 17 LS

description: Subject 17


title: Subject 16 WK 1

description: Subject 16


title: Subject 16 WK 2

description: Subject 16


title: Subject 17 WK 2

description: Subject 17


title: Subject 16 WK 16

description: Subject 16


title: Subject 16 WK 4

description: Subject 16


title: Subject 16 LS

description: Subject 16


title: Subject 16 NL

description: Subject 16


title: Subject 15 WK 4

description: Subject 15


title: Subject 15 WK 2

description: Subject 15


title: Subject 15 LS

description: Subject 15


title: Subject 14 WK 16

description: Subject 14


title: Subject 14 WK 2

description: Subject 14


title: Plk1(+/-) Sample 2 vs Pool wt

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description: Biological replicate 2 of 3. Plk1(+/-) aorta

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 825 ng. Duration: 17 hours.Volume: 100 uL.Temperature (ºC): 65.

scan_protocol: Scanned on an G2565BA DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 9.5.3).

data_processing:
Data processed with GeneSpring GX 9.0.6. Sheet 1. Filtered non-ave. Samples are not averaged.
# Interpretation : Genotype (Non-averaged)
# Experiment : (+/-) vs wt_pool
# Flag Value: Present or Marginal
# Entities where at least 1 out of 3 samples have flags in Present or Marginal

source_name: Pooled WT aortas

label_protocol: Amount of nucleic acid labeled: 1µg. Amplification: by RNA polymerases. Commercial Two-Color Microarray-Based Gene Expression Analysis kit by following manufacturer instructions. Agilent manual G4140-90050 Ver. 5.5 Feb 2007.  Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: ES cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. L

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: WT

value: Aorta

value: 3-5 months

source_name: Aorta Plk1(+/-) 2

value: aorta


title: Subject 15 WK 16

description: Subject 15


title: Subject 14 WK 4

description: Subject 14


title: Subject 14 WK 1

description: Subject 14


title: Subject 15 WK 1

description: Subject 15


title: Plk1(+/-) Sample 3 vs Pool wt

description: Biological replicate 3 of 3. Plk1(+/-) aorta

source_name: Aorta Plk1(+/-) 3


title: Subject 13 WK 4

description: Subject 13

value: MTX


title: Subject 13 WK 16

description: Subject 13


title: Subject 14 NL

description: Subject 14

value: NL


title: Subject 13 WK 2

description: Subject 13


title: Plk1(+/-) Sample 1 vs Pool wt

description: Biological replicate 1 of 3. Plk1(+/-) aorta

source_name: Aorta Plk1(+/-) 1


title: Subject 13 WK 1

description: Subject 13


title: Subject 13 NL

description: Subject 13


title: Subject 12 WK 16

description: Subject 12


title: Subject 13 LS

description: Subject 13

value: LS


title: Subject 12 WK 4

description: Subject 12

value: WK 4


title: Subject 12 WK 2

description: Subject 12


title: Subject 12 NL

description: Subject 12


title: Subject 11 WK 4

description: Subject 11


title: Subject 14 LS

description: Subject 14


title: Subject 11 NL

description: Subject 11


title: Subject 15 NL

description: Subject 15


title: Subject 11 WK 2

description: Subject 11


title: Subject 10 WK 4

description: Subject 10


title: Subject 11 WK 1

description: Subject 11


title: Subject 10 WK 1

description: Subject 10


title: Subject 12 LS

description: Subject 12


title: Subject 11 LS

description: Subject 11


title: Subject 9 WK 1

description: Subject 9


title: Subject 17 NL

description: Subject 17


title: Subject 10 LS

description: Subject 10


title: Subject 10 WK 2

description: Subject 10


title: Subject 12 WK 1

description: Subject 12


title: Subject 9 WK 16

description: Subject 9

value: WK 16


title: Subject 7 WK 16

description: Subject 7


title: Subject 9 LS

description: Subject 9


title: Subject 9 WK 4

description: Subject 9


title: Subject 8 WK 16

description: Subject 8


title: Subject 10 NL

description: Subject 10


title: Subject 8 LS

description: Subject 8


title: Subject 8 WK 4

description: Subject 8


title: Subject 8 WK 2

description: Subject 8


title: Subject 7 WK 4

description: Subject 7


title: Subject 9 WK 2

description: Subject 9


title: Subject 9 NL

description: Subject 9


title: Subject 8 NL

description: Subject 8


title: Subject 7 WK 2

description: Subject 7


title: Subject 8 WK 1

description: Subject 8


title: Subject 7 WK 1

description: Subject 7


title: Subject 7 LS

description: Subject 7


title: Subject 7 NL

description: Subject 7


title: Subject 6 WK 16

description: Subject 6


title: Subject 6 WK 2

description: Subject 6


title: Subject 6 LS

description: Subject 6


title: Subject 6 WK 1

description: Subject 6


title: Subject 5 WK 4

description: Subject 5


title: Subject 5 WK 2

description: Subject 5


title: Subject 6 WK 4

description: Subject 6


title: Subject 5 WK 16

description: Subject 5


title: Subject 4 WK 1

description: Subject 4


title: Subject 4 WK 16

description: Subject 4


title: Subject 4 WK 4

description: Subject 4


title: Subject 4 NL

description: Subject 4


title: Subject 2 WK 4

description: Subject 2


title: Subject 3 WK 1

description: Subject 3


title: Subject 5 LS

description: Subject 5


title: Subject 5 NL

description: Subject 5


title: Subject 5 WK 1

description: Subject 5


title: Subject 4 WK 2

description: Subject 4


title: Subject 3 NL

description: Subject 3


title: Subject 4 LS

description: Subject 4


title: Subject 3 WK 2

description: Subject 3


title: Subject 3 WK 16

description: Subject 3


title: Subject 3 WK 4

description: Subject 3


title: Subject 3 LS

description: Subject 3


title: Subject 2 WK 16

description: Subject 2


title: Subject 2 NL

description: Subject 2


title: Subject 2 WK 2

description: Subject 2


title: Subject 11 WK 16

description: Subject 11


title: Subject 2 LS

description: Subject 2


title: Subject 2 WK 1

description: Subject 2


title: Subject 1 WK 1

description: Subject 1


title: Subject 1 WK 16

description: Subject 1


title: p183AT transfected immortalized multipotent otic progenitors, biological rep3

city: Downers Grove

last: Ebeid

state: IL

address: 555 31st St, Anatomy

department: Anatomy

institute: Midwestern University

hyb_protocol: Hybridization, washing and staining was performed using suggested protocols and reagents recommended for GeneChip Mouse Gene 2.0 ST arrays (Affymetrix ) and the Affymetrix Gene Chip system. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The Affymetrix GeneChip Scanner 3000 7G is used to generate the resultant GeneChip array image

data_processing: The data were analyzed with Affymetrix Expression Console ( version 1.4.1.46) and RMA-Sketch as normalization method

source_name: RFP-positive sorted cells 48 hours post-transfection with p183AT

label_protocol: 200 ng of total RNA was reverse transcribed and processed per manufacturers recommendations using the WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA)

growth_protocol: mESC cells were maintained on feeder layer (arrested fibroblasts) in leukemia inhibitory factor (LIF) to maintain pleuripotency then differentially separated from fibroblasts and grown on gelatin coated flasks 24 hour prior to transfection. iMOP cells grown in suspension in the presence of basic fibroblast growth factor (bFGF)

extract_protocol: mirVana miRNA Isolation Kit (Life Technologies) was used to extract total RNA from RFP-positive sorted cells

treatment_protocol: mESC cells were transfected with different plasmid vectors using Lipofectamine 2000 reagent and kept in culture for 48 hours. iMOP cells were transfected with plasmid vectors using Jet Prime reagent and kept in culture for 48 hours. RFP-positive cells were sorted 48 hours post-transfection using fluorescence activated cell sorting

tag: transfection

value: 48 hours post-transfection with p183AT


title: Subject 1 NL

description: Subject 1


title: Subject 1 WK 2

description: Subject 1


title: Subject 1 LS

description: Subject 1


title: Subject 1 WK 4

description: Subject 1


title: p183AT transfected immortalized multipotent otic progenitors, biological rep1


title: p183AT transfected immortalized multipotent otic progenitors, biological rep2


title: ctrl_4

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: 7pb CT 4

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.

source_name: MCF7 ctrl cells

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

extract_protocol: RNeasy Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: Breast cancer cell line


title: p183T transfected immortalized multipotent otic progenitors, biological rep2

source_name: RFP-positive sorted cells 48 hours post-transfection with p183T

value: 48 hours post-transfection with p183T


title: 5403_Autism

type: genomic

city: Miami

first: Dmitry

last: Velmeshev

state: FL

address: 1501 NW 10th ave, BRB 629

department: Psychiatry

institute: Universtiy of Miami

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing: The arrays were normalized using the Subset-quantile Within Array Normalization (SWAN) method, and poor quality probes were filtered out.

label: Cy5, Cy3

molecule: genomic DNA

source_name: Prefrontal cortex_Autism

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using QIAamp DNA Mini Kit (Qiagen, 51304)

value: Prefrontal cortex

tag: gender

value: M

tag: disease status

value: Autism


title: p183T transfected immortalized multipotent otic progenitors, biological rep1


title: 4899_Autism


title: pAT transfected immortalized multipotent otic progenitors, biological rep3

source_name: RFP-positive sorted cells 48 hours post-transfection with pAT

value: 48 hours post-transfection with pAT


title: ctrl_1

description: 7bp CT   1


title: 5144_Autism


title: ctrl_3

description: 7bp CT 3


title: 4999_Autism


title: pAT transfected immortalized multipotent otic progenitors, biological rep2


title: 1638_Autism

value: F


title: HuH7-F6

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

source_name: drug-resistant cells

label_protocol: Amplified RNA was prepared using 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies). All samples had RNA Integrity Number (RIN) greater than 7.0.

treatment_protocol: After the VEGFR and aurora kinase inhibitor JNJ-28841072 was intraperitoneally injected into NOD/SCID mice bearing tumors of HuH7 cells, the tumors eliciting resistance to this inhibitor were excised into small aliquots and directly engrafted in a second group of NOD/SCID mice. By repeating this process 6 and 12 times, drug-refractory HuH7-F6 and -F12 cells were derived from the parental cancer cells (HuH7-F0), respectively.

value: human hepatocellular carcinoma cell line

tag: genotype/phenotype

value: Subclone resistant to sorafenib


title: 5278_Autism


title: ctrl_2

description: 7bp CT 2


title: HuH7-F12


title: p183T transfected immortalized multipotent otic progenitors, biological rep3


title: dormant cancer cells from tamoxifen

description: Int Dorm Assay

source_name: MCF7 cells treated with tamoxifen 2 months


title: HuH7-F0 (2)

source_name: parental (HuH7-F0)

value: Parental


title: 5308_Autism


title: YSCC27

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12  Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2

source_name: Cholangiocarcinoma

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

extract_protocol: RNA was extracted with Trizol reagent(Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. Quality control was performed with Agilent Bioanalyser.

tag: bile duct vs cholangiolar

value: bile duct


title: 5302_Autism


title: 5173_Control

source_name: Prefrontal cortex_Control

value: Control


title: 5168_Control


title: 4669_Control


title: Subject 6 NL

description: Subject 6

source_name: Skin Tissue Biopsy

value: NL

tag: treatment

value: ADA

value: Skin Tissue


title: pT transfected immortalized multipotent otic progenitors, biological rep3

source_name: RFP-positive sorted cells 48 hours post-transfection with pT

value: 48 hours post-transfection with pT


title: 5419_Autism


title: HuH7-F0 (1)


title: pAT transfected immortalized multipotent otic progenitors, biological rep1


title: 1846_Control


title: University of Arizona Cancer Center (UACC) melanoma cell line 952

city: Rockville

first: Jiyeon

last: Choi

state: Maryland

address: 9615 Medical Center Drive, Rm 3116

institute: NCI

description:
Gene expression data from early passage melanoma cell lines
UACC952

hyb_protocol: This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2).

data_processing: Background correction and quantile normalization of gene expression data were performed using Robust Multi-array Average (RMA) algorithm with the default settings (Affymetrix). Quantile normalization was used. Present and not present (PANP) package was used to determine expression p values, and values with a P >=0.05 were set to missing (NA)

source_name: Early passage melanoma cell line growing in culture at log phase

label_protocol: For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA).

growth_protocol: Melanoma cell line was cultured in RPMI 1640 in the presence of 10% fetal bovine serum.

extract_protocol: RNA extractions were performed using Qiagen RNeasy Midi-kits as per the manufacturer’s instructions. RNA quality and concentration were assessed using a 2100 BioAnalyser (Agilent Technologies).

value: early passage melanoma cell line

tag: genotype

value: various


title: YSCC26


title: YSCC25

value: cholangiolar


title: YSCC24


title: pT transfected immortalized multipotent otic progenitors, biological rep2


title: LC4 Lung Tissue Control sample 4

city: Cambridge

first: Madeline

last: Lancaster

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

department: Cell Biology Division

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description: Lung tissue from a rat with Chow diet after 24 weeks

hyb_protocol: The labeled cDNA product was heated to 95°C and hybridized to the Human Gene 1.0 ST microarray (Affymetrix Inc.) for 17 + 1 hr at 45°C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

scan_protocol: A confocal scanner (Affymetrix GeneChip Scanner 3000 7G plus) was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature

data_processing: The statistical analyses were performed with R 2.11.0. All samples were normalized and summarized by Robust Multiarray Average (RMA). Times series analysis was carried out using bioconductor timecourse package. Differential expression analysis between L_MS and L_C  was performed using LIMMA. The Benjamini and Hochberg multiple hypothesis testing correction procedure was applied to control the false discovery rate (FDR). Data were filtered to include only genes that had a 2-fold-change difference between the groups and an adjusted p value of 0.001

organism: Rattus norvegicus

source_name: lung, rat control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50 ng total RNA

growth_protocol: After weaning the animals were divided into two groups (without differences in weight 70-90 g) and fed with standard rat chow diet that contained protein 28.507%, fat 13.496%, HCO 57.996%, from which sucrose 3.7%, fructose 0.3%, glucose 0.22%, Laboratory Rodent Diet 5001; for induce MetS in group MS the rats had a high sucrose diet (30% sucrose solution) as their only liquid source and the control group (CTL) had water alone, their diets were ad libitum for 24 weeks. The animals were housed in temperature-controlled (20-23oC) room on a 12/12 hours dark-light cycle. After 24 weeks the animals fasting conditions for 7 hours followed sacrificed by decapitation.

extract_protocol: Isolation of RNA from lung tissues was performed with Trizol reagent (Invitrogen, Carlsbad, CA, USA) as recommended by the manufacturer, and finally dissolved in 40μl of Rnase-free water per sample. The total RNA quantification and purity was determined with a ND®-1000 spectrophotometer (Technologies, Inc. Wilmington, DE, USA). Total RNA quality determination was measured on an Agilent's 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA). A RNA Integrity Number (RIN) ≥ 6 was used as a quality filter to perform the microarray assays.

treatment_protocol: for induce MetS in group MS the rats had a high sucrose diet (30% sucrose solution) as their only liquid source during 24 weeks, at libitum.

value: Lung

tag: diet

value: chow diet

tag: group

value: control

value: Wistar


title: LC1_ RT Lung Tissue Control sample 1, technical replicate

source_name: lung, rat control, 258P technical replicate


title: 1347_Control

value: Prefrontal cortex

value: F


title: University of Arizona Cancer Center (UACC) melanoma cell line 929

description:
Gene expression data from early passage melanoma cell lines
UACC929


title: pT transfected immortalized multipotent otic progenitors, biological rep1


title: LC3 Lung Tissue Control sample 3


title: YSCC23


title: University of Arizona Cancer Center (UACC) melanoma cell line 903

description:
Gene expression data from early passage melanoma cell lines
UACC903


title: University of Arizona Cancer Center (UACC) melanoma cell line 91

description:
Gene expression data from early passage melanoma cell lines
UACC91


title: Unmanipulated immortalized multipotent otic progenitors, biological rep3

source_name: Unmanipulated cell culture


title: Unmanipulated immortalized multipotent otic progenitors, biological rep2


title: University of Arizona Cancer Center (UACC) melanoma cell line 827

description:
Gene expression data from early passage melanoma cell lines
UACC827


title: Unmanipulated immortalized multipotent otic progenitors, biological rep1


title: LC2 Lung Tissue Control sample 2


title: University of Arizona Cancer Center (UACC) melanoma cell line 62

description:
Gene expression data from early passage melanoma cell lines
UACC62


title: LC1 Lung Tissue Control sample 1


title: YSCC20


title: p183AT transfected mouse embryonic stem cells, biological rep2

value: mouse embryonic stem cells

value: 48 hours post-transfection with p183AT


title: p183AT transfected mouse embryonic stem cells, biological rep3


title: p183AT transfected mouse embryonic stem cells, biological rep1


title: LMS3 Lung Tissue Metabolic Sindrome sample 3

description: Lung tissue from a male wistar rat with Sucrose diet 30%, after 24 weeks

source_name: lung, rat with MetS

value: sucrose diet 30%

value: Metabolic syndrome


title: p183T transfected mouse embryonic stem cells, biological rep3

value: 48 hours post-transfection with p183T


title: LMS1 _RT  Lung Tissue Metabolic Sindrome sample 1, technical replicate

source_name: lung, rat with MetS, 262P technical replicate


title: YSCC18

value: bile duct


title: YSCC17


title: YSCC21


title: YSCC19


title: 914_Control

value: M

value: Control


title: LMS1 Lung Tissue Metabolic Sindrome sample 1


title: University of Arizona Cancer Center (UACC) melanoma cell line 612

description:
Gene expression data from early passage melanoma cell lines
UACC612

value: early passage melanoma cell line


title: YSCC22


title: LMS2 Lung Tissue Metabolic Sindrome sample 2


title: 1024_Control


title: 1158_Control


title: 5391_Control


title: University of Arizona Cancer Center (UACC) melanoma cell line 457

description:
Gene expression data from early passage melanoma cell lines
UACC457

value: various


title: University of Arizona Cancer Center (UACC) melanoma cell line 558

description:
Gene expression data from early passage melanoma cell lines
UACC558


title: University of Arizona Cancer Center (UACC) melanoma cell line 502

description:
Gene expression data from early passage melanoma cell lines
UACC502


title: YSCC14


title: University of Arizona Cancer Center (UACC) melanoma cell line 3361

description:
Gene expression data from early passage melanoma cell lines
UACC3361


title: pT transfected mouse embryonic stem cells, biological rep2

value: 48 hours post-transfection with pT


title: pAT tranfected mouse embryonic stem cells, biological rep1

value: 48 hours post-transfection with pAT


title: YSCC16


title: YSCC12

value: cholangiolar


title: University of Arizona Cancer Center (UACC) melanoma cell line 3395

description:
Gene expression data from early passage melanoma cell lines
UACC3395


title: pAT tranfected mouse embryonic stem cells, biological rep3


title: YSCC15


title: YSCC13


title: University of Arizona Cancer Center (UACC) melanoma cell line 3291

description:
Gene expression data from early passage melanoma cell lines
UACC3291


title: YSCC11


title: University of Arizona Cancer Center (UACC) melanoma cell line 3312

description:
Gene expression data from early passage melanoma cell lines
UACC3312


title: University of Arizona Cancer Center (UACC) melanoma cell line 3337

description:
Gene expression data from early passage melanoma cell lines
UACC3337


title: p183T transfected mouse embryonic stem cells, biological rep2


title: pT transfected mouse embryonic stem cells, biological rep1


title: pAT tranfected mouse embryonic stem cells, biological rep2


title: pT transfected mouse embryonic stem cells, biological rep3


title: YSCC10


title: Unmanipulated mouse embryonic stem cells, biological rep3


title: YSCC8


title: University of Arizona Cancer Center (UACC) melanoma cell line 3379

description:
Gene expression data from early passage melanoma cell lines
UACC3379


title: University of Arizona Cancer Center (UACC) melanoma cell line 3211

description:
Gene expression data from early passage melanoma cell lines
UACC3211


title: YSCC9


title: YSCC6


title: University of Arizona Cancer Center (UACC) melanoma cell line 3090

description:
Gene expression data from early passage melanoma cell lines
UACC3090


title: University of Arizona Cancer Center (UACC) melanoma cell line 3093

description:
Gene expression data from early passage melanoma cell lines
UACC3093


title: University of Arizona Cancer Center (UACC) melanoma cell line 2994

description:
Gene expression data from early passage melanoma cell lines
UACC2994


title: YSCC5


title: University of Arizona Cancer Center (UACC) melanoma cell line 3074

description:
Gene expression data from early passage melanoma cell lines
UACC3074


title: University of Arizona Cancer Center (UACC) melanoma cell line 2876

description:
Gene expression data from early passage melanoma cell lines
UACC2876


title: Rs632_72h_0μM_A10

city: Research Triangle Park

first: Patrick

last: McMullen

state: North Carolina

address: 6 Davis Drive, P.O. Box 12137

institute: The Hamner Institutes for Health Sciences

hyb_protocol: GeneTitan according to manufacturer’s protocol

scan_protocol: Affymetrix GeneTitan

data_processing: Analysis of gene expression data was performed using Partek software (Partek Inc., St. Louis, MO) utlising GC-RMA normalisation. Arrays with average log2 expression value above 0.06 of median log2 expression values across all arrays were excluded for further analyses. A 1-way ANOVA with interactions was performed to compare gene expression between the treated and control cells. Probability values were adjusted for multiple comparisons using a false discovery rate of 5%.

source_name: Cultured primary hepatocytes exposed to GW7647

label_protocol: RNA samples were prepared for microarray hybridization using the GeneAtlas™ 3’ IVT Express Kit according to manufacturer’s protocol (Applied Biosystems, Carlsbad, CA). Briefly, total RNA was reverse transcribed to synthesize first-strand cDNA. The cDNA was then converted into a double-stranded DNA template for transcription. Amplified cRNA (aRNA) was transcribed in vitro, with incorporation of a biotin-congugated nucleotide. The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate, and samples were fragmented to prepare the biotin-labeled aRNA samples for hybridization onto Affymetrix® GeneChip

growth_protocol: Cells were plated on Rat Collagen IV-coated plates and Geltrex was added for a final concentration of 0.25 mg/ml approximately 6 hours after plating. Cells were maintained at 37˚C in a hμMidified 5% CO2 atmosphere in William E medium supplemented with cell maintenance cocktail B (Invitrogen).

extract_protocol: Total RNA was collected from the treated cells using the Qiaxtractor and the Qiagen VX reagent pack according to the manufacturer’s protocol (Qiagen, Valencia, CA). A DNase 1 incubation was performed on all samples to remove any possible contamination of the RNA samples with cellular DNA

treatment_protocol: GW7647 was obtained from Tocris (Bristol, UK)

tag: biological replicate

tag: exposure time

tag: agent

tag: concentration


title: Rs632_72h_1μM_B12


title: Rs632_72h_0.01μM_G06


title: Rs632_72h_10μM_A07_2


title: Unmanipulated mouse embryonic stem cells, biological rep1

tag: cell type


title: University of Arizona Cancer Center (UACC) melanoma cell line 2993

description:
Gene expression data from early passage melanoma cell lines
UACC2993

tag: tissue


title: Rs632_72h_0.001μM_F05


title: YSCC1


title: Rs631_72h_10μM_F04


title: Unmanipulated mouse embryonic stem cells, biological rep2


title: YSCC4


title: University of Arizona Cancer Center (UACC) melanoma cell line 285

description:
Gene expression data from early passage melanoma cell lines
UACC285


title: YSCC2


title: Rs632_72h_0.1μM_E12


title: University of Arizona Cancer Center (UACC) melanoma cell line 2972

description:
Gene expression data from early passage melanoma cell lines
UACC2972


title: YSCC3


title: YSCC7


title: University of Arizona Cancer Center (UACC) melanoma cell line 2851

description:
Gene expression data from early passage melanoma cell lines
UACC2851


title: MDA-MB-231 Glc-8h

city: Duarte

first: David

middle: Kong

last: Ann

state: CA

address: 1500 E. Duarte Rd.

institute: City of Hope

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

source_name: MDA-MB-231 cell

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

growth_protocol: Cultured in DMEM supplemented with 10% FBS in 37°C, 5% CO2

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

treatment_protocol: Cultured in DMEM without glucose for 8 hours

tag: stress

value: glucose starvation

tag: cell line


title: University of Arizona Cancer Center (UACC) melanoma cell line 2641

description:
Gene expression data from early passage melanoma cell lines
UACC2641


title: MDA-MB-231/shkap1-Glc-8h

value: KAP1 knockdown


title: University of Arizona Cancer Center (UACC) melanoma cell line 2837

description:
Gene expression data from early passage melanoma cell lines
UACC2837


title: Rs631_72h_0.1μM_D05


title: Rs631_72h_1μM_A08


title: University of Arizona Cancer Center (UACC) melanoma cell line 2534

description:
Gene expression data from early passage melanoma cell lines
UACC2534


title: Rs631_72h_0.01μM_A12


title: University of Arizona Cancer Center (UACC) melanoma cell line 2659

description:
Gene expression data from early passage melanoma cell lines
UACC2659


title: University of Arizona Cancer Center (UACC) melanoma cell line 2610

description:
Gene expression data from early passage melanoma cell lines
UACC2610


title: University of Arizona Cancer Center (UACC) melanoma cell line 2528

description:
Gene expression data from early passage melanoma cell lines
UACC2528


title: Rs631_72h_0.001μM_A01


title: University of Arizona Cancer Center (UACC) melanoma cell line 2545

description:
Gene expression data from early passage melanoma cell lines
UACC2545


title: University of Arizona Cancer Center (UACC) melanoma cell line 257

description:
Gene expression data from early passage melanoma cell lines
UACC257


title: MDA-MB-231/shkap1


title: Rs628_72h_10μM_A09


title: Rs628_72h_0μM_F10


title: Tet-Gabpα cKO ES cells: -Tet vs. +Tet

description: Parent cell line is A3-1 ES cells. Strain is 129/SvJ.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: -Tet

growth_protocol: Cells were cultured on gelatin-coated dishes with LIF-supplemented ES cell culture medium.

extract_protocol: Total RNAs were extracted by Sepasol-RNA I Super G according to the manufacturer's instructions.

treatment_protocol: Cells were cultured with or without Tet for 1 day.

tag: strain

value: A3-1 ES cells

tag: tetracycline

source_name: +Tet


title: Rs628_72h_1μM_E05


title: Rs628_72h_0.1μM_E10


title: University of Arizona Cancer Center (UACC) melanoma cell line 383

description:
Gene expression data from early passage melanoma cell lines
UACC383


title: University of Arizona Cancer Center (UACC) melanoma cell line 2512

description:
Gene expression data from early passage melanoma cell lines
UACC2512


title: MDA-MB-231


title: University of Arizona Cancer Center (UACC) melanoma cell line 2427

description:
Gene expression data from early passage melanoma cell lines
UACC2427


title: Rs628_72h_0.001μM_C01


title: University of Arizona Cancer Center (UACC) melanoma cell line 2496

description:
Gene expression data from early passage melanoma cell lines
UACC2496


title: Rs627_72h_1μM_H05


title: University of Arizona Cancer Center (UACC) melanoma cell line 2404

description:
Gene expression data from early passage melanoma cell lines
UACC2404


title: p183T transfected mouse embryonic stem cells, biological rep1

source_name: RFP-positive sorted cells 48 hours post-transfection with p183T

tag: transfection


title: University of Arizona Cancer Center (UACC) melanoma cell line 2331

description:
Gene expression data from early passage melanoma cell lines
UACC2331


title: Rs627_72h_0μM_E02


title: Rs628_72h_0.01μM_A05


title: Rs632_24h_10μM_G01


title: University of Arizona Cancer Center (UACC) melanoma cell line 1729

description:
Gene expression data from early passage melanoma cell lines
UACC1729


title: University of Arizona Cancer Center (UACC) melanoma cell line 1509

description:
Gene expression data from early passage melanoma cell lines
UACC1509


title: University of Arizona Cancer Center (UACC) melanoma cell line 1649

description:
Gene expression data from early passage melanoma cell lines
UACC1649


title: Rs627_72h_0.01μM_G07


title: Rs632_24h_0.01μM_C04


title: Rs632_24h_0.001μM_D12


title: University of Arizona Cancer Center (UACC) melanoma cell line 1816

description:
Gene expression data from early passage melanoma cell lines
UACC1816


title: University of Arizona Cancer Center (UACC) melanoma cell line 1940

description:
Gene expression data from early passage melanoma cell lines
UACC1940


title: Rs631_24h_1μM_H07


title: University of Arizona Cancer Center (UACC) melanoma cell line 1451

description:
Gene expression data from early passage melanoma cell lines
UACC1451


title: University of Arizona Cancer Center (UACC) melanoma cell line 1389

description:
Gene expression data from early passage melanoma cell lines
UACC1389


title: Rs632_24h_1μM_E07


title: Rs627_72h_0.001μM_G09


title: University of Arizona Cancer Center (UACC) melanoma cell line 1265

description:
Gene expression data from early passage melanoma cell lines
UACC1265


title: University of Arizona Cancer Center (UACC) melanoma cell line 1308

description:
Gene expression data from early passage melanoma cell lines
UACC1308


title: Rs631_24h_10μM_G05


title: University of Arizona Cancer Center (UACC) melanoma cell line 1316

description:
Gene expression data from early passage melanoma cell lines
UACC1316


title: University of Arizona Cancer Center (UACC) melanoma cell line 1241

description:
Gene expression data from early passage melanoma cell lines
UACC1241


title: Rs632_24h_0μM_F01


title: Rs631_24h_0.001μM_F06


title: Rs631_24h_0μM_E04


title: University of Arizona Cancer Center (UACC) melanoma cell line 1592

description:
Gene expression data from early passage melanoma cell lines
UACC1592


title: Rs631_24h_0.1μM_E01


title: University of Arizona Cancer Center (UACC) melanoma cell line 1237

description:
Gene expression data from early passage melanoma cell lines
UACC1237


title: Rs631_24h_0.01μM_C09


title: Rs628_24h_1μM_G11


title: Rs628_24h_0.01μM_C10


title: University of Arizona Cancer Center (UACC) melanoma cell line 1190

description:
Gene expression data from early passage melanoma cell lines
UACC1190


title: University of Arizona Cancer Center (UACC) melanoma cell line 1120

description:
Gene expression data from early passage melanoma cell lines
UACC1120


title: Rs628_24h_0.1μM_H11


title: University of Arizona Cancer Center (UACC) melanoma cell line 1118

description:
Gene expression data from early passage melanoma cell lines
UACC1118


title: University of Arizona Cancer Center (UACC) melanoma cell line 1113

description:
Gene expression data from early passage melanoma cell lines
UACC1113


title: University of Arizona Cancer Center (UACC) melanoma cell line 1097

description:
Gene expression data from early passage melanoma cell lines
UACC1097


title: Rs628_24h_10μM_C02


title: Rs628_24h_0.001μM_B10


title: Rs627_24h_0.001μM_G05


title: Rs627_24h_1μM_E06


title: Rs627_24h_0μM_D06


title: University of Arizona Cancer Center (UACC) melanoma cell line 1093

description:
Gene expression data from early passage melanoma cell lines
UACC1093


title: Rs627_24h_0.01μM_F03


title: Rs632_12h_1μM_E05


title: Rs631_72h_0μM_F02


title: Rs632_12h_10μM_D07


title: Rs627_24h_0.1μM_C08


title: Rs632_12h_0.1μM_C12


title: Rs632_12h_0.001μM_H02


title: Rs631_12h_1μM_G03_2


title: Rs631_12h_0μM_A07


title: Rs631_12h_10μM_F12


title: Rs631_12h_0.1μM_H07


title: Mammary epithelial cells non-lactating B

city: Pittsburgh

first: Philip

middle: E.

last: Empey

state: PA

address: 3501 Terrace Street

department: Pharmacy & Therapeutics

institute: University of Pittsburgh School of Pharmacy

description:
Specimen normal per pathology report.
Agilent BioAnalyzer 2100 RNA Integrity Number=9.3

hyb_protocol: cRNA was fragmented and hybridized overnight to Affymetrix U133 Plus 2.0 Genechips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

source_name: Nonlactating mammary epithelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA via Qiagen RNeasy Micro kit with on-column DNAse digestion.   RNA quality was assessed by evaluating the 28s and 18s bands relative to degradation products using an Agilent Bioanalyzer 2100.  Samples were given a RNA Integrity Number (RIN) on a 10 point scale.

tag: sample type

value: Mammary epithelial cells isolated from a surgical breast reduction specimen from a caucasian female.

tag: age

value: 33  years old

value: Mammary epithelial cells


title: Mammary epithelial cells lactating A

description:
Cells isolated from each fresh breast milk sample provided.  RNA from multiple collections overal several weeks pooled.
Agilent BioAnalyzer 2100 RNA Integrity Number=9.8

source_name: Lactating mammary epithelial cells

value: Mammary epithelial cells isolated from breast milk from a healthy caucasian female 39-47 weeks post-partum.

value: 24 years old


title: Mammary epithelial cells non-lactating A

description:
Specimen normal per pathology report.
Agilent BioAnalyzer 2100 RNA Integrity Number=9.2

value: 25  years old


title: 800R.NR mutant_rep1

city: pamplona

first: Ivan

last: Jáuregui Mosquera

state: Navarra

address: Campus de Arrosadia, s/n,  Dpto. Ciencias del Medio Natural

institute: Universidad Pública de Navarra

description: Gene expression after 5 weeks CO2 tratment. Sample collected 4h from the beginning of the light period

hyb_protocol: 1.65 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 the microarrays. They were incubated in SureHyb microarray hybridization chambers with gasket slides (Agilent Technologies) at 65ºC for 17 h in an rotary oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 s with acetonitrile and 30 s in Agilent's stabilization and drying solution, then air dried.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: Normalization and differential expression analysis of the data was done using limma R package (Smyth 2004). Normalization was carried out using quantile method and Bayes statistics were applied to determine the differential expression between the comparisons. Statistical significance was corrected for multiple testing using the Benjamini-Hochberg procedure. For this study, the significant difference in gene expression was Q value < 0.05 and log2 fold change > 0.5.

source_name: Root of Arabidopsis thaliana NR mutant plant exposed to 800 ppm [CO2]. Rep 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by    NucleoSpin® Gel and PCR Clean-up column purification (Macherey-Nagel, Düren, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Arabidopsis thaliana, Columbia 0 ecotype (col 0) and Arabidopsis thaliana NR mutant (NR double mutant G′4-3, nia1- 1/nia2-5) plants grown under hydroponic conditions.

extract_protocol: Total RNA was isolated according to Liao et al.(2004).

value: root

tag: ecotype

value: NR double mutant G′4-3, nia1- 1/nia2-5


title: Mammary epithelial cells non-lactating C

description: Specimen normal per pathology report.


title: Mammary epithelial cells lactating C

description:
Cells isolated from each fresh breast milk sample provided.  RNA from multiple collections overal several weeks pooled.
Agilent BioAnalyzer 2100 RNA Integrity Number=9.7

value: Mammary epithelial cells isolated from breast milk from a healthy caucasian female 9-19 weeks post-partum.

value: 21  years old


title: 800R.NR mutant_rep3

source_name: Root of Arabidopsis thaliana NR mutant plant exposed to 800 ppm [CO2]. Rep 3

tag: genotype


title: Rs631_12h_0.001μM_B08


title: Rs628_12h_1μM_G08


title: Rs631_12h_0.01μM_G10


title: Rs628_12h_10μM_D01


title: Mammary epithelial cells lactating B

description:
Cells isolated from each fresh breast milk sample provided.  RNA from multiple collections overal several weeks pooled.
Agilent BioAnalyzer 2100 RNA Integrity Number=9.5

value: Mammary epithelial cells isolated from breast milk from a healthy caucasian female 27-34 weeks post-partum.

value: 32  years old


title: Rs628_12h_0μM_C06_2


title: Rs627_12h_1μM_A04


title: Rs627_12h_0.001μM_E11


title: Rs632_6h_0μM_B06


title: Rs628_12h_0.01μM_D03


title: 800R.NR mutant_rep2

source_name: Root of Arabidopsis thaliana NR mutant plant exposed to 800 ppm [CO2]. Rep 2


title: 400R.NR mutant_rep3

source_name: Root of Arabidopsis thaliana NR mutant plant exposed to 400 ppm [CO2]. Rep 3


title: Rs632_6h_10μM_D09


title: Rs627_12h_0μM_G02


title: 800R.wt_rep1

source_name: Root of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 1

value: wild type


title: 800R.wt_rep3

source_name: Root of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 3


title: 800R.wt_rep2

source_name: Root of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 2


title: 400R.NR mutant_rep2

source_name: Root of Arabidopsis thaliana NR mutant plant exposed to 400 ppm [CO2]. Rep 2


title: Rs632_6h_0.001μM_G07


title: Rs632_6h_1μM_E05


title: 400R.NR mutant_rep1

source_name: Root of Arabidopsis thaliana NR mutant plant exposed to 400 ppm [CO2]. Rep 1