title: #1 shH2A.B ES cells

city: Ann Arbor

first: Yibin

last: Chen

state: MI

address: 1115 w medical drive

institute: university of Michigan

description: Gene expression from #1 H2A.B KD mouse ES cells

hyb_protocol: Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations on a GeneTitan Instrument.

scan_protocol: Standard Affymetrix protocol

data_processing: Robust Multi-Array (RMA) normalized.

source_name: H2A.B KD ES cells

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA).Affymetrix standard protocol were used.

growth_protocol: Mouse ES cells were maintained on gelatin-coated dishes in Glasgow Minimum Essential medium (GMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum, 55 mM b-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of ESGRO (Chemicon) under feeder-free conditions

extract_protocol: For expression microarray analysis comparing control KD and H2A.B KD mouse ES cells, 2 µg of total RNA purified from G418 treated cells were reverse-transcribed into cDNA with a T7-(dT)24 primer from a custom kit (Life Technologies).

treatment_protocol: For H2A.B knockdown (KD), mouse ES cells were infected with retroviruses with short-hairpin RNA (shRNA) specific for H2A.B. All analyses were performed using H2A.B-depleted ES cells that were treated with G418 for 2-4 weeks. Retroviruses with control RNA sequence was used as a control. Short-hairpin RNA (shRNA) sequences were cloned into pMSCV-neo vector under the control of the U6 promoter.

tag: cell type

value: mouse ES cells

value: H2A.B KD


title: Transfaunation liver, biological rep2

status: Public on Dec 24 2013

type: RNA

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

country: USA

institute: University of Viginia

hyb_protocol: Affymerix protocol

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

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

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Transfaunation liver

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

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

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

tag: genotype/variation

value: wild type

tag: sample group

value: raised under germ-free followed by conventionization

tag: tissue

value: liver


title: Transfaunation liver, biological rep1


title: Heart from naïve mice on 60 days post infection_1

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

country: Japan

institute: Kindai University Faculty of Medicine

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

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

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

source_name: Heart_naïve mice_60 dpi

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

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

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

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

tag: strain

tag: gender

value: male

tag: age (at the timeof infection)

value: 5 weeks

tag: infected with

value: none (naïve control)

tag: time point

value: 60 days post infection

value: heart


title: HaCaT_40hr_Control

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: Gene expression of HaCaT cell lines at 40hr, Control

hyb_protocol: The labeled antisense cRNAs were hybridized to microarrays at 65°C for 17h.

scan_protocol: The arrays were washed and scanned using an Agilent scanner.

data_processing: The scanned images of the arrays were converted and imported into the Institute for Systems Biology’s Systems Biology Experiment Analysis System (SBEAMS) for array data normalization and further analyses.

organism: Homo sapiens

source_name: HaCaT, Control, 40hr

label_protocol: Total RNA was reverse transcribed and followed by generation of cDNAs. The resulting cDNAs were transcribed and labeled with cyanine 3-CTP.

extract_protocol: Total RNA was isolated with miRNeasy kit (Qiagen, Germantown, MD according to the manufacturer's instructions. The quality and quantity of the RNA samples were evaluated by NanoDrop ND-1000 Spectrophotometer (Wilmington, DE), and Agilent Bioanalyzer 2100 (Santa Clara, CA).

treatment_protocol: For TRPV3 mutant overexpression, HaCaT cells were transfected in 6-well dishes at approximately 70% confluence using Lipofectamine 2000 (Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions. Control cells were treated with the same plasmid without insert.

tag: cell line

value: HaCaT

tag: transfection

value: control

tag: time

value: 40 hrs


title: Heart from TMEV-infected mice on 60 days post infection_5

source_name: Heart_TMEV-infected mice_60 dpi

value: Theiler's murine encephalomyelitis virus (TMEV)


title: Heart from naïve mice on 60 days post infection_4


title: Heart from naïve mice on 60 days post infection_3


title: Transfaunation liver, biological rep3


title: HaCaT_16hr_muTRPV3

description: Gene expression of HaCaT cell lines at 16hr, transfected with mutant TRPV3

source_name: HaCaT, transfected with mutant TRPV3, 16hr

value: mutant TRPV3

value: 16 hrs


title: HaCaT_16hr_Control

description: Gene expression of HaCaT cell lines at 16hr, Control

source_name: HaCaT, Control, 16hr


title: HaCaT_40hr_muTRPV3

description: Gene expression of HaCaT cell lines at 40hr, transfected with mutant TRPV3

source_name: HaCaT, transfected with mutant TRPV3, 40hr


title: Control KD ES cells

description: Gene expression from control KD mouse ES cells

source_name: control KD ES cells

value: Control KD


title: Germ free liver, biological rep2

source_name: Germ free liver

value: raised under germ-free


title: Germ free liver, biological rep3


title: 293T_40hr_muTRPV3

description: Gene expression of 293T cell lines at 40hr, transfected with mutant TRPV3

source_name: 293T, transfected with mutant TRPV3, 40hr

treatment_protocol: For TRPV3 mutant overexpression, 293T cells were transfected in 6-well dishes at approximately 70% confluence using Lipofectamine 2000 (Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions. Control cells were treated with the same plasmid without insert.


title: HaCaT_24hr_muTRPV3

description: Gene expression of HaCaT cell lines at 24hr, transfected with mutant TRPV3

source_name: HaCaT, transfected with mutant TRPV3, 24hr

value: 24 hrs


title: RJ28_before

city: Wageningen

first: Milene

last: Catoire

address: Bomenweg 2

department: Human Nutrition

country: Netherlands

institute: Wageningen University

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

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

data_processing: Expression estimates were calculated using RMA

source_name: muscle biopsy

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

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

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

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

tag: ethnicity

value: Caucasian

tag: age

value: 63 years


title: HaCaT_24hr_Control

description: Gene expression of HaCaT cell lines at 24hr, Control

source_name: HaCaT, Control, 24hr


title: Germ free liver, biological rep1

value: wild type

value: liver


title: Heart from TMEV-infected mice on 60 days post infection_4

value: male

value: 5 weeks


title: Heart from TMEV-infected mice on 60 days post infection_2

value: 60 days post infection


title: 293T_16hr_muTRPV3

description: Gene expression of 293T cell lines at 16hr, transfected with mutant TRPV3

source_name: 293T, transfected with mutant TRPV3, 16hr


title: Heart from naïve mice on 60 days post infection_2

value: none (naïve control)

value: heart


title: 293T_24hr_muTRPV3

description: Gene expression of 293T cell lines at 24hr, transfected with mutant TRPV3

source_name: 293T, transfected with mutant TRPV3, 24hr


title: Heart from TMEV-infected mice on 60 days post infection_1


title: Heart from TMEV-infected mice on 60 days post infection_3


title: Bone marrow macrophages 3 days CSF-1 versus 0 days ERT2 Cre Thoc5 (flox/flox) with tamoxifen rep2

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7” (Agilent Technologies).

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction, processing and intra-array normalization of raw fluorescence intensity values were performed with the “Feature Extraction Software V10.7.3.1” by using the recommended default extraction protocol file: GE2_107_Sep09.xml.

label: Alexa fluor 647

source_name: Bone marrow derived macrophages harvested at day 0 of differentiation induction

label_protocol: Synthesis of Cy3- or Cy5-labeled cRNA was performed with the “Amino Allyl MessageAmp™ II aRNA Amplification Kit” (#5190-0444, Life Technologies) according to the manufacturer’s recommendations, except that the molar proportion of aminoallyl-UTP and UTP used was adjusted to 1+11 (instead of 1+1).

extract_protocol: Cytoplasmic RNA was purified by use of the Pure RNA isolation Kit (Roth).

value: Bone marrow macrophages

tag: genotype

value: ERT2 Cre Thoc5 (flox/flox)

tag: differentiation stage

value: day 0

tag: treatment

tag: genetic background

label: Alexa fluor 555

source_name: Bone marrow derived macrophages harvested at day 3 after differentiation induction

value: day 3 (under CSF-1)

value: tamoxifen


title: Bone marrow macrophages 3 days CSF-1 versus 0 days ERT2 Cre Thoc5 (flox/flox) no tamoxifen rep2

tag: cell type


title: 293T_24hr_Control

description: Gene expression of 293T cell lines at 24hr, Control

source_name: 293T, Control, 24hr

value: control


title: 293T_40hr_Control

description: Gene expression of 293T cell lines at 40hr, Control

source_name: 293T, Control, 40hr

value: 40 hrs


title: SGa6-2011

city: Los Angeles

first: Krzysztof

last: Kobielak

state: CA

address: 1425 San Pablo Street

department: Department of Pathology

institute: University of Southern California

description: Sweat gland non-LRCs basal layer cells

hyb_protocol: Hybridiztion was performed at 45ºC for 18h to Mouse Gene 1.0 ST array

scan_protocol: Processed chips were scanned by GeneChip Scanner 3000 7G

data_processing: The raw data were imported into Partek Genomic Suite v6 with default RMA settings (RMA background correction and quantile normalziation, except median is used for probeset summerization), followed by fold change calculations.  Differentially expressed gene lists containing probe sets with 2-fold intensity changes in either direction were generated.

source_name: Sweat gland non-LRCs-2011

label_protocol: Biotinylated cRNA was obtained using Nugen FFPE Reagents

extract_protocol: Total RNA was extracted using Trizol followed by Qiagen's RNeasy Micro Kit.

treatment_protocol: Adult mice was treated with doxycycline for 4 weeks prior to the isolation of sweat gland cells.

value: CD1 and FVB/N


title: 293T_16hr_Control

description: Gene expression of 293T cell lines at 16hr, Control

source_name: 293T, Control, 16hr

value: 16 hrs


title: Bone marrow macrophages 3 days CSF-1 versus 0 days ERT2 Cre with tamoxifen rep2

value: ERT2 Cre


title: Heart from TMEV-infected mice on 4 days post infection_4

source_name: Heart_TMEV-infected mice_4 dpi

value: Theiler's murine encephalomyelitis virus (TMEV)

value: 4 days post infection


title: III-7_Unaffected_Skin

description: unaffected skin from III-7

source_name: Skin biopsy from III-7, Unaffected

value: skin

tag: source

value: unaffected skin from III-7


title: Ifskin-2010

description: Basal layer of the sole's epidermis

source_name: Interfollicular skin-2010

value: Ifskin


title: SGGFPa6-2011

description: Sweat gland LRCs

source_name: Sweat gland LRCs-2011


title: Bone marrow macrophages 3 days CSF-1 versus 0 days ERT2 Cre Thoc5 (flox/flox) with tamoxifen rep1


title: III-7_Affected_Skin

description: affected skin from III-7

source_name: Skin biopsy from III-7, Affected

tag: tissue

value: affected skin from III-7


title: Bone marrow macrophages 3 days CSF-1 versus 0 days ERT2 Cre with tamoxifen rep1


title: Bone marrow macrophages 3 days CSF-1 versus 0 days ERT2 Cre no tamoxifen rep2


title: Bone marrow macrophages 3 days CSF-1 versus 0 days ERT2 Cre Thoc5 (flox/flox) no tamoxifen rep1


title: Heart from TMEV-infected mice on 4 days post infection_3

tag: strain

value: male

value: 5 weeks

value: heart


title: II-7_Affected_Skin

description: affected skin from II-7

source_name: Skin biopsy from II-7, Affected

value: affected skin from II-7


title: Ifskin-2011

description: Basal layer of the sole's epidermis

source_name: Interfollicular skin-2011


title: II-7_Unaffected_Skin

description: unaffected skin from II-7

source_name: Skin biopsy from II-7, Unaffected

value: unaffected skin from II-7


title: SGa6-2010

description: Sweat gland non-LRCs basal layer cells

source_name: Sweat gland non-LRCs-2010


title: SGGFPa6-2010

description: Sweat gland LRCs

source_name: Sweat gland LRCs-2010


title: TIBC5

status: Public on Dec 23 2013

city: Barcelona

first: Ana

last: Rovira

address: Dr. Aiguader 88

country: Spain

institute: IMIM-Hospital del Mar

description: Gene expression data from from human breast tumor

hyb_protocol: Sample was hybridized to Affymetrix Human Gene 1.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

source_name: Total RNA from frozen human breast tumor samples

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: RNA was extracted following Qiagen protocol according to the manufacturer's instructions.

value: breast cancer

tag: condition

value: true interval tumors (TIBC)

tag: phenotype


title: Bone marrow macrophages 3 days CSF-1 versus 0 days ERT2 Cre no tamoxifen rep1

source_name: Bone marrow derived macrophages harvested at day 0 of differentiation induction

value: Bone marrow macrophages

value: day 0

value: day 3 (under CSF-1)


title: SDBC4

value: screen-detected tumors (SDBC)

value: LumA


title: TIBC3


title: SDBC3

value: LumB


title: TIBC4


title: SDBC2


title: TIBC1

value: TN


title: SDBC1


title: TIBC2


title: SDBC5


title: Normal RefDNAc sty

type: genomic

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

institute: University Hospital Essen

description: Hybridized to 250K_Sty

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

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

data_processing: The CEL-Files were analyzed using the BRLMM-algorithm to produce genotype calls, stored in the corresponding CHP-Files.

label: Biotin

molecule: genomic DNA

source_name: Reference DNA provided by Affymetrix

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: QiaAmp DNA Blood Kit

tag: sample type

value: normal reference

value: blood


title: Normal N9 sty

description: Hybridized to 250K_Sty

source_name: whole blood DNA extraction


title: Normal N5 sty

description: Hybridized to 250K_Sty


title: control12

city: Umeå

first: Xiaolian

last: Gu

state: västerbotton

address: Building 6M, 2nd floor, Umeå University

department: Medical Biosciences

country: Sweden

institute: Umeå University

description: SAMPLE 47

hyb_protocol: Standard Illumina hybridization protocol: Illumina whole-genome gene expression direct hybridization assay

scan_protocol: Standard Illumina scanning protocol using the iScan System: iScan Reader, iScan PC, iScan Control Software

data_processing: GenomeStudio software was used to export probe summary profiles (probe profile and control probe profile). Intensities was exported from GenomeStudio without background correction or normalization. Then the Illumina data was background corrected and normalized using the neqc functions in LIMMA (linear models and differential expression for microarray data) package which is available in R through Bioconductor.

source_name: epidermis, healthy control

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano Labeling Kit for Illumina Expression BeadChip (epicentre)

extract_protocol: RNA was extracted using the RNAqueous-Micro Kit (Ambion)

treatment_protocol: Biopsy samples were embedded in Tissue Tek OCT compound and snap-frozen in liquid nitrogen. Samples cut into 10 μm thick sections and placed on membrane-covered glass slides (PALM Membrane Slides, PALM Microlaser Technologies, Bernried, Germany). Laser capture microdissection was then carried out using a PALM® microlaser system (PALM GmbH, Bernried, Germany). Epithelium only was used in further analysis.

tag: disease state

value: healthy control

value: epidermis

tag: gender

value: female

value: untreated

value: control


title: Normal N3 sty

description: Hybridized to 250K_Sty


title: Normal N10 sty

description: Hybridized to 250K_Sty


title: Tumor MPI-410 sty

description: Hybridized to 250K_Sty

source_name: Whole tissue of tumor biopsy

value: tumor

value: aggressive B-cell lymphoma


title: Normal D07-6 sty

description: Hybridized to 250K_Sty


title: Normal N2 sty

description: Hybridized to 250K_Sty


title: Normal B5 sty

description: Hybridized to 250K_Sty


title: Normal N7 sty

description: Hybridized to 250K_Sty


title: Normal D07-7 sty

description: Hybridized to 250K_Sty


title: Tumor MPI-031 sty

description: Hybridized to 250K_Sty


title: Normal B2 sty

description: Hybridized to 250K_Sty


title: Normal N8 sty

description: Hybridized to 250K_Sty


title: control11

description: SAMPLE 46

value: male


title: Normal D07-5 sty

description: Hybridized to 250K_Sty


title: Tumor MPI-115 sty

description: Hybridized to 250K_Sty


title: Normal B4 sty

description: Hybridized to 250K_Sty


title: Tumor MPI-367 sty

description: Hybridized to 250K_Sty


title: Tumor MPI-113 sty

description: Hybridized to 250K_Sty


title: Tumor MPI-032 sty

description: Hybridized to 250K_Sty


title: Normal D07-3 sty

description: Hybridized to 250K_Sty


title: Tumor MPI-528 sty

description: Hybridized to 250K_Sty


title: control10

description: SAMPLE 45


title: Normal B3 sty

description: Hybridized to 250K_Sty


title: control8

description: SAMPLE 43


title: Normal B1 sty

description: Hybridized to 250K_Sty


title: control7

description: SAMPLE 42


title: Tumor MPI-325 sty

description: Hybridized to 250K_Sty


title: Normal N4 sty

description: Hybridized to 250K_Sty


title: Normal N1 sty

description: Hybridized to 250K_Sty


title: Tumor MPI-024 sty

description: Hybridized to 250K_Sty


title: Normal N6 sty

description: Hybridized to 250K_Sty


title: control9

description: SAMPLE 44


title: control6

description: SAMPLE 41


title: control3

description: SAMPLE 38


title: control5

description: SAMPLE 40


title: control2

description: SAMPLE 37


title: D-Limonene-treated replicate 3

city: Wuxi

first: Jidong

last: Liu

address: 1800 Lihu Road

country: China

institute: Jiangnan university

description: Gene expression after 2 h in D-Limonene treated Saccharomyces cerevisiae cell

hyb_protocol: A total of 1μg of labeled cRNA was prepared for fragmentation adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, heated at 60 °C for 30 min, and finally diluted by addition with 55μl 2×GE Hybridization buffer. A volume of 100 μl of hybridization solution was then dispensed in the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 h at 65°C in an 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: The hybridized arrays were washed, fixed and scanned using the Agilent DNA microarray scanner (part number G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%). following Agilent Technologies’ guidelines.

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization), The positive effect of this median normalization is illustrated in Box-plot, and genes marked present or marginal in all samples (“All Targets Value”) were chosen for data analysis. Differentially expressed genes were identified through Fold-change screening.

organism: Saccharomyces cerevisiae

source_name: 0.02% (v/v) D-limonene, 2 h

label_protocol: Sample labeling and hybridization reactions were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, for each sample 1 μg of total RNA was linearly amplified and labeled with Cy3-dCTP. Labelled cRNAs purified with Qiagen RNAeasy Mini Kit, and sample concentration and specific activity (pmol Cy3/μg cRNA) were measured in a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: A single colony of the strain was inoculated to a 250 mL flask with 25 mL YPD media (10 g/L yeast extract, 20 g/L tryptone and 20 g/L glucose) and cultured 24 h at 200 rpm and 30°C as seed for the following culture. The seeds from pre-culture were inoculated into flask with an initial cell density of OD660=0.01. The growth of yeast was monitored by optical density at 600 nm (OD600) with a spectrophotometer. Incubation condition was 30°C with constant shaking at 200 rpm. All experiments were performed in triplicates.

extract_protocol: Total RNA of either control or D-limonene-treated cells was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions, including a DNase digestion step. The RNA was quantified and checked in the Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) at 260 and 280 nm. Integrity of isolated RNA was verified by automated electrophoresis system (Bio-Rad, Hercules, CA, USA).

treatment_protocol: The experiments were preformed in 500 mL flasks with 50 mL YPD medium. Cells grown to early-log phase (OD600=1.0) and then 0.02% (v/v) of D-limonene was added to the cultures, then the cells were incubated at 30°C for 2 h with constant shaking at 200 rpm. Cells were harvested at 2000g for 5 min, then washed twice with double distilled water and stored at -80°C until RNA preparation.

tag: growth cycle

value: Early logarithmic phase


title: D-Limonene-treated replicate 1


title: control1

description: SAMPLE 36

tag: time


title: Control replicate 3

description: control

source_name: control


title: D-Limonene-treated replicate 2


title: lesion_postUV_patient12

description: SAMPLE 35

source_name: psoriatic epidermis, phototherapy, 2 months

value: plaque type psoriasis

tag: years of disease

value: phototherapy

value: post-UV


title: control4

description: SAMPLE 39

tag: age


title: Control replicate 2

description: control


title: Control replicate 1

description: control


title: lesion_postUV_patient9

description: SAMPLE 32


title: lesion_postUV_patient10

description: SAMPLE 33

value: 2 y


title: PitBullTerrier-BI_27396

city: Cambridge

first: Hyun Ji

last: Noh

state: MA

address: 7 Cambridge Center

department: Genome Sequencing and Analysis

institute: Broad Institute

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

organism: Canis lupus familiaris

extract_protocol: Genomic DNA was extracted from blood using the Puregene DNA purification Kit (Gentra Systems) protocol.


title: PitBullTerrier-BI_27398


title: PitBullTerrier-BI_27395


title: PitBullTerrier-BI_27399


title: PitBullTerrier-BI_27397


title: lesion_postUV_patient11

description: SAMPLE 34


title: PitBullTerrier-BI_27394


title: lesion_postUV_patient3

description: SAMPLE 27


title: lesion_postUV_patient7

description: SAMPLE 30


title: lesion_postUV_patient8

description: SAMPLE 31


title: lesion_postUV_patient6

description: SAMPLE 29


title: lesion_postUV_patient1

description: SAMPLE 25


title: PitBullTerrier-BI_27393


title: lesion_postUV_patient4

description: SAMPLE 28


title: lesion_midUV_patient12

description: SAMPLE 24

source_name: psoriatic epidermis, phototherapy, 1 month

value: mid-UV


title: lesion_midUV_patient5

description: SAMPLE 17

value: 1 y


title: lesion_postUV_patient2

description: SAMPLE 26

value: Unknown


title: PitBullTerrier-BI_27392

value: blood


title: lesion_midUV_patient7

description: SAMPLE 19


title: PitBullTerrier-BI_27391


title: lesion_midUV_patient3

description: SAMPLE 15


title: lesion_midUV_patient8

description: SAMPLE 20


title: lesion_midUV_patient10

description: SAMPLE 22


title: lesion_midUV_patient11

description: SAMPLE 23


title: lesion_midUV_patient2

description: SAMPLE 14


title: lesion_midUV_patient4

description: SAMPLE 16


title: PitBullTerrier-BI_27390


title: RAF1KD.SW620.biorep.5

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

description:
RAF1-E4-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

hyb_protocol: standard Affymetrix procedure.

scan_protocol: standard Affymetrix procedure.

data_processing: The data were analyzed with frozen RMA (log2) normalized data using the frma function in the frma package in Biocinductor

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

treatment_protocol: short hairpin RNA complexes with complemen- tary sequence to the mRNA sequence of 8 RAS pathway genes

tag: cell line

tag: genotype/variation

value: RAF1 knockdown


title: RAF1KD.SW480.biorep.6

description:
RAF1-E4-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: lesion_midUV_patient1

description: SAMPLE 13

value: epidermis

tag: treatment


title: RAF1KD.SW480.biorep.5


title: PitBullTerrier-BI_27388


title: RAF1KD.SW620.biorep.6


title: lesion_preUV_patient12

description: SAMPLE 12

source_name: psoriatic epidermis, before phototherapy

value: female

value: pre-UV


title: RAF1KD.SW480.biorep.4

description:
RAF1-E4-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: lesion_preUV_patient7

description: SAMPLE 7


title: lesion_preUV_patient9

description: SAMPLE 9


title: lesion_preUV_patient11

description: SAMPLE 11


title: lesion_midUV_patient9

description: SAMPLE 21


title: RAF1KD.SW620.biorep.4


title: PitBullTerrier-BI_27389


title: RAF1KD.SW480.biorep.3

description:
RAF1-E4-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: lesion_preUV_patient6

description:
SAMPLE 6
treatment suspnded for 3 weeks


title: lesion_preUV_patient8

description: SAMPLE 8


title: PitBullTerrier-BI_27386


title: PitBullTerrier-BI_27385


title: PitBullTerrier-BI_27387


title: PitBullTerrier-BI_27384


title: lesion_preUV_patient4

description: SAMPLE 4


title: lesion_midUV_patient6

description: SAMPLE 18


title: lesion_preUV_patient5

description:
SAMPLE 5
stopped treatment half way


title: RAF1KD.SW620.biorep.3


title: PitBullTerrier-BI_27383


title: RAF1KD.SW480.biorep2

description:
SW480 Raf1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 Raf1


title: lesion_preUV_patient3

description: SAMPLE 3


title: lesion_preUV_patient2

description: SAMPLE 2


title: PitBullTerrier-BI_27382


title: HSF2 siRNA day 8c

city: Turku

first: Matthias

last: Nees

address: Itäinen Pitkäkatu 4C

department: Biotechnology

country: Finland

institute: VTT

description: human cancer cell line PC-3, cultured in 3D organotypic conditions (laminin-rich microenvironment/Matrigel) for 8 days

hyb_protocol: 750 ng cRNA was hybridized on Sentrix HumanHT-12 v4 Expression BeadChips (Illumina) at 58°C overnight.

scan_protocol: Hybridized cRNA was detected with 1 mg/ml Cyanine3-streptavidine (GE Healthcare Biosciences), and arrays were scanned with BeadArray Reader (Illumina).

data_processing:
Data were quality checked and extracted using GenomeStudio software (Illumina), without normalization or background subtraction.
Raw microarray data were quantile-normalized, using the bioconductor R package “beadarray”. Normalized data were further processed using a variance and intensity filter (VST transformation). Statistical analysis of differential gene expression was performed using the limma and lumi R/Bioconductor packages.

source_name: PC3 transfected with siRNA targeting human HSF2, harvested after 8 days

label_protocol: 500 ng RNA was amplified with TotalPrep RNA Amplification kit (Ambion). IVT reaction was performed overnight (16 h) to yield sufficient biotinylated cRNA. RNA and cRNA concentrations were measured with NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc.). RNA integrity was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: For imaging of 3D cultures, cells were embedded between two layers of Matrigel (BD Biosciences) on uncoated Angiogenesis μ-slides (Ibidi Gmbh). Wells were filled with 10 μl of Matrigel/culture medium (1:1) and kept at 37°C until polymerization. Cells were then seeded on top, allowed to attach for 1-2 h at 37°C, and covered with a second layer of Matrigel/culture medium (1:4) before polymerization overnight at 37°C. For RNA and protein extractions, cells were cultured in Millicell hanging cell culture inserts with 1.0 µm PET transparent membranes (Millipore) on 6-well plates (Costar). Membranes were pre-coated with Matrigel/medium (1:1) and incubated at 37°C for 1-2 h to prevent attachment to the membrane. Cell suspension was mixed 1:4 with Matrigel, transferred to the coated well, and allowed to polymerize overnight at 37°C. For all 3D cultures, growth medium was changed every second day.

extract_protocol: 3D cultures of PC3 cells were washed with PBS and incubated on a rocker for 45 min in 5 mM EDTA in PBS to allow the spheroids to detach from the Matrigel. Spheroids were sedimented by centrifugation and RNA from three biological repeats was isolated using the RNeasy Kit (Qiagen). Contaminating genomic DNA was removed with DNase I treatment according to the RNeasy protocol and the samples were sent to the Finnish Microarray and Sequencing Centre (Turku, Finland) for processing.

treatment_protocol: PC3 cells were transfected with siRNA constructs using siLentFect Lipid Reagent (Bio-Rad Laboratories). Cells were suspended in Opti-MEM (Invitrogen) and reverse transfections were performed with 13.3 nM siRNA. For silencing of HSF1, a 1:1 mixture of two different siRNA constructs were used, while HSF2 was silenced as described.  AllStars Negative Control siRNA was used as a scrambled control. All siRNA constructs were purchased from Qiagen. After transfection, the cells were allowed to recover for 48 h before further treatment

tag: sirna transfection

value: HSF2 siRNA


title: PitBullTerrier-BI_27381


title: HSF2 siRNA day 8a


title: RAF1KD.SW620.biorep2

description:
SW620 Raf1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 Raf1


title: HSF1 siRNA day 8c

source_name: PC3 transfected with siRNA targeting human HSF1, harvested after 8 days

value: HSF1 siRNA


title: HSF1 siRNA day 8b


title: PitBullTerrier-BI_27380


title: Scr siRNA day 8b

source_name: PC3 transfected with scrambled control siRNA, harvested after 8 days

value: scrambled siRNA


title: lesion_preUV_patient1

description: SAMPLE 1

value: male


title: HSF1 siRNA day 8a


title: HSF2 siRNA day 8b


title: HSF2 siRNA day 5c

source_name: PC3 transfected with siRNA targeting human HSF2, harvested after 5 days


title: RAF1KD.SW620.biorep1

description:
RAF1_E4_SW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: Scr siRNA day 8a


title: Scr siRNA day 8c


title: NGFRKD.SW620.biorep.5

description:
NGFR-D9-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: NGFR knockdown


title: HSF1 siRNA day 5b

source_name: PC3 transfected with siRNA targeting human HSF1, harvested after 5 days


title: HSF2 siRNA day 5a


title: NGFRKD.SW480.biorep.6

description:
NGFR-D9-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: NGFRKD.SW620.biorep.4

description:
NGFR-D9-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: HSF1 siRNA day 5c


title: HSF2 siRNA day 5b


title: NGFRKD.SW620.biorep.3

description:
NGFR-D9-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: NGFRKD.SW480.biorep.3


title: NGFRKD.SW480.biorep2

description:
SW480 NGFR
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 NGFR


title: NGFRKD.SW480.biorep.4


title: NGFRKD.SW620.biorep2

description:
SW620 NGFR
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 NGFR


title: Scr siRNA day 5c

source_name: PC3 transfected with scrambled control siRNA, harvested after 5 days


title: NGFRKD.SW480.biorep.5


title: Scr siRNA day 5a


title: HSF1 siRNA day 5a


title: slide3-array4

city: Edmonton

first: Stephen

last: Tsoi

address: 4-32G Agriculture/Forestry Centre

department: AFNS

institute: University of Alberta

description: Dye-swap replicate of biological replicate set 3

hyb_protocol: Hybridization mixture was prepared along with Spike-In control according to Agilent Gene Expression Hybridization Kit 60-mer oligo microarray protocol version 4.0.

scan_protocol: Arrays were immediately scanned at 5 μm resolution after slides were washed  and dried with an Axon 4200AL scanner (635 nm for Cy5 and at 532 nm for Cy3) using the autoscan feature from the default setting and images were analysed with Gene Pix Pro 6.0. software

data_processing: FlexArray software was used for data normalization following first with simple background subtraction, LOWESS normalization within and between arrays.

organism: Sus scrofa

label_protocol: Antisense RNA (aRNA) labelling was done under ozone free environmental chamber. Antisense RNA (aRNA) was used for labeling using ULS™ Fluorescent Labeling Kit (Kreatech, Inc., Durham, NC, USA) for Agilent arrays (with Cy3 and Cy5). Labelling was also  done under ozone free environmental chamber.

extract_protocol: ZR-Duet™ DNA/RNA MiniPrep kit (Zymo Research Corporation, Irvine, CA, USA) was used for RNA extraction and at least 200ng of total RNA was used for aRNA synthesis using TargetAmp™ 1-Round aRNA Amplification Kit 103 (Epicentre Biotechnologies, Madison, WI, USA).

treatment_protocol:
Sows were inseminated while in heat and slaughtered 9 days after ovulation and the embryos recovered.
Embryos were collected on Day 9 of post-ovulation from FE group ; n=3  and SE group; n=3. DNA was extracted from more than 20 embryos for each group and individual embryo sexing was performed by PCR using sex specific primers. Five male and five female embryos were pooled separately from individual sows in each treatment group resulting in 12 distinct biological replicates.

tag: developmental stage

value: Day 9 embryo

tag: Sex

tag: treatment group

value: SE

value: FE


title: Scr siRNA day 5b


title: NGFRKD.SW620.biorep1

description:
NGFR_D9_SW4620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: Nr4a-TKO

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

institute: National Center for Global Health and Medicine

hyb_protocol: 480 ng of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse 8x60k Microarrays (G4852) for 17 hours at 65Â°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 37Â°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 (G2539A) using one color scan setting for 8x60k array slides ( Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with GeneSpring GX Ver.12.6.0 (Agilent) using default parameters (protocol GE1_1010_sep10 and Grid: 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Nr4a-TKO Treg cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 600 ng RNA using the Low Input Quick Amp labeling kit, one-color (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.

extract_protocol: RNA was prepared using the RNA-iso (Takara, Japan) following the manufacturer's recommendations. Extracted total RNA was further purified using RNAeasy-micro kit.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Treg cells from wild-type or Nr4a-TKO mice were soreted, and directly lysed with RNA-iso total RNA extraction solution (Takara, Japan).

value: 5 week old

tag: cell type

value: regulatory T cells

tag: genotype


title: slide3-array3

description: Comparing FE and SE in female  (biological replicate set 3)


title: slide3-array2


title: slide3-array1

description: Comparing FE and SE in male  (biological replicate set 3)


title: Wild-type

source_name: Wild-type Treg cells

value: wild-type


title: MAPK3KD.SW620.biorep.6

description:
MAPK3-A1-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: MAPK3 knockdown


title: NGFRKD.SW480.biorep1

description:
NGFR_D9_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: MAPK3KD.SW480.biorep.6


title: slide2-array4

description: Dye-swap replicate of biological replicate set 2


title: slide2-array2

description: Dye-swap replicate of biological replicate set 1


title: slide2-array3

description: Comparing FE and SE in female  (biological replicate set 2)


title: slide2-array1

description: Comparing FE and SE in female  (biological replicate set 1)


title: MAPK3KD.SW620.biorep.5

description:
MAPK3-A1-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: slide1-array4


title: MAPK3KD.SW480.biorep.5


title: MAPK3KD.SW620.biorep.4

description:
MAPK3-A1-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: RWV_24h_rep3

city: San Francisco

first: Tammy

middle: T

last: Chang

address: 513 Parnassus Ave., HSW 1601

department: Surgery

institute: University of California, San Francisco

hyb_protocol: After fragmentation, 10ug of biotinylated aRNA was hybridized on to the Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA) through the UCSF Gladstone Institute Genomics Core. The arrays were stained using a Fluidics Station 400 (Affymetrix).

scan_protocol: Gene arrays were scaned using a GeneArray Scanner (Affymetrix).

data_processing: Microarray data were analyzed using the GeneSpring GX v. 12.0 software (Silicon Genetics, Redwood City, CA) and the GC-RMA algorithm normalized to the median of the control samples (freshly isolated hepatolcytes, t0).

source_name: hepatocyte, RWV, cultured 24h

label_protocol: MessageAmp II-Biotin Enhanced Kit per the manufacturer’s instructions (Ambion, Austin, TX)

extract_protocol: RNeasy Mini Kit per manufacturer's instructions (QIAGEN, Valencia, CA)

treatment_protocol: Primary mouse hepatocytes were cultured as monolayers in TCDs or as 3D aggregates in RWVs for 4 or 24 hours.

tag: strain

value: Male


title: t0_rep3

source_name: hepatocyte, freshly isolated


title: CPZ mouse 3

first: Ewa

last: Szalowska

address: Akkermaalsbos 2

institute: RIKILT-Wageningen UR

description: mouse precision cut liver slices prepared from livers of C57BL/6J

hyb_protocol: Per sample, 7.5ug cRNA of the obtained biotinylated cRNA samples was fragmented and hybridized in a final concentration of 0.0375 ug /ul on the Affymetrix HT Mouse genome 430 PM array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: After an automated process of washing and staining by the GeneTitan machine (Affymetrix, Santa Clara, CA, USA) using the Affymetrix HWS kit for Gene Titan, absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v 3.2 software.

data_processing: Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v 3.2 software.  The data Quality Control was performed in the program Affymetrix Expression Console v 1.1 (Affymetrix, Santa Clara, CA, USA) software to determine if all parameters were within quality specifications. The Probe Logarithmic Intensity Error Estimation (PLIER) algorithm method was used for probe summarisation. Non-normalized data in a form of the Cell Intensity File (*.CEL) were re-annotated (EntrezGene htmg430pm_Mm_ENTREZG) and the data were RMA normalized.

source_name: precision cut liver slices obtained from C57BL/6 treated with chlorpromazine (CPZ)

label_protocol: Biotin- labelled cRNA was generated from high-quality total RNA with the Affymetrix 3’IVT Express Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s specifications with an input of 100 ng total RNA.

growth_protocol: For transcriptome analysis, PCLS were cultured for 24 hours at 80% of oxygen; 5% CO2 and the remaining gas volume was filled up to 95% with N2. PCLS were exposed to model steatogenic compounds. The concentrations used in the exposure experiments were 50 μM for AMI, 200 μM for VA, and 40 μM for TET. Thereafter, RNA was extracted from three slices per each condition and after processing, the samples were hybridized on the HT Mouse Genome 430 PM array plate(s) using the Affymetrix GeneTitan system (Affymetrix, Santa Clara, CA, USA).

extract_protocol: RNA was extracted from three slices using the RNeasy Tissue Mini Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions.

treatment_protocol: Mouse precision cut liver slices (PCLS) were prepared from livers obtained from 5 different C57BL/6 male mice (24 weeks old). PCLS were cultured for 24 hours at 80% of oxygen; 5% CO2 and the remaining gas volume was filled up to 95% with N2. PCLS were exposed to model steatogenic compounds selected based on literature search. As cholestatic model compounds cyclosporin A (CsA), ethinyl estradion (EE), and chlorpromazine (CPZ) were selected. To select a non-toxic dose eventually to be used for exposure experiments and subsequent gene expression profiling experiments, the following concentrations ranges were tested: CsA 0-100 μM,  CPZ 0-80 μM,  EE 0-100 μM,  . CsA, EE, and CPZ were dissolved in DMSO. The compounds were added to the culture medium at a final concentration of 0.1% vol/vol in DMSO. Slices incubated with the solvents at 0.1% vol/vol served as controls. The viability of the slices was assessed by measuring the ATP content normalized on protein.   Dose selection for the three cholestatic  exposures were performed in five independent experiments with slices obtained from five mice.  Concentrations that did not cause a decrease of the level of ATP normalized on protein compared to controls were selected. The concentrations used in the exposure experiments were as follows: 40 μM CsA, 20 μM CPZ, and 10 μM EE.

tag: mouse strain

tag: age of mouse

value: 23 weeks

tag: tissue

value: liver slices

tag: culture time

value: 24 hours


title: t0_rep2


title: slide1-array3

description: Comparing FE and SE in male  (biological replicate set 2)


title: MAPK3KD.SW480.biorep.4


title: RWV_24h_rep2


title: lesion_preUV_patient10

description: SAMPLE 10

tag: disease state

value: plaque type psoriasis

value: epidermis

tag: gender

value: female

value: 2 y

value: phototherapy

tag: time

value: pre-UV


title: slide1-array2

value: Day 9 embryo

value: male


title: slide1-array1

description: Comparing FE and SE in male  (biological replicate set 1)

value: FE

value: SE


title: CPZ mouse 1


title: t0_rep1


title: MAPK3KD.SW620.biorep.3

description:
MAPK3-A1-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

tag: cell line


title: CPZ mouse 4


title: EE mouse 4

source_name: precision cut liver slices obtained from C57BL/6 treated withethinyl estradiol (EE)


title: EE mouse 5


title: TCD_24h_rep3

source_name: hepatocyte, TCD, cultured 24h


title: CPZ mouse 5


title: CPZ mouse 2


title: MAPK3KD.SW480.biorep.3

tag: genotype/variation


title: EE mouse 3


title: EE mouse 1


title: RWV_24h_rep1


title: EE mouse 2


title: CsA mouse 5

source_name: precision cut liver slices obtained from C57BL/6 treated with Cyclosporin A (CsA)


title: CsA mouse 3


title: CsA mouse 2


title: MAPK3KD.SW480.biorep1

description:
MAPK3_A1_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: CsA mouse 4


title: RAF1KD.SW480.biorep1

description:
RAF1_E4_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: RAF1 knockdown


title: RWV_4h_rep1

source_name: hepatocyte, RWV, cultured 4h


title: RWV_4h_rep3


title: DMSO control for CPZ mouse 5

source_name: precision cut liver slices obtained from C57BL/6 treated with DMSO


title: DMSO control for CPZ mouse 4


title: CsA mouse 1


title: MAPK3KD.SW620.biorep2

description:
SW620 MAPK3
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 MAPK3


title: MAPK3KD.SW620.biorep1

description:
MAPK3_A1_SW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: TCD_24h_rep2


title: MAPK3KD.SW480.biorep2

description:
SW480 MAPK3
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 MAPK3


title: NGFRKD.SW620.biorep.6

description:
NGFR-D9-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: NGFR knockdown


title: TCD_4h_rep3

source_name: hepatocyte, TCD, cultured 4h


title: MAPK1KD.SW620.biorep.6

description:
MAPK1-C9-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: MAPK1 knockdown


title: DMSO control for EE mouse 5


title: DMSO control for EE mouse 3


title: DMSO control for CPZ mouse 3


title: DMSO control for CPZ mouse 1


title: MAPK1KD.SW620.biorep.5

description:
MAPK1-C9-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: DMSO control for EE mouse 4


title: RWV_4h_rep2

value: Male


title: MAPK1KD.SW480.biorep.6


title: TCD_24h_rep1


title: DMSO control for EE mouse 1

value: 23 weeks


title: MAPK1KD.SW480.biorep.5


title: DMSO control for EE mouse 2

value: liver slices


title: DMSO control for CPZ mouse 2

value: 24 hours


title: ino24N3

city: Göteborg

first: Pramote

last: Chumnanpuen

address: Kemivägen 10

department: Chemical and Biological Engineering

institute: Chalmers University of Technology

hyb_protocol: Samples were hybridized with GeneChip yeast2 Arrays (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix) by A GeneChip Fluidics Station FS-400 and GeneChip Scanner 3000 7G.

data_processing: Probe Logarithmic Intensity Error (PLIER)

label_protocol: Labelling was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

growth_protocol: Chemostatcultivation on minimal media

extract_protocol: Total RNA was isolated from frozen cell pellets using FastRNA® Pro RED kit (QBiogene, Inc, USA).

treatment_protocol: Biomass samples were taken at steadystate, cooled down imeediately and centrifuged with cooling. The cell prllets were frozen in liquid nitrogen.

value: ino2 and ino4 mutant

tag: growth protocol

value: Nitrogen limited


title: DMSO control for CsA mouse 4


title: DMSO control for CsA mouse 5


title: MAPK1KD.SW480.biorep.4

description:
MAPK1-C9-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

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


title: MAPK1KD.SW620.biorep.4


title: ino24N1


title: DMSO control for CsA mouse 1


title: ino24N2


title: DMSO control for CsA mouse 3


title: MAPK1KD.SW620.biorep.3

description:
MAPK1-C9-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: MAPK1KD.SW480.biorep.3


title: VA mouse 4

source_name: precision cut liver slices obtained from C57BL/6 treated with valproic acid

treatment_protocol: Mouse precision cut liver slices (PCLS) were prepared from livers obtained from 5 different C57BL/6 male mice (24 weeks old). PCLS were cultured for 24 hours at 80% of oxygen; 5% CO2 and the remaining gas volume was filled up to 95% with N2. PCLS were exposed to model steatogenic compounds selected based on literature search. As steatogenic model compounds amiodarone (AMI), valproic acid (VA), and tetracycline (TET) were selected. To select a non-toxic dose eventually to be used for exposure experiments and subsequent gene expression profiling experiments, the following concentrations ranges were tested: AMI 0-100 μM,   VA 0-500 μM, and TET 0-100 μM. AMI was dissolved in DMSO, VA and TET were dissolved in ethanol (EtOH). The compounds were added to the culture medium at a final concentration of 0.1% vol/vol in an appropriate solvent (DMSO or EtOH). Slices incubated with the solvents at 0.1% vol/vol served as controls. The viability of the slices was assessed by measuring the ATP content normalized on protein.   Dose selection for the three steatogenic exposures were performed in five independent experiments with slices obtained from five mice.  Concentrations that did not cause a decrease of the level of ATP normalized on protein compared to controls were selected. The concentrations used in the exposure experiments were 50 μM for AMI, 200 μM for VA, and 40 μM for TET.


title: VA mouse 3


title: VA mouse 5


title: DMSO control for CsA mouse 2


title: ino24C1

value: Carbon limited


title: ino4_N_3

value: ino4 mutant


title: ino24C3


title: ino24C2


title: MAPK1KD.SW480.biorep2

description:
SW480 MAPK1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 MAPK1


title: AMI mouse 5

source_name: precision cut liver slices obtained from C57BL/6 treated with amiodarone


title: MAPK1KD.SW620.biorep2

description:
SW620 MAPK1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 MAPK1


title: VA mouse 1


title: ino4_N_2


title: ino4_N_1


title: ino4_C_2


title: MAPK1KD.SW620.biorep1

description:
MAPK1_C9_SW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: ino4_C_1


title: ino4_C_3


title: AMI mouse 4

description: mouse precision cut liver slices prepared from livers of C57BL/6J


title: MAP2K2KD.SW620.biorep.6

description:
MAP2K2-C3-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: MAP2K2 knockdown


title: AMI mouse 2


title: MAP2K2KD.SW480.biorep.6


title: VA mouse 2


title: ino2_N_3

value: ino2 mutant


title: human bone marrow stromal cells from patient 2 treated with LuCaP 23.1 conditioned media

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
PT2_23.1CM
bone marrow stromal cells isolated from patient 2 treated with LuCaP 23.1 conditioned medium

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505B (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid, extract, and normalize data using the GE2_105_Jan09 protocol with default settings.

label_protocol: amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: sample type

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: molecule subtype

value: second round aRNA

extract_protocol: Total RNA from osteoblasts was extracted using STAT-60 (Tel-Test, INC. Friendswood, TX) according to the manufacturer's protocol followed by two rounds of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer's specifications.

tag: treated with

value: LuCaP 23.1 conditioned medium


title: MAP2K2KD.SW480.biorep.5

description:
MAP2K2-C3-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: MAP2K2KD.SW620.biorep.5


title: human bone marrow stromal cells from patient 1 treated with LuCaP 23.1 conditioned media

description:
PT1_23.1CM
bone marrow stromal cells isolated from patient 1 treated with LuCaP 23.1 conditioned medium

value: male


title: AMI mouse 1


title: ino2_N_2


title: human bone marrow stromal cells from patient 3 treated with LuCaP 23.1 conditioned media

description:
PT3_23.1CM
bone marrow stromal cells isolated from patient 3 treated with LuCaP 23.1 conditioned medium


title: MAP2K2KD.SW480.biorep.4

description:
MAP2K2-C3-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: AMI mouse 3


title: MAP2K2KD.SW620.biorep.4


title: TET mouse 5

source_name: precision cut liver slices obtained from C57BL/6 treated with tetracycline


title: human bone marrow stromal cells from patient 3 treated with mineralization media

description:
PT3_23.1MM
bone marrow stromal cells isolated from patient 3 treated with control medium

value: mineralization media


title: MAP2K2KD.SW620.biorep.3

description:
MAP2K2-C3-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: human bone marrow stromal cells from patient 2 treated with mineralization media

description:
PT2_23.1MM
bone marrow stromal cells isolated from patient 2 treated with control medium


title: ino2_C_3


title: TET mouse 4


title: human bone marrow stromal cells from patient 1 treated with mineralization media

description:
PT1_23.1MM
bone marrow stromal cells isolated from patient 1 treated with control medium


title: ino2_N_1


title: opi1N3

value: opi1 mutant


title: MAP2K2KD.SW620.biorep2

description:
SW620 MAP2K2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 MAP2K2


title: TET mouse 1


title: Ethanol control mouse 4

source_name: precision cut liver slices obtained from C57BL/6 treated with ethanol


title: RPE/choroid-control-7

city: Iowa City

first: S. Scott

last: Whitmore

state: IA

address: 375 Newton Road

department: The University of Iowa Institute for Vision Research

institute: The University of Iowa

description: Age-related maculopathy: Normal fundus exam <2 years

hyb_protocol: Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA)

scan_protocol: Affymetrix Model 3000 scanner with 7G upgrade running GeneChip operating system (ver. 1.4; Affymetrix, Inc.)

data_processing:
(1) RMA normalization using AltAnalyze (ver. 2.0.7 beta); (2) Batch correction using ComBat algorithm in R, preserving AMD status, CFH genotype, and gender as covariates; (3) Batch-corrected expression data imported into AltAnalyze and processed (Ensembl 65 database, genome build Hg19, using only probesets mapping to consitutive exons [shared by all Ensembl transcripts for a given gene; see AltAnalyze documentation], masking-cross hybridizing probesets, filtering probesets expressed below non-log level of 70); (4) Samples CTRL3 and CTRL9 identified as outliers by arrayQualityMetrics and removed. Steps 1-3 repeated.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: Hs_gene_core.mps

source_name: RPE/choroid, normal tissue

label_protocol: (1) RNA to cDNA conversion (WT-Ovation Pico RNA Amplification System [NuGEN Technologies, San Carlos, CA); (2) cDNA purification (QIAGEN QIAquick PCR purification column); (3) sense target (ST)-cDNA conversion (WT-Ovation Exon Module v1 (NuGEN Technologies); (4) purification; (5) fragmentation (85 nt mean length); (6) biotin labelling (NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies).

growth_protocol: not applicable

extract_protocol: During eye dissection, macula region was removed using a 6mm trephine punch. RPE/choroid was separated from the retina and flash frozen in liquid nitrogen within 4 hours of death. Tissue was subsequently stored at -80°C. RNA was extracted using an Rneasy Mini Kit (QIAGEN, Valencia, CA) following to manufacture's protocol.

treatment_protocol: not applicable

value: retinal pigment epithelium (RPE)/choroid

tag: age

value: HY

tag: batch

value: A


title: RPE/choroid-control-8

value: female

tag: genotype

value: YY

value: B


title: TET mouse 2

value: 23 weeks

value: liver slices

value: 24 hours


title: MAP2K2KD.SW480.biorep.3

value: MAP2K2 knockdown


title: TET mouse 3


title: opi1N1

value: Nitrogen limited


title: ino2_C_1

value: ino2 mutant

value: Carbon limited


title: ino2_C_2


title: Ethanol control mouse 3


title: TCD_4h_rep1

tag: strain

tag: Sex

value: Male


title: RPE/choroid-control-6

value: HH


title: RPE/choroid-control-4

description: Age-related maculopathy: Normal fundus exam but old records; normal gross appearance


title: MAP2K2KD.SW480.biorep2

description:
SW480 MAP2K2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 MAP2K2


title: MAP2K2KD.SW620.biorep1

description:
MAP2K2_C3_SW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: Ethanol control mouse 2

tag: mouse strain

tag: age of mouse

value: male


title: RPE/choroid-control-5

tag: tissue


title: Ethanol control mouse 1

tag: culture time


title: RPE/choroid-control-2

description: Age-related maculopathy: Normal fundus exam <2 years; large cup to disc ratio

tag: gender


title: opi1N2

value: opi1 mutant


title: TCD_4h_rep2


title: MAP2K2KD.SW480.biorep1

description:
MAP2K2_C3_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: MAP2K1KD.SW620.biorep.6

description:
MAP2K1-C1-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: MAP2K1 knockdown


title: DMSO control mouse 4

description: mouse precision cut liver slices prepared from livers of C57BL/6J


title: MAP2K1KD.SW480.biorep.6


title: opi1CB3

description: opi1_Clim_bottom phase of CO2 profile

source_name: opi1_Clim_bottom phase of CO2 profile

value: Carbon limited_bottom phase of CO2


title: opi1CB2

description: opi1_Clim_bottom phase of CO2 profile


title: RPE/choroid-AMD-9

description: Age-related maculopathy: RPE changes

source_name: RPE/choroid, AMD affected

value: retinal pigment epithelium (RPE)/choroid


title: opi1CT3

description: opi1_Clim_top phase of CO2 profile

source_name: opi1_Clim_top phase of CO2 profile

value: Carbon limited_top phase of CO2


title: opi1CB1

description: opi1_Clim_bottom phase of CO2 profile


title: DMSO control mouse 2


title: DMSO control mouse 1


title: opi1CT2

description: opi1_Clim_top phase of CO2 profile


title: opi1CT1

description: opi1_Clim_top phase of CO2 profile


title: RPE/choroid-AMD-6

description: Age-related maculopathy: RPE changes

value: A


title: MAP2K1KD.SW480.biorep.5

description:
MAP2K1-C1-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: DMSO control mouse 3


title: RPE/choroid-control-1

value: HY

value: B


title: RPE/choroid-AMD-7

description: Age-related maculopathy: RPE changes

value: female

value: YY


title: RPE/choroid-AMD-8

description: Age-related maculopathy: Numerous large drusen, no atrophy or exudate


title: MAP2K1KD.SW620.biorep.5


title: RPE/choroid-AMD-5

description: Age-related maculopathy: RPE changes; neovascular membrane in contralateral eye


title: PQ mouse 5

source_name: precision cut liver slices obtained from C57BL/6 treated with PQ

treatment_protocol: Mouse precision cut liver slices (PCLS) were prepared from livers obtained from 5 different C57BL/6 male mice (24 weeks old). PCLS were cultured for 24 hours at 80% of oxygen; 5% CO2 and the remaining gas volume was filled up to 95% with N2. PCLS were exposed to model necrotic compounds selected based on published reports. As necrotic model compounds acetaminophen (APAP), isoniazid (ISND) , and paraquat (PQ)  were selected. To select a non-toxic dose eventually to be used for exposure experiments and subsequent gene expression profiling experiments, the following concentrations ranges were tested: PQ 0-10 μM,  APAP 0-3000 μM and ISND 0-1000 μM. APAP and PQ were dissolved in DMSO, and ISND was dissolved in PBS. The compounds were added to the culture medium at a final concentration of 0.1% vol/vol in an appropriate solvent (DMSO or PBS). Slices incubated with the solvents at 0.1% vol/vol served as controls. The viability of the slices was assessed by measuring the ATP content normalized on protein.   Dose selection for the three necrotic exposures were performed in five independent experiments with slices obtained from five mice.  Concentrations that did not cause a decrease of the level of ATP normalized on protein compared to controls were selected. The concentrations used in the exposure experiments were as follows: 1000 μM APAP, 1000 μM ISND, and 5 μM PQ.

value: 23 weeks

value: liver slices

value: 24 hours


title: MAP2K1KD.SW480.biorep.4

description:
MAP2K1-C1-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: MAP2K1KD.SW620.biorep.4


title: refN3

value: Reference

value: Nitrogen limited


title: refN2


title: MAP2K1KD.SW620.biorep.3

description:
MAP2K1-C1-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: refN1


title: RPE/choroid-AMD-4

description: Age-related maculopathy: Macular drusen


title: PQ mouse 4


title: MAP2K1KD.SW480.biorep.3


title: PQ mouse 2


title: PQ mouse 1


title: ISND mouse 5

source_name: precision cut liver slices obtained from C57BL/6 treated with ISND


title: RPE/choroid-AMD-1

description: Age-related maculopathy: RPE changes


title: PQ mouse 3


title: MAP2K1KD.SW480.biorep2

description:
SW480 MAP2K1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 MAP2K1


title: RPE/choroid-AMD-3

description: Age-related maculopathy: Macular drusen


title: refC2

value: Carbon limited


title: MAPK1KD.SW480.biorep1

description:
MAPK1_C9_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: MAPK1 knockdown


title: MAP2K1KD.SW620.biorep1

description:
MAP2K1_C1_SW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: MAP2K1KD.SW620.biorep2

description:
SW620 MAP2K1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 MAP2K1


title: RPE/choroid-AMD-2

description: Age-related maculopathy: RPE changes


title: ISND mouse 4

value: male


title: MAP2K1KD.SW480.biorep1

description:
MAP2K1_C1_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: MAP2K1 knockdown


title: refC3


title: refC1


title: HRASKD.SW620.biorep.6

description:
HRAS-A1-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments

value: HRAS knockdown


title: EPS Mutant Wet Replicate 4

city: Kgs Lyngby

first: Gamze

last: Gulez

address: Miljoevej 113

department: Environmental Engineering

country: Denmark

institute: Technical University of Denmark

description:
This sample is of  EPS mutantPseudomonas putida KT2440. It is the fourth of four  biological replicates used in this experiment and grown without water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period

hyb_protocol: Labeled cDNA was hybridized to the array probes on the array per manufacturer’s protocol (Nimblegen Hybridization System, WI, USA).

scan_protocol: Scanning was performed by  using GenePix 4000B Scanner (Molecular Devices, CA, USA).

data_processing: Gene expression data were analyzed with the statistical software R (www.r-project.org) using the oligo and limma packages available in Bioconducter (www.bioconductor.org). Data were normalized using Robust Multiarray Average (RMA) approach with the quantile method

organism: Pseudomonas putida KT2440

source_name: Pseudomonas putida KT2440 EPS mutant without water stress

label_protocol: Labeling and cDNA synthesis was performed per manufacturer’s protocol (One Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, Agilent, CA).

extract_protocol: RNA extraction was performed using Agilent MiniRNA Kit (CA, USA) following the manufacturer‘s protocol. RNA concentrations and integrities were checked using NanoDrop 1000 (Thermo Fisher Scientific, DE, USA), Qubit 2.0 Fluorometer (Invitrogen, USA), Agilent 2100 Bioanalzyer (CA, USA), and gel electrophoresis.

tag: treatment

value: Wet

value: Knockout mutant deficient in EPS synthesis


title: ISND mouse 2


title: EPS Mutant Wet Replicate 3

description:
This sample is of EPS mutantPseudomonas putida KT2440. It is the third of four biological replicates used in this experiment and grown without water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: HRASKD.SW620.biorep.5

description:
HRAS-A1-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments

tag: cell line


title: ISND mouse 1


title: EPS Mutant Wet Replicate 1

description:
This sample is of  EPS mutantPseudomonas putida KT2440. It is the first of four biological replicates used in this experiment and grown without water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: HRASKD.SW480.biorep.6

tag: genotype/variation


title: EPS Mutant Wet Replicate 2

description:
This sample is of EPS mutantPseudomonas putida KT2440. It is the second of four biological replicates used in this experiment and grown without water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: APAP mouse 5

description: mouse precision cut liver slices prepared from livers of C57BL/6J

source_name: precision cut liver slices obtained from C57BL/6 treated with APAP


title: EPS Mutant Dry Replicate 4

description:
This sample is of EPS mutant Pseudomonas putida KT2440. It is the fourth of four  biological replicates used in this experiment and grown under water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period

source_name: Pseudomonas putida KT2440 EPS mutant under water stress

value: Dry


title: HRASKD.SW480.biorep.5


title: ISND mouse 3


title: Alginate Mutant Wet Replicate 4

description:
This sample is of  alginate mutantPseudomonas putida KT2440. It is the fourth of four biological replicates used in this experiment and grown without water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period

source_name: Pseudomonas putida KT2440 alginate mutant without water stress

value: Knockout mutant deficient in alginate synthesis


title: EPS Mutant Dry Replicate 1

description:
This sample is of EPS mutant Pseudomonas putida KT2440. It is the first of four  biological replicates used in this experiment and grown under water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: EPS Mutant Dry Replicate 2

description:
This sample is of  EPS mutant Pseudomonas putida KT2440. It is the second of four biological replicates used in this experiment and grown under water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: EPS Mutant Dry Replicate 3

description:
This sample is ofEPS mutant Pseudomonas putida KT2440. It is the third of four  biological replicates used in this experiment and grown under water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: APAP mouse 4


title: HRASKD.SW620.biorep.3

description:
HRAS-A1-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: APAP mouse 2


title: HRASKD.SW620.biorep.4

description:
HRAS-A1-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: APAP mouse 3


title: HRASKD.SW480.biorep.3


title: Alginate Mutant Wet Replicate 3

description:
This sample is of  alginate mutantPseudomonas putida KT2440. It is the third of four  biological replicates used in this experiment and grown without water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: HRASKD.SW480.biorep.4


title: APAP mouse 1


title: Alginate Mutant Wet Replicate 2

description:
This sample is of  alginate mutantPseudomonas putida KT2440. It is the sedond of four  biological replicates used in this experiment and grown without water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: Alginate Mutant Dry Replicate 3

description:
This sample is of  alginate mutant Pseudomonas putida KT2440. It is the third of four  biological replicates used in this experiment and grown under water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period

source_name: Pseudomonas putida KT2440 alginate mutant under water stress


title: control PBS mouse 2

source_name: precision cut liver slices obtained from C57BL/6 treated with PBS


title: control PBS mouse 3


title: HRASKD.SW480.biorep2

description:
SW480 HRAS
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 HRAS


title: Alginate Mutant Dry Replicate 4

description:
This sample is of  alginate mutant Pseudomonas putida KT2440. It is the fourth of four  biological replicates used in this experiment and grown under water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: Alginate Mutant Wet Replicate 1

description:
This sample is of  alginate mutantPseudomonas putida KT2440. It is the first of four wild-type biological replicates used in this experiment and grown without water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: control PBS mouse 1


title: HRASKD.SW620.biorep2

description:
SW620 HRAS
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 HRAS


title: HRASKD.SW620.biorep1

description:
HRAS_B3_SW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: control PBS mouse 4


title: HRASKD.SW480.biorep1

description:
HRAS_B3_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: control.nontrans.SW620.biorep.7

description:
SW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: Alginate Mutant Dry Replicate 2

description:
This sample is of  alginate mutant Pseudomonas putida KT2440. It is the second of four biological replicates used in this experiment and grown under water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: control DMSO mouse 4

description: mouse precision cut liver slices prepared from livers of C57BL/6J

source_name: precision cut liver slices obtained from C57BL/6 treated with DMSO


title: control DMSO mouse 3


title: Alginate Mutant Dry Replicate 1

description:
This sample is of alginate mutant Pseudomonas putida KT2440. It is the first of four  biological replicates used in this experiment and grown under water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: control.nontrans.SW480.biorep.7

description:
SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: WT Wet Replicate 4

description:
This sample is of wild-type Pseudomonas putida KT2440. It is the fourth of four wild-type biological replicates used in this experiment grown without water stress.
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period

source_name: Pseudomonas putida KT2440 WT without water stress

value: Wild type


title: control DMSO mouse 2


title: WT Wet Replicate 3

description:
This sample is of wild-type Pseudomonas putida KT2440. It is the third of four wild-type biological replicates used in this experiment grown without water stress.
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: WT Wet Replicate 2

description:
This sample is of wild-type Pseudomonas putida KT2440. It is the second of four wild-type biological replicates used in this experiment grown without water stress.
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: control.nontrans.SW480.biorep2

description:
SW480 Neg Cntrl
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 Neg Cntrl


title: Leghorn, biological rep5

city: Knoxville

first: Bo

last: Ji

state: TN

address: 2640 Morgan Circle Drive

department: Animal Science

institute: University of Tennessee

description: Gene expression data from adipose tissue of 3 week Leghorn

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Statistical analysis of the microarray data was performed using R 2.13.2 and routines contained in Bioconductor (bioconductor.org). GC robust multi-array average (GCRMA) was used to normalize and scale the raw data from CEL files.

organism: Gallus gallus

source_name: Leghorn GHs 13

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was isolated from chicken adipose samples using the RNeasy Lipid kit and incorporating an on-column DNase treated with the RNase-free DNase Set according to the manufacturer's protocol.

treatment_protocol: At 3 week of age, male birds from three distinct genetic lines of chickens (Broiler, Fayoumi and Leghorn) were used.

value: adipose

tag: breed

value: Leghorn

value: 3 weeks


title: control.nontrans.SW620.biorep1

description:
NonTransducedControlSW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: Leghorn, biological rep6


title: control.nontrans.SW620.biorep2

description:
SW620 Neg Cntrl
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 Neg Cntrl


title: Leghorn, biological rep4


title: control DMSO mouse 1

city: Wageningen

value: 23 weeks

value: liver slices


title: Leghorn, biological rep3


title: Normal N9 nsp

description: Hybridized to 250K_Nsp

source_name: whole blood DNA extraction

tag: sample type

value: normal reference

value: blood


title: Normal N10 nsp

description: Hybridized to 250K_Nsp


title: control.nontrans.SW480.biorep1

description:
NonTransducedControlSW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: Normal N8 nsp

description: Hybridized to 250K_Nsp


title: WT Wet Replicate 1

description:
This sample is of wild-type Pseudomonas putida KT2440. It is the first of four wild-type biological replicates used in this experiment grown without  water stress.
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: WT Dry Replicate 3

description:
This sample is of wild-type Pseudomonas putida KT2440. It is the third of four wild-type biological replicates used in this experiment grown under water stress.
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period

source_name: Pseudomonas putida KT2440 WT under water stress


title: WT Dry Replicate 4

description:
This sample is of wild-type Pseudomonas putida KT2440. It is the fourth of four wild-type biological replicates used in this experiment grown under water stress.
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: Leghorn, biological rep2


title: Leghorn, biological rep1


title: root_6h_rep3

city: New York

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

hyb_protocol: 1.5 ug of Cy3-labelled 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 ATH NAT array for 17 hours at 65Â°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 37Â°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 using one color scan setting for 8x60k array slides.

data_processing: Raw data of processed signal intensities are obtained by analysis using Feature Extraction Software (Agilent) with default parameters. Standard QC analysis, background normalization and quantile normalization were performed using GeneSpring GX Software (Agilent) with default parameters.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: root, white light 6h, replicate 3

label_protocol: We performed RNA labeling, hybridization and scaning using protocols according to the Agilent's instructions. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).

growth_protocol: Arabidopsis thaliana ecotype Col-0 plants were used in this study. For sampling etiolated and de-etiolated seedlings, seeds were surface-sterilized in a 70% ethanol briefly and placed directly into a 30% Clorox with 0.1% Triton X-100 for 10 min and rinsed five times with sterilized water. Seeds were resuspended in a sterilized 0.15% (w/v) agarose and then sown in rows onto Murashige and Skoog (MS; MB biomedical, LLC, 263324) medium with 1% sucrose, Myo-inositol (Sigma, I3011), MES (Sigma, M8250) and 0.8% Bactoagar.

extract_protocol: Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen).

treatment_protocol: Seeds on plate were stratified at 4℃ for 3 days and exposed to white light (100 umol m-2 s-1) for 1h at 22℃ to initiate germination before being transferred to continuous darkness at 22℃ for 4 day. After sampling of etiolated seedlings in the dark, seedlings on plates were exposed to continuous white light (100 umol m-2 s-1) for 1 and 6h. Prior to sampling, de-etiolated seedlings were divided into cotyledons, hypocotyls and roots, and organ samples were harvested and frozen immediately in liquid nitrogen and stored at -80℃.

tag: organ

value: root

tag: light treatment

value: white light 6h


title: WT Dry Replicate 2

description:
This sample is of wild-type Pseudomonas putida KT2440. It is the second of four wild-type biological replicates used in this experiment grown under water stress.
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: Normal N6 nsp

description: Hybridized to 250K_Nsp

extract_protocol: QiaAmp DNA Blood Kit


title: Normal N4 nsp

description: Hybridized to 250K_Nsp


title: control.nontarget.SW620.biorep.6

description:
NONTARGET-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: root_6h_rep1

source_name: root, white light 6h, replicate 1


title: Fayoumi, biological rep5

description: Gene expression data from adipose tissue of 3 week Fayoumi

source_name: Fayoumi M 5.1

value: Fayoumi

tag: age

value: male


title: control.nontarget.SW480.biorep.6


title: Fayoumi, biological rep4


title: control.nontarget.SW620.biorep.5

description:
NONTARGET-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: WT Dry Replicate 1

description:
This sample is of wild-type Pseudomonas putida KT2440. It is the first of four wild-type biological replicates used in this experiment and grown under water stress
Aliquots of overnight grown P. putida KT2440 and its mutant cells were inoculated (approx. 1x107 cells in 100 µl) on the surface of ceramic plates. Total duration of the incubation was always 5 days, after which the cells were harvested (see below). The cells were either maintained at -0.5 kPa (wet) until the termination of experiment (control) or subjected to -0.4 MPa Ψm (dry) for the last 4 hr of the 5-day incubation period


title: control.nontarget.SW480.biorep.5


title: Normal N7 nsp

description: Hybridized to 250K_Nsp


title: Normal N5 nsp

description: Hybridized to 250K_Nsp


title: Fayoumi, biological rep3


title: control.nontarget.SW620.biorep.4

description:
NONTARGET-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: control.nontarget.SW480.biorep.4


title: Normal N3 nsp

description: Hybridized to 250K_Nsp


title: Normal N2 nsp

description: Hybridized to 250K_Nsp


title: Tumor MPI-528 nsp

description: Hybridized to 250K_Nsp

source_name: Whole tissue of tumor biopsy

value: tumor

tag: disease state

value: aggressive B-cell lymphoma


title: hypocotyl_6h_rep2

source_name: hypocotyl, white light 6h, replicate 2

value: hypocotyl


title: hypocotyl_6h_rep3

source_name: hypocotyl, white light 6h, replicate 3


title: Tumor MPI-032 nsp

description: Hybridized to 250K_Nsp


title: root_6h_rep2

source_name: root, white light 6h, replicate 2


title: Fayoumi, biological rep2


title: control.nontarget.SW620.biorep.3

description:
NONTARGET-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: Fayoumi, biological rep1


title: hypocotyl_6h_rep1

source_name: hypocotyl, white light 6h, replicate 1


title: cotyledon_6h_rep3

source_name: cotyledon, white light 6h, replicate 3

value: cotyledon


title: control.nontarget.SW480.biorep.3


title: Normal N1 nsp

description: Hybridized to 250K_Nsp


title: Tumor MPI-031 nsp

description: Hybridized to 250K_Nsp


title: control.nontarget.SW480.biorep2

description:
SW480 NT Cntrl
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 NT Cntrl


title: cotyledon_6h_rep2

source_name: cotyledon, white light 6h, replicate 2


title: broiler, biological rep5

description: Gene expression data from adipose tissue of 3 week broiler

source_name: Broiler

value: Broiler


title: control.nontarget.SW620.biorep2

description:
SW620 NT Cntrl
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 NT Cntrl


title: root_1h_rep3

source_name: root, white light 1h, replicate 3

value: white light 1h


title: cotyledon_6h_rep1

source_name: cotyledon, white light 6h, replicate 1


title: control.nontarget.SW620.biorep1

description:
pLKO_NonTarget_SW620
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: broiler, biological rep2

value: adipose


title: root_1h_rep1

source_name: root, white light 1h, replicate 1


title: broiler, biological rep4


title: cotyledon_1h_rep2

source_name: cotyledon, white light 1h, replicate 2


title: control.ev.SW620.biorep.5

description:
EMPTYPLKO-B1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: control.ev.SW480.biorep.5


title: control.ev.SW620.biorep.6

description:
EMPTYPLKO-B2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: cotyledon_1h_rep3

source_name: cotyledon, white light 1h, replicate 3


title: control.ev.SW480.biorep.4

description:
EMPTYPLKO-A2
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: control.ev.SW620.biorep.3

description:
EMPTYPLKO-A1
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: cotyledon_1h_rep1

source_name: cotyledon, white light 1h, replicate 1


title: hypocotyl_1h_rep2

source_name: hypocotyl, white light 1h, replicate 2


title: root_dark_rep2

source_name: root, dark, replicate 2

value: dark


title: root_dark_rep3

source_name: root, dark, replicate 3


title: control.nontarget.SW480.biorep1

description:
pLKO_NonTarget_SW480
Gene expression data from colorectal cancer cell lines used for knock-down experiments


title: hypocotyl_1h_rep3

source_name: hypocotyl, white light 1h, replicate 3


title: control.ev.SW620.biorep.4


title: control.ev.SW480.biorep.6


title: root_dark_rep1

source_name: root, dark, replicate 1


title: hypocotyl_1h_rep1

source_name: hypocotyl, white light 1h, replicate 1


title: control.ev.SW480.biorep.3


title: broiler, biological rep1

value: 3 weeks


title: control.ev.SW620.biorep2

description:
SW620 EV Cntrl
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW620 EV Cntrl


title: control.ev.SW480.biorep2

description:
SW480 EV Cntrl
Gene expression data from colorectal cancer cell lines used for knock-down experiments

source_name: SW480 EV Cntrl


title: hypocotyl_dark_rep3

source_name: hypocotyl, dark, replicate 3