title: Glomerulus WT mouse, 16 weeks, replicate 4

source_name: Glomerulus, WT 16 weeks

value: 16 weeks


title: Glomerulus ob mouse, 8 weeks, replicate 4

status: Public on Dec 10 2017

type: RNA

city: Regensburg

first: Dominik

last: Chittka

address: Franz-Josef-Strauss-Allee 11

department: Nephrology

country: Germany

institute: University hospital Regensburg

hyb_protocol: 5,2 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Mouse Whole Transcriptome 1.0 ST array for 16 h at 45°C in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the SST-RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Glomerulus, ob 8 weeks

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 15 µg of subsequently synthesized cDNA was purified, and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: After cervical dislocation kidneys were explanted and passed through a series of stainless steel sieves (150 µm, 100 µm, 70 µm, 50 µm). Glomeruli were collected, and the purity of the respective isolated glomeruli fractions was controlled by an Axiostar plus microscope (Zeiss, Jena, Germany).  Subsequent RNA extraction was conducted using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). RNA concentration and purity were determined by a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA) prior to storage at  80°C.

extract_protocol: Total RNA extraction was conducted using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions.

tag: tissue

value: isolated glomeruli

tag: strain

value: BTBR ob/ob

tag: gender

value: female

tag: age

value: 8 weeks


title: G6_blood_normal_rep1

status: Public on Dec 12 2017

type: genomic

city: Tongliao

first: Batudeligen

last: Duan

state: Inn Mongolian

address: 1742 Huolinhe Street

department: Affiliated hospital of Inner Mongolian University for the nationalities

country: China

institute: Institute of clinical pharmacology of traditional Mongolian Medicine

hyb_protocol: 1 Preheat the heat block to 95°C.  2 Preheat the Illumina Hybridization Oven to 48°C and set the rocker speed to 5.Assemble the Hybridization Chambers  3 .Place the resuspended MSA4 plate on the heat block to denature the samples at 95°C for  20 minutes.   4 Remove the BeadChips from 2°C to 8°C storage, leaving the BeadChips in their plastic bags  and mylar packages until you are ready to begin hybridization3 During the 20-minute incubation, prepare the Hyb Chambers.   a Place the BeadChip Hyb Chamber gaskets into the BeadChip Hyb Chambers.   b Dispense 400 μl PB2 into the humidifying buffer reservoirs in the Hyb Chambers.  c After you fill the Hyb Chamber reservoirs with PB2, place the lid on the Hyb Chamber  right away to prevent evaporation. It is not necessary to lock the lid.  d Leave the closed Hyb Chambers on the bench at room temperature until the BeadChips  are loaded with DNA sample. Load BeadChips into the Hyb Chamber within 1 hour.4 After the 20-minute incubation, remove the MSA4 plate from the heat block and place it on  the benchtop at room temperature for 30 minutes.  5 After the 30-minute cool down, pulse centrifuge the MSA4 plate to 280 × g. Remove the foil  seal.

scan_protocol: scanned with iScan (Illumina) in accordance with the manufacturer’s protocol. Following scanning,  raw data in the form of IDAT files were funnelled through the ChAMP analysis  pipeline implemented in R (http://www.R-project.org/). ChAMP is an integrated  workflow that ues a number of Bioconductor packages. Within ChAMP, IDAT files  were loaded and normalized using minfi

data_processing:
SWAN (subset-quantile within array normalization) introduced sub-quantile normalization for the methylated and unmethylated channels separately, assuming that the distribution of the probes with similar number of CpGs should be similar, irrespective of probe type
Raw Illumina data files were processed with the minfi Bioconductor package. Using the P-values of detection from this package, we next estimated coverage of each sample and probe. All samples and probes had reasonable coverage. P-values larger than 0.05 were assigned not available (NAs) and later imputed using the impute.knn (k=5) function from the impute Bioconductor package
the non_normalized.txt contain Unmethylated and methylated signal intensities and Average Beta value

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: normal blood sample

label_protocol: 1 Follow the instructions in the Zymo EZ DNA Methylation Kit to denature the genomic DNA  and add conversion reagent.  2 Incubate in a thermal cycler using the following conditions for 16 cycles:  • 95°C for 30 seconds  • 50°C for 1 hour   3 Hold DNA at 4°C for 10 minutes in the thermal cycler until you are ready to do the clean-up.  1 Follow the instructions in the Zymo EZ DNA Methylation Kit to do the following:  a Wash off the conversion reagent.  b Desulphonate the column or plate with desulphonation buffer. Incubate at room  temperature for 15 minutes.  c Wash off the desulphonation buffer.  d Add elution buffer.  e Centrifuge to elute.  2 Transfer the bisulfite-converted DNA (BCD) samples to the BCD plate.  3 Heat-seal the plate and store it at -25C° to -15°C.  4 Proceed to Make MSA4 Plate (Pre-AMP).

growth_protocol: Pulmonary tuberculosis patient and normal people who have genetic relationship wtih each other.

extract_protocol: 1. Cut tissue (up to 25 mg; up to 10 mg spleen) into small pieces, and place in 1.5 ml microcentrifuge tube. For rodent tails, use one (rat) or two (mouse) 0.4–0.6 cm lengths of tail. Add 180 μl Buffer ATL.  2. Add 20 μl proteinase K. Mix by vortexing, and incubate at 56°C until completely lysed. Vortex occasionally during incubation, or place in a thermomixer, in a shaking water bath, or on a rocking platform. Lysis is usually complete in 1–3 h or, for rodent tails, 6–8 h. Samples can be lysedovernight.  3. Vortex for 15 s. Add 200 μl Buffer AL to the sample. Mix thoroughly by vortexing. Then add 200 μl ethanol (96–100%). Mix again thoroughly. Alternatively, premix Buffer AL and ethanol, and add together.  4. Pipet the mixture into a DNeasy Mini spin column in a 2 ml collection tube. Centrifuge at _6000 x g (8000 rpm) for 1 min. Discard flow-through and collection tube.  5. Place the spin column in a new 2 ml collection tube. Add 500 μl Buffer AW1. Centrifuge for 1 min at _6000 x g. Discard flow-through and collection tube.  6. Place the spin column in a new 2 ml collection tube. Add 500 μl Buffer AW2. Centrifuge for 3 min at 20,000 x g (14,000 rpm). Discard flow-through and collection tube. Remove the spin column carefully so that it does not come into contact with the flow-through.  7. Transfer the spin column to a new 1.5 ml or 2 ml microcentrifuge tube, and add 200 μl Buffer AE for elution. Incubate for 1 min at room temperature. Centrifuge for 1 min at _6000 x g.  Recommended: Repeat this step for maximum yield.

treatment_protocol: Blood samples were obtained in January 2017 in a Blood RNA tube (4 ml) and an EDTA-containing tube (2 ml). Samples were stored at -80°C.

tag: subject id

tag: genotype

value: has a genetic relationship with G1

tag: disease state

value: normal

value: blood


title: Liver, growing, rep4

status: Public on Dec 11 2017

city: Lexington

first: James

last: Matthews

state: KY

address: 207 W.P. Garrigus Buidling

department: Animal and Food Sciences

country: USA

institute: University of Kentucky

description: steer

hyb_protocol: Following fragmentation, 10 µg of labeled cRNA was hybridized to Affymetrix Bovine Gene 1.0 ST Array for 16 hr at 45°C using the gene chips in the GeneChip Hybridization Oven 640, using 1 chip per RNA sample. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were stained with R-Phycoerythrin Streotavidin, followed by an antibody solution and a second R-Physcoerythrin Streptavidin solution, with all lquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip Scanner (GCS) with AGCC software (Command Console).

data_processing: The raw data were collected with the GeneChip Operating Software (GCOS, version 1.2). The expression intensity values from the software (i.e., the .cel files) were imported into Partek Genomics Suite software (version 6.4; Partek Inc., St. Louis, MO, USA). The algorithm of Robust Multichip Averaging data were further converted into expression values via the algorithms of Quantile normalization of different chips and then Median Polish summarization of multiple probes.

organism: Bos taurus

source_name: Liver, growing

label_protocol: Biotinylated cRNA were prepared from 3 µg of total RNA according to Affymetrix protocol. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA, USA) and oligo(dT)24 primers. Bio-labeled cRNA was prepared by cDNA in vitro transcription biotinylated UTP.

growth_protocol: The growth protocol has been described in the overall design section above.

extract_protocol: Trizol extraction of total RNA was perfomed according to the manufacturer's instruction.

treatment_protocol: The treatment protocol has been described in the overall design section above.

value: Liver

value: male

tag: developmental stage

value: growing


title: Glomerulus ob mouse, 8 weeks, replicate 2


title: Glomerulus WT mouse, 8 weeks, replicate 1

source_name: Glomerulus, WT 8 weeks

value: BTBR WT


title: Glomerulus WT mouse, 16 weeks, replicate 1


title: Glomerulus WT mouse, 16 weeks, replicate 2


title: G1_blood_ disease_rep1

source_name: Pulmonary tuberculosis blood sample

value: has a genetic relationship with G6

value: Pulmonary tuberculosis


title: Glomerulus WT mouse, 24 weeks, replicate 2

source_name: Glomerulus, WT 24 weeks

value: 24 weeks


title: Glomerulus ob mouse, 16 weeks, replicate 3

source_name: Glomerulus, ob 16 weeks


title: Glomerulus ob mouse, 16 weeks, replicate 1


title: Glomerulus WT mouse, 24 weeks, replicate 1


title: Glomerulus ob mouse, 16 weeks, replicate 2


title: Glomerulus ob mouse, 24 weeks, replicate 4

source_name: Glomerulus, ob 24 weeks


title: Glomerulus WT mouse, 24 weeks, replicate 3


title: Glomerulus ob mouse, 24 weeks, replicate 3


title: Glomerulus ob mouse, 24 weeks, replicate 2


title: Glomerulus ob mouse, 24 weeks, replicate 1


title: Wild type stressed, biological rep3

status: Public on Dec 09 2017

city: Athens

first: Aristotelis

last: Chatziioannou

address: 48 Vas. Constantinou Ave.

department: Institute of Biology, Medicinal Chemistry and Biotechnology

country: Greece

institute: National Hellenic Research Foundation

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the wild type of IRE1a under stress conditions

hyb_protocol: Affymetrix HG-U133 Plus GeneChip arrays hybridization was performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 7G and image analysis performed with the GeneChip Operating Software (GCOS).

data_processing: Background correction was performed with the RMA method, normalization was performed with the Quantile method and summarization was performed with median polish.

source_name: U87-MG glioblastoma cells overexpressing wild type IRE1a, stress conditions

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

growth_protocol: U87 cells were grown in DMEM glutamax (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA II, total RNA isolation kit (Macherey-Nagel, Düren, Germany)

treatment_protocol: U87 were stably transfected at MOI = 0.3 with pCDH-CMV-MCS-EF1-Puro-copGFP (System biosciences) empty vector (EV), pCDH-CMV-MCS-EF1-Puro-copGFP containing IRE1alpha wild-type sequence (WT) or mutated sequence (P336L, A414T, S769F or Q780) or a Dominant Negative form of IRE1a.

tag: cell line

tag: genotype/variation

value: overexpressing the wild type of IRE1a

tag: condition

value: stress conditions

tag: cell type

value: glioblastoma


title: Glomerulus WT mouse, 16 weeks, replicate 3

value: isolated glomeruli

value: 16 weeks


title: Glomerulus ob mouse, 16 weeks, replicate 4

value: BTBR ob/ob

value: female


title: Wild type stressed, biological rep2

source_name: U87-MG glioblastoma cells overexpressing wild type IRE1a, stess conditions


title: S_39, IUS PND7

city: Cologne

first: Kai

middle: Dietrich

last: Nüsken

state: NRW

address: Kerpener Str. 62

department: Department of Pediatrics

institute: University of Cologne, Medical Faculty

description: Gene expression data from rat kidney from an animal of the intrauterine stress group on postnatal day 7

hyb_protocol: The hybridization was conducted by the Cologne Center of Genomics (Germany) according to a NuGEN protocol (Applause WT-Amp ST System #part no.5500)

scan_protocol: The scanning was performed by the Cologne Center of Genomics (Germany) using an Affymetrix GeneChip Scanner 7G

data_processing:
The data were processed by BioAtlas in Berlin, Germany.
Command Console CHP file version 1
algorithm-name-0 = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish

organism: Rattus norvegicus

source_name: Rat kidney from animal S_39 of the intrauterine stress group on postnatal day 7

label_protocol: The labeling was conducted by the Cologne Center of Genomics (Germany) according to a NuGEN protocol (Applause WT-Amp ST System #part no.5500)

growth_protocol: Wistar rat dams (Janvier Labs, France) were time-mated [presence of sperm plug = gestational day (GD) 1] and either fed a defined diet (no. C1000, Altromin, Germany) containing 17,6% protein throughout pregnancy in groups LIG, IUS and C, or a diet containing 8,1% protein (no. C1003, Altromin) in group LP. IUGR in the LIG group was induced by bilateral vessel ligation and in the IUS group by sham operation.

extract_protocol: RNA isolation using a RNA Kit from Macherey Nagel, Germany, NuceloSpin RNA #740955.250

treatment_protocol: All dams received control diet (no. C1000, Altromin) after giving birth. On PND 1 and PND 7 all pups were narcotized with pentobarbital and decapitated. Then kidneys were obtained, weighed, shock frozen in liquid nitrogen and stored at -80°C.

value: Wistar

tag: group

value: Intrauterine stress

value: Male

value: Postnatal day 7

value: Kidney


title: S_34, LP PND7

description: Gene expression data from rat kidney from an animal of the low protein group on postnatal day 7

source_name: Rat kidney from animal S_34 of the low protein group on postnatal day 7

value: Low protein


title: Wild type, biological rep2

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the wild type of IRE1a under basal conditions

source_name: U87-MG glioblastoma cells overexpressing wild type IRE1a, basal conditions

value: basal conditions


title: Wild type stressed, biological rep1


title: S_36, IUS PND7

source_name: Rat kidney from animal S_36 of the intrauterine stress group on postnatal day 7


title: S_35, LP PND7

source_name: Rat kidney from animal S_35 of the low protein group on postnatal day 7


title: S_37, IUS PND7

source_name: Rat kidney from animal S_37 of the intrauterine stress group on postnatal day 7


title: Wild type, biological rep3


title: Empty vector stressed, biological rep3

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing an empty vector of IRE1a under stress conditions

source_name: U87-MG glioblastoma cells overexpressing an empty vector of IRE1a, stress conditions

value: overexpressing an empty vector of IRE1a


title: Empty vector stressed, biological rep2


title: S_40, IUS PND7

source_name: Rat kidney from animal S_40 of the intrauterine stress group on postnatal day 7


title: S_38, IUS PND7

source_name: Rat kidney from animal S_38 of the intrauterine stress group on postnatal day 7


title: Saos2-derived iPSC_OSKM-transduced_Clone2_rep3

city: Kuala Lumpur

first: Pei Feng

last: Choong

address: PPUKM-MAKNA Cancer Centre

department: Research

country: Malaysia

institute: MAKNA

description:
Saos2 C2-3 P30
gene expression of OSKM-transduced reprogrammed iSaos2

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = PrimeView
program-name = Expression Console
program-version = 1.3.1.187
program-company = Affymetrix

source_name: Saos2 transduced with OSKM, Clone 2

label_protocol: Not provided

growth_protocol: OS parental cell lines were maintained in basal medium, supplemented with 10% FBS, 1% penicilin-streptomycin, 1% L-glutamine. OS-iPSC clones were maintained in standard hESC medium, on irradiated MEF feeder layer.

extract_protocol: Total RNA was isolated using the miRNeasy Mini kit (Qiagen, California, USA) following manufacturer's instruction

treatment_protocol: OS cell lines were transduced with retrovirus supernatant of OSKM with 1:1:1:1 ratio. The OSKM-transduced cells were supplemented with 5 µg/ml polybrene. Upon confluency, the OSKM-transduced cells were passaged to inactivated MEF and cultured using the hESC protocol.

value: Saos-2 transduced with OSKM, Clone 2

tag: morphology

value: adherent colony

tag: disease

value: osteosarcoma-derived


title: Wild type, biological rep1

value: overexpressing the wild type of IRE1a


title: Saos2-derived iPSC_OSKM-transduced_Clone2_rep2

description:
Saos2 C2-2 P38
gene expression of OSKM-transduced reprogrammed iSaos2


title: S_32, LP PND7

source_name: Rat kidney from animal S_32 of the low protein group on postnatal day 7


title: Empty vector stressed, biological rep1

value: stress conditions

value: glioblastoma


title: S_31, LP PND7

source_name: Rat kidney from animal S_31 of the low protein group on postnatal day 7


title: osteosarcoma cell line Saos2_non-OSKM-transduced_rep2

description:
Saos2 Par v2
gene expression of non-OSKM transduced parental Saos2

source_name: Saos2 non-OSKM transduced

value: Parental Saos-2

value: adherent monolayer

value: osteosarcoma, from 11 year old


title: osteosarcoma cell line Saos2_non-OSKM-transduced_rep1

description:
Saos2 Par v1
gene expression of non-OSKM transduced parental Saos2


title: Empty vector, biological rep1

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing an empty vector of IRE1a under basal conditions

source_name: U87-MG glioblastoma cells overexpressing an empty vector of IRE1a, basal conditions


title: Empty vector, biological rep2


title: Saos2-derived iPSC_OSKM-transduced_Clone2_rep1

description:
Saos2 C2 P22
gene expression of OSKM-transduced reprogrammed iSaos2


title: S_33, LP PND7

source_name: Rat kidney from animal S_33 of the low protein group on postnatal day 7

value: Wistar


title: G292-derived iPSC_OSKM-transduced_Clone2_rep3

description:
G292 C2-2 P28
gene expression of OSKM-transduced reprogrammed iG292

source_name: G292 transduced with OSKM, Clone 2

value: G-292 transduced with OSKM, Clone 2


title: S_30, LIG PND7

description: Gene expression data from rat kidney from an animal of the ligatur group on postnatal day 7

source_name: Rat kidney from animal S_30 of the ligatur group on postnatal day 7

value: Ligatur

value: Male


title: S_26, LIG PND7

source_name: Rat kidney from animal S_26 of the ligatur group on postnatal day 7

value: Postnatal day 7

value: Kidney


title: Empty vector, biological rep3

value: basal conditions


title: S_27, LIG PND7

source_name: Rat kidney from animal S_27 of the ligatur group on postnatal day 7


title: G292-derived iPSC_OSKM-transduced_Clone2_rep2

description:
G292 C2 P42
gene expression of OSKM-transduced reprogrammed iG292


title: Dominant negative stressed, biological rep2

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the dominant negative form of IRE1a under stress conditions

source_name: U87-MG glioblastoma cells overexpressing dominant negative form of IRE1a, stress conditions


title: S_29, LIG PND7

source_name: Rat kidney from animal S_29 of the ligatur group on postnatal day 7


title: S_28, LIG PND7

source_name: Rat kidney from animal S_28 of the ligatur group on postnatal day 7


title: S_24, C PND7

description: Gene expression data from rat kidney from an animal of the control group on postnatal day 7

source_name: Rat kidney from animal S_24 of the control group on postnatal day 7

value: Control


title: Dominant negative stressed, biological rep3

value: overexpressing the dominant negative form of IRE1a


title: osteosarcoma cell line G292_non-OSKM-transduced_rep1

description:
G292 Par v1
gene expression of non-OSKM transduced parental G292

source_name: G292 non-OSKM transduced

value: Parental G-292

value: osteosarcoma, from 9 year old female


title: osteosarcoma cell line G292_non-OSKM-transduced_rep2

description:
G292 Par v2
gene expression of non-OSKM transduced parental G292


title: clone 7 stressed, biological rep3

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the IRE1a mutant (A414T) under stress conditions

source_name: U87-MG glioblastoma cells overexpressing IRE1a bearing  A414T mutation, stress conditions

value: overexpressing the IRE1a mutant (A414T)


title: Dominant negative, biological rep2

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the dominant negative form of IRE1a under basal conditions

source_name: U87-MG glioblastoma cells overexpressing dominant negative form of IRE1a, basal conditions


title: Dominant negative, biological rep3


title: S_25, C PND7

source_name: Rat kidney from animal S_25 of the control group on postnatal day 7


title: G292-derived iPSC_OSKM-transduced_Clone2_rep1

description:
G292 C2 P30
gene expression of OSKM-transduced reprogrammed iG292

value: adherent colony

value: osteosarcoma-derived


title: S_20, IUS PND1

description: Gene expression data from rat kidney from an animal of the intrauterine stress group on postnatal day 1

source_name: Rat kidney from animal S_20 of the intrauterine stress group on postnatal day 1

value: Intrauterine stress

value: Postnatal day 1


title: S_19, IUS PND1

source_name: Rat kidney from animal S_19 of the intrauterine stress group on postnatal day 1


title: S_23, C PND7

source_name: Rat kidney from animal S_23 of the control group on postnatal day 7


title: clone 6 stressed, biological rep1

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the IRE1a mutant (P336L) under stress conditions

source_name: U87-MG glioblastoma cells overexpressing IRE1a bearing  P336L mutation, stress conditions

value: overexpressing the IRE1a mutant (P336L)

value: stress conditions

value: glioblastoma


title: S_16, IUS PND1

source_name: Rat kidney from animal S_16 of the intrauterine stress group on postnatal day 1

value: Wistar


title: clone 7, biological rep1

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the IRE1a mutant (A414T) under basal conditions

source_name: U87-MG glioblastoma cells overexpressing IRE1a bearing  A414T mutation, basal conditions


title: S_18, IUS PND1

source_name: Rat kidney from animal S_18 of the intrauterine stress group on postnatal day 1

value: Male


title: clone 7, biological rep3


title: S_11, LP PND1

description: Gene expression data from rat kidney from an animal of the low protein group on postnatal day 1

source_name: Rat kidney from animal S_11 of the low protein group on postnatal day 1

value: Low protein


title: clone 7, biological rep2


title: S_15, LP PND1

source_name: Rat kidney from animal S_15 of the low protein group on postnatal day 1

value: Kidney


title: Glomerulus WT mouse, 24 weeks, replicate 4

source_name: Glomerulus, WT 24 weeks

value: isolated glomeruli

value: BTBR WT

value: female

value: 24 weeks


title: clone 6, biological rep2

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the IRE1a mutant (P336L) under basal conditions

source_name: U87-MG glioblastoma cells overexpressing IRE1a bearing  P336L mutation, basal conditions

value: basal conditions


title: clone 6, biological rep1


title: S_17, IUS PND1

source_name: Rat kidney from animal S_17 of the intrauterine stress group on postnatal day 1


title: S_14, LP PND1

source_name: Rat kidney from animal S_14 of the low protein group on postnatal day 1


title: S_12, LP PND1

source_name: Rat kidney from animal S_12 of the low protein group on postnatal day 1


title: clone 6 stressed, biological rep2


title: S_22, C PND7

source_name: Rat kidney from animal S_22 of the control group on postnatal day 7

value: Control

value: Postnatal day 7


title: clone 6 stressed, biological rep3


title: clone 7 stressed, biological rep1

source_name: U87-MG glioblastoma cells overexpressing IRE1a bearing  A414T mutation, stress conditions

value: overexpressing the IRE1a mutant (A414T)


title: S_10, LIG PND1

description: Gene expression data from rat kidney from an animal of the ligatur group on postnatal day 1

source_name: Rat kidney from animal S_10 of the ligatur group on postnatal day 1

value: Ligatur


title: S_9, LIG PND1

source_name: Rat kidney from animal S_9 of the ligatur group on postnatal day 1

value: Postnatal day 1


title: clone 7 stressed, biological rep2


title: S_7, LIG PND1

source_name: Rat kidney from animal S_7 of the ligatur group on postnatal day 1


title: S_8, LIG PND1

source_name: Rat kidney from animal S_8 of the ligatur group on postnatal day 1


title: S_13, LP PND1

source_name: Rat kidney from animal S_13 of the low protein group on postnatal day 1


title: clone 4, biological rep1

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the IRE1a mutant (Q780Stop) under basal conditions

source_name: U87-MG glioblastoma cells overexpressing IRE1a bearing  Q780Stop mutation, basal conditions


title: clone 4, biological rep2

value: overexpressing the IRE1a mutant (Q780Stop)


title: clone 4 stressed, biological rep2

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the IRE1a mutant (Q780Stop) under stress conditions

source_name: U87-MG glioblastoma cells overexpressing IRE1a bearing  Q780Stop mutation, stress conditions

value: stress conditions


title: clone 4 stressed, biological rep3

value: glioblastoma


title: clone 4 stressed, biological rep1


title: clone 4, biological rep3


title: clone 6, biological rep3

value: overexpressing the IRE1a mutant (P336L)


title: clone 3 stressed, biological rep3

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the IRE1a mutant (S769F) under stress conditions

source_name: U87-MG glioblastoma cells overexpressing IRE1a bearing S769F mutation, stress conditions

value: overexpressing the IRE1a mutant (S769F)


title: clone 3, biological rep1

description: RMA log2 signal intensities from U87-MG glioblastoma cells overexpressing the IRE1a mutant (S769F) under basal conditions

source_name: U87-MG glioblastoma cells overexpressing IRE1a bearing S769F mutation, basal conditions


title: S_3, C PND1

description: Gene expression data from rat kidney from an animal of the control group on postnatal day 1

source_name: Rat kidney from animal S_3 of the control group on postnatal day 1

value: Wistar

value: Male


title: S_2, C PND1

source_name: Rat kidney from animal S_2 of the control group on postnatal day 1

value: Kidney


title: S_5, C PND1

source_name: Rat kidney from animal S_5 of the control group on postnatal day 1


title: clone 3 stressed, biological rep2


title: S_4, C PND1

source_name: Rat kidney from animal S_4 of the control group on postnatal day 1


title: S_6, LIG PND1

source_name: Rat kidney from animal S_6 of the ligatur group on postnatal day 1


title: clone 3, biological rep2


title: S_1, C PND1

source_name: Rat kidney from animal S_1 of the control group on postnatal day 1


title: clone 3, biological rep3


title: CD45-CD31-Ter119-, Osx+ cells sample 2 (Osteolineage precursor cells)

status: Public on Dec 08 2017

city: Houston

first: Dongsu

last: Park

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: Osx+ osteolineage precursor cells

hyb_protocol: Labeled by terminal deoxynucleotidyl transferase (TdT) with Affymetrix proprietary DNA labeling reagent linked to biotin

scan_protocol: Gene chips were scanned using Affymetrix Scanner 3000 7G at the Dana-Farber Cancer Institute Microarray Core

data_processing: CEL files were analyzed by R software using the affy library and limma statistics

source_name: Mouse periosteal tissue

label_protocol: Transcripts were labeled with Affymetrix Gene Chip whoe transcript sense labeling kit

growth_protocol: Cells were analyzed from primary isolate from male and female mice without further tissue culture.

extract_protocol: RNA was isolated from sorted cells using Rneasy Microkit (Qiagen) by manufacturer's instruction

treatment_protocol: Bone marrow and periosteal skeletal stem cells were isolated from bone marrow and periosteal tissue, respectively. (Bone marrow skeletal stem cells were CD45-/CD31-/Ter119-/Mx1+/Nes+; Periosteal skeletal stem cells were CD45-/CD31-/Ter119-/Mx1+/Ocn-/CD105+/CD140a+)

value: Osx+ osteolineage precursor cells


title: CD45-CD31-Ter119-, CD105+CD140a+, Nes+ (Mx1+/-) cells from bone marrow (Nes+ BM SSCs)

description: Nes+ bone marrow skeletal stem cells

value: Nes+ bone marrow skeletal stem cells


title: CD45-CD31-Ter119-, Osx+ cells sample 1 (Osteolineage precursor cells)

description: Osx+ osteolineage precursor cells


title: CD45-CD31-Ter119-, CD51+ cells from bone marrow (CD51+ BM SSCs) sample 2

description: CD51+ bone marrow skeletal stem cells

source_name: Mouse bone marrow

value: CD51+ bone marrow skeletal stem cells


title: clone 3 stressed, biological rep1


title: CD45-CD31-Ter119-, CD105+CD140a+, Mx1+Osteocalcin- cells from periosteal tissue (Mx1+Ocn- P-SSCs) sample 1

description: Mx1+Ocn- Periosteal skeletal stem cells

value: Mx1+Ocn- Periosteal skeletal stem cells


title: CD45-CD31-Ter119-, CD105+CD140a+, Mx1+Nes+ cells from bone marrow (Mx1+Nes+ BM SSCs) sample 1

description: Mx1+Nes+ bone marrow skeletal stem cells


title: CD45+ cells from bone marrow sample 1

description: hematopoietic lineage cells

value: hematopoietic lineage cells


title: CD45-CD31-Ter119-, CD51+ cells from bone marrow (CD51+ BM SSCs) sample 1

description: CD51+ bone marrow skeletal stem cells


title: CD45-CD31-Ter119-, CD105+CD140a+, Mx1+Osteocalcin- cells from periosteal tissue (Mx1+Ocn- P-SSCs) sample 2

description: Mx1+Ocn- Periosteal skeletal stem cells


title: CD45-CD31-Ter119-, CD105+CD140a+, Mx1+Nes+ cells from bone marrow (Mx1+Nes+ BM SSCs) sample 2

value: Mx1+Nes+ bone marrow skeletal stem cells


title: Mutant 6, Wild-type 2

city: Philadelphia

first: Natalie

middle: A

last: Terry

state: PA

address: 3615 Civic  Center Blvd

institute: The Children's Hospital of Philadelphia

description: Biologic replicate 1 of 4

hyb_protocol: 2-color Agilent-026655 Whole Mouse Genome Microarray 4x44K v2.

scan_protocol: Samples were scanned at the Next Generation Sequencing Core at the University of Pennsylvania.

data_processing:
GeneSpring GX - The analysis is done with the ratio of sample pairs rather than with individual samples
Fold change was determined by comparing test mean intensity and test control intensity. An FDR cut of 10% was used after analyzing by student's t Q-Q plot and Volcano Plot of log fold change to log odds.

source_name: villin-Cre; Arx loxP duodenum 6

label_protocol: Agilent protocol

growth_protocol: Whole duodenum from postnatal day 5 mice was analyzed.

extract_protocol: Whole duodenum was homogenized in Trizol then total RNA was extracted with phenol:chloroform and precipitated with ethanol. RNA quality was tested via bioanalysis for a RIN greater than 9.0.

treatment_protocol: No specific treatment

value: villin-Cre; Arx loxP

value: intestine

tag: development stage

value: postnatal day 5

source_name: wild-type duodenum 2

value: wild type


title: miR-139-5p mimic vs negative control

city: Darlinghurst

first: Tim

last: Molloy

state: NSW

address: Level 8, 405 Liverpool St

department: Haematology

country: Australia

institute: St Vincent's Centre for Applied Medical Research

hyb_protocol: miRNA was hybridized as per Agilent miRNA hydribization instructions

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner G2505C US80603148

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalization (LOWESS) was performed using BRB-Array-Tools version 4.5.1.

label_protocol: Cyanine-3/5 (Cy3/Cy5) labeled cRNA was prepared from 0.5 ug RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MCF7 cells were cultured in RPMI medium supplemented with 10% fetal calf serum

extract_protocol: 24 hours post-transfection total RNA was extracted using RNeasy RNA extraction kit (Qiagen) as per manufacturer's instructions

treatment_protocol: A miR-139-5p or negative control miScript miRNA mimic (Qiagen) at a final concentration of 10 nmol/L was transfected into cells using HiPerFect transfection reagent (Qiagen) as per manufacturer's instructions

tag: transfection

value: Negative control mimic

value: miR-139-5p mimic


title: CD45+ cells from bone marrow sample 2

description: hematopoietic lineage cells


title: Wild-type 4, Mutant 8

description: Biologic replicate 1 of 4

source_name: wild-type duodenum 4

value: wild-type

tag: tissue

source_name: villin-Cre; Arx loxP duodenum 8


title: Mutant 5, Wild-type 1

description: Biologic replicate 1 of 4

source_name: villin-Cre; Arx loxP duodenum 5

source_name: wild-type duodenum 1


title: Wild-type 3, Mutant 7

description: Biologic replicate 1 of 4

source_name: wild-type duodenum 3

source_name: villin-Cre; Arx loxP duodenum 7


title: Sample 335

status: Public on Dec 07 2017

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

hyb_protocol: Labeled products were pooled and served as a final Master Mix for the array, The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybridization master for a given source and biological replicate.

scan_protocol: Axon GenePix 4200 Professional, 5 micron resolution.

data_processing: Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data

organism: Daphnia pulex

source_name: Cyano DelxNod Rep1

label_protocol: cDNA labeling using 1 O.D. Cy-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.

growth_protocol: 4 day old animals were isolated from synchronized cultures of brood mothers. Mothers were fed a control diet of the non toxic green algae at an optimal diet ratio under constant light and temperature conditions

extract_protocol: Tissue was homogenized and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

treatment_protocol: Animals were exposed for 10 days to a control diet or a diet containing 50% of one of the five cyanobacteria, an insecticide treatment of one of 8 eight insecticide at EC50 level for reproduction or a binary mixture treatment of an insecticide and a cyanobacteria . Animals were fed daily and experimental jars were changed out three times a week. After 10 days RNA was extracted.

tag: Sex

value: female

value: adult

value: whole body

source_name: Mixture DelxNod Rep2


title: Sample 329

source_name: Cyano CarbxNod Rep1

source_name: Mixture CarbxNod Rep2


title: Sample 334

source_name: Pesticide DelxNod Rep2


title: Sample 330

source_name: Control ChlorxNod Rep1

source_name: Pesticide ChlorxNod Rep1


title: S_21, C PND7

description: Gene expression data from rat kidney from an animal of the control group on postnatal day 7

source_name: Rat kidney from animal S_21 of the control group on postnatal day 7

tag: strain

value: Wistar

value: Control

tag: gender

value: Male

value: Postnatal day 7

value: Kidney


title: Sample 332

source_name: Cyano ChlorxNod Rep1

source_name: Mixture ChlorxNod Rep2


title: Sample 327

source_name: Control CarbxNod Rep2

source_name: Cyano CarbxNod Rep2


title: Sample 333

source_name: Control DelxNod Rep1

source_name: Pesticide DelxNod Rep1


title: Sample 325

source_name: Mixture DelxOsl Rep4

source_name: Cyano DelxOsl Rep3


title: Sample 326

source_name: Control CarbxNod Rep1

source_name: Pesticide CarbxNod Rep1


title: Sample 318

source_name: Mixture CarbxOsl Rep3

source_name: Pesticide CarbxOsl Rep4


title: Sample 331

source_name: Pesticide ChlorxNod Rep2

source_name: Mixture ChlorxNod Rep1


title: Sample 328

source_name: Pesticide CarbxNod Rep2

source_name: Mixture CarbxNod Rep1


title: Sample 314

source_name: Mixture FenxCyl Rep3

source_name: Pesticide FenxCyl Rep4


title: Sample 317

source_name: Cyano CarbxOsl Rep4

source_name: Control CarbxOsl Rep4


title: Sample 323

source_name: Pesticide DelxOsl Rep3

source_name: Control DelxOsl Rep3


title: Sample 321

source_name: Mixture ChlorxOsl Rep3

source_name: Pesticide ChlorxOsl Rep4


title: Sample 309

source_name: Mixture AcexCyl Rep4

source_name: Cyano AcexCyl Rep3


title: Sample 316

source_name: Pesticide CarbxOsl Rep3

source_name: Control CarbxOsl Rep3


title: Sample 311

source_name: Mixture EndoxCyl Rep3

source_name: Pesticide EndoxCyl Rep4


title: Sample 319

source_name: Mixture CarbxOsl Rep4

source_name: Cyano CarbxOsl Rep3


title: Sample 315

source_name: Mixture FenxCyl Rep4

source_name: Cyano FenxCyl Rep3


title: Sample 313

source_name: Pesticide FenxCyl Rep3

source_name: Control FenxCyl Rep3


title: Sample 322

source_name: Mixture ChlorxOsl Rep4

source_name: Cyano ChlorxOsl Rep3


title: Sample 312

source_name: Mixture EndoxCyl Rep4

source_name: Cyano EndoxCyl Rep3


title: Sample 310

source_name: Pesticide EndoxCyl Rep3

source_name: Control EndoxCyl Rep3


title: Sample 304

source_name: Pesticide DelxMc Rep2

source_name: Mixture DelxMc Rep1


title: Sample 299

source_name: Cyano CarbxMc Rep1

source_name: Mixture CarbxMc Rep2


title: Sample 305

source_name: Cyano DelxMc Rep1

source_name: Mixture DelxMc Rep2


title: Sample 320

source_name: Pesticide ChlorxOsl Rep3

source_name: Control ChlorxOsl Rep3


title: Sample 324

source_name: Mixture DelxOsl Rep3

source_name: Pesticide DelxOsl Rep4


title: Sample 298

source_name: Pesticide CarbxMc Rep2

source_name: Mixture CarbxMc Rep1


title: Sample 306

source_name: Pesticide AcexCyl Rep3

source_name: Control AcexCyl Rep3


title: Sample 308

source_name: Mixture AcexCyl Rep3

source_name: Pesticide AcexCyl Rep4


title: Sample 307

source_name: Cyano AcexCyl Rep4

source_name: Control AcexCyl Rep4


title: Sample 303

source_name: Control DelxMc Rep1

source_name: Pesticide DelxMc Rep1


title: Sample 301

source_name: Pesticide ChlorxMc Rep2

source_name: Mixture ChlorxMc Rep1


title: Sample 300

source_name: Control ChlorxMc Rep1

source_name: Pesticide ChlorxMc Rep1


title: Sample 302

source_name: Cyano ChlorxMc Rep1

source_name: Mixture ChlorxMc Rep2


title: Sample 291

source_name: Pesticide EndoxMc Rep3

source_name: Control EndoxMc Rep3


title: Sample 292

source_name: Mixture EndoxMc Rep4

source_name: Cyano EndoxMc Rep3


title: Sample 295

source_name: Mixture FenxMc Rep4

source_name: Cyano FenxMc Rep3


title: Sample 290

source_name: Mixture AcexMc Rep4

source_name: Cyano AcexMc Rep3


title: Sample 284

source_name: Pesticide TebxMc Rep3

source_name: Control TebxMc Rep3


title: Sample 285

source_name: Mixture TebxMc Rep3

source_name: Pesticide TebxMc Rep4


title: Sample 286

source_name: Mixture TebxMc Rep4

source_name: Cyano TebxMc Rep3


title: Sample 288

source_name: Cyano AcexMc Rep4

source_name: Control AcexMc Rep4


title: Sample 287

source_name: Pesticide AcexMc Rep3

source_name: Control AcexMc Rep3


title: Sample 293

source_name: Pesticide FenxMc Rep3

source_name: Control FenxMc Rep3


title: Sample 289

source_name: Mixture AcexMc Rep3

source_name: Pesticide AcexMc Rep4


title: Sample 277

source_name: Cyano TetraxCyl Rep4

source_name: Control TetraxCyl Rep4


title: Sample 294

source_name: Mixture FenxMc Rep3

source_name: Pesticide FenxMc Rep4


title: Sample 280

source_name: Mixture TebxNod Rep4

source_name: Cyano TebxNod Rep3


title: Sample 278

source_name: Cyano TebxMc Rep4

source_name: Control TebxMc Rep4


title: Sample 296

source_name: Control CarbxMc Rep1

source_name: Pesticide CarbxMc Rep1


title: Sample 275

source_name: Pesticide TebxNod Rep3

source_name: Control TebxNod Rep3


title: Sample 297

source_name: Control CarbxMc Rep2

source_name: Cyano CarbxMc Rep2


title: Sample 279

source_name: Mixture TebxNod Rep3

source_name: Pesticide TebxNod Rep4


title: Sample 283

source_name: Mixture TetraxCyl Rep4

source_name: Cyano TetraxCyl Rep3


title: Sample 272

source_name: Control DelxAph Rep1

source_name: Pesticide DelxAph Rep1


title: Sample 276

source_name: Cyano TebxNod Rep4

source_name: Control TebxNod Rep4


title: Sample 281

source_name: Pesticide TetraxCyl Rep3

source_name: Control TetraxCyl Rep3


title: Sample 273

source_name: Pesticide DelxAph Rep2

source_name: Mixture DelxAph Rep1


title: Sample 270

source_name: Pesticide ChlorxAph Rep2

source_name: Mixture ChorxAph Rep1


title: Sample 264

source_name: Control CarbxAph Rep2

source_name: Cyano CarbxAph Rep2


title: Sample 268

source_name: Cyano CarbxAph Rep1

source_name: Mixture CarbxAph Rep2


title: Sample 282

source_name: Mixture TetraxCyl Rep3

source_name: Pesticide TetraxCyl Rep4


title: Sample 267

source_name: Pesticide CarbxAph Rep2

source_name: Mixture CarbxAph Rep1


title: Sample 271

source_name: Cyano ChlorxAph Rep1

source_name: Mixture ChlorxAph Rep2


title: Sample 269

source_name: Control ChlorxAph Rep1

source_name: Pesticide ChlorxAph Rep1


title: Sample 274

source_name: Cyano DelxAph Rep1

source_name: Mixture DelxAph Rep2


title: Sample 265

source_name: Control CarbxAna Rep1

source_name: Pesticide CarbxAna Rep1


title: Sample 260

source_name: Control FenxAph Rep1

source_name: Pesticide FenxAph Rep1


title: Sample 254

source_name: Pesticide TetraxOsl Rep3

source_name: Control TetraxOsl Rep3


title: Sample 255

source_name: Pesticide AcexAph Rep2

source_name: Mixture AcexAph Rep1


title: Sample 257

source_name: Control EndoxAph Rep1

source_name: Pesticide EndoxAph Rep1


title: Sample 266

source_name: Pesticide ChlorxAna Rep2

source_name: Mixture ChlorxAna Rep1


title: Sample 263

source_name: Control CarbxAph Rep1

source_name: Pesticide CarbxAph Rep1


title: Sample 251

source_name: Control AcexAph Rep1

source_name: Pesticide AcexAph Rep1


title: Sample 242

source_name: Control AcexCyl Rep1

source_name: Pesticide AcexCyl Rep1


title: Sample 246

source_name: Pesticide EndoxCyl Rep2

source_name: Mixture EndoxCyl Rep1


title: Sample 262

source_name: Cyano FenxAph Rep1

source_name: Mixture FenxAph Rep2


title: Sample 256

source_name: Cyano AcexAph Rep1

source_name: Mixture AcexAph Rep2


title: Sample 249

source_name: Pesticide FenxCyl Rep2

source_name: Mixture FenxCyl Rep1


title: Sample 247

source_name: Cyano EndoxCyl Rep1

source_name: Mixture EndoxCyl Rep2


title: Sample 252

source_name: Control AcexAph Rep2

source_name: Cyano AcexAph Rep2


title: Sample 248

source_name: Control FenxCyl Rep1

source_name: Pesticide FenxCyl Rep1


title: Sample 261

source_name: Pesticide FenxAph Rep2

source_name: Mixture FenxAph Rep1


title: Sample 253

source_name: Cyano ChlorxOsl Rep1

source_name: Mixture ChlorxOsl Rep2


title: Sample 243

source_name: Pesticide AcexCyl Rep2

source_name: Mixture AcexCyl Rep1


title: Sample 259

source_name: Cyano EndoxAph Rep1

source_name: Mixture EndoxAph Rep2


title: Sample 237

source_name: Mixture TetraxCyl Rep3

source_name: Pesticide TetraxCyl Rep4


title: Sample 239

source_name: Pesticide TetraxAna Rep3

source_name: Control TetraxAna Rep3


title: Sample 250

source_name: Cyano FenxCyl Rep1

source_name: Mixture FenxCyl Rep2


title: Sample 235

source_name: Mixture TetraxAph Rep3

source_name: Pesticide TetraxAph Rep4


title: Sample 234

source_name: Cyano TetraxAna Rep4

source_name: Control TetraxAna Rep4


title: Sample 236

source_name: Mixture TetraxAph Rep4

source_name: Cyano TetraxAph Rep3


title: Sample 258

source_name: Pesticide EndoxAph Rep2

source_name: Mixture EndoxAph Rep1


title: Sample 241

source_name: Mixture TetraxAna Rep4

source_name: Cyano TetraxAna Rep3


title: Sample 245

source_name: Control EndoxCyl Rep1

source_name: Pesticide EndoxCyl Rep1


title: 48hpi infection, biological rep1

city: Kansas City

first: Jianming

last: Qiu

state: KS

address: 3901 rainbow blvd

department: Microbiology

institute: University of Kansas Medical Center

description: Expression profiling by array

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2.

data_processing: The data were analyzed with R Affy package using RMA. Intensity values were log2 transformed, and were normalized by quantile in limma package.

source_name: B19V_48hr, CD36+ EPCs

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

growth_protocol: Primary human CD133+ hematopoietic stem cells were isolated from bone marrow of healthy donors according to the protocol (04-H-0179) approved by the National Heart, Lung, and Blood Institute institutional review board. Primary human CD36+ erythroid progenitor cells (EPCs) were expanded ex vivo through culturing the cells in Wong medium under normoxia incubator (5% CO2 and 21% O2) up to Day 4 and frozen in liquid nitrogen. In each experiment, Day 4 cells were seeded under normoxia for 2-3 days, prior to incubation under hypoxia (5% CO2 and 1% O2) for 2 days.

extract_protocol: The mock- and B19V-infected CD36+ EPCs were collected at 6, 12, 24, and 48 hpi. RNA samples were extracted using the miRNeasy Mini Kit by following the manufacturer’s instruction. At each time points, 3 repeat samples were prepared. All RNA samples were analyzed on an Agilent 2100 Bioanalyzer with an Agilent RNA 6000 Nano Kit to ensure an RNA Intergrity Number (RIN) ≥ 8.0.

treatment_protocol: After 2 days under hypoxic incubation, CD36+ EPCs were infected with B19V at a multiplicity of infection (MOI) of 1,000 vgc per cell or mock infected.

value: bone marrow-derived, CD36+ EPCs

tag: infection

tag: time


title: 24hpi infection, biological rep3

description: Expression profiling by array

source_name: B19V_24hr, CD36+ EPCs


title: 48hpi infection, biological rep3

description: Expression profiling by array


title: 12hpi infection, biological rep3

description: Expression profiling by array

source_name: B19V_12hr, CD36+ EPCs


title: 48hpi infection, biological rep2

description: Expression profiling by array


title: Sample 240

source_name: Mixture TetraxAna Rep3

source_name: Pesticide TetraxAna Rep4


title: Sample 238

source_name: Mixture TetraxCyl Rep4

source_name: Cyano TetraxCyl Rep3


title: 12hpi infection, biological rep2

description: Expression profiling by array


title: 12hpi infection, biological rep1

description: Expression profiling by array


title: 6hpi infection, biological rep2

description: Expression profiling by array

source_name: B19V_6hr, CD36+ EPCs


title: 24hpi infection, biological rep1

description: Expression profiling by array


title: 24hpi infection, biological rep2

description: Expression profiling by array


title: 6hpi infection, biological rep3

description: Expression profiling by array


title: mock infection, biological rep3

description: Expression profiling by array

source_name: Control_0hr, CD36+ EPCs

value: control


title: 6hpi infection, biological rep1

description: Expression profiling by array


title: Sample 231

source_name: Pesticide TetraxAph Rep3

source_name: Control TetraxAph Rep3


title: Sample 229

source_name: Pesticide TebxAna Rep2

source_name: Mixture TebxAna Rep1


title: Sample 233

source_name: Cyano TetraxCyl Rep4

source_name: Control TetraxCyl Rep4


title: mock infection, biological rep2

description: Expression profiling by array


title: Sample 226

source_name: Pesticide TebxOsl Rep2

source_name: Mixture TebxOsl Rep1


title: Sample 244

source_name: Cyano AcexCyl Rep1

source_name: Mixture AcexCyl Rep2


title: mock infection, biological rep1

description: Expression profiling by array


title: Sample 223

source_name: Pesticide TebxAph Rep2

source_name: Mixture TebxAph Rep1


title: Sample 228

source_name: Control TebxAna Rep1

source_name: Pesticide TebxAna Rep1


title: Sample 224

source_name: Cyano TebxAph Rep1

source_name: Mixture TebxAph Rep2


title: Sample 232

source_name: Cyano TetraxAph Rep4

source_name: Control TetraxAph Rep4


title: Sample 225

source_name: Control TebxOsl Rep1

source_name: Pesticide TebxOsl Rep1


title: Sample 227

source_name: Cyano TebxOsl Rep1

source_name: Mixture TebxOsl Rep2


title: Sample 230

source_name: Cyano TebxAna Rep1

source_name: Mixture TebxAna Rep2


title: Sample 222

source_name: Control TebxAna Rep2

source_name: Cyano TebxAna Rep2


title: Sample 219

source_name: Cyano DelxAna Rep1

source_name: Mixture DelxAna Rep2


title: Sample 221

source_name: Control TebxOsl Rep2

source_name: Cyano TebxOsl Rep2


title: Sample 217

source_name: Control DelxAna Rep1

source_name: Pesticide DelxAna Rep1


title: Sample 220

source_name: Control TebxAph Rep1

source_name: Pesticide TebxAph Rep1


title: Sample 214

source_name: Cyano CarbxAna Rep1

source_name: Mixture CarbxAna Rep2


title: Sample 213

source_name: Pesticide CarbxAna Rep2

source_name: Mixture CarbxAna Rep1


title: Sample 209

source_name: Pesticide FenxAna Rep3

source_name: Control FenxAna Rep3


title: Sample 216

source_name: Cyano ChlorxAna Rep1

source_name: Mixture ChlorxAna Rep2


title: Sample 215

source_name: Control ChlorxAna Rep1

source_name: Pesticide ChlorxAna Rep1


title: Sample 206

source_name: Pesticide EndoxAna Rep3

source_name: Control EndoxAna Rep3


title: Sample 218

source_name: Pesticide DelxAna Rep2

source_name: Mixture DelxAna Rep1


title: Sample 212

source_name: Control CarbxAna Rep2

source_name: Cyano CarbxAna Rep2


title: Sample 205

source_name: Mixture AcexAna Rep4

source_name: Cyano AcexAna Rep3


title: Sample 207

source_name: Mixture EndoxAna Rep3

source_name: Pesticide EndoxAna Rep4


title: Sample 196

source_name: Mixture FenxNod Rep3

source_name: Pesticide FenxNod Rep4


title: Sample 211

source_name: Mixture FenxAna Rep4

source_name: Cyano EndoxAna Rep3


title: Sample 208

source_name: Mixture EndoxAna Rep4


title: Sample 202

source_name: Pesticide FenxOsl Rep2

source_name: Mixture FenxOsl Rep1


title: Sample 204

source_name: Mixture AcexAna Rep3

source_name: Pesticide AcexAna Rep4


title: Sample 203

source_name: Control TebxAph Rep2

source_name: Cyano  TebxAph Rep2


title: Sample 201

source_name: Cyano AcexAna Rep4

source_name: Control AcexAna Rep4


title: Sample 199

source_name: Mixture EndoxMc Rep3

source_name: Pesticide EndoxMc Rep4


title: Sample 189

source_name: Cyano AcexNod Rep4

source_name: Control AcexNod Rep4


title: Sample 195

source_name: Pesticide FenxNod Rep3

source_name: Control FenxNod Rep3


title: Sample 210

source_name: Mixture FenxAna Rep3

source_name: Pesticide FenxAna Rep4


title: Sample 197

source_name: Mixture FenxNod Rep4

source_name: Cyano FenxNod Rep3


title: Sample 200

source_name: Pesticide AcexAna Rep3

source_name: Control AcexAna Rep3


title: Sample 187

source_name: Mixture DelxMc Rep4

source_name: Cyano DelxMc Rep3


title: Sample 192

source_name: Pesticide EndoxNod Rep3

source_name: Control EndoxNod Rep3


title: Sample 194

source_name: Mixture EndoxNod Rep4

source_name: Cyano EndoxNod Rep3


title: Sample 198

source_name: Cyano CarbxCyl Rep2

source_name: Control CarbxCyl Rep3


title: Sample 183

source_name: Mixture ChlorxMc Rep3

source_name: Pesticide ChlorxMc Rep4


title: Sample 193

source_name: Mixture EndoxNod Rep3

source_name: Pesticide EndoxNod Rep4


title: Sample 186

source_name: Mixture DelxMc Rep3

source_name: Pesticide DelxMc Rep4


title: Sample 188

source_name: Pesticide AcexNod Rep3

source_name: Control AcexNod Rep3


title: Sample 182

source_name: Pesticide ChlorxMc Rep3

source_name: Control ChlorxMc Rep3


title: Sample 190

source_name: Mixture AcexNod Rep3

source_name: Pesticide AcexNod Rep4


title: Sample 181

source_name: Mixture CarbxMc Rep4

source_name: Cyano CarbxMc Rep3


title: Sample 179

source_name: Control AcexMc Rep1

source_name: Pesticide AcexMc Rep1


title: Sample 191

source_name: Mixture AcexNod Rep4

source_name: Cyano AcexNod Rep3


title: Sample 184

source_name: Mixture ChlorxMc Rep4

source_name: Cyano ChlorxMc Rep3


title: Sample 185

source_name: Pesticide DelxMc Rep3

source_name: Control DelxMc Rep3


title: Sample 177

source_name: Pesticide CarbxMc Rep3

source_name: Control CarbxMc Rep3


title: Sample 175

source_name: Pesticide TetraxAna Rep2

source_name: Mixture TetraxAna Rep1


title: Sample 178

source_name: Cyano CarbxMc Rep4

source_name: Control CarbxMc Rep4


title: Sample 165

source_name: Control TetraxMc Rep1

source_name: Pesticide TetraxMc Rep1


title: Sample 180

source_name: Mixture CarbxMc Rep3

source_name: Pesticide CarbxMc Rep4


title: Sample 176

source_name: Cyano TetraxAna Rep1

source_name: Mixture TetraxAna Rep2


title: Sample 170

source_name: Control TetraxAna Rep2

source_name: Cyano TetraxAna Rep2


title: Sample 168

source_name: Control TetraxAph Rep1

source_name: Pesticide TetraxAph Rep1


title: Sample 162

source_name: Control TebxCyl Rep1

source_name: Pesticide TebxCyl Rep1


title: Sample 156

source_name: Control TetraxNod Rep1

source_name: Pesticide TetraxNod Rep1


title: Sample 171

source_name: Pesticide TetraxAph Rep2

source_name: Mixture TetraxAph Rep1


title: Sample 166

source_name: Pesticide TetraxMc Rep2

source_name: Mixture TetraxMc Rep1


title: Sample 169

source_name: Control TetraxCyl Rep2

source_name: Cyano TetraxCyl Rep2


title: Sample 172

source_name: Control TetraxCyl Rep1

source_name: Pesticide TetraxCyl Rep1


title: Sample 174

source_name: Control TetraxAna Rep1

source_name: Pesticide TetraxAna Rep1


title: Sample 159

source_name: Control TetraxMc Rep2

source_name: Cyano TetraxMc Rep2


title: Sample 164

source_name: Cyano TebxCyl Rep1

source_name: Mixture TebxCyl Rep2


title: Sample 163

source_name: Pesticide TebxCyl Rep2

source_name: Mixture TebxCyl Rep1


title: Sample 155

source_name: Mixture DelxNod Rep4

source_name: Cyano DelxNod Rep3


title: Sample 154

source_name: Mixture DelxNod Rep3

source_name: Pesticide DelxNod Rep4


title: Sample 161

source_name: Cyano TetraxNod Rep1

source_name: Mixture TetraxNod Rep2


title: Sample 150

source_name: Pesticide ChlorxNod Rep3

source_name: Control ChlorxNod Rep3


title: Sample 173

source_name: Cyano TetraxCyl Rep1

source_name: Mixture TetraxCyl Rep2


title: Sample 157

source_name: Control TetraxNod Rep2

source_name: Cyano TetraxNod Rep2


title: Sample 152

source_name: Mixture ChlorxNod Rep4

source_name: Cyano ChlorxNod Rep3


title: Sample 149

source_name: Mixture CarbxNod Rep4

source_name: Cyano CarbxNod Rep3


title: Sample 158

source_name: Control TebxCyl Rep2

source_name: Cyano TebxCyl Rep2


title: Sample 147

source_name: Cyano CarbxNod Rep4

source_name: Control CarbxNod Rep4


title: Sample 151

source_name: Mixture ChlorxNod Rep3

source_name: Pesticide ChlorxNod Rep4


title: Sample 160

source_name: Pesticide TetraxNod Rep2

source_name: Mixture TetraxNod Rep1


title: Sample 167

source_name: Cyano TetraxMc Rep1

source_name: Mixture TetraxMc Rep2


title: Sample 145

source_name: Mixture DelxAph Rep4

source_name: Cyano DelxAph Rep3


title: Sample 144

source_name: Mixture DelxAph Rep3

source_name: Pesticide DelxAph Rep4


title: Sample 143

source_name: Pesticide DelxAph Rep3

source_name: Control DelxAph Rep3


title: Sample 148

source_name: Mixture CarbxNod Rep3

source_name: Pesticide CarbxNod Rep4


title: Sample 146

source_name: Pesticide CarbxNod Rep3

source_name: Control CarbxNod Rep3


title: Sample 153

source_name: Pesticide DelxNod Rep3

source_name: Control DelxNod Rep3


title: Sample 139

source_name: Mixture CarbxAph Rep4

source_name: Cyano CarbxAph Rep3


title: Sample 140

source_name: Pesticide ChlorxAph Rep3

source_name: Control ChlorxAph Rep3


title: Sample 135

source_name: Mixture TebxAna Rep4

source_name: Cyano TebxAna Rep3


title: Sample 137

source_name: Cyano CarbxAph Rep4

source_name: Control CarbxAph Rep4


title: Sample 138

source_name: Mixture CarbxAph Rep3

source_name: Pesticide CarbxAph Rep4


title: Sample 142

source_name: Mixture ChlorxAph Rep4

source_name: Cyano ChlorxAph Rep3


title: Sample 133

source_name: Pesticide TebxAna Rep3

source_name: Control TebxAna Rep3


title: Sample 132

source_name: Mixture TebxOsl Rep4

source_name: Cyano TebxOsl Rep3


title: Sample 129

source_name: Mixture TebxAph Rep4

source_name: Cyano TebxAph Rep3


title: Sample 123

source_name: Mixture DelxCyl Rep4

source_name: Cyano DelxCyl Rep3


title: Sample 134

source_name: Mixture TebxAna Rep3

source_name: Pesticide TebxAna Rep4


title: Sample 136

source_name: Pesticide CarbxAph Rep3

source_name: Control CarbxAph Rep3


title: Sample 122

source_name: Mixture DelxCyl Rep3

source_name: Pesticide DelxCyl Rep4


title: Sample 119

source_name: Mixture ChlorxCyl Rep3

source_name: Pesticide ChlorxCyl Rep4


title: Sample 125

source_name: Cyano TebxAph Rep4

source_name: Control TebxAph Rep4


title: Sample 130

source_name: Pesticide TebxOsl Rep3

source_name: Control TebxOsl Rep3


title: Sample 116

source_name: Mixture CarbxCyl Rep3

source_name: Pesticide CarbxCyl Rep4


title: Sample 118

source_name: Pesticide ChlorxCyl Rep3

source_name: Control ChlorxCyl Rep3


title: Sample 120

source_name: Mixture ChlorxCyl Rep4

source_name: Cyano ChlorxCyl Rep3


title: Sample 128

source_name: Mixture TebxAph Rep3

source_name: Pesticide TebxAph Rep4


title: Sample 131

source_name: Mixture TebxOsl Rep3

source_name: Pesticide TebxOsl Rep4


title: Sample 115

source_name: Cyano CarbxCyl Rep4

source_name: Control CarbxCyl Rep4


title: Sample 109

source_name: Pesticide ChlorxAna Rep3

source_name: Control ChlorxAna Rep3


title: Sample 127

source_name: Cyano TebxAna Rep4

source_name: Control TebxAna Rep4


title: Sample 110

source_name: Mixture ChlorxAna Rep3

source_name: Pesticide ChlorxAna Rep4


title: Sample 124

source_name: Pesticide TebxAph Rep3

source_name: Control TebxAph Rep3


title: Sample 105

source_name: Pesticide CarbxAna Rep3

source_name: Control CarbxAna Rep3


title: Sample 106

source_name: Cyano CarbxAna Rep4

source_name: Control CarbxAna Rep4


title: Sample 111

source_name: Mixture ChlorxAna Rep4

source_name: Cyano ChlorxAna Rep3


title: Sample 114

source_name: Mixture DelxAna Rep4

source_name: Cyano DelxAna Rep3


title: Sample 126

source_name: Cyano TebxOsl Rep4

source_name: Control TebxOsl Rep4


title: Sample 117

source_name: Mixture CarbxCyl Rep4

source_name: Cyano CarbxCyl Rep3


title: Sample 121

source_name: Pesticide DelxCyl Rep3

source_name: Control DelxCyl Rep3


title: Sample 141

source_name: Mixture ChlorxAph Rep3

source_name: Pesticide ChlorxAph Rep4


title: Sample 104

source_name: Cyano TebxMc Rep1

source_name: Mixture TebxMc Rep2


title: Sample 108

source_name: Mixture CarbxAna Rep4

source_name: Cyano CarbxAna Rep3


title: Sample 107

source_name: Mixture CarbxAna Rep3

source_name: Pesticicide CarbxAna Rep4


title: Sample 112

source_name: Pesticide DelxAna Rep3

source_name: Control DelxAna Rep3


title: Sample 113

source_name: Mixture DelxAna Rep3

source_name: Pesticide DelxAna Rep4


title: Sample 96

source_name: Control TetraxCyl Rep2

source_name: Cyano TetraxCyl Rep2


title: Sample 98

source_name: Cyano TebxNod Rep1

source_name: Mixture TebxNod Rep2


title: Sample 91

source_name: Cyano EndoxOsl Rep1

source_name: Mixture EndoxOsl Rep2


title: Sample 93

source_name: Cyano FenxOsl Rep1

source_name: Mixture FenxOsl Rep2


title: Sample 103

source_name: Pesticide TebxMc Rep2

source_name: Mixture TebxMc Rep1


title: Sample 95

source_name: Control TebxNod Rep2

source_name: Cyano TebxNod Rep2


title: Sample 102

source_name: Control TebxMc Rep1

source_name: Pesticide TebxMc Rep1


title: Sample 101

source_name: Cyano TetraxCyl Rep1

source_name: Mixture TetraxCyl Rep2


title: cutaneous squamous cell carcinoma cells ID 2

city: Salzburg

first: Christina

last: Guttmann-Gruber

address: Muellner Hauptstrasse 48

country: Austria

institute: EB House Austria

description: Gene expression data from cutaneous SCC cells ID 2

hyb_protocol: Hybridization on GeneChip Human Gene 1.0 ST Array was performed according to standard protocols. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250 according to the GeneChip Expression Wash, Stain, and Scan User Manual (P/N 702731).

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were generated with Affymetrix GeneChip Command Console 1.3 and Expression Console 1.2.1 Software.

label: Biotin

source_name: tumor biopsy

label_protocol: Labeled ssDNA was prepared according to the standard protocols from the Ambion WT Expression Kit and the Gene Chip WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 2)

growth_protocol: All cells were routinely subcultured and maintained in EpiLife medium.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy kit according to manufacturer's protocols.

treatment_protocol: no treatment

value: cutaneous squamous cell carcinoma

tag: disease status

value: RDEB-SCC


title: cutaneous squamous cell carcinoma cells ID 53

description: Gene expression data from cutaneous SCC cells ID 53


title: Sample 97

source_name: Pesticide TebxNod Rep2

tag: developmental stage

source_name: Mixture TebxNod Rep1


title: cutaneous squamous cell carcinoma cells ID 1

description: Gene expression data from cutaneous SCC cells ID 1


title: Sample 81

source_name: Pesticide DelxOsl Rep2

source_name: Mixture DelxOsl Rep1


title: Sample 99

source_name: Control TetraxCyl Rep1

source_name: Pesticide TetraxCyl Rep1


title: Sample 79

source_name: Pesticide ChlorxOsl Rep2

source_name: Mixture ChlorxOsl Rep1


title: Sample 89

source_name: Control EndoxOsl Rep1

source_name: Pesticide EndoxOsl Rep1


title: Sample 88

source_name: Cyano AcexOsl Rep1

source_name: Mixture AcexOsl Rep2


title: Sample 85

source_name: Cyano TetraxAph Rep1

source_name: Mixture TetraxAph Rep2


title: recessive dystrophic EB keratinocytes cell line 4

description: Gene expression data from RDEB keratinocyte cell line 4

source_name: skin

value: keratinocytes

value: recessive dystrophic EB


title: Sample 94

source_name: Control TebxNod Rep1

source_name: Pesticide TebxNod Rep1


title: Sample 87

source_name: Pesticide AcexOsl Rep2

source_name: Mixture AcexOsl Rep1


title: Sample 84

source_name: Control AcexOsl Rep2

source_name: Cyano AcexOsl Rep2


title: Sample 92

source_name: Control FenxOsl Rep1

source_name: Pesticide FenxOsl Rep1


title: recessive dystrophic EB keratinocytes cell line 3

description: Gene expression data from RDEB keratinocyte cell line 3


title: Sample 80

source_name: Control DelxOsl Rep1

source_name: Pesticide DelxOsl Rep1


title: Sample 82

source_name: Cyano DelxOsl Rep1

source_name: Mixture DelxOsl Rep2


title: Sample 86

source_name: Pesticide TetraxOsl Rep2

source_name: Mixture TetraxOsl Rep1


title: normal human keratinocytes cell line 1

description: Gene expression data from normal human keratinocytes cell line 1

value: healthy


title: recessive dystrophic EB keratinocytes cell line 2

description: Gene expression data from RDEB keratinocyte cell line 2


title: Sample 76

source_name: Pesticide CarbxOsl Rep2

source_name: Mixture CarbxOsl Rep1


title: Sample 90

source_name: Pesticide EndoxOsl Rep2

source_name: Mixture EndoxOsl Rep1


title: Sample 77

source_name: Cyano CarbxOsl Rep1

source_name: Mixture CarbxOsl Rep2


title: Sample 78

source_name: Control ChlorxOsl Rep1

source_name: Pesticide ChlorxOsl Rep1


title: Sample 72

source_name: Mixture FenxAph Rep3

source_name: Pesticide FenxAph Rep4


title: Sample 100

source_name: Pesticide TetraxCyl Rep2

source_name: Mixture TetraxCyl Rep1


title: Sample 83

source_name: Control AcexOsl Rep1

source_name: Pesticide AcexOsl Rep1


title: Sample 75

source_name: Control CarbxOsl Rep2

source_name: Cyano CarbxOsl Rep2


title: IRF1-/- BMDM infected with influenza A virus PR8, rep 1

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Five micrograms of cDNA was hybridized for 16h at 45C on a Mouse Gene 2.0 ST GeneChip array

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.5

source_name: bone marrow derived macrophages infected for 9 hour with influenza A virus PR8

label_protocol: Sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671)

growth_protocol: Primary BMDMs were grown for 5–6 days in DMEM (Gibco) supplemented with 1% non-essential amino acids (Gibco), 10% FBS (Atlanta Biologicals), 30% medium conditioned by L929 mouse fibroblasts, and 1% penicillin and streptomycin (Sigma).

extract_protocol: Total RNA was extracted using the Qiagen Rneasy protocol according to the manufacturer's recommended methods

treatment_protocol: BMDMs in antibiotic–free medium were seeded onto 12-well plates at a density of 1 × 106 cells per well, followed by incubation overnight. Cells were then infected with influenza A virus PR8 (MOI, 25) and cultured for an additional 9 hours before extracting total RNA.

tag: strain background

value: IRF1-/- mouse backcrossed to the C57BL/6 background

value: bone marrow derived macrophages

tag: infected with

value: influenza A virus PR8 for 9 hrs


title: Sample 74

source_name: Control CarbxOsl Rep1

value: female

value: adult

source_name: Pesticide CarbxOsl Rep1


title: Sample 66

source_name: Mixture AcexAph Rep3

value: whole body

source_name: Pesticide AcexAph Rep4


title: IRF1-/- BMDM infected with influenza A virus PR8, rep 2

tag: genotype/variation


title: Sample 73

source_name: Cyano FenxAph Rep3


title: Sample 58

source_name: Pesticide EndoxNod Rep2

source_name: Mixture EndoxNod Rep1


title: Sample 69

source_name: Mixture EndoxAph Rep3

source_name: Pesticide EndoxAph Rep4


title: Sample 60

source_name: Control FenxNod Rep1

source_name: Pesticide FenxNod Rep1


title: Sample 65

source_name: Control TetraxOsl Rep2

source_name: Cyano TetraxOsl Rep2


title: Sample 67

source_name: Mixture AcexAph Rep4

source_name: Cyano AcexAph Rep3


title: Sample 71

source_name: Pesticide FenxAph Rep3

source_name: Control FenxAph Rep3


title: Sample 70

source_name: Cyano EndoxAph Rep3


title: Sample 62

source_name: Cyano FenxNod Rep1

source_name: Mixture FenxNod Rep2


title: Sample 52

source_name: Control AcexNod Rep1

source_name: Pesticide AcexNod Rep1


title: Sample 61

source_name: Pesticide FenxNod Rep2

source_name: Mixture FenxNod Rep1


title: Sample 64

source_name: Cyano AcexAph Rep4

source_name: Control AcexAph Rep4


title: Sample 55

source_name: Pesticide AcexNod Rep2

source_name: Mixture AcexNod Rep1


title: Sample 50

source_name: Pesticide FenxMc Rep2

source_name: Mixture FenxMc Rep1


title: Sample 63

source_name: Pesticide AcexAph Rep3

source_name: Control AcexAph Rep3


title: Sample 49

source_name: Control FenxMc Rep1

source_name: Pesticide FenxMc Rep1


title: Sample 54

source_name: Pesticide TetraxMc Rep3

source_name: Control TetraxMc Rep3


title: Sample 59

source_name: Cyano EndoxNod Rep1

source_name: Mixture EndoxNod Rep2


title: Sample 45

source_name: Cyano AcexMc Rep1

source_name: Mixture AcexMc Rep2


title: Sample 46

source_name: Control EndoxMc Rep1

source_name: Pesticide EndoxMc Rep1


title: Sample 51

source_name: Cyano FenxMc Rep1

source_name: Mixture FenxMc Rep2


title: Sample 68

source_name: Pesticide EndoxAph Rep3

source_name: Control EndoxAph Rep3


title: Sample 56

source_name: Cyano AcexNod Rep1

source_name: Mixture AcexNod Rep2


title: Sample 48

source_name: Cyano EndoxMc Rep1

source_name: Mixture EndoxMc Rep2


title: Sample 57

source_name: Control EndoxNod Rep1

source_name: Pesticide EndoxNod Rep1


title: Sample 53

source_name: Control AcexNod Rep2

source_name: Cyano AcexNod Rep2


title: Sample 40

source_name: Mixture TebxCyl Rep4

source_name: Cyano TebxCyl Rep3


title: Sample 47

source_name: Pesticide EndoxMc Rep2

source_name: Mixture EndoxMc Rep1


title: Sample 43

source_name: Control AcexMc Rep2

source_name: Cyano AcexMc Rep2


title: Sample 44

source_name: Pesticide AcexMc Rep2

source_name: Mixture AcexMc Rep1


title: Sample 39

source_name: Mixture TebxCyl Rep3

source_name: Pesticide TebxCyl Rep4


title: Sample 35

source_name: Cyano TetraxMc Rep4

source_name: Control TetraxMc Rep4


title: Sample 42

source_name: Mixture TetraxMc Rep4

source_name: Cyano TetraxMc Rep3


title: Sample 34

source_name: Cyano TebxCyl Rep4

source_name: Control TebxCyl Rep4


title: Sample 37

source_name: Mixture TetraxNod Rep4

source_name: Cyano TetraxNod Rep3


title: Sample 36

source_name: Mixture TetraxNod Rep3

source_name: Pesticide TetraxNod Rep4


title: Sample 30

source_name: Mixture FenxOsl Rep3

source_name: Pesticide FenxOsl Rep4


title: Sample 38

source_name: Pesticide TebxCyl Rep3

source_name: Control TebxCyl Rep3


title: Sample 41

source_name: Mixture TetraxMc Rep3

source_name: Pesticide TetraxMc Rep4


title: Sample 28

source_name: Mixture EndoxOsl Rep4

source_name: Cyano EndoxOsl Rep3


title: Sample 18

source_name: Cyano ChlorxCyl Rep1

source_name: Mixture ChlorxCyl Rep2


title: Sample 17

source_name: Pesticide ChlorxCyl Rep2

source_name: Mixture ChlorxCyl Rep1


title: Sample 22

source_name: Pesticide AcexOsl Rep3

source_name: Control AcexOsl Rep3


title: Sample 19

source_name: Control DelxCyl Rep1

source_name: Pesticide DelxCyl Rep1


title: Sample 13

source_name: Control AcexCyl Rep2

source_name: Cyano AcexCyl Rep2


title: Sample 32

source_name: Pesticide TetraxNod Rep3

source_name: Control TetraxNod Rep3


title: Sample 20

source_name: Pesticide DelxCyl Rep2

source_name: Mixture DelxCyl Rep1


title: Sample 33

source_name: Cyano TetraxNod Rep4

source_name: Control TetraxNod Rep4


title: Sample 26

source_name: Pesticide EndoxOsl Rep3

source_name: Control EndoxOsl Rep3


title: Sample 10

source_name: Cyano FenxAna Rep1

source_name: Mixture FenxAna Rep2


title: Sample 14

source_name: Pesticide CarbxCyl Rep2

source_name: Mixture CarbxCyl Rep1


title: Sample 31

source_name: Mixture FenxOsl Rep4

source_name: Cyano FenxOsl Rep3


title: BC20

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalization (Quantile) was performed using BRB-Array-Tools version 4.5.1.

source_name: tumour

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: miRNA was extracted from tissue samples using the mirVana miRNA Isolation Kit (Ambion) as per the manufacturer's instructions.

value: Relapse


title: BC18


title: Sample 27

source_name: Mixture EndoxOsl Rep3

source_name: Pesticide EndoxOsl Rep4


title: Sample 12

source_name: Control CarbxCyl Rep2

source_name: Cyano CarbxCyl Rep2


title: Sample 7

source_name: Cyano EndoxAna Rep1

source_name: Mixture EndoxAna Rep2


title: Sample 25

source_name: Mixture AcexOsl Rep4

source_name: Cyano AcexOsl Rep3


title: Sample 15

source_name: Cyano CarbxCyl Rep1

source_name: Mixture CarbxCyl Rep2


title: BC16


title: Sample 5

source_name: Control EndoxAna Rep1

source_name: Pesticide EndoxAna Rep1


title: BC15


title: Sample 24

source_name: Mixture AcexOsl Rep3

source_name: Pesticide AcexOsl Rep4


title: BC19


title: Sample 23

source_name: Cyano AcexOsl Rep4

source_name: Control AcexOsl Rep4


title: Sample 29

source_name: Pesticide FenxOsl Rep3

source_name: Control FenxOsl Rep3


title: Sample 6

source_name: Pesticide EndoxAna Rep2

source_name: Mixture EndoxAna Rep1


title: Sample 4

source_name: Cyano AcexAna Rep1

source_name: Mixture AcexAna Rep2


title: Sample 21

source_name: Cyano DelxCyl Rep1

source_name: Mixture DelxCyl Rep2


title: Sample 8

source_name: Control FenxAna Rep1

source_name: Pesticide FenxAna Rep1


title: Sample 2

source_name: Control AcexAna Rep2

source_name: Cyano AcexAna Rep2


title: BC12

source_name: tumour


title: Sample 9

source_name: Pesticide FenxAna Rep2

source_name: Mixture FenxAna Rep1


title: Sample 16

source_name: Control ChlorxCyl Rep1

source_name: Pesticide ChlorxCyl Rep1


title: BC14


title: BC7

value: NoRelapse


title: BC1


title: BC3


title: Sample 11

source_name: Control CarbxCyl Rep1

source_name: Pesticide CarbxCyl Rep1


title: BC8


title: BC17


title: BC10


title: BC11


title: BC13


title: BC4


title: AE3

status: Public on Dec 06 2017

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in dentate gyrus of EB-treated OVX adult female rat

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two pups were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.

source_name: EB treated_ Replicate 3

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: 150-200g adult female Sprague-Dawley rats purchased from Taconic Farms were kept on a 12-h light/dark cycle (lights on at 0700) and housed in groups of four with food and water ad libitum. Rats were ovariectomized (OVX) under ketamine/xylazine anesthesia one week prior to hormonal replacement

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Female rats were ovariectomized and treated either with estrogen replacement (four doses of 2 microg of estradiol every 24 h: two doses before SE, two doses after) or oil. SE was induced by I.P. administration of kainic acid (KA, 16 mg/kg) and terminated after 5 h with pentobarbital.

value: Sprague-Dawley

tag: status

value: ovaryectomized, seizured

value: dentate gyrus

tag: treatment

value: EB


title: AO4

description: Gene expression in dentate gyrus of oil-treated seizured OVX adult female rat

source_name: Oil treated _ Replicate 4

value: oil


title: AO2

source_name: Oil treated _ Replicate 2


title: AE1

source_name: EB treated_ Replicate 1


title: BC6

tag: group


title: BC9


title: AO1

source_name: Oil treated _ Replicate 1


title: BC2


title: Sample 3

source_name: Pesticide AcexAna Rep2

source_name: Mixture AcexAna Rep1


title: intact DP

city: Tokyo

first: Masahiro

last: Kiso

address: 1-21-1 Toyama Shinjuku-ku

department: Regenerative Medicine, Research Institute

country: Japan

institute: National Center for Global Health and Medicine

description: Gene expression in intact DPs

hyb_protocol: 2.0ug of Cy3-labelled cDNA was filled up to 50 ul containing 1x Agilent blocking agent and 1x Agilent hybridization buffer, and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: intact dermal papilla

label_protocol: cDNA were amplified by Ovation® Pico WTA System V2（NuGEN Technologies) from XXng total RNA according to the manufacturer's instructions. Amplified cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer. Cyanine-3 (Cy3) labeled cDNA was prepared with SureTag Complete DNA Labeling Kit (Agilent) according to the manufacturer's instructions, followed by Amicon Ultra-0.5 mL Centrifugal Filters for DNA Purification and Concentration (Merck Millipore). Dye incorporation and cDNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Vibrissal dermal papillae were obtained from 4-week-old C57BL/6J mice and GFP mice as described previously. The mystical pad was cut open, and the skin was inverted. Follicles were removed with fine forceps. The collagen capsules surrounding the vibrissae follicles were removed to expose the follicle bases, and the dermal papillae (DPs) were dissected using thin needles. Isolated DPs were placed on the bottoms of cell culture dishes. DPCs were cultured for 10-14 days.The culture medium was exchanged every four days.

extract_protocol: Total RNA was prepared from DPCs using ISOGEN (WAKO, Shiga, Japan) and following the manufacturer’s protocol. cDNA was synthesized from 2 μg of total RNA using PrimeScript (Takara Bio; Osaka, Japan) with a mixture of random hexamers (Takara Bio), oligo dT primers (Takara Bio), and ribonuclease inhibitor (Takara Bio).

treatment_protocol: They were cultured in D-MEM (low glucose) supplemented with 10% fetal bovine serum and FGF2 10 ng/ml (Peprotech, Rocky Hill, CA)

value: Vibrissal dermal papillae

tag: culture stage

value: wild-DPC


title: Kras G12D Lung Tumor Associated Macrohages  replicate 4

city: Baltimore

first: Michael

middle: Jonathan

last: Topper

state: MD

address: 1650 Orleans St., Suite 530

department: Oncology

institute: Johns Hopkins University

description: replicate 2

hyb_protocol: Agilent Mouse GE 4x 44K v2 microarrays were used, which contain 41,000 unique probes targeting 27,958 Entrez gene RNAs. 825 ng of each Cyanine-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.

scan_protocol: Microarrays were scanned using an Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

source_name: Mouse Lung Macrophages (CD45+CD11b+F4/80+)

label_protocol: Sample amplification and labeling procedures were carried out by using Quick RNA Amplification and Labeling Kit (Cat# 5190-0447, Agilent Technologies) with minor modifications. Briefly, 400 ng total RNA was reverse-transcribed into cDNA by MMLV-RT using oligo dT primers (Cat# RA300A-2, System Bioscience) that incorporate T7 promoter sequence. The cDNA is then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine-labeled CTP (Perkin Elmer). The labeled cRNA is purified using RNeasy mini kit (Qiagen). RNA spike-in controls (Agilent Technologies) are added to RNA samples before amplification and labeling according to manufacturer’s protocol.

growth_protocol: LSL-KrasG12D mice were instilled with Cre expressing adenovirus to induce the formation of adenomas, thereafter, mice were treated with vehicle or combination Azacitidine plus ITF-2357 for 3 months. Lungs were digested and the resulting single cell suspensions were sorted for viable macrophages (CD45+, CD11b+, F4/80+) and viable lymphocytes (CD45+, CD3+, CD8+).

extract_protocol: RNA was extracted and purified using using the RNeasy Mini kit (Qiagen). The extracted RNA was amplified using Sigma WTA2 kit and processed for hybridization on an Mouse Gene Expression v2 4x44K Microarray chip.

value: 0.5mg/kg Azacitidine + 2.0 mg/kg ITF-2357


title: Combo Mouse Kras G12D Lung Tumors replicate 1

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

source_name: Mouse Kras G12D Lung Tumors

growth_protocol: LSL-KrasG12D mice were instilled with Cre expressing adenovirus to induce the formation of adenomas, thereafter, mice were treated with vehicle or combination Azacitidine plus ITF-2357 for 3 months.

extract_protocol: RNA was extracted and purified using using the RNeasy Mini kit (Qiagen) and processed for hybridization on an Mouse Gene Expression v2 4x44K Microarray chip.


title: AO3

source_name: Oil treated _ Replicate 3


title: AE4

source_name: EB treated_ Replicate 4


title: AE2

source_name: EB treated_ Replicate 2


title: tP18

description: Gene expression transfected DPCs P18

source_name: transfected dermal papilla P18


title: P0

description: Gene expression in cultured DPCs P0

source_name: cultured dermal papilla P0


title: BC5

source_name: tumour


title: Sample 1

source_name: Control AcexAna Rep1

source_name: Pesticide AcexAna Rep1


title: Mock Mouse Kras G12D Lung Tumors replicate 2

value: Vehicle


title: S273A Carbo 3

city: Boston

first: Melin

middle: J.

last: Khandekar

state: MA

address: 100 Blossom St. Cox 3

institute: Massachusetts General Hospital

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.0.38

source_name: Fibroblast from S273A PPARG knock in mouse_carboplatin

label_protocol: standard Affymetrix protocol

growth_protocol: Grown in DMEM

extract_protocol: RNA extracted using Trizol follwed by Qiagen RNA prep

treatment_protocol: Treated with carboplatin 25µM for 24 hours or saline

value: S273A PPARG knock in

tag: cell type

value: fibroblast

tag: treated with

value: 25µM carboplatin for 24 hours


title: Kras G12D Lung Tumor Associated Macrohages  replicate 1

description: replicate 1


title: S273A No Carbo 3

source_name: Fibroblast from S273A PPARG knock in mouse

value: saline (control)


title: WT No Carbo 3

source_name: Fibroblast from WT PPARg mouse

value: WT PPARg


title: WT Carbo 1

source_name: Fibroblast from WT PPARg mouse_carboplatin


title: P5

description: Gene expression in cultured DPCs P5

source_name: cultured dermal papilla P5

tag: tissue


title: Combo Mouse Kras G12D Lung Tumors replicate 2


title: Kras G12D Lung Tumor Associated T Lymphocytes replicate 4

description: replicate 2

source_name: Mouse Lung Lymphocytes (CD45+CD3+CD8+)


title: Kras G12D Lung Tumor Associated T Lymphocytes replicate 3

description: replicate 1


title: S273A Carbo 1


title: Aire-/- mTEChi 1

city: Stanford

first: Andrew

middle: S.

last: Koh

state: CA

address: 279 Campus Drive B203

institute: Stanford University

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: Expression signals were normalized using the Signal Space Transformation-Robust Multi-Chip Average (SST-RMA) algorithm on the Affymetrix Expression Console software.  Normalized signals were analyzed using the Transcriptome Analysis Console software (Affymetrix).

source_name: Thymus

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: mTECs were sorted into Trizol LS (Life Technologies), RNA was extracted according to manufacturer’s instructions, then purified using the RNeasy Micro Kit (Qiagen).

treatment_protocol: Thymi were tissue-digested, enriched for stroma and sorted for DAPIneg, CD45neg, Epcam+, UEA+, Ly51lo, MHCIIhi and MHCIIlo mTECs

tag: genotype

value: Aire-/-

value: mTEChi

tag: age

value: 4 weeks


title: Brg1+/+ mTEChi 1

tag: strain


title: Kras G12D Lung Tumor Associated T Lymphocytes replicate2


title: Aire-/- mTEChi 2


title: Brg1+/+ mTEChi 2


title: Kras G12D Lung Tumor Associated Macrohages  replicate 3

description: replicate 1

source_name: Mouse Lung Macrophages (CD45+CD11b+F4/80+)


title: Mock Mouse Kras G12D Lung Tumors replicate 1

source_name: Mouse Kras G12D Lung Tumors


title: Brg1+/+ mTEClo 1

value: mTEClo


title: S273A No Carbo 2


title: Adrenals harvested before dexamethasone treatment (control), biological replicate 4

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

description: Gene expression data from adrenal before dexamethasone treatment

hyb_protocol: Targets were assayed on a Affymetrix Mouse Gene ST 2.1 Plate

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

data_processing: Data was RMA-normalized using the oligo package from Bioconductor.

source_name: Adrenal glands from wt C57BL/6J male mouse

label_protocol: Biotinylated cRNA was prepared with  WT Pico Kit (Affymetrix)

extract_protocol: Total RNA was extracted with RNAeasy mini kit (Qiagen) following the manufacturer's protocol. Quality of RNA was assessedwith Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Adrenal glands were collected from mice before dexamethasone treatment, immediatey after its suspension and 3 and 7 days into the recovery process.

value: Adrenal gland

value: WT

value: 6 weeks


title: Adrenals harvested before dexamethasone treatment (control), biological replicate 2


title: WT Carbo 2


title: Brg1-/- mTEClo 1


title: WT Carbo 3


title: WT No Carbo 1


title: WT No Carbo 2


title: Kras G12D Lung Tumor Associated T Lymphocytes replicate 1

description: replicate 1


title: Kras G12D Lung Tumor Associated Macrohages  replicate2


title: S273A No Carbo 1


title: S273A Carbo 2


title: Aire-/- mTEClo 1


title: A549 Mock v. 500nM Azacitidine + 100nM ITF-2357

hyb_protocol: Agilent human GE 4x 44K v2 microarrays (Agilent design ID 026652, part number G4845A) were used, which contain 41,000 unique probes targeting 27,958 Entrez gene RNAs. 825 ng of each Cyanine-labeled samples was used for hybridization at 65ºC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.

source_name: Mock

growth_protocol: NSCLC cell lines were treated as defined for each condition, Azacitidine treatments were applied for 5 days duration and HDACi treatments were applied for 2 days duration. RNA was extracted on day 8.

extract_protocol: RNA was extracted and purified using using the RNeasy Mini kit (Qiagen) and processed for hybridization on an Human Gene Expression v2 4x44K Microarray chip.

tag: cell line

tag: day


title: A549 Mock v. 500nM Azacitidine + 100nM MS-275 rep4


title: Brg1-/- mTEChi 2


title: H1299 Mock v. 100nM ITF-2357 rep3


title: H1299 Mock v. 500nM Azacitidine + 100nM MS-275 rep3


title: H1299 Mock v. 500nM Azacitidine + 100nM ITF-2357 rep3


title: Adrenals harvested at the end of dexamethasone treatment, biological replicate 1

description: Gene expression data from adrenal after 14 days of dexamethasone treatment


title: Adrenals harvested at the end of dexamethasone treatment, biological replicate 2


title: A549 Mock v. 100nM MS-275 rep4


title: H1299 Mock v. 100nM MS-275 rep3


title: Adrenals harvested before dexamethasone treatment (control), biological replicate 3


title: Brg1-/- mTEChi 1


title: Aire+/+ mTEClo 1

value: Aire+/+


title: Aire+/+ mTEChi 2


title: Adrenals harvested before dexamethasone treatment (control), biological replicate 1


title: H23 Mock v. 500nM Azacitidine rep2

source_name: Azacitidine


title: Adrenals harvested 7 days after dexamethasone treatment, biological replicate 4

description: Gene expression data from adrenal after 7 days of recovery following  dexamethasone treatment


title: H460 Mock v. 100nM MS-275  rep1


title: H460 Mock v. 500nM Azacitidine + 100nM MS-275 rep1


title: H23 Mock v. 100nM ITF-2357 rep2


title: T28

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

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

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

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

source_name: Esophagus

label_protocol: Extracted total RNA was labeled with Hy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: SPF condition

extract_protocol: Total RNA, including small RNA, was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA) for tissue samples, and miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany)

tag: disease state

value: Barrett’s esophagus

value: L2-IL-1β mice

value: 28 week old

value: Esophagus


title: T46

value: 46 week old


title: Aire+/+ mTEChi 1


title: Adrenals harvested 3 days after dexamethasone treatment, biological replicate 4

description: Gene expression data from adrenal after 3 days of recovery following  dexamethasone treatment


title: Adrenals harvested 3 days after dexamethasone treatment, biological replicate 3


title: H23 Mock v. 500nM Azacitidine + 100nM ITF-2357 rep2


title: A549 Mock v. 100nM ITF-2357 rep4


title: Adrenals harvested at the end of dexamethasone treatment, biological replicate 3


title: Adrenals harvested 7 days after dexamethasone treatment, biological replicate 3


title: blood_disease_rep3

city: Tongliao

first: Batudeligen

last: Duan

address: 1742 Huolinhe Street

institute: Institute of clinical pharmacology of traditional Mongolian Medicine

description: Gene expression data from Pulmonary tuberculosis patient's blood cells

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

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

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

source_name: blood from Pulmonary tuberculosis patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA (Expression Analysis Technical Manual, 2013, Affymetrix).

growth_protocol: Pulmonary tuberculosis patient and normal people who have genetic relationship wtih each other.

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

treatment_protocol: Blood samples were obtained in January 2017 in a Blood RNA tube (4 ml) and an EDTA-containing tube (2 ml). Samples were stored at -80°C.

tag: diagnosis

value: Pulmonary tuberculosis

value: blood

tag: subject id

tag: subject relationship

value: has a genetic relationship with G5


title: Adrenals harvested 7 days after dexamethasone treatment, biological replicate 2


title: Adrenals harvested 3 days after dexamethasone treatment, biological replicate 2


title: H1299 Mock v. 500nM Azacitidine rep3


title: H460 Mock v. 500nM Azacitidine rep1


title: Adrenals harvested 3 days after dexamethasone treatment, biological replicate 1


title: A549 Mock v. 500nM Azacitidine rep4


title: H23 Mock v. 500nM Azacitidine + 100nM MS-275 rep2


title: S28

source_name: Serum

value: Serum


title: Adrenals harvested 7 days after dexamethasone treatment, biological replicate 1


title: H460 Mock v. 500nM Azacitidine + 100nM ITF-2357 rep1


title: H23 Mock v. 100nM MS-275 rep2


title: H460 Mock v. 100nM ITF-2357 rep1


title: blood_disease_rep1

value: has a genetic relationship with G6


title: S46


title: blood_normal_rep1

description: Gene expression data from normal people's blood cells

source_name: blood from normal people

value: normal

value: has a genetic relationship with G1


title: blood_normal_rep2

value: has a genetic relationship with G2


title: blood_disease_rep2

value: has a genetic relationship with G4


title: blood_normal_rep3

value: has a genetic relationship with G3


title: FOL-005 (3uM) 24 hours 2

status: Public on Dec 05 2017

city: Münster

first: Majid

last: Alam

address: Mendelstraße 17

institute: Monasterium Laboratory

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix  GeneArray Scanner 3000

data_processing: The data were analyzed with Transcriptome Analysis Console 3.0 (Affymetrix) and gene expression profiling was performed using human transcriptome arrays 2.0 (HTA-2_0) from Affymetrix with RMA.

source_name: HFs 3uM FOL 24hr 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5ug total RNA

growth_protocol: Hair follicles (HFs) were microdissected from human occipital scalp skin and inbated in supplemented Williams E media overnight

treatment_protocol: After overnight incubation HFs were treated with corresponding groups of vehicle, FOL-005 (300nM) and FOL-005 (3uM) for 6 and 24 hours

value: Hair Follicle


title: Vehicle 6 hours 2

source_name: HFs Vehicle 6hr 2


title: FOL-005 (300nM) 24 hours 2

source_name: HFs 300nM FOL 24hr 2


title: Vehicle 24 hours 2

source_name: HFs Vehicle 24hr 2