title: Patient1 post separator

status: Public on Apr 11 2016

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: A patients with systemic lupus erythematosus who were undergoing double filtration plasmapheresis once every 2 weeks.

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: systemic lupus erythematosus

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

value: plasma

tag: status

value: post plasma separator

value: 39 years

tag: Sex


title: genomic DNA from placental biopsy 8

status: Public on Apr 12 2016

type: genomic

city: Penrith

first: Christine

middle: L

last: Chiu

state: New South Wales

address: Locked Bag 1797

department: School of Medicine

country: Australia

institute: Western Sydney University

description: preeclampsia placenta

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

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

data_processing: Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization). Data was then pre-processed in the R package wateRmelon using the dasen function. processed data: dasen normalized beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: placental biopsy collected <30mins of delivery

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA extracted from placental biopsies using Qiagen DNA mini kit as per manufacturer's protocols

value: Male

tag: disease

value: preeclampsia

tag: gestation (wk)

tag: tissue

value: placenta


title: Patient2 pre separator

type: RNA

country: Japan

molecule: total RNA

value: pre plasma separator

tag: age

value: 29 years

value: Female


title: Patient3 pre separator

description: A patients with systemic lupus erythematosus who were undergoing immuneadsorption once every 2 weeks.

value: 51 years


title: Patient3 post separator


title: Control CV125 Strain Replicate 4

city: CHATENAY-MALABRY

first: Claudine

last: DELOMENIE

address: 5, rue Jean-Baptiste Clément

department: Transcriptomique

country: France

institute: University Paris Sud 11

description: Biological replicate (culture batch) 1 of 2. Individual culture 4 of 4. Control wild-type CV125 strain, untreated, cultured in an individual vial and harvested.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After washing, slides were scanned using the Agilent Microarray Scanner (G2565CA) at 5-µm resolution.

scan_protocol: After washing, slides were scanned using the Microarray Scanner (G2565CA) from Agilent at 5-µm resolution and at high and low photomultiplier voltages. Images were quantified using Agilent Feature Extraction 10.7.3.1. software with default protocols and settings.

data_processing: Data were computed using Genespring GX software version 12.6 (Agilent Technologies). Fluorescence signals were background-subtracted and a filtering procedure excluded data points considered unreliable as they corresponded to probe sets associated with low signal intensities or bad quality features. A within-array loess normalization was performed, followed by an inter-array scaling normalization.

organism: Aspergillus nidulans

source_name: control CV125 strain (WT)

label_protocol: 200 ng of total RNA were labelled using the Low Input Quick Amp Labelling Kit, Two-Color (Agilent Technologies), using Cy5-CTP for the reference RNA pool  made of a mix of all samples, and Cy3-CTP for individual samples.

growth_protocol: Mycelia were grown at 30°C for 15 h in 400 mL minimal medium with shaking at 150 rpm, in the presence of fructose (0.1%) as the carbon source and urea (5 mM) as the nitrogen source. Media composition, supplements and basic growth conditions were as described by Cove DJ (Biochim Biophys Acta. 1966 Jan 11;113(1):51-6. PMID: 5940632 1966). For each strain, 4 cultures were carried out in each one of two independent experiments.

extract_protocol: Total RNA was isolated as previously described (Total RNA was isolated with guanidine as  described (Robellet X et al. 2010 Curr Genet. 2010 56(4):341-8. doi: 10.1007/s00294-010-0303-5. Epub 2010 May 22). An additional purification step was performed using Trizol following manufacturer's instructions

tag: strain

value: CV125 (pabaA1)

value: mycelium

source_name: pooled WT and TG strains

value: mix of 4 strains  CV125 (pabaA1) and 3 transgenic (pabaA1) strains harbouring a gpdAp-lacZ-trpCt.riboB construct integrated in different chromosomes (NA1363, in chromosome VIII; NA1360, in chromosome V; NA1359, in chromosome II).


title: Transgenic NA1363 Strain Replicate 2

description: Biological replicate (culture batch) 2 of 2. Individual culture 2 of 4. Control wild-type CV125 strain, untreated, cultured in an individual vial and harvested.

source_name: transgenic NA1363 strain (LacZ)

value: NA1363 (pabaA1) harbouring a gpdAp-lacZ-trpCt.riboB construct integrated in chromosome VIII. This construct, carried out in a derivative of the pBR322 vector, contained the E. coli lacZ sequence (encoding ß-galactosidase) fused to the A. nidulans trpC terminator and placed under the control of the strong and constitutive promoter of the A. nidulans gpdA gene, and the riboB gene as selection marker.


title: Patient1 pre separator


title: Patient2 post separator


title: Control CV125 Strain Replicate 3

description: Biological replicate (culture batch) 1 of 2. Individual culture 3 of 4. Control wild-type CV125 strain, untreated, cultured in an individual vial and harvested.


title: Control CV125 Strain Replicate 1

description: Biological replicate (culture batch) 1 of 2. Individual culture 1 of 4. Control wild-type CV125 strain, untreated, cultured in an individual vial and harvested.


title: RPMI8226 normoxia

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

description: SAMPLE 1

hyb_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).

scan_protocol: Agilent G2600A SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent), computed normalized signal intensity with 75%tile normalization.

source_name: RPMI8226 normoxia

growth_protocol: normoxia: 21%O2, hypoxia: 1%O2.

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: RPMI1640 plus 10% FCS.

tag: oxygen status

value: normoxia

tag: cell line

tag: cell type

value: myeloma


title: KMS12BM normoxia

description: SAMPLE 2

source_name: KMS12BM normoxia

label_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).


title: Control CV125 Strain Replicate 2

description: Biological replicate (culture batch) 1 of 2. Individual culture 2 of 4. Control wild-type CV125 strain, untreated, cultured in an individual vial and harvested.


title: genomic DNA from placental biopsy 11

description: normal placenta

value: normal/healthy


title: Muscle-AR113Q-high fat diet-rep5

city: Trento

first: maria

last: pennuto

state: --Choose--

address: Centre for Integrative Biology

department: CIBIO

country: Italy

institute: University of Trento

hyb_protocol: 1.65 mg of Cy3-labeled cRNA (specific activity: 24.4 ±1.7 pmol Cy3 per mg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Fragmentation Buffer and 2x GE (Gene Expression) Blocking Agent (Gene Expression Hybridization Kit, p/n 5188-5242, Agilent Technologies) following manufacturer’s instructions. On completion of the fragmentation reaction, 55 ml of 2x Hi-RPM Hybridization Buffer were added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K V2 Microarray kit (G4846A, Agilent Technologies) for 17 hours at 65°C in a rotating hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C, Agilent Technologies) using the AgilentHD_GX_1Color Profile (Scan Area: 61x21.6 mm; Scan resolution: 5 mm, dye channel set to 100% Green PMT) of Agilent ScanControl software 8.1.3 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09). The output of Agilent Feature Extraction Software has been analyzed using the Bioconductor limma package. Signals have been background-corrected with the normexp algorithm. The probes that resulted as not found on the majority of the arrays were filtered out. Quantile normalization has been applied to the data.

organism: Mus musculus

source_name: quadriceps muscle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 g RNA using the One-Color Low Input Quick Amp Labeling Kit (p/n 5190-2331, Agilent Technologies)

growth_protocol: Congenic C57Bl6J wilt type (CTRL) and AR113Q (SBMA) mice were used in this study.

extract_protocol: Total RNA was extracted Tryzol and purified using RNeasy MinElute Cleanup Kit (Qiagen). RNA quality was analyzed by microfluidic gel electrophoresis on RNA 6000 Nano chip using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA).

treatment_protocol: Mice were fed the NCD or the HFD starting at 40 days of age and sacrificed at 180 dyas of age. Tissues were collectd, snap-frozen in liquid nitrogen, and stored at -80C.

tag: genotype/variation

tag: diet

value: high fat

value: 180 day old


title: Muscle-AR113Q-high fat diet-rep3


title: Muscle-AR113Q-high fat diet-rep2


title: Muscle-AR113Q-high fat diet-rep1


title: Muscle-AR113Q-normal diet-rep5

value: normal


title: Muscle-control-high fat diet-rep4

value: wild type


title: Muscle-AR113Q-normal diet-rep3


title: RPMI8226 hypoxia

description: SAMPLE 5

source_name: RPMI8226 hypoxia

value: hypoxia


title: Muscle-control-high fat diet-rep1


title: Muscle-control-normal diet-rep5


title: Muscle-AR113Q-normal diet-rep4


title: Muscle-AR113Q-normal diet-rep1


title: Muscle-control-normal diet-rep2


title: Muscle-control-high fat diet-rep2


title: Muscle-control-normal diet-rep4


title: Muscle-control-high fat diet-rep3


title: Muscle-AR113Q-high fat diet-rep4


title: Muscle-AR113Q-normal diet-rep2


title: Muscle-control-normal diet-rep3


title: HVT_12

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

country: United Kingdom

institute: GSK

description: Gene expression data from PMNs

hyb_protocol: Labelled cDNA was hybridized onto Hg-U133 Plus 2.0 GeneChip oligonucleotide arrays (Affymetrix).

scan_protocol: Standard protocols

data_processing: Data were analyzed in R/Bioconductor, normalized by RMA= Data were analyzed in R/Bioconductor, normalized by RMA

label: Biotin

source_name: PMNs from HVT

label_protocol: FL-Ovation cDNA Biotin Module V2 kit (NuGen).

growth_protocol: Standard culturing conditions

extract_protocol: WT-Ovation Pico RNA Amplification System (NuGen).

treatment_protocol: The agents were added to the cell culture medium and incubated for the desired time.

tag: study part

value: Part A

tag: disease state

value: HVT

tag: donor pair (part a)

value: l

value: PMN

tag: rna rin value


title: GM-CSF + PI3Kg_10

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + GM-CSF + PI3Kg Inhibitor, t=6h

value: Part B

tag: donor (part b)

tag: agent

value: GM-CSF + PI3Kg Inhibitor

tag: time

value: 6 h


title: ARDS_12

description: Gene expression data from PMNs

source_name: PMNs from ARDS patient

value: ARDS


title: HVT_11

description: Gene expression data from PMNs

value: k


title: OVOL2 transduced-NPCs_rep1

city: Kyoto

first: Koji

last: Kitazawa

state: Kyoto

address: 465 Kajiicho Kamigyoku

department: Ophthalmology

institute: Kyoto Prefectural University of Medicine

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: GeneSpring GX. Signals were normalized to percentile.

label: biotin

source_name: OVOL2 transduced-NPCs

label_protocol: Standard Affymetrix protocol.

growth_protocol: All the cells were cultured in CEC medium which consists of Dulbecco’s modified Eagle’s medium and Ham’s F-12 media (1:1 mixture) (Life Technologies) containing B27-supplement (Life Technologies), Rho-kinase (ROCK) inhibitor (10 uM) (Nacalai Tesque), epidermal growth factor (10 ng/ml) (Life Technologies), Epigallocatechin gallate (SIGMA) and penicillin-streptomycin (50 IU/ml) (Nakalai Tesque),

extract_protocol: Each sample was resuspended in a Qiagen lysis buffer, and RNA was prepared using the RNeasy Purification kit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: Retrovirus carrying OVOL2 was transduced to the NPCs

value: neural progenitor cells

tag: transduction


title: Gfi1_WT_Th

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

description: gene expression in Gfi1_WT_Thn

hyb_protocol: Hybridization and washing were done according to Agilent One-Color Gene Expression protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan microarray scanner (G2600D) using one color scan setting

data_processing: Raw signal intensities were extracted with Agilent Feature Extraction Software 11.5.1.1 (protocol GE1_1105_Oct12) using default parameters

source_name: splenic naïve CD4 T cell

label_protocol: 100 ng of total RNA was amplifies and labeled using Low Input Quick Amp Labeling Kit, One-Color

growth_protocol: Naïve CD4 T (CD44lowCD62LhighCD25negative) cells were prepared using a CD4+CD62L+ T cell isolation kit II (cat#130-093-227; Miltenyi Biotec).  Naïve CD4 T cells  were stimulated with an immobilized anti-TCR-β mAb (3 μg/ml, H57-597; BioLegend),  an anti-CD28 mAb (1 μg/ml, 37.5; BioLegend),  IL-2 (10 ng/ml), anti-IL-4 mAb (5μg/ml, 11B11; BioLegend), and anti-IFN-γ mAb (5 μg/ml, R4-6A2; BioLegend) for two days.

extract_protocol: Total RNA was isolated with PureLink RNA Mini Kit (lifetechnologies) according to the manufacture's protocol

value: Gfi1 wild type

value: spleen


title: Muscle-control-normal diet-rep1


title: Gfi1_KO_Th

description: gene expression in Gfi1_KO_Thn

value: Gfi1 knock out


title: OVOL2 transduced-NPCs_rep2


title: ARDS_11

description: Gene expression data from PMNs


title: GM-CSF_10

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + GM-CSF, t=6h

value: GM-CSF


title: GM-CSF + PI3Kd_10

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + GM-CSF + PI3Kd Inhibitor, t=6h

value: GM-CSF + PI3Kd Inhibitor


title: Fibroblasts_rep2

source_name: Fibroblasts

treatment_protocol: Retrovirus carring each TF was transduced to the fibroblasts.

value: fibroblasts


title: NPCs_rep2

source_name: NPCs

value: control


title: 6TFs transduced-fibroblasts_rep1

source_name: 6TFs transduced-fibroblasts


title: CEC_Donor E_passage 2_rep2

source_name: CEC, Donor E, passage 2

value: corneal epithelium cells


title: 6TFs transduced-fibroblasts_rep2


title: NPCs_rep1


title: CEC_Donor E_passage 2_rep1


title: CEC_Donor E_passage 0_rep2

source_name: CEC, Donor E, passage 0


title: Vehicle_10

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT, DMSO, t=6

value: HVT

value: DMSO


title: Fibroblasts_rep1


title: GM-CSF + PI3Kg_09

description: Gene expression data from PMNs

value: PMN


title: CEC_Donor B_passage 2_rep1

source_name: CEC, Donor B, passage 2


title: GM-CSF + PanPI3K_10

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + GM-CSF + PanPI3K Inhibitor, t=6h

value: Part B

value: GM-CSF + PanPI3K Inhibitor


title: Vehicle_09

description: Gene expression data from PMNs

value: 6 h


title: GM-CSF_09

description: Gene expression data from PMNs


title: CEC_Donor E_passage 0_rep1


title: CEC_Donor B_passage 2_rep2


title: PanPI3K_09

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + panPI3K Inhibitor, t=6h

value: panPI3K Inhibitor


title: GM-CSF + PanPI3K_09

description: Gene expression data from PMNs


title: Fresh_10

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT, DMSO, t=0

value: 0 h


title: GM-CSF + PI3Kg_08

description: Gene expression data from PMNs

value: GM-CSF + PI3Kg Inhibitor


title: GM-CSF_08

description: Gene expression data from PMNs


title: GM-CSF + PI3Kd_08

description: Gene expression data from PMNs


title: GM-CSF + PI3Kd_09

description: Gene expression data from PMNs


title: PanPI3K_08

description: Gene expression data from PMNs


title: Fresh_09

description: Gene expression data from PMNs


title: GM-CSF + PI3Kd_07

description: Gene expression data from PMNs


title: Fresh_08

description: Gene expression data from PMNs


title: GM-CSF + PI3Kg_07

description: Gene expression data from PMNs


title: GM-CSF + PanPI3K_07

description: Gene expression data from PMNs


title: Vehicle_08

description: Gene expression data from PMNs


title: Fresh_07

description: Gene expression data from PMNs


title: GM-CSF + PI3Kd_05

description: Gene expression data from PMNs


title: Vehicle_07

description: Gene expression data from PMNs


title: PanPI3K_07

description: Gene expression data from PMNs


title: GM-CSF + PI3Kg_05

description: Gene expression data from PMNs


title: Vehicle_06

description: Gene expression data from PMNs


title: Vehicle_05

description: Gene expression data from PMNs


title: GM-CSF + PI3Kg_04

description: Gene expression data from PMNs


title: GM-CSF + PI3Kd_06

description: Gene expression data from PMNs


title: GM-CSF + PanPI3K_05

description: Gene expression data from PMNs


title: GM-CSF + PanPI3K_06

description: Gene expression data from PMNs


title: PanPI3K_06

description: Gene expression data from PMNs


title: GM-CSF + PI3Kd_04

description: Gene expression data from PMNs


title: GM-CSF_04

description: Gene expression data from PMNs


title: PanPI3K_05

description: Gene expression data from PMNs


title: GM-CSF + PanPI3K_04

description: Gene expression data from PMNs


title: Fresh_05

description: Gene expression data from PMNs


title: GM-CSF + PI3Kg_06

description: Gene expression data from PMNs


title: GM-CSF_06

description: Gene expression data from PMNs


title: Fresh_06

description: Gene expression data from PMNs


title: PanPI3K_04

description: Gene expression data from PMNs


title: GM-CSF + PanPI3K_08

description: Gene expression data from PMNs


title: GM-CSF_05

description: Gene expression data from PMNs


title: GM-CSF_07

description: Gene expression data from PMNs


title: GM-CSF + PI3Kg_03

description: Gene expression data from PMNs


title: Fresh_04

description: Gene expression data from PMNs


title: GM-CSF + PI3Kd_03

description: Gene expression data from PMNs


title: GM-CSF + PanPI3K_03

description: Gene expression data from PMNs


title: PanPI3K_03

description: Gene expression data from PMNs


title: HMGB1fl3

city: New York

first: Robert

middle: F.

last: Schwabe

state: NY

address: 1150 St. Nicholas Avenue-412C

department: Medicine

country: USA

institute: Columbia University

hyb_protocol: 60 ul (25 ng/ul) of fragemented and labeled cDNA was hybridized to Mouse Genome 1.0ST GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the RMA algorithm as implemented in Bioconductor/R.

source_name: Liver from Hmgb1 floxed mice

label_protocol: 150 ng RNA was amplified, biotin labeled and fragmented using the Ambion WT Expression kit and GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by column purification (Qiagen) and quantification by NanoDrop spectrophotometer.

treatment_protocol: Whole liver tissue was used from 2 groups of 8 week old male littermates, on C57Bl/6 background (backcrossed 5 times)  Group 1: Liver from mice with Albumin-Cre-mediated deletion of Hmgb1. Group 2: Liver from Hmgb1 floxed mice.

value: Balb/c

tag: gender

value: male

value: liver stellate cells


title: HMGB1fl2

tag: tissue


title: GM-CSF + PI3Kd_02

description: Gene expression data from PMNs


title: Vehicle_03

description: Gene expression data from PMNs


title: Vehicle_04

description: Gene expression data from PMNs


title: HMGB1fl4


title: GM-CSF_03

description: Gene expression data from PMNs

value: GM-CSF


title: GM-CSF + PI3Kg_02

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + GM-CSF + PI3Kg Inhibitor, t=6h


title: Fresh_03

description: Gene expression data from PMNs


title: CEC-OVOL2_3

description: OVOL2_knockdown CEC cell

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8 x 60 K allay for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The array data were analyzed using GeneSpring software ver.13.0 (Agilent). Gene expression values were normalized by excluding low-signal intensity data and percentile shifts.

source_name: corneal epithelium cells_OVOL2 knockdown

label_protocol: Microarray experiments were performed according to the manufacturer’s instruction. Twenty to one hundred nanograms of total RNA was labelled with cyanine 3-CTP and hybridized in SurePrint G3 Human GE 8 x 60 K (Agilent Technologies).

growth_protocol: Human peripheral corneal epithelial cells (CECs) were isolated from donor cornea, respectively, by treatment with 1000 protease units (PU)/ml of dispase (Dispase type Ⅱ; Godo Shusei) at 4 ºC overnight and TrypLE Express (Life Technologies) at 4 ºC for 30 minute. CECs were cultured in CEC medium, which consisted of Dulbecco’s modified Eagle’s medium and Ham’s F-12 media (1:1 mixture) (Life Technologies) containing B27-supplement (Life Technologies), Rho-kinase (ROCK) inhibitor (10 mM) (Nacalai Tesque), epidermal growth factor (10 ng/ml) (Life Technologies), Epigallocatechin gallate (SIGMA) and penicillin-streptomycin (50 IU/ml) (Nakalai Tesque), at 37 ºC in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted using the RNeasy Kit (QIAGEN) and was assessed by Agilent 2100 Bioanalyzer and the RNA 6000 LabChip Kit (Agilent Technologies).


title: AlbCRE+2

source_name: Liver from mice with Albumin-Cre-mediated deletion of Hmgb1


title: AlbCRE+3


title: CEC-OVOL2_4

description: OVOL2_knockdown CEC cell


title: CEC-Nega2

description: negative control CEC cell

source_name: corneal epithelium cells_negative control


title: CEC-Nega4

description: negative control CEC cell


title: CEC-Nega1

description: negative control CEC cell


title: GM-CSF + PanPI3K_02

description: Gene expression data from PMNs


title: PanPI3K_10

description: Gene expression data from PMNs


title: TLR7ko_IAV_AECII_d3_repl_1

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

hyb_protocol: Hybridization and washing was performed according to Affymetrix company's recommendations. GeneChips were washed in an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner and GCOS v1.1.1 software.

data_processing: Microarray data were analyzed using GeneSpring GX software (Agilent technologies). Data were summarized and normalized with the RMA algorithm.

source_name: AECII from d3 IAV infected Tlr7ko C57BL/6 mouse

label_protocol: Labeling was performed using the GeneChip HT 3' IVT Express Kit (Affymetrix) according to manufacturers instructions.

growth_protocol: For AECII isolation lungs were perfused with PBS through the heart and instilled with 2 ml dispase solution and 500 µl liquefied low-melt agarose (1 %) through the trachea using a 22 G indwelling cannula. When the agarose was solidified, lungs were excised and incubated in 2 ml dispase solution for 45 min at room temperature. The lung tissue of single lungs was then disintegrated using forceps and incubated at room temperature for 10 minutes gently rocking in DMEM medium supplemented with DNase and anti CD16/32 antibody for blocking of Fc receptors while. Lung cell suspensions were filtered subsequently through nylon meshes of 100 µm, 70 µm, 45 µm and 30 µm size. At this step, 5 mice per group were pooled for each experimental condition. Following filtration, cells were stained for CD16/32, F4/80, CD11b, CD11c, CD19 and CD45. Primary murine AECII were isolated by negative selection by sorting for SSChigh cells negative for the antibody-staining using a FACS sorter and stored in RNAlater buffer (Qiagen). In case of whole lung material lungs were perfused with PBS through the heart and stored in RNAlater buffer.

extract_protocol: Total RNA was isolated by using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations. DNA was digested by using the RNase-Free DNase Set (Qiagen). RNA was eluted in 100 μl nuclease-free water and further concentrated by ethanol precipitation. RNA integrity was tested by using the Agilent  2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany) with an Agilent RNA 6000 Nano/Pico Kit (Agilent Technologies).

treatment_protocol: Mice were used for experiments at an age between 8 and 12 weeks and control groups were age- and sex-matched. Mice were intranasally infected with a lethal dose of IAV PR8/A/34(H1N1) in a volume of 40 µl. For anesthesia, the animals were intraperitoneally injected with a mixture of ketamine/xylazine and the virus in PBS or PBS alone for control groups was administered onto the nostrils to be taken up upon breathing. Samples (lungs, AECII cells) were prepared at indicated time points.

tag: genotype

tag: treatment

value: IAV infection

tag: days after infection

tag: cell material

value: alveolar type II epithelial cells


title: AlbCRE+4

tag: strain


title: AlbCRE+1


title: HMGB1fl1


title: TLR7ko_IAV_AECII_d3_repl_2


title: CEC-Nega3

description: negative control CEC cell

tag: cell type


title: CEC-OVOL2_1

description: OVOL2_knockdown CEC cell


title: GM-CSF_02

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + GM-CSF, t=6h


title: TLR7ko_IAV_AECII_d2_repl_2

source_name: AECII from d2 IAV infected Tlr7ko C57BL/6 mouse


title: conjunctival epithelium_rep2

hyb_protocol: Manufacturer’s recommended condition.

scan_protocol: Manufacturer’s recommended condition.

source_name: conjunctival epithelium, replicate 2

label_protocol: Manufacturer’s recommended condition.

extract_protocol: Human CECs and  conjunctival epithelial cells were isolated from donor cornea, conjunctival tissues via the treatment of 1000 protease units (PU)/ml of dispase at 4ºC overnight and TrypLE Express (Life Technologies) at 4ºC for 30 minutes. Each sample was resuspended in a Qiagen lysis buffer, and RNA was prepared using the RNeasy Purification kit (Qiagen) following the manufacturer's recommendations.

tag: pathology

value: Normal

value: conjunctival epithelium


title: CEC-OVOL2_2

description: OVOL2_knockdown CEC cell

value: corneal epithelium cells


title: conjunctival epithelium_rep1

source_name: conjunctival epithelium, replicate 1


title: corneal epithlium_rep2

source_name: peripheral corneal epithelium, replicate 2

value: peripheral corneal epithelium


title: TLR7ko_IAV_AECII_d2_repl_1


title: TLR7ko_IAV_AECII_d1_repl_2

source_name: AECII from d1 IAV infected Tlr7ko C57BL/6 mouse


title: TLR7ko_IAV_AECII_d1_repl_1


title: WT_IAV_AECII_d3_repl_2

source_name: AECII from d3 IAV infected WT C57BL/6 mouse

value: WT


title: PanPI3K_02

description: Gene expression data from PMNs

tag: study part

value: Part B

value: HVT

value: PMN


title: TLR7ko_PBS_AECII_d0_repl_1

source_name: AECII from uninfected Tlr7ko C57BL/6 mouse

value: uninfected


title: corneal epithlium_rep1

source_name: peripheral corneal epithelium, replicate 1


title: TLR7ko_PBS_AECII_d0_repl_2


title: Vehicle_02

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT, DMSO, t=6

tag: disease state

value: DMSO

value: 6 h


title: Fresh_02

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT, DMSO, t=0

value: 0 h


title: WT_IAV_AECII_d3_repl_1


title: WT_IAV_AECII_d2_repl_2

source_name: AECII from d2 IAV infected WT C57BL/6 mouse


title: GM-CSF + PI3Kd_01

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + GM-CSF + PI3Kd Inhibitor, t=6h

value: GM-CSF + PI3Kd Inhibitor


title: GM-CSF_01

description: Gene expression data from PMNs


title: GM-CSF + PI3Kg_01

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + GM-CSF + PI3Kg Inhibitor, t=6h

value: GM-CSF + PI3Kg Inhibitor


title: WT_IAV_AECII_d2_repl_1


title: GM-CSF + PanPI3K_01

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + GM-CSF + PanPI3K Inhibitor, t=6h

value: GM-CSF + PanPI3K Inhibitor


title: Vehicle_01

description: Gene expression data from PMNs


title: HVT_10

description: Gene expression data from PMNs

source_name: PMNs from HVT

value: Part A

tag: donor pair (part a)

value: j


title: WT_PBS_AECII_d0_repl_2

source_name: AECII from uninfected WT C57BL/6 mouse

value: alveolar type II epithelial cells


title: WT_IAV_AECII_d1_repl_2

source_name: AECII from d1 IAV infected WT C57BL/6 mouse

value: IAV infection


title: WT_IAV_AECII_d1_repl_1


title: Fresh_01

description: Gene expression data from PMNs

tag: rna rin value


title: PanPI3K_01

description: Gene expression data from PMNs

source_name: Cultured PMNs from HVT + panPI3K Inhibitor, t=6h

tag: donor (part b)

value: panPI3K Inhibitor


title: TLR7ko_IAV_Lung_d3_repl_2

source_name: whole lung from d3 IAV infected Tlr7ko C57BL/6 mouse

value: lung


title: ARDS_10

description: Gene expression data from PMNs

source_name: PMNs from ARDS patient

value: ARDS


title: TLR7ko_IAV_Lung_d3_repl_3


title: ARDS_09

description: Gene expression data from PMNs

value: i


title: ARDS_08

description: Gene expression data from PMNs

value: h


title: HVT_09

description: Gene expression data from PMNs

value: HVT

value: PMN


title: TLR7ko_IAV_Lung_d3_repl_1


title: WT_IAV_Lung_d3_repl_3

source_name: whole lung from d3 IAV infected WT C57BL/6 mouse

value: WT


title: WT_IAV_Lung_d3_repl_2


title: WT_PBS_AECII_d0_repl_1

value: uninfected


title: HVT_06

description: Gene expression data from PMNs

value: f


title: TLR7ko_PBS_Lung_d0_repl_3

source_name: whole lung from uninfected Tlr7ko C57BL/6 mouse


title: WT_IAV_Lung_d3_repl_1


title: HVT_07

description: Gene expression data from PMNs

value: g


title: HVT_08

description: Gene expression data from PMNs


title: TLR7ko_PBS_Lung_d0_repl_2


title: ARDS_07

description: Gene expression data from PMNs


title: ARDS_06

description: Gene expression data from PMNs


title: HVT_05

description: Gene expression data from PMNs

value: e


title: WT_PBS_Lung_d0_repl_2

source_name: whole lung from uninfected WT C57BL/6 mouse


title: WT_PBS_Lung_d0_repl_3


title: HVT_04

description: Gene expression data from PMNs

value: d


title: ARDS_04

description: Gene expression data from PMNs

value: Part A


title: ACY-957_rep3

city: Boston

first: Jeff

last: Shearstone

state: MA

address: 70 Fargo Street

department: Biology

institute: Acetylon Pharmaceuticals

description: cells were treated with ACY-957

hyb_protocol: Affymetrix sample labeling, hybridization, and scanning was performed by Covance (Seattle, WA)

data_processing: BRB-ArrayTools was used for RMA data reduction and downstream analysis (BRB-ArrayTools developed by Dr. Richard Simon and the BRB-ArrayTools Development Team)

source_name: Erythroid progenitors

growth_protocol: CD34+ cells isolated from human bone marrow of healthy normal donors were cultured in a 2-phase system. This system has been described previously (Sankaran, Menne et al. 2008).  Cells were expanded for 7 days in StemSpan SFEM (StemCell, Vancouver, Canada) supplemented with CC100 (StemCell), 100 U/ml penicillin and 100 ug/ml streptomycin. CC100 is a mix of Flt-3 ligand, stem cell factor (SCF), interleukin-3 (IL3), and interleukin-6 (IL6). Cells were then cultured for an additional 5 days in erythroid differentiation media, composed of StemSpan SFEM supplemented with 1 U/ml erythropoietin (EPO), 5 ng/ml (IL3), 20 ng/ml (SCF), 2 uM dexamethasone, 1 uM beta-estradiol, 100 U/ml penicillin and 100 ug/ml streptomycin.

extract_protocol: RNA was extracted using Qiagen RNeasy kit with on-column DNase digestion

treatment_protocol: Cells were treated with vehicle (DMSO) or the HDAC1/2-selective inhibitor ACY-957 at 1 micromolar for 5 days in erythroid differentiation media.

value: Erythroid progenitors derived from human CD34+ bone marrow cells


title: ACY-957_rep2

description: cells were treated with ACY-957

scan_protocol: Affymetrix sample labeling, hybridization, and scanning was performed by Covance (Seattle, WA)


title: vehicle_rep3

description: cells were treated with vehicle

label_protocol: Affymetrix sample labeling, hybridization, and scanning was performed by Covance (Seattle, WA)


title: ARDS_05

description: Gene expression data from PMNs


title: ACY-957_rep1

description: cells were treated with ACY-957


title: WT_PBS_Lung_d0_repl_1


title: TLR7ko_PBS_Lung_d0_repl_1


title: ARDS_02

description: Gene expression data from PMNs

value: b


title: ARDS_03

description: Gene expression data from PMNs

value: c


title: HVT_02

description: Gene expression data from PMNs


title: ARDS_01

description: Gene expression data from PMNs

value: a


title: vehicle_rep2

description: cells were treated with vehicle


title: HVT_03

description: Gene expression data from PMNs


title: placebo_4R_liver_array

status: Public on Apr 10 2016

city: chapel hill

first: Yunjung

last: Kim

state: North Carolina

address: 120 Mason farm road

institute: UNC at Chapel Hill

description: gene expression data

hyb_protocol: Total RNA were hybridized to Affymetrix Mouse Gene 1.1 ST 96-Array Plate arrays using a GeneTitan instrument from Affymetrix according to the manufacturer’s protocols

data_processing: Robust multiarray average method (RMA) implemented in the Affymetrix gene expression console with default settings (median polish and sketch-quantile normalization) to estimate normalized expression levels of transcripts

source_name: C57BL/6J, liver

extract_protocol: Tissues were rapidly dissected, snap-frozen in liquid nitrogen, and pluverized using a BioPulverizer unit (BioSpec Products, Bartlesville, OK)

treatment_protocol: All animals were bred at UNC from mice that were less than six generations removed from founders acquired from the Jackson Laboratory (Bar Harbor, ME).

value: placebo

value: liver


title: HVT_01

description: Gene expression data from PMNs


title: drug_4N_liver_array

description: gene expression data

value: drug


title: placebo_3L_liver_array

description: gene expression data


title: placebo_3N_liver_array

description: gene expression data


title: drug_4L_liver_array

description: gene expression data


title: drug_3B_liver_array

description: gene expression data


title: drug_3R_liver_array

description: gene expression data


title: drug_2N_liver_array

description: gene expression data


title: placebo_4B_liver_array

description: gene expression data


title: placebo_1N_liver_array

description: gene expression data


title: placebo_3T_liver_array

description: gene expression data


title: drug_1R_liver_array

description: gene expression data


title: drug_2T_liver_array

description: gene expression data


title: placebo_1T_liver_array

description: gene expression data


title: vehicle_rep1

description: cells were treated with vehicle


title: drug_2L_liver_array

description: gene expression data


title: placebo_4R_brain_array

description: gene expression data

source_name: C57BL/6J, whole brain

value: whole brain


title: placebo_1L_liver_array

description: gene expression data


title: drug_4L_brain_array

description: gene expression data


title: drug_4N_brain_array

description: gene expression data


title: drug_4T_brain_array

description: gene expression data


title: placebo_3T_brain_array

description: gene expression data


title: drug_3R_brain_array

description: gene expression data


title: placebo_2B_liver_array

description: gene expression data


title: drug_1B_liver_array

description: gene expression data


title: placebo_4B_brain_array

description: gene expression data


title: placebo_2R_brain_array

description: gene expression data


title: drug_3B_brain_array

description: gene expression data


title: placebo_3L_brain_array

description: gene expression data


title: placebo_1T_brain_array

description: gene expression data


title: drug_2L_brain_array

description: gene expression data


title: placebo_2B_brain_array

description: gene expression data


title: drug_1B_brain_array

description: gene expression data


title: placebo_3N_brain_array

description: gene expression data


title: placebo_1L_brain_array

description: gene expression data


title: drug_2T_brain_array

description: gene expression data


title: placebo_1N_brain_array

description: gene expression data


title: drug_1R_brain_array

description: gene expression data


title: drug_2N_brain_array

description: gene expression data


title: Tam sensitive MCF7 replicate6

city: Odense C

first: Daniel

last: Elias

address: J. B. Winsløwsvej 25

department: Cancer and Inflammation Research

country: Denmark

institute: University of Southern Denmark

description: MCF7 breast cancer cell line sensitive to tamoxifen

hyb_protocol: Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174  Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000175

scan_protocol: Affymetrix Gene ChIP Scanner 3000 Dx. Standard Affymetrix Cel file scan protocol.

data_processing: Microarray data were normalized and processed by Partek® Genomics Suite using RMA normalization methods

source_name: ER+ breast cancer cell line

growth_protocol: The human breast cancer cell line MCF-7 was originally obtained from The Breast Cancer Task Force Cell Culture Bank, Mason Research Institute (Edinburgh, UK). The MCF-7 cells were gradually adapted to grow in low serum concentration and the tamoxifen-sensitive subline MCF-7/S0.5 was used to establish the four TamR cell lines: MCF-7/TAMR-1 (TamR1), MCF-7/TAMR-4 (TamR4), MCF-7/TAMR-7 (TamR7) and MCF-7/TAMR-8 (TamR8) by long-term treatment with 10-6M tamoxifen. Cells were kept within 10 passages throughout the experiments to reduce variability between experimental results.

extract_protocol: Total RNA was extracted by lysing cells in Trizol and total RNA was precipitated using 75% ethanol.

treatment_protocol: TamR cells were treated with 10-6M tamoxifen prior to RNA extraction

value: Human breast cancer cell line

tag: cell line

tag: tamoxifen sensitivity

value: sensitive


title: Tam sensitive MCF7 replicate7

label_protocol: Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP00000174  Microarray Protocol for Affymetrix In Situ Synthesized Oligo Arrays, AfCS Procedure Protocol PP0000017


title: hiPS_p3_uF_402

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

institute: University of Bologna

description: Gene expression of hiPS p3 reprogrammed in microfluidics and expanded in well, clone 402

hyb_protocol: Cy3-labelled cDNA was hybridized (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 8x60K v2.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: Agilent Feature Extraction Software (FES) was used to read out the microarray image files.

source_name: hiPS p3 uF 402

label_protocol: 250 ng of each of the cDNAs were labeled with Cyanine 3.

extract_protocol: Each colony was lysed using SuperAmp Lysis Buffer (Miltenyi Biotec) and stored appropriately according to the instructions of the SuperAmp Preparation Kit. The samples were sent on dry ice to Miltenyi Biotec, where amplification, cDNA quantification using ND-1000 Spectrophotometer (NanoDrop Technologies), evaluation of cDNA integrity using a 2100 Bioanalyzer (Agilent Technologies), and microarray analysis were performed.

value: human foreskin BJ fibroblasts


title: Tam sensitive MCF7 replicate4


title: Tam sensitive MCF7 replicate8


title: Tam sensitive MCF7 replicate5


title: hiPS_p3_uF_405

description: Gene expression of hiPS p3 reprogrammed in microfluidics and expanded in well, clone 405

source_name: hiPS p3 uF 405


title: hiPS_p3_uF_403

description: Gene expression of hiPS p3 reprogrammed in microfluidics and expanded in well, clone 403

source_name: hiPS p3 uF 403


title: hiPS_p3_well_503

description: Gene expression of hiPS p3 reprogrammed in well and expanded in well, clone 503

source_name: hiPS p3 well 503


title: Tam sensitive MCF7 replicate2


title: hiPS_p3_uF_401

description: Gene expression of hiPS p3 reprogrammed in microfluidics and expanded in well, clone 401

source_name: hiPS p3 uF 401


title: Tam sensitive MCF7 replicate1

description: MCF7 breast cancer cell lines resistant to tamoxifen


title: hiPS_p0_uF_405

description: Gene expression of hiPS p0 reprogrammed in microfluidics, clone 405

source_name: hiPS p0 uF 405


title: hiPS_p3_well_506

description: Gene expression of hiPS p3 reprogrammed in well and expanded in well, clone 506

source_name: hiPS p3 well 506


title: hiPS_p0_uF_401

description: Gene expression of hiPS p0 reprogrammed in microfluidics, clone 401

source_name: hiPS p0 uF 401


title: hiPS_p3_well_502

description: Gene expression of hiPS p3 reprogrammed in well and expanded in well, clone 502

source_name: hiPS p3 well 502


title: TamR8 replicate1

value: TamR8 (derived from MCF-7/S0.5)

value: resistant


title: hiPS_p0_uF_403

description: Gene expression of hiPS p0 reprogrammed in microfluidics, clone 403

source_name: hiPS p0 uF 403


title: TamR7 replicate1

value: TamR7 (derived from MCF-7/S0.5)


title: Tam sensitive MCF7 replicate3


title: TamR8 replicate2


title: TamR4 replicate3

value: TamR4 (derived from MCF-7/S0.5)


title: hiPS_p3_well_501

description: Gene expression of hiPS p3 reprogrammed in well and expanded in well, clone 501

source_name: hiPS p3 well 501


title: hiPS_p0_uF_402

description: Gene expression of hiPS p0 reprogrammed in microfluidics, clone 402

source_name: hiPS p0 uF 402


title: hiPS_p0_well_506

description: Gene expression of hiPS p0 reprogrammed in well, clone 506

source_name: hiPS p0 well 506


title: TamR1 replicate3

value: TamR1 (derived from MCF-7/S0.5)


title: TamR4 replicate2


title: hiPS_p0_well_503

description: Gene expression of hiPS p0 reprogrammed in well, clone 503

source_name: hiPS p0 well 503


title: TamR7 replicate2


title: TamR4 replicate1


title: TamR1 replicate1


title: TamR1 replicate2


title: hiPS_p0_well_502

description: Gene expression of hiPS p0 reprogrammed in well, clone 502

source_name: hiPS p0 well 502


title: hiPS_p0_well_501

description: Gene expression of hiPS p0 reprogrammed in well, clone 501

source_name: hiPS p0 well 501


title: Cortex 13 days 21% O2 No.3

status: Public on Apr 09 2016

city: Dresden

first: Lena

last: Braunschweig

address: Fetscherstr. 74

department: Neurology

institute: TU Dresden

description:
12 (2. Array)
Lena_12_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, normoxic NSCs

hyb_protocol: 5.5 ug of biotinylated and fragmented cDNA were hybridized for 17 hr at 45C on Affymetrix Mouse Gene ST 1.0  Arrays according to the GeneChip WT Terminal Labeling and Hybridization User Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Statistical data analysis was done with the Agilent GeneSpring software version 12.5 using Affymetrix default analysis settings and quantile normalization. No baseline transformation was done.

source_name: Cortex_13 days_21% O2

label_protocol: Biotinylated cDNA samples were prepared according to the Ambion WT Expression Kit (4411973) protocol  inconjunction with the GeneChip WT Terminal Labeling and Hybridization User Manual from 100 ng total RNA.

growth_protocol: Cells were isolated from murine fetal cortex and mesencephalon at embryonic day 14 and maintained in expansion medium for 48 hours or 13 days after dissection. Medium change was done three times per week.

extract_protocol: RNA was isolated from a 6-well with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA concentration was measured using Nanodrop spectrometer (Agilent Technologies) and RNA quality was approved by Agilent 2100 Bioanalyzer.

treatment_protocol: For hypoxic culture, cells were maintained in a gas mixture composed of 92% N2, 5% CO2 and 3% O2.

tag: strain background

tag: developmental stage

value: embryonic day 14

value: fetal cortex

value: Cortex primary culture

tag: culture time

value: 13 days

tag: oxygen


title: Cortex 13 days 3% O2 No.2

description:
8 (2. Array)
Lena_8_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, hypoxic NSCs

source_name: Cortex_13 days_3% O2

tag: tissue


title: Cortex 13 days 3% O2 No.3

description:
9 (2. Array)
Lena_9_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, hypoxic NSCs


title: Cortex 13 days 21% O2 No.2

description:
11 (2. Array)
Lena_11_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, normoxic NSCs


title: ♂ 14/14 Untreated vs ♂ Oregon reference rep2

city: Bucharest

first: Attila

middle: Cristian

last: Ratiu

address: Intrarea Portocalelor, No. 1-3

department: Department of Genetics

country: Romania

institute: University of Bucharest

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). Raw data are then loaded into limma (Bioconductor) and normalised with the vsn package (Bioconductor). The resulting ratios are log2 ratio of sample/control.

organism: Drosophila melanogaster

source_name: male Oregon reference pool

label_protocol: To 3 to 5 µg of total RNA, add 1 µl 500 ng/ µl of Oligo(dT)23 anchored primer (Sigma) and adjust volume to 5 µl with DEPC- water. Incubate at 65 °C for 10 min, then snap cool on ice. Add 4 µl 5x First Strand Buffer (Invitrogen), 2 µl 0.1M DTT (Invitrogen), 1 µl 10 mM dNTP mix, 0.25 µl 40 U/µl RNasin (Promega) and 0.75 µl 200 U/µl Superscript III (Invitrogen). Incubate at 46 °C for 2 hours, then at 65 °C for 15 minutes, snap cool on ice. For second strand synthesis: Add 7.5 µl Second Strand Buffer (Invitrogen), 0.75 µl 10 mM dNTP mix, 2 µl 10 U/µl DNA Polymerase I (Invitrogen), 0.1 µl 5 U/µl RnaseH (Promega), 0.5 µl 10 U/µl E. coli Ligase (NEB) adjust volume to 40 µl with DEPC-water. Incubate at 16 °C for 2 hours, then purification using QIAquick PCR Purification Kit. For the labeling use the Nimblegen Dual Colour Labelling Kit. In PCR tubes take 1 µg double stranded DNA, add 40 diluted Cy3 or Cy5-Random Nonamers (Nimblegen) and make up to a volume of 80 µl with Nuclease-free Water (Nimblegen). Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quickchill on ice for 10 minutes. Add 10 µl 10mM dNTP Mix (Nimblegen), 8 µl Nuclease-free Water (Nimblegen) and 2 µl 50U/μl Klenow Fragment (3’->5’ exo-) (Nimblegen), mix gently by pipetting. Incubate at 37°C for 3 hours in thermocycler. Stop the reaction by adding 21.5 µl Stop Solution (Nimblegen). Transfer samples to 1.5 ml tubes and add 110 µl Isopropanol, mix and incubate for 10 minutes at room temperature in the dark. Centrifuge at 13,000rpm for 10 minutes and discard supernatant. Add 500 µl ice-cold 80% ethanol and centrifuge at 13,000rpm for 2 minutes. Discard supernatant and dry pellet for 5 minutes in the dark. Resuspend labeled DNA in 50 µl Nuclease-free Water (Nimblegen) and measure the concentration on the Nanodrop. Combine 34 µg of sample with 34 µg control and dry samples in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

growth_protocol: The flies were maintained on Nutri-Fly Bloomington Formulation medium (Genesee Scientific) at a temperature of 22-23 degrees Celsius.

extract_protocol: Homogenise tissue in 300 µl TRIzol (Invitrogen) in a 1.5 ml tube using an RNAase-free polypropylene pellet pestle and add up to 700 µl of TRIzol. Centrifuge at 13,000 rpm in a microcentriuge for 10 minutes at 4 °C to pellet debris. Transfer supernatant to a fresh 1.5 ml tube. Add 0.2 volumes chloroform, shake vigorously for 15 seconds and incubate at room temperature for 2-3 minutes. Centrifuge at 13,000 rpm for 15 minutes at 4 °C. Transfer upper phase to a new RNase-free tube, being careful not to touch the interface. Add 0.7 volumes of isopropanol to precipitate the RNA. Incubate at room temperature for 5 minutes or 1 hour at -20 °C and then centrifuge at 13,000 rpm for 15 minutes at 4 °C. Discard the supernatant and wash the RNA pellet with 1 ml 70% ethanol/DEPC MilliQ water. Centrifuge at 13,000 rpm for 10 minute at 4 °C. Air-dry the pellet briefly (~ 5 minutes). Resuspend in an appropriate volume of DEPC MilliQ water, e.g. 20 to 50 µl. The RNA will dissolve more readily if the DEPC MilliQ water is preheated to 55 °C. Verify quality of RNA on a 1 % agarose gel and quantify with a Nanodrop.

treatment_protocol: During the experimental feeding, the males pertaining to the treated biological replicates were transferred in vials with 5 ml of solidified agar containing 5% sucrose. On top of the medium we placed a sterile filter paper spotted with 230 µl of 5% sucrose solution containing 9 X 10^9 CFU of P. aeruginosa in suspension. Alternatively, sterile filter papers previously spotted with 230 µl of 5% sucrose were used for males from the untreated biological replicates . The vials were placed at 25°C for about 63 hours, to allow the males to ingest the inoculated or raw sucrose solution.

tag: Sex

value: male

tag: genotype/variation

value: wild type Oregon

tag: sample type

value: reference pool

source_name: male 14/14 Untreated

tag: treatment

value: Untreated


title: ♂ 057302/Tb Untreated vs ♂ Oregon reference rep1

source_name: male 057302/Tb Untreated


title: ♂ 057302/Tb Untreated vs ♂ Oregon reference rep3

description: dye-swap


title: Cortex 48 hours 21% O2 No.3

description:
18 (2. Array)
Lena_18_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, normoxic NSCs

source_name: Cortex_48 hours_21% O2

tag: cell type

value: 48 hours


title: ♂ 14/14 Untreated vs ♂ Oregon reference rep1


title: Cortex 13 days 3% O2 No.1

description:
7 (2. Array)
Lena_7_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, hypoxic NSCs


title: ♂ 057302/Tb Untreated vs ♂ Oregon reference rep2


title: ♂ 14/14 Untreated vs ♂ Oregon reference rep4

description: dye-swap


title: ♂ 057302/Tb Untreated vs ♂ Oregon reference rep4

description: dye-swap


title: Cortex 13 days 21% O2 No.1

description:
10 (2. Array)
Lena_10_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, normoxic NSCs


title: ♂ Oregon Treated vs ♂ Oregon reference rep4

description: dye-swap

source_name: male Oregon Treated

value: fed with P. aeruginosa suspension


title: Cortex 48 hours 21% O2 No.2

description:
17 (2. Array)
Lena_17_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, normoxic NSCs


title: ♂ Oregon Treated vs ♂ Oregon reference rep3

description: dye-swap


title: ♂ 14/14 Untreated vs ♂ Oregon reference rep3

description: dye-swap


title: Cortex 48 hours 3% O2 No.3

description:
15 (2. Array)
Lena_15_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, hypoxic NSCs

source_name: Cortex_48 hours_3% O2


title: Cortex 48 hours 3% O2 No.2

description:
14 (2. Array)
Lena_14_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, hypoxic NSCs


title: Cortex 48 hours 21% O2 No.1

description:
16 (2. Array)
Lena_16_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, normoxic NSCs


title: Midbrain 13 days 21% O2 No.2

description:
5 (1. Array)
21.2_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, normoxic NSCs

source_name: Midbrain_13 days_21% O2

value: mesencephalon

value: Midbrain primary culture


title: ♂ Oregon Treated vs ♂ Oregon reference rep2


title: ♂ Oregon Treated vs ♂ Oregon reference rep1


title: Midbrain 13 days 21% O2 No.3

description:
6 (1. Array)
21.3_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, normoxic NSCs


title: Cortex 48 hours 3% O2 No.1

description:
13 (2. Array)
Lena_13_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, hypoxic NSCs


title: Midbrain 13 days 21% O2 No.1

description:
4 (1. Array)
21.1_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, normoxic NSCs


title: Midbrain 13 days 3% O2 No.3

description:
3 (1. Array)
3.3_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, hypoxic NSCs

source_name: Midbrain_13 days_3% O2


title: Midbrain 13 days 3% O2 No.1

description:
1 (1. Array)
3.1_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, hypoxic NSCs


title: ♂ 057302/Tb Treated vs ♂ Oregon reference rep3

description: dye-swap

source_name: male 057302/Tb Treated


title: ♂ 14/14 Treated vs ♂ Oregon reference rep4

description: dye-swap

source_name: male 14/14 Treated


title: Midbrain 48 hours 21% O2 No.2

description:
5 (2. Array)
Lena_5_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, normoxic NSCs

source_name: Midbrain_48 hours_21% O2


title: Midbrain 48 hours 3% O2 No.1

description:
1 (2. Array)
Lena_1_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, hypoxic NSCs

source_name: Midbrain_48 hours_3% O2


title: ♂ 057302/Tb Treated vs ♂ Oregon reference rep1


title: ♂ 057302/Tb Treated vs ♂ Oregon reference rep4

description: dye-swap


title: Midbrain 48 hours 3% O2 No.2

description:
2 (2. Array)
Lena_2_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, hypoxic NSCs


title: Midbrain 48 hours 21% O2 No.3

description:
6 (2. Array)
Lena_6_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, normoxic NSCs


title: Midbrain 13 days 3% O2 No.2

description:
2 (1. Array)
3.2_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of long-term, hypoxic NSCs


title: Midbrain 48 hours 21% O2 No.1

description:
4 (2. Array)
Lena_4_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, normoxic NSCs


title: ♂ 14/14 Treated vs ♂ Oregon reference rep1


title: ♂ 057302/Tb Treated vs ♂ Oregon reference rep2


title: ♂ 14/14 Treated vs ♂ Oregon reference rep3

description: dye-swap


title: ♂ 14/14 Treated vs ♂ Oregon reference rep2


title: Midbrain 48 hours 3% O2 No.3

description:
3 (2. Array)
Lena_3_(MoGene-1_0-st-v1).CEL(normalized)
Whole transcript expression profiling of short-term, hypoxic NSCs


title: patients 11 Z011

status: Public on Apr 08 2016

city: Hangzhou

first: Ping

last: Wang

address: 38 West Lake Avenue

country: China

institute: Affiliated 3rd Hospital of Hangzhou

hyb_protocol: Fluorescent targets were hybridized to the Phalanx Human OneArray v6.1 with Phalanx hybridization buffer using Phalanx Hybridization System.

scan_protocol: The scanned images were analyzed with Agilent Scanner and processing by GenePix software 4.1 to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Data were analyzed with the Rosetta Resolver System software (Rosetta Biosoftware, USA). The Rosetta Resolver System Error Model was used to calculate the normalized intensities, CV, log2 ratio and p-value (differential expressed). Briefly, probes whose flags were -50 within all arrays were excluded; replicated probes within one chip were averaged; intensities were normalized by median scaling and taking the mean intensities.

source_name: Blood

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated from peripheral blood leukocyte. The quality of RNA was determined by an optical density (OD) 260/280 ratio >1.8, and OD 260/230 ratio >1.5.RNA integrity was examined on an Agilent Bioanalyzer.

tag: disease

value: healthy individual


title: patients 12 Z012


title: patients 9 Z009


title: patients 10 Z010


title: patients 6 J006

value: segmental vitiligo


title: patients 8 J008


title: patients 4 X004

value: generalized vitiligo


title: patients 3 X003


title: patients 1 X001


title: patients 2 X002


title: Normal_RF_case8

city: Guangzhou

first: Jin

address: No.651 Dongfeng East Road

department: Department of Breast Oncology

institute: Sun Yat-sen University Cancer Center

description: miRNA expression in normal breast tissue of case8

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Cat # G2565CA，Agilent technologies, Santa Clara, CA, US) using one color scan setting (Scan resolution 3um, and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) with default settings. Raw data were normalized by Quantile algorithm using Gene Spring Software 12.6 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm.

source_name: normal breast tissue, recurrence-free group, case8

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using RecoverAllTM Total Nucleic Acid Isolation (Cat # AM1975, Ambion, Austin, TX, US) |, following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: All the specimens were fixed in 10% buffered formalin and embedded in paraffin.

value: formalin-fixed paraffin-embedded tissue blocks

tag: gender

value: female

tag: age

tag: tnm stage

value: IIA

tag: pathology

value: infiltrating ductal carcinoma of breast

tag: molecular subtype

value: triple neagtive

tag: survival outcome

value: recurrence-free survival > 10 years


title: Tumor_RF_case5

description: miRNA expression in primary tumor of case5

source_name: primary tumor, recurrence-free group, case5


title: patients 5 J005


title: Tumor_LM_case3

description: miRNA expression in primary tumor of case3

source_name: primary tumor, lung metastasis group, case3

value: IIB

value: lung metastasis


title: Tumor_RF_case6

description: miRNA expression in primary tumor of case6

source_name: primary tumor, recurrence-free group, case6


title: patients 7 J007


title: Normal_RF_case6

description: miRNA expression in normal breast tissue of case6

source_name: normal breast tissue, recurrence-free group, case6


title: Met_LM_case2

description: miRNA expression in lung metastasis of case2

source_name: lung metastasis, lung metastasis group, case2

value: IIIA


title: Tumor_RF_case7

description: miRNA expression in primary tumor of case7

source_name: primary tumor, recurrence-free group, case7


title: Normal_RF_case7

description: miRNA expression in normal breast tissue of case7

source_name: normal breast tissue, recurrence-free group, case7


title: Tumor_LM_case4

description: miRNA expression in primary tumor of case4

source_name: primary tumor, lung metastasis group, case4


title: Ctf4_IP

city: London

first: Catarina

last: Samora

address: 44 Lincoln's Inn Fields

institute: The Francis Crick Institute

hyb_protocol: Hybridization was performed as previously described (Katou et al. 2003). Samples were hybridized in buffer containing SSPE, TritonX-100, denatured salmon sperm DNA and biotin-labelled control oligonucleotide, oligo B2. Samples were denatured at 95ºC for 10 minutes before being hybridized to the arrays for 16 hours at 42C in a GeneChip Hybridization Oven 640.

scan_protocol: The washing and scanning protocol (FlexMidi_euk2v3_450), provided by Affymetrix, was performed automatically on a GeneChip Fluidics Station 450. Arrays were scanned using the GeneChip Scanner 3000 7G, and primary analysis of tiling chip data was performed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Signal intensities between the ChIP and supernatant samples were normalized across all probe sets. Changes and change p-values were called as detailed in the Affymetrix Statistical Algorithms Reference Guide (http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf). Probe sets and changes were averaged within adjacent 100 bp windows for graphical depiction. VALUE=Normalized signal intensity against SUPernatant fraction

organism: Saccharomyces cerevisiae

source_name: ChIP DNA from yeast cells

label_protocol: 10 ng of amplified DNA was digested with DNase I and end-labeled using biotin-N6-ddATP using terminal transferase TdT (Roche, 400 U/µl) and Biotin-N6-ddATP (Enzo Life Sciences).

growth_protocol: Cells were grown in YP + 2% Glucose to an OD600 of 0.3. Cells were then arrested in G1 by adding alpha-factor to a final concentration of 0.05mg/ml during 2h. Cells were released into YP + 2% Glucose + 200 mM HU + 0.4 M BrdU for 30min.

extract_protocol: Chromatin Immunoprecipitation followed by hybridization to a high-density oligonucleotide microarray (ChIP on chip) were performed as previously described (Katou et al. 2003; Lengronne et al. 2004; Lengronne et al. 2006). Briefly, cross-linked cells were disrupted using a Multi-Beads Shocker, and whole cell extracts were sonicated to obtain 400-600 bp genomic DNA fragments. Chromatin immunoprecipitation (ChIP) was performed with anti-PK monoclonal antibody (clone SV5-Pk1, Serotec) coupled to protein A Dynabeads. Immunoprecipates were eluted and incubated overnight at 65ºC to reverse the cross-link. An aliquot of the supernatant fraction of the immunoprecipitation was treated in parallel to provide a whole genome DNA sample for comparison. The ChIP and supernatant samples were then incubated with proteinase K, extracted twice with phenol/chloroform/isoamylalcohol, precipitated, resuspended in TE and incubated with RNaseA. The DNA was purified, concentrated by ethanol precipitation and amplified by PCR after random priming.

treatment_protocol: HU arrested cells were cross-linked with 1% Formaldehide for 30 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.

tag: strain

value: MATa CTF4-Pk9::TRP

tag: antibody

value: anti-Pk Clone V5 vendor:Serotec


title: Met_LM_case1

description: miRNA expression in lung metastasis of case1

source_name: lung metastasis, lung metastasis group, case1


title: Chl1_input

source_name: input DNA from yeast cells

value: MATa HA6-CHL1


title: Chl1_IP

value: anti-HA CloneF-7 vendor:Santa Cruz


title: Tumor_RF_case8

description: miRNA expression in primary tumor of case8

source_name: primary tumor, recurrence-free group, case8


title: Tumor_LM_case1

description: miRNA expression in primary tumor of case1

source_name: primary tumor, lung metastasis group, case1


title: Tumor_LM_case2

description: miRNA expression in primary tumor of case2

source_name: primary tumor, lung metastasis group, case2


title: Met_LM_case4

description: miRNA expression in lung metastasis of case4

source_name: lung metastasis, lung metastasis group, case4


title: Normal_RF_case5

description: miRNA expression in normal breast tissue of case5

source_name: normal breast tissue, recurrence-free group, case5


title: BrdU30min_HU_IP

value: anti-BrdU Clone 2B1 vendor:MBL


title: Met_LM_case3

description: miRNA expression in lung metastasis of case3

source_name: lung metastasis, lung metastasis group, case3


title: Normal_LM_case1

description: miRNA expression in normal breast tissue of case1

source_name: normal breast tissue, lung metastasis group, case1


title: genomic data from + HIV- patient FOX206, neutrophils

city: La Jolla

first: Andrew

middle: M

last: Gross

state: California

address: 9500 Gilman Drive #0688

institute: UCSD

hyb_protocol: 500ng of DNA was bisulfite converted using EZ DNA Methylation Kits (Zymo Research) and subsequently processed for HumanMethylation450 BeadChips following manufacturer’s instructions.

scan_protocol: BeadChips were scanned using the Illumina HiScan System

data_processing:
Minfi R package, custom R/python scripts available  on Github (https://github.com/theandygross)
The matrix_signal_update.csv contains unmethylated and methylated signal intensities

source_name: HIV- patient FOX206

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was purified from whole blood or flow sorted blood samples using PaxGene collection tubes (Qiagene) and FlexiGene DNA extraction kits (Qiagene).

tag: subject status/id

value: HIV- patient FOX206

value: male

tag: age (yrs)

value: flow sorted neutrophils


title: Ctf4_input


title: genomic data from + HIV+ patient FOX382, neutrophils

source_name: HIV+ patient FOX382

value: HIV+ patient FOX382


title: genomic data from + HIV+ patient FOX379, neutrophils

source_name: HIV+ patient FOX379

value: HIV+ patient FOX379


title: genomic data from + HIV- patient FOX204, neutrophils

source_name: HIV- patient FOX204

value: HIV- patient FOX204


title: genomic data from + HIV+ patient FOX376, neutrophils

source_name: HIV+ patient FOX376

value: HIV+ patient FOX376


title: genomic data from + HIV+ patient FOX381, neutrophils

source_name: HIV+ patient FOX381

value: HIV+ patient FOX381


title: genomic data from + HIV+ patient FOX365, neutrophils

source_name: HIV+ patient FOX365

value: HIV+ patient FOX365


title: BrdU30min_HU_input


title: genomic data from + HIV+ patient FOX362, neutrophils

source_name: HIV+ patient FOX362

value: HIV+ patient FOX362


title: genomic data from + HIV+ patient FOX354, neutrophils

source_name: HIV+ patient FOX354

value: HIV+ patient FOX354


title: genomic data from + HIV- patient FOX217, neutrophils

source_name: HIV- patient FOX217

value: HIV- patient FOX217


title: genomic data from + HIV- patient FOX218, neutrophils

source_name: HIV- patient FOX218

value: HIV- patient FOX218


title: genomic data from + HIV- patient FOX209, neutrophils

source_name: HIV- patient FOX209

value: HIV- patient FOX209


title: genomic data from + HIV- patient FOX215, neutrophils

source_name: HIV- patient FOX215

value: HIV- patient FOX215


title: genomic data from + HIV- patient FOX208, neutrophils

source_name: HIV- patient FOX208

value: HIV- patient FOX208


title: Normal_LM_case2

description: miRNA expression in normal breast tissue of case2

source_name: normal breast tissue, lung metastasis group, case2

tag: tissue

value: formalin-fixed paraffin-embedded tissue blocks

value: female

value: IIIA

value: infiltrating ductal carcinoma of breast

value: triple neagtive

value: lung metastasis


title: 526-2011

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: Isolated Breast cancer cells

hyb_protocol: 2.2 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Fold changes between expression estimates for individual samples were computed after MA mean and variance normalization using the GAM method. An empirical Bayes partial density model was used to obtain differentially expressed genes with an FDR of 5% and |FC|>2.

source_name: Isolated Breast cancer cells

label_protocol: 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

growth_protocol: MCF7 and MDA231 cells with a doxycycline-inducible shRNA vector targeting either FoxA1 or FoxA2 and MCF7 and MDA231 cells with a doxycycline-inducible shRNA vector targeting either FoxA1 or FoxA2  with the overexression of FoxA2 in MCF7 cells and FoxA1 in MDA231 cells were inoculated in Balb/c nude mice treated with or without doxycycline to analyze tumor growth

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

treatment_protocol: Tumor were extracted and human breast cancer cells were isolated based on the GFP expression (cancer cell-specific) and tRFP expression ( FoxA1- and FoxA2-depleted cell-specific)

tag: sh

tag: oe

tag: dox

value: dox-

tag: cell line


title: 524-2011

description: Isolated Breast cancer cells

value: Ctrl


title: 525-2011

description: Isolated Breast cancer cells

value: dox+

value: KD


title: Normal_LM_case3

description: miRNA expression in normal breast tissue of case3

source_name: normal breast tissue, lung metastasis group, case3

value: IIB


title: 521-2011B

description: Isolated Breast cancer cells

value: OE

value: MDA


title: 518-2011B

description: Isolated Breast cancer cells


title: 517-2011B

description: Isolated Breast cancer cells


title: 520-2011B

description: Isolated Breast cancer cells


title: genomic data from + HIV- patient FOX201, neutrophils

source_name: HIV- patient FOX201

value: HIV- patient FOX201

value: male

tag: cell type

value: flow sorted neutrophils


title: genomic data from + HIV+ patient FOX384, neutrophils

source_name: HIV+ patient FOX384

value: HIV+ patient FOX384


title: genomic data from + HIV+ patient FOX380, neutrophils

source_name: HIV+ patient FOX380

value: HIV+ patient FOX380


title: genomic data from + HIV+ patient FOX366, neutrophils

source_name: HIV+ patient FOX366

value: HIV+ patient FOX366


title: 527-2011

description: Isolated Breast cancer cells


title: genomic data from + HIV+ patient FOX356, neutrophils

source_name: HIV+ patient FOX356

value: HIV+ patient FOX356


title: genomic data from + HIV+ patient FOX353, neutrophils

source_name: HIV+ patient FOX353

value: HIV+ patient FOX353


title: genomic data from + HIV- patient FOX227, neutrophils

source_name: HIV- patient FOX227

value: HIV- patient FOX227


title: genomic data from + HIV- patient FOX216, neutrophils

source_name: HIV- patient FOX216

value: HIV- patient FOX216


title: genomic data from + HIV- patient FOX219, neutrophils

source_name: HIV- patient FOX219

value: HIV- patient FOX219


title: genomic data from + HIV- patient FOX202, neutrophils

source_name: HIV- patient FOX202

value: HIV- patient FOX202


title: genomic data from + HIV+ patient FOX361, neutrophils

source_name: HIV+ patient FOX361

value: HIV+ patient FOX361


title: genomic data from + HIV+ patient FOX375, neutrophils

source_name: HIV+ patient FOX375

value: HIV+ patient FOX375


title: genomic data from + HIV+ patient FOX383, neutrophils

source_name: HIV+ patient FOX383

value: HIV+ patient FOX383


title: genomic data from + HIV+ patient FOX374, neutrophils

source_name: HIV+ patient FOX374

value: HIV+ patient FOX374


title: genomic data from + HIV- patient FOX221, neutrophils

source_name: HIV- patient FOX221

value: HIV- patient FOX221


title: genomic data from + HIV+ patient FOX385, neutrophils

source_name: HIV+ patient FOX385

value: HIV+ patient FOX385


title: genomic data from + HIV+ patient FOX352, neutrophils

source_name: HIV+ patient FOX352

value: HIV+ patient FOX352

value: male


title: genomic data from + HIV+ patient FOX369, neutrophils

source_name: HIV+ patient FOX369

value: HIV+ patient FOX369

value: flow sorted neutrophils


title: genomic data from + HIV+ patient FOX363, neutrophils

source_name: HIV+ patient FOX363

value: HIV+ patient FOX363


title: genomic data from + HIV- patient FOX222, neutrophils

source_name: HIV- patient FOX222

value: HIV- patient FOX222


title: genomic data from + HIV- patient FOX213, neutrophils

source_name: HIV- patient FOX213

value: HIV- patient FOX213


title: genomic data from + HIV- patient FOX212, neutrophils

source_name: HIV- patient FOX212

value: HIV- patient FOX212


title: genomic data from + HIV- patient FOX211, neutrophils

source_name: HIV- patient FOX211

value: HIV- patient FOX211


title: genomic data from + HIV- patient FOX225, neutrophils

source_name: HIV- patient FOX225

value: HIV- patient FOX225


title: genomic data from + HIV- patient FOX214, neutrophils

source_name: HIV- patient FOX214

value: HIV- patient FOX214


title: genomic data from + HIV- patient FOX205, neutrophils

source_name: HIV- patient FOX205

value: HIV- patient FOX205


title: genomic data from + HIV- patient FOX207, neutrophils

source_name: HIV- patient FOX207

value: HIV- patient FOX207


title: genomic data from + HIV- patient FOX203, neutrophils

source_name: HIV- patient FOX203

value: HIV- patient FOX203


title: Normal_LM_case4

description: miRNA expression in normal breast tissue of case4

source_name: normal breast tissue, lung metastasis group, case4

value: formalin-fixed paraffin-embedded tissue blocks

value: female

value: IIB

value: infiltrating ductal carcinoma of breast

value: triple neagtive

value: lung metastasis


title: genomic data from + HIV+ patient FOX357, neutrophils

source_name: HIV+ patient FOX357

value: HIV+ patient FOX357

value: male

value: flow sorted neutrophils


title: genomic data from + HIV+ patient FOX370, CD4 t-cells

source_name: HIV+ patient FOX370

value: HIV+ patient FOX370

value: flow sorted CD4 t-cells


title: genomic data from + HIV- patient FOX224, neutrophils

source_name: HIV- patient FOX224

value: HIV- patient FOX224


title: genomic data from + HIV+ patient FOX377, neutrophils

source_name: HIV+ patient FOX377

value: HIV+ patient FOX377


title: genomic data from + HIV- patient FOX212, CD4 t-cells

value: HIV- patient FOX212


title: genomic data from + HIV+ patient FOX351, neutrophils

source_name: HIV+ patient FOX351

value: HIV+ patient FOX351


title: genomic data from + HIV+ patient FOX382, CD4 t-cells

source_name: HIV+ patient FOX382

value: HIV+ patient FOX382


title: genomic data from + HIV+ patient FOX355, neutrophils

source_name: HIV+ patient FOX355

value: HIV+ patient FOX355


title: genomic data from + HIV- patient FOX206, CD4 t-cells

source_name: HIV- patient FOX206

value: HIV- patient FOX206


title: genomic data from + HIV+ patient FOX352, CD4 t-cells (failed QC)

source_name: HIV+ patient FOX352

value: HIV+ patient FOX352


title: genomic data from + HIV- patient FOX223, CD4 t-cells

source_name: HIV- patient FOX223

value: HIV- patient FOX223


title: genomic data from + HIV+ patient FOX351, CD4 t-cells


title: genomic data from + HIV- patient FOX211, CD4 t-cells

source_name: HIV- patient FOX211

value: HIV- patient FOX211


title: genomic data from + HIV+ patient FOX367, CD4 t-cells

source_name: HIV+ patient FOX367

value: HIV+ patient FOX367


title: genomic data from + HIV+ patient FOX366, CD4 t-cells

source_name: HIV+ patient FOX366

value: HIV+ patient FOX366


title: Treated Gen2.2 replicate 1

city: Granada

first: Pedro

last: Carmona

address: Avda. de la Ilustración 114

institute: GENYO

description: replicate

hyb_protocol: Standard Illumina Human-HT12 Version 4

scan_protocol: Standard Illumina Genome Studio

data_processing: The data were background corrected and normalized using the Limma package

source_name: Gen2.2 cell culture

label_protocol: Illumina TotalPrep RNA Amplification Kit

growth_protocol: Cells were mantained in RPMI 1640 supplemented with 10% FBS

extract_protocol: RNA was extracted high pure RNA isolation kit from Roche, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cultured cells at log phase

value: pDC leukemia

tag: treatment

value: 1µM ODN2006


title: Treated Gen2.2 replicate 2

description: replicate


title: Treated Gen2.2 replicate 3

description: replicate


title: genomic data from + HIV- patient FOX220, CD4 t-cells

source_name: HIV- patient FOX220

value: HIV- patient FOX220

tag: gender

value: male


title: genomic data from + HIV- patient FOX213, CD4 t-cells

source_name: HIV- patient FOX213

value: HIV- patient FOX213

value: flow sorted CD4 t-cells


title: genomic data from + HIV- patient FOX201, CD4 t-cells

source_name: HIV- patient FOX201

value: HIV- patient FOX201


title: genomic data from + HIV+ patient FOX369, CD4 t-cells

source_name: HIV+ patient FOX369

value: HIV+ patient FOX369


title: genomic data from + HIV- patient FOX208, CD4 t-cells

source_name: HIV- patient FOX208

value: HIV- patient FOX208


title: genomic data from + HIV- patient FOX227, CD4 t-cells

source_name: HIV- patient FOX227

value: HIV- patient FOX227


title: genomic data from + HIV- patient FOX218, CD4 t-cells

source_name: HIV- patient FOX218

value: HIV- patient FOX218


title: genomic data from + HIV- patient FOX224, CD4 t-cells

source_name: HIV- patient FOX224

value: HIV- patient FOX224


title: genomic data from + HIV+ patient FOX354, CD4 t-cells

source_name: HIV+ patient FOX354

value: HIV+ patient FOX354


title: genomic data from + HIV+ patient FOX384, CD4 t-cells

source_name: HIV+ patient FOX384

value: HIV+ patient FOX384


title: genomic data from + HIV- patient FOX219, CD4 t-cells

source_name: HIV- patient FOX219

value: HIV- patient FOX219


title: genomic data from + HIV+ patient FOX365, CD4 t-cells

source_name: HIV+ patient FOX365

value: HIV+ patient FOX365


title: genomic data from + HIV- patient FOX216, CD4 t-cells

source_name: HIV- patient FOX216

value: HIV- patient FOX216


title: genomic data from + HIV+ patient FOX385, CD4 t-cells

source_name: HIV+ patient FOX385

value: HIV+ patient FOX385


title: genomic data from + HIV+ patient FOX383, CD4 t-cells

source_name: HIV+ patient FOX383

value: HIV+ patient FOX383


title: genomic data from + HIV+ patient FOX357, CD4 t-cells

source_name: HIV+ patient FOX357

value: HIV+ patient FOX357


title: genomic data from + HIV- patient FOX204, CD4 t-cells

source_name: HIV- patient FOX204

value: HIV- patient FOX204

value: male


title: genomic data from + HIV+ patient FOX378, neutrophils

source_name: HIV+ patient FOX378

value: HIV+ patient FOX378

value: flow sorted neutrophils


title: genomic data from + HIV- patient FOX205, CD4 t-cells

source_name: HIV- patient FOX205

value: HIV- patient FOX205

value: flow sorted CD4 t-cells


title: genomic data from + HIV+ patient FOX358, CD4 t-cells

source_name: HIV+ patient FOX358

value: HIV+ patient FOX358


title: genomic data from + HIV- patient FOX209, CD4 t-cells

source_name: HIV- patient FOX209

value: HIV- patient FOX209


title: genomic data from + HIV- patient FOX217, CD4 t-cells

source_name: HIV- patient FOX217

value: HIV- patient FOX217


title: genomic data from + HIV- patient FOX222, CD4 t-cells

source_name: HIV- patient FOX222

value: HIV- patient FOX222


title: genomic data from + HIV+ patient FOX372, CD4 t-cells

source_name: HIV+ patient FOX372

value: HIV+ patient FOX372


title: genomic data from + HIV+ patient FOX356, CD4 t-cells

source_name: HIV+ patient FOX356

value: HIV+ patient FOX356


title: genomic data from + HIV- patient FOX203, CD4 t-cells

source_name: HIV- patient FOX203

value: HIV- patient FOX203


title: genomic data from + HIV+ patient FOX381, CD4 t-cells (failed QC)

source_name: HIV+ patient FOX381

value: HIV+ patient FOX381


title: genomic data from + HIV+ patient FOX353, CD4 t-cells

source_name: HIV+ patient FOX353

value: HIV+ patient FOX353


title: T.8MemKLRG1-CD127+.Sp.d8.LisOVA#3

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

hyb_protocol: Affymetrix WT Sense Target Labeling Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Spleen

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: Spleen

tag: age

value: 45 Days Old

tag: exclusion markers

tag: genetic background

tag: phenotype markers

tag: separation method

value: FACSAria

tag: Sex

value: Male


title: genomic data from + HIV+ patient FOX368, CD4 t-cells

source_name: HIV+ patient FOX368

value: HIV+ patient FOX368

value: male


title: T.8MemKLRG1-CD127+.Sp.d8.LisOVA#1


title: T.8EffKLRG1+CD127-.Sp.d8.LisOVA#3


title: T.8MemKLRG1-CD127+.Sp.d8.LisOVA#2


title: T.8EffKLRG1+CD127-.Sp.d8.LisOVA#2


title: genomic data from + HIV+ patient FOX371, CD4 t-cells

source_name: HIV+ patient FOX371

value: HIV+ patient FOX371


title: genomic data from + HIV- patient FOX214, CD4 t-cells

source_name: HIV- patient FOX214

value: HIV- patient FOX214

value: flow sorted CD4 t-cells


title: 1/3PH pooled sample

first: Zhikun

last: Liu

address: Qingchun Road 79#

institute: Zhejiang University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0

organism: Rattus norvegicus

source_name: remnant liver tissue at 24H after 1/3PH

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by submitter

treatment_protocol: Total RNA was amplified, labeled and purified using the GeneChip 3’IVT Express Kit (Affymetrix) followed the manufacturer’s instructions to obtain biotin labeled cRNA. Array hybridization and wash were performed using the GeneChip® Hybridization, Wash and Stain Kit (Affymetrix) in a Hybridization Oven 645 (Affymetrix) and with a Fluidics Station 450 (Affymetrix) according to the manufacturer’s instructions. Slides were scanned using the GeneChip® Scanner 3000 (Affymetrix) and Command Console Software 3.1 (Affymetrix) with default settings. Raw data were normalized by MAS 5.0 algorithm in Gene Spring Software 11.0 (Agilent Technologies)

value: liver


title: T.8Eff.Tbet-.Sp.OT1.d6LisOVA#3


title: T.8Eff.Tbet-.Sp.OT1.d6LisOVA#2


title: 2/3PH pooled sample

source_name: remnant liver tissue at 24H after 2/3PH


title: T.8Eff.Tbet+.Sp.OT1.d6LisOVA#3


title: T.8Eff.Tbet-.Sp.OT1.d6LisOVA#1


title: T.4Mem49d+11a+.Sp.d30.LCMV#1

value: 6 Weeks Old


title: genomic data from + HIV- patient FOX207, CD4 t-cells

source_name: HIV- patient FOX207

value: HIV- patient FOX207


title: genomic data from + HIV- patient FOX215, CD4 t-cells

source_name: HIV- patient FOX215

value: HIV- patient FOX215


title: genomic data from + HIV+ patient FOX361, CD4 t-cells

source_name: HIV+ patient FOX361

value: HIV+ patient FOX361


title: genomic data from + HIV+ patient FOX355, CD4 t-cells

source_name: HIV+ patient FOX355

value: HIV+ patient FOX355


title: T.8Eff.Tbet+.Sp.OT1.d6LisOVA#2


title: T.8Eff.Tbet+.Sp.OT1.d6LisOVA#1


title: T.4Nve44-49d-11a-.Sp#3


title: T.4Eff49d+11a+.Sp.d8.LCMV#2


title: genomic data from + HIV- patient FOX202, CD4 t-cells

source_name: HIV- patient FOX202

value: HIV- patient FOX202


title: genomic data from + HIV+ patient FOX360, CD4 t-cells

source_name: HIV+ patient FOX360

value: HIV+ patient FOX360


title: genomic data from + HIV+ patient FOX359, CD4 t-cells

source_name: HIV+ patient FOX359

value: HIV+ patient FOX359


title: genomic data from + HIV- patient FOX225, CD4 t-cells

source_name: HIV- patient FOX225

value: HIV- patient FOX225


title: T.4Nve44-49d-11a-.Sp#1

value: Spleen

value: FACSAria


title: T.4Eff49d+11a+.Sp.d8.LCMV#1

value: Male


title: T.4Mem49d+11a+.Sp.d30.LCMV#2


title: MF.480int.LV.Naive#2

source_name: Liver

value: Liver

value: CD45+ Mertk+ CD64+ F480lo


title: MF.480hi.LV.Naive#3

value: PI

value: CD45+ Mertk+ CD64+ F480hi


title: MF.480int.LV.Naive#3


title: MF.480int.LV.Naive#1

value: PI- CD45+ CD64+ Mertk+ F480lo


title: MEChi.GFP-.Adult#7

source_name: Thymic Medulla

value: Thymic Medulla

value: 5 Weeks Old

value: CD45- Ly51- MHCIIhi GFP-

value: MoFlo Sorter

value: Mixed


title: MEChi.GFP+.Adult.KO#3

value: CD45- Ly51- MHCIIhi GFP+


title: MF.480hi.LV.Naive#1

value: 6 Weeks Old

value: PI- CD45+ CD64+ Mertk+ F480hi


title: MEChi.GFP-.Adult#6


title: MF.480hi.LV.Naive#2


title: MEChi.GFP+.Adult.KO#1


title: MEChi.GFP+.Adult.KO#2


title: MEChi.GFP+.Adult#7


title: MC.Tr#3

source_name: Whole Tissue

value: Whole Tissue

value: CD4 CD8 CD19 CD11b CD11c


title: MEChi.GFP+.Adult#8


title: MEChi.GFP-.Adult#8


title: MC.digest.PC#1

source_name: Peritoneal Cavity

value: Peritoneal Cavity

value: CD45+ CD117+ FcER1a+

value: FACSAria


title: MC.digest.PC#4

value: IgE/FcER1a+ CD117+ CD45+ CD4- CD8- CD19- CD11b/c-

value: Male


title: MC.Tr#2

value: CD11b CD11c CD4 CD8 CD19


title: MEChi.GFP+.Adult#6


title: MC.Tr#1


title: MC.To#5


title: MC.digest.PC#5


title: 3ABDKO infected with DNMT3L control Day 42 post 24 treatment with 5-Aza-CdR

city: Los Angeles

first: Peter

middle: A

last: Jones

address: 1441 Eastlake Ave NOR7344

department: Urology

institute: University of Southern California

description: 3ABDKO 3L DAY 42

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: MethylLumi Package

label: cy5 and cy3

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: HCT derivative cell line 3ABDKO


title: 3ABDKO infected with DNMT3B1M control Day 42 PBS control

description: 3ABDKO 3B1M DAY 42 CTRL


title: PB_91d_5

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: 10 µg of fragmented, biotinylated aRNA were hybridized for approximately 16 hrs at 45ºC to the GeneChip® Mouse430_2 arrays. The arrays were then washed and stained with the GeneChip® Hybridization Wash and Stain kit (Affymetrix). The washing and staining steps were performed with GeneChip® Fluidics Workstation 450 (Affymetrix).

scan_protocol: Arrays were then scanned using a solid-state laser scanner (GeneArray® Scanner 3000 combined with the GeneChip® autoloader, Affymetrix). The Affymetrix GeneChip® Operating Software (GCOS) was used to generate the primary and secondary raw data files.

data_processing: The raw microarray data was normalized using the RMA method implemented in R/Bioconductor.

source_name: liver, Phenobarbital, 91 days, 0.05 % w/v

label_protocol: Processing of GeneChip® experiments was conducted as recommended by the manufacturer of the GeneChip® system (Affymetrix, Santa Clara, CA). For tissue samples, double stranded cDNA was synthesized with a starting amount of 0.1 µg total RNA. For RNA reverse transcription, the GeneChip® 3' IVT Express Labelling Assay (lot ID 0904012, Affymetrix) was used in the presence of a T7-(dT)24 DNA oligonucleotide primer (Affymetrix). The cDNA was then transcribed in vitro in the presence of biotinylated ribonucleotides to form biotin-labelled amplified RNA (aRNA). The labelled aRNA was then purified and quantified by UV spectrophotometry at 260 nm and fragmented.

growth_protocol: 29- to 32-day-old male B6C3F1/Crl (C57BL/6 female × C3H/He male) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatize for 5 days prior to being randomly divided into treatment groups.

extract_protocol: Blood was withdrawn for PK analysis, and liver was removed, split into several sections, either frozen in liquid nitrogen and stored at −80°C for subsequent analyses or fixed in neutral phosphate-buffered formalin, and embedded in paraffin wax. To ensure sample homogeneity for different molecular profiling methods, frozen liver samples were reduced to powder with Covaris Cryoprep (Covaris Inc., Woburn, MA) system and aliquoted on dry ice. Frozen liver samples were homogenized in TRIzol reagent (Invitrogen, Carlsbad, CA) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: PB (Sigma [St Louis, MO] #04710, 0.05% [wt/vol] in drinking water) was administered to one group through ad libitum access to drinking water. Mice were checked daily for activity and behavior and sacrificed on the indicated dates.

tag: strain

value: liver

value: PB

value: Phenobarbital

tag: group

tag: treatment_duration [days]

tag: treatment_dose [% w/v]


title: MC.To#2

source_name: Muscle

tag: tissue

value: Muscle

value: FcER1a+ CD117+ CD45+


title: MC.Sk#4

source_name: Skin

value: Skin


title: MC.To#1

value: 6 Weeks Old


title: PB_91d_3


title: PB_91d_1


title: MC.Sk#2


title: PB_91d_2


title: MC.Sk#3


title: PB_91d_4


title: 3ABDKO infected with DNMT3B3 control Day 10 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3B3 DAY 10


title: 3ABDKO infected with DNMT3L control Day 10 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3L DAY 10


title: PB_57d_5

source_name: liver, Phenobarbital, 57 days, 0.05 % w/v


title: 3ABDKO infected with DNMT3B3 control Day 42 PBS control

description: 3ABDKO 3B3 DAY 42 CTRL


title: 3ABDKO infected with EV control Day 42 post 24 treatment with 5-Aza-CdR

description: 3ABDKO EV DAY 42


title: 3ABDKO infected with DNMT3B1 control Day 42 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3B1 DAY 42


title: 3ABDKO infected with DNMT3B1 control Day 42 PBS control

description: 3ABDKO 3B1 DAY 42 CTRL


title: 3ABDKO infected with DNMT3L control Day 42 PBS control

description: 3ABDKO 3L DAY 42 CTRL


title: MC.PC#6

source_name: Blood

value: Blood


title: 3ABDKO infected with DNMT3B1M control Day 10 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3B1M DAY 10


title: 3ABDKO infected with DNMT3L control Day 5 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3L DAY 5


title: PB_57d_4


title: 3ABDKO infected with EV control Day 10 post 24 treatment with 5-Aza-CdR

description: 3ABDKO EV DAY 10


title: MC.PC#3

value: CD11c, CD11b, CD4, CD8, CD19


title: MC.PC#4


title: MC.PC#5


title: 3ABDKO infected with EV control Day 5 post 24 treatment with 5-Aza-CdR

description: 3ABDKO EV DAY 5


title: MC.PC#13


title: PB_57d_1


title: PB_28d_3

source_name: liver, Phenobarbital, 28 days, 0.05 % w/v


title: 3ABDKO infected with DNMT3B3 control Day 42 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3B3 DAY 42


title: 3ABDKO infected with DNMT3B1 control Day 10 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3B1 DAY 10


title: PB_28d_4


title: MC.Es#2

value: Whole Tissue

value: CD4 CD8 CD19 CD11b CD11c


title: 3ABDKO infected with DNMT3L control Day 0 PBS control

description: 3ABDKO 3L CTRL


title: PB_28d_2


title: 3ABDKO infected with DNMT3B1M control Day 5 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3B1M DAY 5


title: Ep.8wk.MEClo.Th#2

source_name: Thymus

value: Thymus

value: 8 Weeks Old

value: PI- CD45-

value: EpCAM+ Ly51+ MHCII+ Sca1+


title: 3ABDKO infected with DNMT3B3 control Day 0 PBS control

description: 3ABDKO 3B3 CTRL


title: 3ABDKO infected with DNMT3B1M control Day 42 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3B1M DAY 42


title: 3ABDKO infected with DNMT3B1 control Day 0 PBS control

description: 3ABDKO 3B1 CTRL


title: PB_28d_1


title: 3ABDKO infected with DNMT3B1M control Day 0 PBS control

description: 3ABDKO 3B1M CTRL


title: 3ABDKO infected with DNMT3B1 control Day 5 post 24 treatment with 5-Aza-CdR

description: 3ABDKO 3B1 DAY 5


title: Ep.8wk.MEClo.Th#1

value: FACSAria

value: Male


title: IDH1 (R132H/WT)

city: Oviedo

first: Agustin

middle: F

last: Fernandez

email: affernandez@hca.es, agusff@gmail.com

state: Asturias

address: Avenida de Roma s/n

department: IUOPA

institute: Oviedo University-HUCA

data_processing: Illumina Genome Studio

label: Cy3, Cy5

source_name: MCF10A breast cancer cell line

label_protocol: Standard Illumina labelling protocol

growth_protocol: Cells were routinely maintained in DMEM/F-12 including 2.5 mmol/L L-glutamine and 15 mmol/L HEPES, supplemented with 5% horse serum, 10 μg/mL insulin, 20 ng/mL hEGF, 0.5 μg/mL hydrocortisone, 0.1 μg/mL cholera toxin

extract_protocol: Total DNA was isolated by standard procedures

treatment_protocol: No treatment

value: mammary gland; breast


title: IDH1 (WT/WT)


title: PB_14d_5

source_name: liver, Phenobarbital, 14 days, 0.05 % w/v

value: liver

value: PB


title: Ep.8wk.CEChi.Th#2


title: Ep.8wk.MEChi.Th#2


title: Ep.8wk.MEChi.Th#1


title: PB_14d_4

value: Phenobarbital


title: 3ABDKO infected with EV control Day 0 PBS control

description: 3ABDKO EV CTRL

value: HCT derivative cell line 3ABDKO


title: PB_57d_2


title: PB_14d_3


title: 3BKO infected with DNMT3B3 control Day 42 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B3 DAY 42

data_processing:
MethylLumi Package
Unmethylated and methylated signal intensities in MethylationIntensities.txt file


title: PB_14d_1


title: PB_14d_2


title: 3BKO infected with DNMT3B4 control Day 42 post 24 treatment with 5-Aza-CdR

description: 3BK0 3B4 DAY 42


title: PB_57d_3


title: Ep.8wk.CEChi.Th#1


title: Ep.8wk.CEC.Sca1+.Th#2


title: PB_7d_5

source_name: liver, Phenobarbital, 7 days, 0.05 % w/v


title: PB_7d_4


title: Ep.5wk.MEClo.Th#2

value: 5 Weeks Old


title: PB_28d_5


title: Ep.5wk.MEClo.Th#1