title: Corrected AWS iPSC replicate 2

city: San Diego

first: Sachin

last: Kumar

state: California

address: 10010 N.Torrey Pines Road

department: Gene Expression Laboratory

institute: Salk Institute for Biological Studies

description: cell culture

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip® Expression Analysis Technical Manual)

scan_protocol: Affymetrix® GeneChip® Scanner 3000 with GCOS software according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label: Biotin

label_protocol: Affymetrix GeneChip® IVT Labeling Kit, according to manufactuer's protocol (GeneChip® Expression Analysis Technical Manual)

growth_protocol: iPSCs were maintained on a layer of mitotically inactivated MEFs in DMEM/F12 (Invitrogen) supplemented with 0.1 mM non-essential amino acids (Invitrogen), 1 mM glutamax (Invitrogen), 20% Knockout Serum Replacement (Invitrogen), 55 μM b-mercaptoethanol (Invitrogen) and 10 ng/ml bFGF (Joint Protein Central). iPSCs were also cultured in Matrigel (BD Biosciences) with mTeSR medium (Stem Cell Technologies).

extract_protocol: Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA) and purified further using the Rneasy Mini Kit (Invitrogen).

treatment_protocol:
iPSCs Generation. For the generation of human iPSCs, human fibroblasts were seeded in a 6-well plate and spin-infected with a mix of high-quality retroviruses encoding OCT4, SOX2, KLF4, c-MYC, and GFP in the presence of 4 ug/ml polybrene. Three infections on consecutive days were performed. 6 days after the first spin-infection, fibroblasts were gently individualized with TrypLE (invitrogen) and seeded onto fresh MEFs in the fibroblast culture medium. After 24 h, the medium was switched to hESC medium. The media was changed every 1–2 days depending on cell density. To establish the iPSC lines, colonies were manually picked and transferred onto MEF feeder cells for several passages before further transfer to Matrigel/mTesR conditions.
Targeted gene correction of LMNA mutations in HGPS-iPSC and AWS-iPSC were accomplished using Helper-Dependent Adenovirus (HDAd)-based gene correction vector.

value: iPSC

tag: lmna mutation status

value: after correction


title: AWS iPSC replicate 2

status: Public on Mar 30 2012

type: RNA

country: USA

description: cell culture

molecule: total RNA

organism: Homo sapiens

tag: cell type

value: before correction


title: Corrected AWS iPSC replicate 1

description: cell culture


title: AWS iPSC replicate 1

description: cell culture


title: Corrected HGPS iPSC replicate 1

description: cell culture


title: RNA isolated from PBMCs (Micro2)

city: Valenzano-Bari

first: Sharon

middle: Natasha

last: Cox

department: Renal Lab

country: Italy

institute: Schena Foundation

description: After hybridization, the microarray chips were washed using the Affymetrix fluidics station in a buffer containing biotinylated antistreptavidin antibody and stained with streptavidin-PE

hyb_protocol: After a step of purification, 20 mg of newly synthesized cRNA were fragmented by metal-induced hydrolisis and hybridized for 16 hours at 45°C to the GeneChip Human Genome U133A ol igonucleotide microarray (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The intensity of the fluorescence was measured with an Affymetrix scanner at 570 nm.

data_processing: Scaled gene expression values were calculated using the default setting of Affymetrix Microarray Suite (MAS) software version 5.0

source_name: IgAN Patient with a Nomal Renal Function and microscopic hematuria

label_protocol: cDNA was obtained using the GeneChip One-Cycle cDNA Synthesis kit (Affymetrix, Santa Clara, California). After that an in vitro transcription was performed to generate biotinylated cRNA to be hybridated on microarrays using the Gene Chip IVT Labelling kit (Affymetrix). The T7 fagus promoter triggered the process of transcription.

extract_protocol: PBMCs were isolated by density separation over a Ficoll–Hypaque (Flow Laboratories, Irvine, UK) gradient (460 g for 30 min). The PBMCs were washed three times with PBS pH 7.4/1 mM EDTA (Sigma, Milan, Italy). Cells were then counted and their viability was determined by trypan blue exclusion (>90% PBMCs were viable). PBMCs were used for total RNA extraction by means of RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol

tag: gender

value: Female

tag: creatinine clearance

value: >90 ml/min/1.73 m2 body surface area (evaluated by Cockcroft-Gault formula)

tag: serum creatinine

tag: clinical follow up

value: At least 7 years

tag: disease state

value: IgA nephropathy

tag: disease stage

value: macroscopic hematuria

tag: patient

value: PBMC


title: HGPS iPSC replicate 2

description: cell culture


title: RNA isolated from PBMCs (Micro3)

value: Male


title: wildtype macrophages treated with RI-BPI peptide, technical replicate 1

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

description: technical replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

label: biotin

organism: Mus musculus

source_name: primary bone marrow derived macrophages

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

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

tag: strain

tag: age

value: 10 week old males

tag: tissue

value: macrophages


title: HGPS iPSC replicate 1

description: cell culture


title: RNA isolated from PBMCs (MACRO3)

source_name: IgAN Patient with a Nomal Renal Function and macroscopic hematuria

treatment_protocol: Blood was collected during gross hematuria episode

value: microscopic hematuria


title: Neurons at 48h_untreated

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

country: France

institute: INSERM

description: Gene expression data from cerebellar neurons culture 48h, untreated

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChip were scanned using an Affymetrix Genechip 3000 7G scanner.

data_processing: Data were analyzed using Affymetrix GeneChip Operating Software (GCOS) and Microarray Suite version 5.0 (MAS5.0) softwares and results were pairwise compared to extract up- and down-regulated genes.

source_name: Cerebellar neurons from newborns, untreated, cultured for 48 hours

label_protocol: Biotinylated cDNA were prepared according to the two-cycle cDNA synthesis Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Cerebellar neurons were retrieved from newborns by mechanic dissociation, plated in serum-free medium for 48 hours and then treated

extract_protocol: Total RNA was extracted using the Qiagen RNeasy micro-kit and quality was assessed by Agilent BioAnalyzer

treatment_protocol: Cultures were either treated with 10-7 M thyroid hormone (T3) for 6, 16, 24 or 48 hours or left untreated the same amount of time as control cultures.

value: Primary culture of cerebellar neurons

value: Prepared from P4-P7 pups

tag: genotype

value: Wild-type


title: wildtype macrophages treated with control peptide, technical replicate 2

description: technicall replicate 2


title: wildtype macrophages treated with RI-BPI peptide, technical replicate 2

description: technicall replicate 2


title: AWS Fibroblast replicate 2

description: cell culture

value: Fibroblast


title: RNA isolated from PBMCs (MACRO2)


title: TCF7 shRNA Rep2

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description: biological replicate 2

hyb_protocol: Arrays were hybridized at the Stanford Functional Genomics Facility using standard Illumina protocols

scan_protocol: Arrays were scanned at the Stanford Functional Genomics Facility using standard Illumina protocols

data_processing: Unbackground corrected data was exported from Beadstudio. The data was processed using the Bioconductor R lumi package. The data was subjected to background correction to make the data positive, a variance stabilizing transformation and quantile normalization.

source_name: murine EML  Lin-SCA+CD34+ cells  multipotential hematopoietic precursor treated with TCF7 shRNA

label_protocol: Samples were labelled at the Stanford Functional Genomics Facility using standard Illumina protocols

growth_protocol: EML cell culture was maintained in  expansion medium (IMDB, 20% heat inactivated horse serum, 100 ng/ml SCF [PeproTech])

extract_protocol: Total RNA from Tcf7 shRNA knockdown cells and control cells (transfected with scrambled shRNA) was purified using the RNeasy Plus kit from Qiagen.

treatment_protocol: Total EML cells were washed twice in FACS buffer (0.5 % BSA, 1 mM EDTA, 1X PBS) and resuspended in 100 µl FACS buffer per 1x106 cells.  CD34-FITC (1 µg per 1 x 106 cells; Ebiosciences) was added to the cells and incubated for 1 hour at 4 °C. Sca1-PE (0.06 µg per 1 x 106 cells; Ebiosciences) and Lineage Cocktail APC (5 µl per 1 x 106 cells; Miltenyi Biotec) were added to the cells and incubated for an additional 30 minutes.  Lin-SCA+CD34+ and Lin-SCA-CD34- cells were collected using FACS Aria (Beckman).  Lin-SCA+CD34+ cells (1x105) cells were transduced at an MOI=1 with a Tcf7 targeting shRNA construct TRCN0000012679 or a shRNA negative control. After a 24-hour incubation with the shRNA-containing virus, the cells were grown in EML GM for 24 hours, then cells were selected for 24 hours in puromycin (1.2 μg/ml). Cells were harvested (a total of four days after initial sort) and total RNA extracted.

tag: shRNA

tag: cell line

value: EML

value: murine EML  Lin-SCA+CD34+ cells  multipotential hematopoietic precursor cell


title: RNA isolated from PBMCs (MACRO1)


title: Corrected HGPS iPSC replicate 2

description: cell culture

value: iPSC

value: after correction


title: AWS Fibroblast replicate 1

description: cell culture

value: before correction


title: RNA isolated from PBMCs (Micro1)

value: >90 ml/min/1.73 m2 body surface area (evaluated by Cockcroft-Gault formula)

value: At least 7 years


title: wildtype macrophages treated with RI-BPI peptide, technical replicate 3

description: technical replicate 3


title: wildtype macrophages treated with control peptide, technical replicate 3

description: technical replicate 3


title: Scrambled shRNA

description: negative control

source_name: murine EML  Lin-SCA+CD34+ cells  multipotential hematopoietic precursor treated with scrambled control shRNA

value: Scrambed


title: Neurons at 24h_untreated

description: Gene expression data from cerebellar neurons culture 24h, untreated

source_name: Cerebellar neurons from newborns, untreated, cultured for 24 hours


title: TCF7 shRNA Rep1

description: biological replicate 1

source_name: murine EML  Lin-SCA+CD34+ cells  multipotential hematopoietic precursor cells treated with TCF7 shRNA


title: CD11b+L6G+Ly6C- cells, 3wks tumor-bearing mice, rep2

city: Seoul

first: Chang-Yuil

last: Kang

address: 29-102, Seoul National University, Shillim-dong, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
ER2-2
Gene expression data from MDSCs.

hyb_protocol: Hybridization cocktails containing 5 to 5.5 µg of fragmented, end-labeled single-stranded cDNA were prepared and hybridized to GeneChip Human Gene 1.0 ST arrays for 17hr at 45°C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The RMA algorithm was used for expression summary and signal calculation of Affymetrix MoGene 1.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

source_name: CD11b+L6G+Ly6C- cells from 3wks tumor-bearing mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Wt_sensetarget_label_manual(updated manual)_1, 2007, Affymetrix).

growth_protocol: BALB/c mice were subcutaneously injected with 1x10^5 Her-2/CT26 cells.

extract_protocol: Total RNA was purified from CD11b+Ly-6C(high)Ly-6G(low) and CD11b+Ly-6C(low)Ly-6G(high) cells using Qiagen RNeasy kits (Qiagen, Valencia, CA).

treatment_protocol: To obtain MDSC subpopulations, CD11b+ cells, enriched by the MACS system, were stained with APC-conjugated anti-CD11b Ab, FITC-conjugated anti-Ly-6C Ab and PE-conjugated anti-Ly-6G Ab and sorted using a FACSAria II (BD Bioscience).

value: BALB/c

value: female

value: spleen

value: CD11b+L6G+Ly6C- PMN-MDSCs

tag: tumor injection

value: 1x10^5 Her-2/CT26 cells

tag: days after tumor injection

value: 3 weeks


title: wildtype macrophages treated with control peptide, technical replicate 1

description: technical replicate 1

value: 10 week old males

value: macrophages


title: Neurons at 24h_T3 treatment

description: Gene expression data from cerebellar neurons cultured 24h with T3

source_name: Cerebellar neurons from newborns, treated 24 hours with thyroid hormone T3

value: Primary culture of cerebellar neurons

value: Prepared from P4-P7 pups

value: Wild-type


title: CD11b+L6G+Ly6C- cells, 6wks tumor-bearing mice, rep2

description:
LR2-2
Gene expression data from MDSCs.

source_name: CD11b+L6G+Ly6C- cells from 6wks tumor-bearing mice

value: 6 weeks


title: CD11b+L6G+Ly6C- cells, 6wks tumor-bearing mice, rep1

description:
LR2-1
Gene expression data from MDSCs.


title: CD11b+L6G+Ly6C- cells, naïve mice, rep3

description:
NR2-3
Gene expression data from MDSCs.

source_name: CD11b+L6G+Ly6C- cells from naïve mice


title: Neurons at 16h_T3 treatment

description: Gene expression data from cerebellar neurons cultured 16h with T3

source_name: Cerebellar neurons from newborns, treated 16 hours with thyroid hormone T3


title: CD11b+L6G+Ly6C- cells, naïve mice, rep1

description:
NR2-1
Gene expression data from MDSCs.


title: CD11b+L6G+Ly6C- cells, naïve mice, rep2

description:
NR2-2
Gene expression data from MDSCs.


title: Root at 100%RWC Replicate 1 [single channel]

city: Rondebosch

first: Nicola

last: Illing

state: Western Cape

address: Chemistry Rd

department: Molecular and Cell Biology

country: South Africa

institute: University of Cape Town

description: Biological replicate 1 of 3. Gene expression levels in 100%RWC root.

hyb_protocol: The X. humilis cDNA microarrays were hybridized with Cy3 fluorescently labeled probes of desiccated leaf, hydrated leaf, desiccated root, hydrated root and seed. Three biological replicates were examined for all experimental conditions apart from the hydrated root condition.  In this case, one biological replicate was hybridised to three separate slides. The statistical analysis was based on a total of three replicates per experimental condition (three biological replicates for all conditions except the hydrated root condition which has three technical replicates). The processed microarray slide was prehybridized with 100 ul of hybridization buffer (50% formamide, 50% SSC, 0.2% SDS) for 2 h at 42°C to reduce background. Slides were washed in dH20 and dried by centrifugation at 1000 rpm for 5 minutes. A total of 100 ul denatured probe mix (80 pmol labelled cDNA, 25% formamide, 5X SSC, 0.1% SDS) was injected under the lifterslip (Erie Scientific, USA) covering the array and the slide was incubated horizontally in a Telechem hybridisation chamber (Telechem International Inc, USA) at 42°C for 16 h in the dark. Slides were subsequently transferred to a fresh dish and washed in a series of wash buffers preheated to 55°C beginning with 2X SSC, 0.5% SDS, followed by 0.5.X SSC and finally 0.05X SDS for 5min each with agitation at room temperature. They were dipped in 100% ethanol and dried by centrifugation at 1000 rpm for 5 minutes.

scan_protocol: Axon confocal scanning system (Genepix 4000B) and GenePix Pro 6.0 data acquisition software (Molecular Devices Products, USA) were used according to the manufacturer’s instructions to capture the X. humilis data. Normalisation of the Cy3 fluorescent dye emission intensities across all the slides was achieved by adjusting the level of the photomuliplier gains. The signal intensities for all 7200 spots were quantified and the mean fluorescence values were extracted.

data_processing: A feature-indicator grid was aligned onto the image of each scanned slide to capture fluorescent intensity data from the scanned slides. Each printed cDNA spot was identified and the foreground, background signal intensities as well as other information for each spot were quantified and extracted by the GenePix Pro 6.0 software according to manufacturer’s instructions. Raw expression data captured and extracted after slide scanning were imported into and processed in R version 2.2.1. Spatial correction of the X. humilis data was conducted using the spat.norm function followed by background correction (bkg.norm function) using the “deterministic” approach in smida. The data sets were normalised using affy quantile normalisation using the normalize.quantiles function in the affy package. Normalized log2 expression values for all technical replicates were merged by averaging.

organism: Xerophyta humilis

source_name: Single root at 100%RWC harvested from desiccating plants

label_protocol: RNA samples extracted from X humilis leaf, root and seed were assessed by visualisation on denaturing formamide gels and spectrophotometrically with a Nanodrop ND-1000 (Nanodrop, USA). The ratios of A260 nm/A280 nm and A260 nm/A230 nm were recorded. Fifteen micrograms of total RNA was fluorescently labeled by reverse transcription in the presence of 5-(3-aminoallyl)-dUTP (Sigma-Aldrich, St. Louis) and 500ng oligodT primer using Superscript III (Invitrogen) overnight at 42ºC.  The RNA was hydrolysed with 500 nM NaOH and 250 nM EDTA at 65°C for 15 minutes and the cDNA was purified through QIAquick PCR Purification columns (Qiagen, Germany) according to the manufacturers recommendations with the replacement wash buffer and elution buffer by phosphate wash buffer (5 mM KPO4, pH 8.0, 80% ethanol) and phosphate elution buffer (4 mM M KPO4, pH 8.5), respectively. Cy3 monofunctional dye (Amersham, Germany) was linked to the aminomodified nucleotides of the purified cDNA in 0.2 M sodium carbonate buffer (pH 9.0) for 1 hour at room temperature in a separate coupling step to generate fluorescently labeled cDNA. The labelled cDNA was separated from uncoupled Cy3 by purification through QIAquick PCR Purification columns (Qiagen, Germany) following the manufacturers protocol and measured at 260 nm and 550 nm on a nanodrop to quantitate both cDNA concentration and Cy dye incorporation.

growth_protocol: X. humilis plants collected from Barakalalo National Park, Limpopo, South Africa, were maintained in trays with good drainage under glasshouse conditions at the University of Cape Town.  Plants were watered every second day for two weeks, prior to the commencement of the desiccation treatment.

extract_protocol: For vegetative tissue: X. humilis leaf and root tissue was ground up with liquid nitrogen and thawed in 5M Na-perchlorate, 0.3M Tris-HCl (pH 8.3), 1% [v/v] SDS, 8.5% [w/v] PVPP, 2% [v/v] PEG-6000, 1% [v/v] beta-ME.  The samples were incubated at room temperature with shaking for 30 minutes, and centrifuged at 10,000 x g for 10 minutes at 4oC. The supernatant was subjected to two rounds of phenol:chloroform:isoamylalcohol (PCI) precipitation followed by an overnight isopropanol precipitation at -20oC.  The precipitated RNA was recovered by centrifugation at 10,000 x g for 10 minutes at 4oC, and the pellet resuspended in 1ml dH2O at 65oC for 5 minutes.  The RNA was selectively precipitated overnight at 4oC with 2.5M LiCl and recovered by centrifugation at 12,000 x g at 4oC for 30 minutes. For seed tissue: Approximately 200 mg X. humilis seeds were ground up in liquid nitrogen and together with 700 ul XT buffer (0.2 M sodium borate decahydrate, 30 mM EGTA, 1% SDS, 1% sodium deoxycholate, 2% PVP, 10 mM DTT, 1% IGEPAL, pH 9.0). The powder was decanted to a 15 ml falcon tube, thawed at room temperature and an additional 700 ul XT buffer added.  The liquid was divided into two eppendorf tubes, 56 ul 2M KCL added to each tube, mixed and incubated on ice for 60 min.  The supernatant was recovered by centrifugation at 13 000 rpm for 20 min at 4ºC and the RNA selectively precipitated by the addition of LiCl to a final of 2.5M and incubation at -20ºC overnight.  The RNA was collected by centrifugation at 13 000 rpm for 20 min at 4ºC and the pellets resuspended in 100 ul RNase-free water.  The RNA was subsequently purified following the RNeasy kit protocol (Qiagen, Germany).

treatment_protocol: Three trays of plants were allowed to dry naturally by withholding water until fully desiccated (~5%RWC) for a total of three weeks and an additional three trays of plants were maintained in a hydrated state (~90%RWC) with watering three times a week.  Desiccated leaf and root samples and hydrated leaf and root samples were harvested simultaneously and flash frozen and stored at -80oC. To calculate the RWC three leaves were removed from the plant and weighed to obtain the fresh weight. These leaves were then placed in a beaker of water for 24 hours and weighed to obtain the weight at full turgour. Subsequently the leaves were placed at 105°C for 24 hours and weighed to obtain the dry weight. The RWC was determined by subtracting average dry weight from the average fresh weight, which is divided by the average fresh weight subtracted from the average weight at full turgor, multiplied by 100. Mature seeds were collected over several flowering intervals from genetically diverse populations of X. humilis plants.

value: root

tag: %rwc


title: Neurons at 48h_T3 treatment

description: Gene expression data from cerebellar neurons cultured 48h with T3

source_name: Cerebellar neurons from newborns, treated 48 hours with thyroid hormone T3


title: Neurons at 16h_untreated

description: Gene expression data from cerebellar neurons culture 16h, untreated

source_name: Cerebellar neurons from newborns, untreated, cultured for 16 hours


title: CD11b+L6G-Ly6C+ cells, 6wks tumor-bearing mice, rep3

description:
LR1-3
Gene expression data from MDSCs.

source_name: CD11b+L6G-Ly6C+ cells from 6wks tumor-bearing mice

tag: cell type

value: CD11b+L6G-Ly6C+ Mo-MDSCs


title: CD11b+L6G+Ly6C- cells, naïve mice, rep4

description:
NR2-4
Gene expression data from MDSCs.

tag: gender


title: CD11b+L6G-Ly6C+ cells, 3wks tumor-bearing mice, rep3

description:
ER1-3
Gene expression data from MDSCs.

source_name: CD11b+L6G-Ly6C+ cells from 3wks tumor-bearing mice


title: CD11b+L6G-Ly6C+ cells, 3wks tumor-bearing mice, rep2

description:
ER1-2
Gene expression data from MDSCs.


title: Neurons at 6h_untreated

description: Gene expression data from cerebellar neurons culture 6h, untreated

source_name: Cerebellar neurons from newborns, untreated, cultured for 6 hours


title: CD11b+L6G-Ly6C+ cells, 6wks tumor-bearing mice, rep2

description:
LR1-2
Gene expression data from MDSCs.


title: CD11b+L6G-Ly6C+ cells, 3wks tumor-bearing mice, rep1

description:
ER1-1
Gene expression data from MDSCs.


title: CFTR+/+, biological replicate 6

city: Iowa City

first: Shyam

last: Ramachandran

address: 240G EMRB

department: Pediatrics

institute: Univ of Iowa

description: The GeneChip® Porcine Genome Array

hyb_protocol: The resultant biotinylated cRNA is fragmented and then hybridized to The GeneChip® Porcine Genome Array. The GeneChip® Porcine Genome Array provides comprehensive coverage of the Sus scrofa transcriptome. The array contains 23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 S. scrofa genes.

scan_protocol: The arrays are washed, stained, and scanned using the Affymetrix Model 450 Fluidics Station and Affymetrix Model 3000 scanner using the manufacturer’s recommended protocols, and the data collected using the GeneChip Operating Software (GCOS), v.1.4.

data_processing: Data processing and analysis was performed using the Partek Genomics Suite (RMA normalization).

organism: Sus scrofa

source_name: Primary airway epithelial culture (trachea)

label_protocol: Total RNA (5 μg) is processed using the Affymetrix GeneChip one-cycle target labeling kit (Affymetrix) according to the manufacturer’s recommended protocols.

growth_protocol: Primary cultures were maintained in USG media

extract_protocol: TriZOL and manufacturer's recommended protocol was followed to extract RNA from primary cultures

value: trachea

value: CFTR+/+


title: CFTR-/-, biological replicate 4

description: The GeneChip® Porcine Genome Array

value: CFTR-/-


title: CD11b+L6G-Ly6C+ cells, 6wks tumor-bearing mice, rep1

description:
LR1-1
Gene expression data from MDSCs.

value: BALB/c


title: Neurons at 6h_T3 treatment

description: Gene expression data from cerebellar neurons cultured 6h with T3

source_name: Cerebellar neurons from newborns, treated 6 hours with thyroid hormone T3


title: CD11b+L6G-Ly6C+ cells, naïve mice, rep1

description:
NR1-1
Gene expression data from MDSCs.

source_name: CD11b+L6G-Ly6C+ cells from naïve mice

value: female


title: CFTR+/+, biological replicate 4

description: The GeneChip® Porcine Genome Array


title: CFTR-/-, biological replicate 3

description: The GeneChip® Porcine Genome Array


title: CFTR+/+, biological replicate 5

description: The GeneChip® Porcine Genome Array


title: CFTR-/-, biological replicate 5

description: The GeneChip® Porcine Genome Array


title: CFTR-/-, biological replicate 1

description: The GeneChip® Porcine Genome Array


title: CFTR-/-, biological replicate 2

description: The GeneChip® Porcine Genome Array


title: CFTR+/+, biological replicate 3

description: The GeneChip® Porcine Genome Array


title: CD11b+L6G-Ly6C+ cells, naïve mice, rep2

description:
NR1-2
Gene expression data from MDSCs.

value: spleen


title: CFTR+/+, biological replicate 1

description: The GeneChip® Porcine Genome Array


title: CFTR+/+, biological replicate 2

description: The GeneChip® Porcine Genome Array


title: CD11b+L6G+Ly6C- cells, 3wks tumor-bearing mice, rep1

description:
ER2-1
Gene expression data from MDSCs.

value: CD11b+L6G+Ly6C- PMN-MDSCs


title: GC-rep10

city: Cambridge

first: Massimiliano

last: di Pietro

address: Hills Road

country: United Kingdom

institute: MRC Cancer Cell Unit

hyb_protocol: Samples were hybridized to Affymetrix Human GeneChip 1.0ST arrays using Affymetrix Hybridization Kit following manufacturer's instructions for the 49/64 format array. Wash and stain of arrays was carried out on geneChip Fluidics 450 Workstation using protocol FS450_0007

scan_protocol: Arrays were scanned on Affymetrix GeneChip GCS3000

data_processing: Softwares/Tools used for the data processing were Affymetrix GeneChip Command Console Software (AGCC), and Partek Genomic Suite 6.5. For the creation of the summarized log-signal, the Robust Multichip Average (RMA) with Quantile normalisation and Median Polish for Probe set summarisation were used

source_name: GC

label_protocol: WT Expression Kit (Ambion) was used to obtain ss cDNA which was then labelled and fragmented using Affymetrix WT Terminal Labelling Kit according to manufacturing instructions

growth_protocol: N/A - samples were biopsies collected at the time of endoscopy from the normal oesophagus, Barrett's oesophagus and gastric cardia

extract_protocol: Biopsies were homogenised in Trizol using the Precellys. A standard Trizol extraction method was used.

treatment_protocol: Samples were snap frozen in liquid nitrogen at the time of collection

value: gastric cardia


title: GC-rep6


title: GC-rep9


title: GC-rep5


title: GC-rep8


title: NE-rep4

source_name: NE

value: normal esopahgus


title: GC-rep7


title: GC-rep3


title: GC-rep1


title: NE-rep8


title: GC-rep4


title: NE-rep7


title: GC-rep2


title: NE-rep3


title: NE-rep5


title: NE-rep6


title: NE-rep2


title: H0-882

city: Ottawa

first: Morie

last: Malowany

state: Ontario

address: 50 Colombine Driveway, Tunney's Pasture

department: Environmental Health Science and Research Bureau

country: Canada

institute: Health Canada

hyb_protocol: Agilent Whole Mouse Genome Microarrays (G4122F; containing over 41,000 genes and transcripts) were hybridized with 825 ng Cy5-labelled exposed (hypo, hyper or hypo+) RNA and 825 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays.  Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned using Agilent DNA Microarray Scanner (G2565CA) and data was acquired with Feature Extraction 10.1.1 (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

data_processing: The median signal intensity of each microarray sample was used. Technical replicates were not averaged.  Data for each probe was flagged (flag=1) if the median signal intensity for that probe was less than the mean of the negative controls ((-)3xSLv1) plus three standard deviations. RawCy5 and RawCy3 are the median signal intensities for the Cy5 and Cy3 channels on each microarray. NormCy5 and NormCy3 are the loess normalized signal intensities for the Cy5 and Cy3 channels within each array; this is a within-array normalization performed separately for each array. Flag indicates whether the median signal intensity falls in the background, i.e below threshold calculated from the negative controls (mean plus three standard deviations of the negative controls). Ratio is calculated as log2(NormCy5/NormCy3) (Relative Intensity, logged).

source_name: liver from a euthyroid mouse

label_protocol: Individual 200 ng aliquots of RNA from each samples were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada).  RNA was quantified using UV spectrophotometer and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

value: Control

tag: microarray barcode

tag: microarray slide block

value: Female

source_name: stratagene mouse reference

extract_protocol: Material was purchased as total RNA (universal mouse reference total RNA (Stratagene, CA, USA))


title: H1-499

source_name: liver from a hyperthyroid mouse

value: Hyper (H1)


title: BE-rep9

source_name: BE

value: Barrett's


title: H2-575

source_name: liver from hypothyroid mice

value: Hypo (H2)


title: BE-rep10


title: NE-rep1


title: H1-783


title: H2-316


title: H3-601

source_name: liver from hypo-replacement mouse

value: Hypo+ (H3)


title: H2-893


title: H0-394


title: BE-rep8


title: H1-861


title: BE-rep5


title: BE-rep6


title: BE-rep7


title: H3-763


title: H2-721


title: BE-rep3


title: H1-585


title: BE-rep2


title: H1-621


title: H3-363

value: Male


title: H3-543


title: H0-831


title: H2-743


title: BE-rep1


title: H1-583


title: BE-rep4


title: H0-523


title: H3-761


title: H1-696


title: H0-391


title: H1-498


title: H2-723


title: H0-522


title: H2-311


title: H3-454


title: H1-784


title: H2-576


title: GenAu MB BCELL v5.0 H3K4me3 Pax5-/- Rag2-/- 300105

type: genomic

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

description: Chip-chip Pax5-/- Rag2-/- pro-B cells H3K4me3

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
custom R-script
log2(Signal Cy5/Signal Cy3) - tukey.biweight(Signal Cy5/Signal Cy3)

molecule: genomic DNA

source_name: H3K4me3 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: pro-B cells were cultured for 5 days in the presence of IL-7 on OP9 feeder cells.

extract_protocol: 5x10E6 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer(500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: pro-B cells were MACs sorted from the bone marrow of 3-5 week old mice.

tag: genotype/variation

value: 5 days in culture

value: pro-B cells

tag: antibody

tag: type

value: ChIP

tag: amplification

value: wga

tag: antibody  vendor

value: Upstate

tag: antibody  lot#

source_name: Input DNA from Pax5-/- Rag2-/- pro-B cells

growth_protocol: see channel 1

extract_protocol: see channel 1

treatment_protocol: see channel 1

value: Input


title: H0-832

tag: disease state


title: GenAu MB BCELL v5.0 H3K4me3 Rag2-/- 226727

description: Chip-chip Rag2-/- pro-B cells H3K4me3

source_name: H3K4me3 ChIP DNA from Rag2-/- pro-B cells

tag: age

tag: strain

source_name: Input DNA from Rag2-/- pro-B cells


title: CD11b+L6G-Ly6C+ cells, naïve mice, rep3

description:
NR1-3
Gene expression data from MDSCs.

value: BALB/c

value: female

tag: tissue

value: spleen

value: CD11b+L6G-Ly6C+ Mo-MDSCs


title: H2-891


title: H3-546


title: ampR mutant, induced, biological repl 3

city: Miami

first: Deepak

last: Balasubramanian

state: Fl

institute: FLORIDA INTERNATIONAL UNIVERSITY

description: Gene expression data from mutant cells exposed to sub-MIC ß-lactams

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Pseudomonas aeruginosa GeneChip (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneSpring GX 10.0 Expression Analysis Software. Data normalization and sumarization was performed using GC-RMA. Other analysis parameters used were: expression cutoff of 50-100% stringency; p-value < 0.01 of one-way ANOVA data corrected by Benjamini Hochberg FDR; fold-change >2.0

organism: Pseudomonas aeruginosa

source_name: PAO∆ampR induced

label_protocol: cDNA was prepared using SuperScript III reverse transcriptase, fragmented with RQ1 Dnase and biotin labeled.

growth_protocol: P. aeruginosa PAO1 and PAO∆ampR were grown in LB medium in baffled flasks at 37 ˚C, 300 RPM

extract_protocol: Total RNA was extracted from penicillin-treated and untreated cells using Rneasy Mini Kit (Qiagen) following manufacturer protocols.

treatment_protocol: Mid log cells were exposed to sub-MIC concentrations of penicillin G. Untreated controls were maintained.

value: Whole cell

tag: genotype

value: ampR mutant

value: Late log/ early stationary

tag: agent

value: exposed to sub-MIC ß-lactams


title: H0-881

value: Control


title: ampR mutant, induced, biological repl 2


title: H1-864

value: Hyper (H1)


title: GenAu MB BCELL v5.0 H3K9ac Rag2-/- 226557

description: Chip-chip Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Rag2-/- pro-B cells

tag: antibody cat#


title: GenAu MB BCELL v5.0 H3K4me3 Rag2-/- 226561

description: Chip-chip Rag2-/- pro-B cells H3K4me3

tag: cell type


title: ampR mutant, uninduced, biological repl 3

description: Gene expression data from mutant cells unexposed to ß-lactams

source_name: PAO∆ampR uninduced


title: ampR mutant, induced, biological repl 1


title: ampR mutant, uninduced, biological repl 1


title: GenAu MB BCELL v5.0 H3K27me3 Rag2-/- 181972

description: Chip-chip Rag2-/- pro-B cells H3K27me3

source_name: H3K27me3 ChIP DNA from Rag2-/- pro-B cells

tag: antibody provider

value: T. Jenuwein


title: Wild type, induced, biological repl 2

description: Gene expression data from wild type cells exposed to sub-MIC ß-lactams

source_name: PAO1 induced

value: Wild type


title: Wild type, induced, biological repl 3


title: Wild type, induced, biological repl 1


title: GenAu MB BCELL v5.0 Pax-bio Pax5bio/bio Rag2-/- 226775

description: Chip-chip Pax5bio/bio Rag2-/- pro-B cells Pax-bio

source_name: Pax-bio ChIP DNA from Pax5bio/bio Rag2-/- pro-B cells

value: Pax5bio/bio Rag2-/-

value: 5 days in culture

value: pro-B cells

tag: antibody-like reagent

value: streptavidin pulldown of in-vivo bio-tagged protein (Pax-bio)

source_name: Input DNA from Pax5bio/bio Rag2-/- pro-B cells


title: Wild type, uninduced, biological repl 3

description: Gene expression data from wild type cells unexposed to ß-lactams

source_name: PAO1 uninduced


title: GenAu MB BCELL v5.0 Ctcf Rag2-/- 147888

description: Chip-chip Rag2-/- pro-B cells Ctcf

source_name: Ctcf ChIP DNA from Rag2-/- pro-B cells

value: Ctcf

value: ChIP

value: wga

value: Milipore

value: Input


title: BMP2(+),LOXL2(+)

city: Tokyo

first: Dai

last: Suzuki

address: 1-5-8 Hatanodai, Shinagawa

department: Biochemistry

country: Japan

institute: Showa University

description:
Osteoblastgenesis
US11060402_252800512938_S01_GE1_107_Sep09_1_4

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul of  Agilent 2x HI-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (20 bit, Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100% ).

data_processing: The scanned images were analyzed with Feature Extraction Software v 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20110722) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: primary osteoblasts

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Liner Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Primary osteoblasts were harvested and cultured in the presence of 10% FBS for culture.

extract_protocol: Rneasy mini kit (Qiagen) extraction of total RNA was performed according to the manufacture's instructions.

treatment_protocol: Primary osteoblasts were treated with BMP2 (200 ng/ml) and or LOXL2 (4 μg/ml) for 72h.

value: osteoblasts

tag: treatment


title: Wild type, uninduced, biological repl 2

value: Whole cell


title: ampR mutant, uninduced, biological repl 2

value: ampR mutant

value: Late log/ early stationary


title: GenAu MB BCELL v5.0 H3K36me3 Rag2-/- 226556

description: Chip-chip Rag2-/- pro-B cells H3K36me3

source_name: H3K36me3 ChIP DNA from Rag2-/- pro-B cells

tag: genotype/variation

value: Abcam


title: Wild type, uninduced, biological repl 1


title: GenAu MB BCELL v5.0 H3K4me2 Pax5-/- Rag2-/- 226302

description: Chip-chip Pax5-/- Rag2-/- pro-B cells H3K4me2

source_name: H3K4me2 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

tag: antibody

value: Upstate


title: BMP2(+),LOXL2(-)

description:
Osteoblastgenesis
US11060402_252800512938_S01_GE1_107_Sep09_1_3


title: GenAu MB BCELL v5.0 H3K27me3 Pax5-/- Rag2-/- 181956

description: Chip-chip Pax5-/- Rag2-/- pro-B cells H3K27me3

source_name: H3K27me3 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

tag: type

value: T. Jenuwein


title: GenAu MB BCELL v5.0 Pax5 Rag2-/- 147460

description: Chip-chip Rag2-/- pro-B cells Pax5

source_name: Pax5 ChIP DNA from Rag2-/- pro-B cells

tag: amplification

value: IgG purified


title: GenAu MB BCELL v5.0 H3K4me2 Rag2-/- 226562

description: Chip-chip Rag2-/- pro-B cells H3K4me2

source_name: H3K4me2 ChIP DNA from Rag2-/- pro-B cells

tag: antibody  vendor


title: BMP2(-),LOXL2(-)

description:
Osteoblastgenesis
US11060402_252800512938_S01_GE1_107_Sep09_1_1

value: pre-osteoblasts


title: GenAu MB BCELL v5.0 Ctcf Pax5-/- Rag2-/- 182394

description: Chip-chip Pax5-/- Rag2-/- pro-B cells Ctcf

source_name: Ctcf ChIP DNA from Pax5-/- Rag2-/- pro-B cells

value: 5 days in culture

tag: antibody  lot#

source_name: Input DNA from Pax5-/- Rag2-/- pro-B cells


title: GenAu MB BCELL v5.0 H3K4me3 Pax5-/- Rag2-/- 142343

source_name: H3K4me3 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

value: pro-B cells


title: GenAu MB BCELL v5.0 H3K4me2 Pax5-/- Rag2-/- 141263


title: GenAu MB BCELL v5.0 H3K4me2 Rag2-/- 142171

description: Chip-chip Rag2-/- pro-B cells H3K4me2

source_name: Input DNA from Rag2-/- pro-B cells


title: ob/ob chow diet Group 4

city: Palo Alto

first: Haiyan

last: Zhang

address: 3801 Miranda Ave

department: Geriatric Research, Education and Clinical Center

institute: VA Palo Alto Health Care System

description: Mouse Whole Genome Onearray

hyb_protocol: Phalanx hybridization protocol

scan_protocol: Phalanx scanning protocol

data_processing: Quantile normalization, averaged

source_name: ob/ob mouse liver

label_protocol: AminoAllyl aRNA labeling. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP was used to conjugate the purified aRNA with the NHS-CyDye.

extract_protocol: Liver tissue homogenized with Qiashredder homogenizer, RNA extracted with RNeasy Mini Kit. RNA verified with NanoDrop ND-1000, Agilent RNA 6000 Nano Assay and agarose electrophoresis.

treatment_protocol: Using wild type (WT, C57BL/6) fed with chow diet as control, WT mice were either fed with high-fat diet or high-fat diet with NDGA (2.5g/kg food); ob/ob mice were fed with either chow or chow with NDGA (2.5 g/kg food), and maintained on the respective diets for 16 weeks.

value: chow diet

value: ob/ob

tag: genetic background

value: liver


title: WT high-fat NDGA diet Group 2

description: Mouse Whole Genome Onearray

source_name: WT mouse liver

value: high-fat NDGA diet

value: wild type


title: Heart, 8 wpi, fish 4-7, high responder

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with either Agilent G2565BA or GenePix 4100A DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1 and GenePix Pro 6.0. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Heart of infected salmon

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol using Agilent Quick Amp Labelling Kit

growth_protocol: Salmon (average weight 50g) was kep in tanks with sea water

extract_protocol: RNA was isolated using the iPrep™ TRIzol® Plus kit (Invitrogen), and purified with PureLink RNA mini kits

treatment_protocol: Injection of PMCV was performed after sedation (benzocaine, 30-40 mg L-1). Infected groups received an intraperitoneal (i.p.) injection dose (0.2 ml) of a supernatant from a GF-1 cell line (derived from the fin tissue of orange-spotted grouper, Epinephelus coioides) infected with PMCV. The infected individuals were denoted as high and low responders by scores of heart histopathology.

value: Heart

tag: development stage

value: post-smolt

tag: infection

value: piscine myocarditis virus (PMCV)

tag: time(wpi)

value: 8 wpi

source_name: Heart of control salmon


title: WT chow diet Group 3

description: Mouse Whole Genome Onearray

tag: genotype

tag: tissue


title: Heart, 8 wpi, fish 4-4, low responder


title: Heart, 8 wpi, fish 4-14, low responder


title: WT high-fat diet Group 1

description: Mouse Whole Genome Onearray

value: high-fat diet


title: GenAu MB BCELL v5.0 H3K9ac Rag2-/- 226757

description: Chip-chip Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Rag2-/- pro-B cells

tag: age

tag: strain

value: ChIP

value: wga

tag: antibody cat#

value: Input


title: GenAu MB BCELL v5.0 Pax-bio Pax5bio/bio Rag2-/- 226361

source_name: Pax-bio ChIP DNA from Pax5bio/bio Rag2-/- pro-B cells

value: Pax5bio/bio Rag2-/-

tag: cell type

tag: antibody-like reagent

value: streptavidin pulldown of in-vivo bio-tagged protein (Pax-bio)

source_name: Input DNA from Pax5bio/bio Rag2-/- pro-B cells


title: Heart, 8 wpi, fish 4-3, high responder


title: Heart, 6 wpi, fish 8, low responder, direct labeling

value: 6 wpi


title: GenAu MB BCELL v5.0 Su(z)12 Rag2-/- 130369

description: Chip-chip Rag2-/- pro-B cells Su(z)12

source_name: Su(z)12 ChIP DNA from Rag2-/- pro-B cells

tag: genotype/variation

value: 5 days in culture

value: pro-B cells

value: Upstate


title: Heart, 8 wpi, fish 3-11, low responder


title: F-M0

city: PARIS

first: Nicolas

last: DERIAN

address: 15 Avenue Pitié

department: Biotherapy

hyb_protocol: Labelled cRNA were hybridized overnight to Illumina Human HT-12 V3 BeadChip arrays (Illumina)

scan_protocol: Beadchips were scanned on the Illumina BeadArray 500GX Reader using Illumina BeadScan image data acquisition software (version 2.3.0.13).

data_processing:
Data were process using BeadStudio software and R package Lumi.
Normalized matrix contains expression value normalized by quantiles, transformed by log2 and detection p-values after removing outliers, merging these data with an other experiment performed on Illumina HT12 V4.0 (GPL13475), 39396 probes remained.

source_name: patient F before treatment

label_protocol: Total RNA was amplified and converted to biotinylated cRNA according to the manufacturer’s protocol (Illumina TotalPrep RNA Amplification Kit; Ambion).

extract_protocol: RNA was extracted from fresh PBMCs using the NucleoSpin RNA II  kit (Macherey-Nagel, Hoerd, France) according to the manufacturer’s instructions. RNA integrity was assessed using an Agilent Bioanalyser showing a quality RNA integrity number of 8–10 (Agilent Technologies). RNA yield was assessed using a NanoDrop 1000 spectrophotometer (NanoDrop Products, Thermo Fisher Scientific).

treatment_protocol: Vitamin D supplementation using 100 000 IU of cholecalciferol per week

value: PBMC

tag: treatment


title: ob/ob chow NDGA diet Group 5

description: Mouse Whole Genome Onearray

value: chow NDGA diet

value: ob/ob

value: liver


title: GenAu MB BCELL v5.0 Su(z)12 Pax5bio/bio Rag2-/- 140091

description: Chip-chip Pax5bio/bio Rag2-/- pro-B cells Su(z)12

source_name: Su(z)12 ChIP DNA from Pax5bio/bio Rag2-/- pro-B cells

tag: antibody

tag: type


title: BMP2(-),LOXL2(+)

description:
Osteoblastgenesis
US11060402_252800512938_S01_GE1_107_Sep09_1_2

source_name: primary osteoblasts

value: pre-osteoblasts


title: Heart, 8 wpi, fish 3-9, high responder

value: Heart

value: post-smolt

value: piscine myocarditis virus (PMCV)


title: D-M2

source_name: patient D 2 month after treatment

value: Vitamin D supplementation using 100 000 IU of cholecalciferol per week

tag: sample time

value: 2 month after treatment


title: GenAu MB BCELL v5.0 H3K4me3 Rag2-/- 142355

description: Chip-chip Rag2-/- pro-B cells H3K4me3

source_name: H3K4me3 ChIP DNA from Rag2-/- pro-B cells

value: ChIP

tag: amplification

value: wga

tag: antibody  vendor

tag: antibody  lot#

value: Input


title: F-M2

source_name: patient F 2 month after treatment


title: Heart, 6 wpi, fish 7, low responder, reverse labeling

tag: development stage

tag: infection

value: 6 wpi


title: Heart, 6 wpi, fish 8, low responder, reverse labeling

tag: time(wpi)


title: Heart, 6 wpi, fish 6, low responder, reverse labeling

tag: tissue


title: Heart, 6 wpi, fish 5, low responder, reverse labeling


title: Heart, 6 wpi, fish 6, low responder, direct labeling


title: Heart, 6 wpi, fish 5, low responder, direct labeling


title: Heart, 6 wpi, fish 7, low responder, direct labeling


title: Heart, 6 wpi, fish 3, high responder, reverse labeling


title: C-M0

source_name: patient C before treatment


title: A-M2

source_name: patient A 2 month after treatment


title: Heart, 6 wpi, fish 3, high responder, direct labeling


title: B-M2

source_name: patient B 2 month after treatment


title: GenAu MB BCELL v5.0 H3K9ac Rag2-/- 141262

description: Chip-chip Rag2-/- pro-B cells H3K9ac

tag: age

value: 5 days in culture

source_name: Input DNA from Rag2-/- pro-B cells


title: Heart, 6 wpi, fish 2, high responder, direct labeling


title: Heart, 6 wpi, fish 1, high responder, direct labeling


title: Heart, 6 wpi, fish 1, high responder, reverse labeling


title: Heart, 10 wpi, fish 4-5, low responder

value: 10 wpi


title: Heart, 4 wpi, fish 6, reverse labeling

value: 4 wpi


title: Heart, 6 wpi, fish 2, high responder, reverse labeling


title: A-M0

source_name: patient A before treatment

value: PBMC


title: Heart, 6 wpi, fish 4, high responder, direct labeling

source_name: Heart of infected salmon


title: B-M0

source_name: patient B before treatment


title: Heart, 4 wpi, fish 6, direct labeling

source_name: Heart of control salmon


title: Heart, 10 wpi, fish 4-4, low responder


title: Heart, 6 wpi, fish 4, high responder, reverse labeling


title: Heart, 8 wpi, fish 4-11, high responder

value: 8 wpi


title: Heart, 4 wpi, fish 5, reverse labeling


title: Heart, 4 wpi, fish 5, direct labeling


title: Heart, 10 wpi, fish 4-14, low responder


title: Heart, 10 wpi, fish 4-15, low responder


title: Heart, 4 wpi, fish 4, direct labeling


title: C-M2

source_name: patient C 2 month after treatment


title: Wt/Delta3_1 replicate

city: Parkville

first: Matthew

middle: J

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

hyb_protocol: Hybridization was conducted as per Agilent 2 color microarray-based gene expression analysis manual (version 5.7) with the modification 4 microg of labeled total RNA was used per hybridization.

scan_protocol: Images were quantified using Agilent Feature Extraction Software

organism: Escherichia coli O157:H7 str. EDL933

source_name: liquid culture of Escherichia coli EHEC EDL933 Δstx1-2

label_protocol: 5microg of total RNA was labeled with Cy3-ULS or Cy5-ULS (Kreatech) as per manufacturers instructions

growth_protocol: overnight cultures of E.Coli EHEC EDL933 were inoculated into LB medium 1:100 and grown until the OD600 was 0.85-0.95

extract_protocol: 10mL of a culture was incubated with 20mL of RNAprotect solution (Qiagen) at room temperature for 15min. Cells were pelleted and RNA was purified using a FastRNA Pro Blue kit (Qbiogene). RNA samples were Dnase treated (Qiagen) and further purified using an RNeasy MiniElute kit (Qiagen)

treatment_protocol: Bicarbonate was added to a final concentration of 45mM

value: wt

tag: bicarbonate

value: neg


title: Heart, 4 wpi, fish 4, reverse labeling


title: Heart, 8 wpi, fish 4-15, low responder


title: GenAu MB BCELL v5.0 H3K9ac Pax5-/- Rag2-/- 141193

description: Chip-chip Pax5-/- Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Pax5-/- Rag2-/- pro-B cells

value: pro-B cells

tag: strain

value: Upstate

tag: antibody cat#

source_name: Input DNA from Pax5-/- Rag2-/- pro-B cells


title: Delta3_1/Wt replicate


title: Delta3_1/Delta3 replicate


title: Wt/Bicarb replicate

value: pos


title: Heart, 4 wpi, fish 3, reverse labeling

value: Heart

value: post-smolt

value: piscine myocarditis virus (PMCV)


title: Heart, 10 wpi, fish 3-9, high responder


title: Heart, 4 wpi, fish 3, direct labeling


title: Heart, 4 wpi, fish 2, direct labeling


title: Heart, 4 wpi, fish 1, direct labeling


title: Heart, 4 wpi, fish 2, reverse labeling


title: Heart, 10 wpi, fish 4-12, high responder


title: Bicarb/Wt replicate


title: delta3vWt replicate


title: Heart, 4 wpi, fish 1, reverse labeling


title: Heart, 2 wpi, fish 6, direct labeling

value: 2 wpi


title: Heart, 2 wpi, fish 6, reverse labeling


title: D-M0

source_name: patient D before treatment


title: Heart, 2 wpi, fish 5, reverse labeling


title: Heart, 2 wpi, fish 4, reverse labeling


title: Heart, 10 wpi, fish 3-3, high responder


title: Heart, 10 wpi, fish 3-4, high responder


title: Delta3_1/Delta3


title: Delta3_1/Wt


title: Wt/Delta3_1


title: delta3vWt


title: Heart, 2 wpi, fish 5, direct labeling


title: Heart, 2 wpi, fish 4, direct labeling


title: Heart, 2 wpi, fish 3, reverse labeling


title: Heart, 2 wpi, fish 3, direct labeling


title: Wt/Delta3 replicate


title: Heart, 2 wpi, fish 2, reverse labeling


title: Wt/Bicarb


title: Dmel_S2_TopoIIRNAi_rep2

city: Atlanta

first: Edward

last: Ramos

state: GA

address: 1510 Clifton Rd NE

department: Biology

institute: Emory University

hyb_protocol: cDNA was hybridized to a NimbleGen D. melanogaster gene expression 12X135K array at the Florida State University-NimbleGen Microarray Facility.

scan_protocol: Arrays were scanned at the Florida State University-NimbleGen Microarray Facility.

data_processing: The data was generated using Partek Genomic Suites 6.5 software using log2 RMA normalization.

organism: Drosophila melanogaster

source_name: S2 cells, TopoII RNAi

label_protocol: cDNA was labeled at the Florida State University-NimbleGen Microarray Facility.

growth_protocol: Drosophila Schneider line 2 (S2) cells were grown in HyQ SFX-insect medium (HyClone) with penicillin-streptomycin antibiotic at 25C without CO2.

extract_protocol: RNA was isolated from the S2 cells using the Qiagen RNeasy kit (catalog #74104) with on-column DNA digestion (catalog #79254) following the manufacturer's protocols. mRNA was then isolated using Sera-Mag Magnetic Oligo(dT) beads (catalog # 2815-2103) following the manufacturer’s protocol. cDNA synthesis was then performed using the Applied Biosystems High-Capacity cDNA Reverse Transcription Kit (catalog #4368814).

treatment_protocol: Cells were treated with 10 µg/ml double-stranded RNA (dsRNA). Additional dsRNA was added throughout the experiment to maintain the 10 µg/ml concentration. dsRNA was made following Ambion's MEGAscript protocol. The primers used to synthesize dsRNAs for the TopoII and green fluorescent protein (GFP) genes are: GFP forward: 5'ACGTAAACGGCCACAAGTTC 3' reverse: 5' TGCTCAGGTAGTGGTTGTCG 3', TopoII forward: 5' TAGTGGCTCGATCTTTTGGC 3' reverse: 5' TTGCCAGAGCGATATCTCTACA 3'.

tag: cell line

tag: RNAi

value: TopoII


title: Dmel_S2_TopoIIRNAi_rep1


title: Dmel_S2_gfp_rep2

source_name: S2 cells, gfp RNAi

value: gfp


title: emf2 7-day-old seedlings

city: Taipei

first: Mao-Sen

last: Liu

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

description:
7D emf2
Gene expression data from 7-day-old emf2 seedlings grown under short day conditions.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip Arabidopsis  ATH1 Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Arabidopsis thaliana

source_name: 7-day-old seedlings of emf2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Seedlings were grown on 0.8% agar plates with half-strength MS and 1.5% sucrose under short day conditions (8h light/ 16h dark) at 21 degrees Celsius.

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

treatment_protocol: Seedlings of rescued emf2 and transWT were grown on plates with 20 mg/mL hygromycin, while those of WT and emf2 were grown on MS-only plates, under short day conditions (8h/16h) for 7 days.

value: whole seedlings

tag: genotype/variation

value: emf2 mutant background

value: 7 days


title: Dmel_S2_gfp_rep1


title: Rescued emf2 7-d-old seedlings

description:
7D Rescued emf2
Gene expression data from 7-day-old rescued emf2 seedlings grown under short day conditions.

source_name: 7-day-old seedlings of rescued emf2 harboring 35S::BoEMF2.1

value: emf2 mutant background harboring 35S::BoEMF2.1


title: delta3/Wt replicate


title: Heart, 2 wpi, fish 2, direct labeling


title: delta3/Wt


title: Wt/Delta3


title: Heart, 2 wpi, fish 1, reverse labeling


title: Bicarb/Wt


title: Heart, 2 wpi, fish 1, direct labeling


title: GenAu MB BCELL v2.5 H3K9ac Rag2-/- 95879

description: Chip-chip Rag2-/- pro-B cells H3K9ac

source_name: H3K9ac ChIP DNA from Rag2-/- pro-B cells

value: 5 days in culture

tag: cell type

tag: antibody

value: ChIP

value: IVT

value: Input


title: transWT 7-day-old seedlings

description:
7D transWT
Gene expression data from 7-day-old transWT seedlings grown under short day conditions.

source_name: 7-day-old seedlings of WT harboring 35S::BoEMF2.1

value: wild type background harboring 35S::BoEMF2.1


title: GenAu MB BCELL v2.5 H3K4me2 Pax5-/- Rag2-/- 96063

source_name: H3K4me2 ChIP DNA from Pax5-/- Rag2-/- pro-B cells

value: pro-B cells

tag: type

value: Upstate


title: WT 7-day-old seedlings

description:
7D WT
Gene expression data from 7-day-old WT seedlings grown under short day conditions.

source_name: 7-day-old seedlings of WT Columbia ecotype

tag: ecotype

value: Columbia

value: wild type background


title: GenAu MB BCELL v2.5 H3K4me3 Rag2-/- 92002

description: Chip-chip Rag2-/- pro-B cells H3K4me3

source_name: H3K4me3 ChIP DNA from Rag2-/- pro-B cells

tag: amplification

tag: antibody  vendor

source_name: Input DNA from Rag2-/- pro-B cells


title: GenAu MB BCELL v2.5 H3K9ac Pax5-/- Rag2-/- 87920

tag: antibody  lot#


title: MRS1814

status: Public on Mar 29 2012

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

description: Biological replicate 1 of 2, technical replicate 3 of 3.

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celsius for 17 h. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on a ScanArray Express microarray scanner (PE). Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: Signals of the scanned slides were corrected for background signal, log2 transformed and subsequently normalised using quantile normalization as described in Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64.

organism: Lactiplantibacillus plantarum WCFS1

source_name: bacterial cells

label_protocol: Annealing Mix x µl RNA preparation (=5µg) y µl nuclease-free water 1 µl Random Nonamers 11 µl TOTAL 1. mix Annealing Mix in a 200 µl PCR tube gently by pipetting up and down 2. incubate for 5' 70°C 3. cool at room temperature for 10' (annealing) 4. spin down the mixture to the bottom of the tube 5. place on ice Reverse transcription Reverse Transcription Mix 4 µl 5x buffer 2 µl 0.1 M DTT 1 µl dNTP-mix 1 µl AA-dUTP 1 µl TMIII (keep only briefly outside 20°C) 20 µl TOTAL 1. Mix by very gently by pipetting up and down (vigorous pipetting will denature the enzyme!) 2. Incubate for 3 hrs at 42°C (in PCR-machine) 3. Cool on ice for immediate purification or place at 20°C for storage Degradation of mRNA 1. Add 2 µl 2,5 M NaOH 2. Mix (vortex) and spin down 3. Incubate for 15 min. at 37°C 4. Add 10 µl 2 M HEPES free acid 5. Mix (vortex) and spin down 6. Ready for purification or store at 20°C Labelling and purification of cDNA with cyanine dyes Followed GE Healthcare kit Amersham CyDye (Cy3/Cy5) Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA and Aminoallyl-aRNA code RPN5661 Labelling of amino allyl-modified cDNA with CyDye 1. Add the amino allyl modified cDNA (in 0.1 M sodium bicarbonate) directly into one aliquot of CyDye NHS Ester. Resuspend the ester completely by pipetting several times and transfer the solution to an amber 1.5 ml tube 2. Incubate at room temperature, in the dark for 60 to 90 minutes 3. Add 15 µl 4 M Hydroxylamine to each coupling reaction 4. Mix by stirring and incubate at room temperature, in the dark, for 15 minutes 5. Proceed directly to purification of CyDye-labelled cDNA Purification of CyDye labelled cDNA Followed GE Healthcare kit Amersham CyDye (Cy3/Cy5) Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA and Aminoallyl-aRNA code RPN5661.

growth_protocol: Cultures were grown in MRS at 37˚C without agitation.

extract_protocol: Cultures were lysed by beat-beating, and total RNA was isolated by subsequent phenol-chloroform extraction.

treatment_protocol: Harvested cultures were immediately pelleted at 4570xg and 4˚C.


title: MRS1812

description: Biological replicate 1 of 2, technical replicate 1 of 3.


title: GenAu MB BCELL v2.5 H3K4me3 Pax5-/- Rag2-/- 91992

description: Chip-chip Pax5-/- Rag2-/- pro-B cells H3K4me3

source_name: H3K4me3 ChIP DNA from Pax5-/- Rag2-/- pro-B cells


title: MRS1813

description: Biological replicate 1 of 2, technical replicate 2 of 3.


title: Aniger_Xylan_rep3

city: Kgs. Lyngby

first: Mikael

middle: R

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

description: Part of a study of transcriptional profiling across six carbon-sources.

hyb_protocol: Affymetrix standard

scan_protocol: As described in Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J. A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4387-92. PMID: 18332432

data_processing: Affymetrix CEL-data files were preprocessed by using the statistical language and environment R (R Development Core Team, 2007) version 2.6.1. The probe intensities were normalized for background by using the robust multiarray average method (Irizarry, 2003) by using only perfect match (PM) probes. Normalization was performed subsequently by using the quantiles algorithm (Bolstad, 2003). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

label: Affymetrix standard

organism: Aspergillus niger

source_name: A. niger mycelium grown on a xylan medium

label_protocol: Affymetrix standard

tag: Strain

tag: Carbon source

value: Xylan

tag: Sample time

value: Mid-exponential phase

tag: Cultivation

value: Shake-flask

tag: Replicate


title: Aniger_GlucoseCarb_rep3

source_name: A. niger mycelium grown on a glucose medium

extract_protocol:
As described in Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J. A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4387-92.
PMID: 18332432

value: Glucose


title: Aniger_Starch_rep2

source_name: A. niger mycelium grown on a starch medium

value: Starch


title: Aniger_XyloseCarb_rep3

source_name: A. niger mycelium grown on a xylose medium

value: Xylose


title: Aniger_XyloseCarb_rep1


title: Aniger_Xylan_rep1


title: Aniger_XyloseCarb_rep2


title: Kdm1a KD 1

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

hyb_protocol: Fragmented and biotin-labeled cDNA was hybridized to GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix, CA) according to manufacturer’s instructions.

scan_protocol: Hybridized arrays were washed using the GeneChip Fluidics Station 450 (Affymetrix) using protocol 001 and scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Exon array data were processed using an R/Bioconductor package, as previously described (Okoniewski and Miller, 2008). Background adjustment, quantile normalization and summarization of probe-level intensity were performed using the robust multi-array average algorithm (Irizarry et al., 2003). 267,824 probesets annotated in Ensembl mouse genome build 56 as “exonic” and not “multitarget”, with their expression values, were extracted in CSV file format. The CSV file was used to calculate “gene level summaries”, which represent the mean expression of all exonic probe sets mapping to each of 23,770 Ensembl annotated genes. The gene-level summaries are available from the Series record as a supplementary file.

Probe group file: MoEx-1_0-st-v1.r2.pgf
Genome build: Ensembl mouse genome build 56

source_name: Murine MLL-AF9 AML cells, Kdm1a KD

label_protocol: RNA quality was confirmed using an Agilent Bioanalyzer (Agilent Technologies, CA) prior to cDNA amplification of 40ng RNA using the Ovation Pico WTA System (NuGEN, CA), according to manufacturer’s instructions. A WT-Ovation Exon Module kit (NuGEN) was used to generate sense transcript cDNA, which was then fragmented and biotin labeled using an Encore Biotin Module kit (NuGEN), according to manufacturer’s instructions.

growth_protocol: For experiments involving viral infection of cryopreserved AML cells, cells were thawed, spinoculated and cultured overnight with viral supernatant containing 5% X63 supernatant.

extract_protocol: RNA was extracted using QIAshredder spin columns and an RNeasy Plus Micro kit (Qiagen, UK).

tag: background/strain

value: Kdm1a KD

value: MLL-AF9 AML cells enriched for leukemia stem cells (LSCs)


title: Aniger_Arabinose_rep3

source_name: A. niger mycelium grown on an arabinose medium

value: Arabinose


title: Aniger_Xylan_rep2


title: Control 3

source_name: Murine MLL-AF9 AML cells, control

value: control


title: Kdm1a KD 3


title: Kdm1a KD 2


title: GenAu MB BCELL v2.5 H3K4me2 Rag2-/- 90982

description: Chip-chip Rag2-/- pro-B cells H3K4me2

source_name: H3K4me2 ChIP DNA from Rag2-/- pro-B cells

tag: age

value: 5 days in culture

tag: strain

value: ChIP

value: IVT

tag: antibody cat#


title: Aniger_GlucoseCarb_rep2


title: Control 2

tag: genotype/variation


title: Aniger_Arabinan_rep3

source_name: A. niger mycelium grown on an arabinan medium

value: Arabinan


title: Aniger_Starch_rep1


title: Aniger_GlucoseCarb_rep1


title: Aniger_Arabinose_rep2


title: Aniger_Arabinan_rep1


title: Aniger_Arabinose_rep1


title: Aniger_Arabinan_rep2


title: Control 1

tag: cell type


title: 24CB-451B

city: Philadelphia

first: Nahid

last: Turan

state: PA

address: 3307 North Broad Street, AHB

department: Fels Institute

institute: Temple University School of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: We used Illumina's GenomeStudio Gene Expression Module v1.0 to obtain our raw expression data. Our paper used different bioinformatics models with the raw unnormalized data.

source_name: Cord Blood

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

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

tag: birth weight (g)

tag: gestational age (wks)

tag: birth weight (%)

tag: tissue

value: cord blood


title: 22CB-422B


title: 23CB-449B


title: 21CB-415B


title: 20AB-342B


title: 19CB-409B


title: 24AB-429B


title: 20CB-414B


title: 22AB-390B


title: 19AB-335B


title: 18CB-400B


title: 17AB-271B


title: 15CB-351B


title: 21AB-347B


title: 16AB-172B


title: 15AB-168B


title: 17CB-397B


title: 11CB-295B


title: 16CB-394B


title: 18AB-329B


title: 11AB-135B


title: 13AB-162B


title: 13CB-307B


title: 12CB-299B


title: 14CB-349B


title: 12AB-151B


title: 10AB-104B


title: 10CB-290B


title: 14AB-166B


title: 9CB-273B


title: 7AB-A14B


title: 8AB-101B


title: 23AB-399B


title: 6CB-178B


title: 5AB-A12B


title: 4CB-C30B


title: 6AB-A13B


title: 3CB-C24B


title: 7CB-184B


title: 4AB-A9B


title: 8CB-211B


title: 2AB-A3B


title: 5CB-159B


title: 1CB-C11B


title: 20CP-414P

source_name: Placenta

value: placenta


title: 23CP-449P


title: 24CP-451P


title: 22CP-422P


title: 23AP-399P


title: 1AB-A1B


title: 3AB-A7B


title: 2CB-C18B


title: 19AP-335P


title: 24AP-429P


title: 20AP-342P


title: 19CP-409P


title: 21CP-415P


title: 22AP-390P


title: 18CP-400P


title: 21AP-347P


title: 17CP-397P


title: 17AP-271P


title: 18AP-329P


title: 16CP-394P


title: 16AP-172P


title: 15CP-351P


title: 14CP-349P


title: Newborn placenta gDNA for sample_Y9_b

description: replicate 2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina's GoldenGate Methylation Assay using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadExpress scanner using standard recommended Illumina scanner setting

data_processing: GenomeStudio software

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

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

value: Placenta


title: 13CP-307P


title: Newborn placenta gDNA for sample_Y9_a

description: replicate 1


title: 14AP-166P


title: Newborn cord blood gDNA for sample_Y9_a

description: replicate 1

value: Cord Blood


title: Newborn placenta gDNA for sample_X23_b

description: replicate 2


title: Newborn cord blood gDNA for sample_Y9_b

description: replicate 2


title: Newborn placenta gDNA for sample_X23_a

description: replicate 1


title: 15AP-168P


title: 12CP-299P


title: Newborn cord blood gDNA for sample_X23_b

description: replicate 2


title: 13AP-162P


title: Newborn placenta gDNA for sample_Y16B_b

description: replicate 2


title: 10CP-290P


title: 11CP-295P


title: 11AP-135P


title: 12AP-151P


title: Newborn cord blood gDNA for sample_Y16B_b

description: replicate 2


title: Newborn cord blood gDNA for sample_X23_a

description: replicate 1


title: Newborn placenta gDNA for sample_Y2A_b

description: replicate 2


title: 10AP-104P


title: Newborn cord blood gDNA for sample_Y16B_a

description: replicate 1


title: Newborn placenta gDNA for sample_Y16B_a

description: replicate 1


title: Newborn cord blood gDNA for sample_Y2A_b

description: replicate 2


title: Newborn placenta gDNA for sample_Y2A_a

description: replicate 1


title: 8AP-101P


title: 9AP-102P


title: 9CP-273P


title: Newborn placenta gDNA for sample_X22_b

description: replicate 2


title: 7AP-A14P


title: 6CP-178P


title: Newborn cord blood gDNA for sample_Y2A_a

description: replicate 1


title: 7CP-184P


title: Newborn placenta gDNA for sample_X22_a

description: replicate 1


title: 8CP-211P


title: Newborn cord blood gDNA for sample_X22_a

description: replicate 1


title: Newborn cord blood gDNA for sample_X22_b

description: replicate 2


title: Newborn placenta gDNA for sample_Y16A_b

description: replicate 2


title: Newborn placenta gDNA for sample_Y16A_a

description: replicate 1


title: Newborn cord blood gDNA for sample_Y16A_b

description: replicate 2


title: Newborn cord blood gDNA for sample_Y16A_a

description: replicate 1


title: 3CP-C24P


title: 6AP-A13P


title: 4CP-C30P


title: 5CP-159P


title: 2AP-A3P


title: 4AP-A9P


title: 1CP-C11P


title: Newborn cord blood gDNA for sample_Y1_b

description: replicate 2


title: 451P_genomic placenta DNA sample

description: placenta DNA

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

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

data_processing: BeadStudio software v3.2

source_name: placenta sample 24CB-451B

extract_protocol: Genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions. The Zymo Bisulphite Conversion Kit was used to convert the DNA samples.


title: Newborn placenta gDNA for sample_Y1_a

description: replicate 1


title: Newborn placenta gDNA for sample_Y1_b

description: replicate 2


title: 415P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 23CB-449B


title: 2CP-C18P


title: 3AP-A7P


title: Newborn cord blood gDNA for sample_Y1_a

description: replicate 1


title: 9AB-102B


title: Newborn placenta gDNA for sample_X21_b

description: replicate 2


title: Newborn placenta gDNA for sample_Y15_b

description: replicate 2


title: 178P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 18CB-400B


title: 273P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 19CB-409B


title: Newborn cord blood gDNA for sample_X21_a

description: replicate 1


title: 5AP-A12P


title: Newborn cord blood gDNA for sample_Y15_a

description: replicate 1


title: 299P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 20CB-414B


title: Newborn cord blood gDNA for sample_Y15_b

description: replicate 2


title: Newborn placenta gDNA for sample_Y15_a

description: replicate 1


title: 449P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 16CB-394B


title: 351P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 21CB-415B


title: Newborn placenta gDNA for sample_X21_a

description: replicate 1


title: Newborn cord blood gDNA for sample_X21_b

description: replicate 2


title: 414P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 15CB-351B


title: C24P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 17CB-397B


title: 349P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 13CB-307B


title: Newborn cord blood gDNA for sample_X34_a

description: replicate 1


title: Newborn placenta gDNA for sample_X34_b

description: replicate 2


title: Newborn placenta gDNA for sample_X34_a

description: replicate 1


title: Newborn placenta gDNA for sample_X18_a

description: replicate 1


title: 400P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 22CB-422B


title: 1AP-A1P


title: 397P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 14CB-349B


title: 159P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 10CB-290B


title: 422P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 8CB-211B


title: 295P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 12CB-299B


title: Newborn cord blood gDNA for sample_X18_b

description: replicate 2

source_name: Cord Blood


title: Newborn cord blood gDNA for sample_X18_a

description: replicate 1


title: Newborn placenta gDNA for sample_X32_a

description: replicate 1

source_name: Placenta


title: 307P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 5CB-159B


title: 394P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 6CB-178B


title: 409P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 7CB-184B


title: 211P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 11CB-295B


title: Newborn placenta gDNA for sample_X32_b

description: replicate 2


title: Newborn cord blood gDNA for sample_Y14_b

description: replicate 2


title: Newborn cord blood gDNA for sample_Y14_a

description: replicate 1


title: Newborn placenta gDNA for sample_Y14_b

description: replicate 2


title: C18P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 9CB-273B


title: C11P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 1CB-C11B


title: C30P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 2CB-C18B


title: 347P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 23AB-399B


title: 184P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 3CB-C24B


title: 429P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 24AB-429B


title: 329P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 22AB-390B


title: Newborn placenta gDNA for sample_Y14_a

description: replicate 1


title: 168P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 21AB-347B


title: 290P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 4CB-C30B


title: Newborn cord blood gDNA for sample_X32_b

description: replicate 2


title: Newborn cord blood gDNA for sample_X32_a

description: replicate 1


title: Newborn placenta gDNA for sample_X14_a

description: replicate 1


title: A13P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 18AB-329B


title: Newborn cord blood gDNA for sample_X14_b

description: replicate 2


title: 102P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 19AB-335B


title: 151P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 20AB-342B


title: A7P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 17AB-271B


title: Newborn cord blood gDNA for sample_X14_a

description: replicate 1

source_name: Cord Blood


title: Newborn placenta gDNA for sample_X14_b

description: replicate 2

source_name: Placenta


title: Newborn placenta gDNA for sample_Y12_b

description: replicate 2


title: Newborn cord blood gDNA for sample_X27_b

description: replicate 2


title: Newborn placenta gDNA for sample_Y12_a

description: replicate 1


title: Newborn cord blood gDNA for sample_X27_a

description: replicate 1


title: Newborn placenta gDNA for sample_X27_a

description: replicate 1


title: Newborn cord blood gDNA for sample_Y12_a

description: replicate 1


title: Newborn placenta gDNA for sample_X27_b

description: replicate 2


title: 399P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 16AB-172B


title: 101P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 11AB-135B


title: 271P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 14AB-166B


title: A12P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 10AB-104B


title: 342P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 15AB-168B


title: Newborn placenta gDNA for sample_X9_a

description: replicate 1


title: Newborn placenta gDNA for sample_X9_b

description: replicate 2


title: 335P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 7AB-A14B


title: 135P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 12AB-151B


title: Newborn cord blood gDNA for sample_Y12_b

description: replicate 2


title: A3P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 9AB-102B


title: 390P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 8AB-101B


title: 166P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 13AB-162B


title: Newborn cord blood gDNA for sample_X9_b

description: replicate 2


title: Newborn cord blood gDNA for sample_X9_a

description: replicate 1


title: 172P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 6AB-A13B


title: 104P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 4AB-A9B


title: Newborn placenta gDNA for sample_Y11A_b

description: replicate 2


title: A14P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 3AB-A7B


title: 162P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 5AB-A12B


title: Newborn placenta gDNA for sample_Y11A_a

description: replicate 1


title: Newborn cord blood gDNA for sample_Y11A_b

description: replicate 2


title: Newborn cord blood gDNA for sample_Y11A_a

description: replicate 1


title: A1P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 1AB-A1B


title: A9P_genomic placenta DNA sample

description: placenta DNA

source_name: placenta sample 2AB-A3B


title: Newborn placenta gDNA for sample_X26_b

description: replicate 2

source_name: Placenta


title: Newborn placenta gDNA for sample_X26_a

description: replicate 1


title: Newborn placenta gDNA for sample_X6_b

description: replicate 2


title: Newborn cord blood gDNA for sample_X26_a

description: replicate 1

source_name: Cord Blood


title: genomic DNA from cord blood sample 23CB-449B

description:
Cord Blood DNA
23CB-449B

source_name: cord blood sample 23CB-449B


title: Newborn cord blood gDNA for sample_X26_b

description: replicate 2


title: genomic DNA from cord blood sample 22CB-422B

description:
Cord Blood DNA
22CB-422B

source_name: cord blood sample 22CB-422B


title: genomic DNA from cord blood sample 24CB-451B

description:
Cord Blood DNA
24CB-451B

source_name: cord blood sample 24CB-451B


title: Newborn cord blood gDNA for sample_X6_b

description: replicate 2


title: Sensitive-Drought_rep3

city: Lucknow

first: Samir

middle: V

last: Sawant

state: UP

address: Rana Pratap Marg

department: Plant Molecular Biology

country: India

institute: CSIR-NBRI

description: Gene expression data from root tissue under drought condition of drought sensitive genotype

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

scan_protocol: GeneChips were scanned using the Gene chip scanner 3000.

data_processing: The data were analyzed with MAS5.

organism: Gossypium herbaceum

source_name: Root tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual,  Affymetrix).

growth_protocol: The seeds of both genotype (Gossypium herbaceum)  were sown for germination in mixture of solarite, vermiculite, garden soil and sand soil (1:1:1:1 ratio). After germination of seeds, plants were grown  for four week in glass house at 28±2 oC and 16/8 h of light and dark photoperiod respectively.

extract_protocol: Total RNA  was isolated from Spectrum plant total RNA isolation  Kit (Sigma-Aldrich) according to the manufacturer’s instructions.

treatment_protocol: Drought stress was given to potted plants by withholding water to maintain the soil moisture always less than 30%. The drought treated plants were watered only once in every alternate week while the control pots were irrigated daily. A total 12 plants were grown in earthen pots, including six plants from each genotype. Drought stress, was given to plants by withhold watering in six pots including three from both accession. The drought treatment was given till the visible differences became apparent. Remaining six pots including three pots from both genotype were watered normally and considered as control

tag: genotype

value: Sensitive to drought stress

value: one month old plants

value: root

tag: stress

value: drought


title: Tolerant-Drought_rep3

description: Gene expression data from root tissue under drought condition of drought tolerant genotype

value: Tolerant to drought stress


title: Tolerant-Water_rep3

description: Gene expression data from root tissue under water condition of drought tolerant genotype


title: genomic DNA from cord blood sample 21CB-415B

description:
Cord Blood DNA
21CB-415B

source_name: cord blood sample 21CB-415B


title: Tolerant-Water_rep2


title: Tolerant-Drought_rep1


title: Sensitive-Drought_rep2


title: Sensitive-Water_rep3

description: Gene expression data from root tissue under water condition of drought sensitive genotype


title: Sensitive-Water_rep2


title: Tolerant-Water_rep1


title: Tolerant-Drought_rep2


title: Sensitive-Drought_rep1


title: genomic DNA from cord blood sample 20CB-414B

description:
Cord Blood DNA
20CB-414B

source_name: cord blood sample 20CB-414B


title: genomic DNA from cord blood sample 18CB-400B

description:
Cord Blood DNA
18CB-400B

source_name: cord blood sample 18CB-400B


title: Sensitive-Water_rep1


title: genomic DNA from cord blood sample 19CB-409B

description:
Cord Blood DNA
19CB-409B

source_name: cord blood sample 19CB-409B


title: Newborn placenta gDNA for sample_X6_a

description: replicate 1


title: genomic DNA from cord blood sample 16CB-394B

description:
Cord Blood DNA
16CB-394B

source_name: cord blood sample 16CB-394B


title: wild-type liver_ZT20_rep 2

city: La Jolla

first: Ruth

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute

description:
6033102053-H
technical replicate 2

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

source_name: wild-type liver_ZT20

tag: background strain

value: Reverbalpha/beta Alb Cre-

value: wild-type

tag: gender

value: male

value: 20 week-old

value: liver


title: Newborn cord blood gDNA for sample_X34_b

description: replicate 2


title: genomic DNA from cord blood sample 17CB-397B

description:
Cord Blood DNA
17CB-397B

source_name: cord blood sample 17CB-397B


title: Newborn placenta gDNA for sample_Y10A_b

description: replicate 2


title: Newborn cord blood gDNA for sample_Y10A_b

description: replicate 2


title: Newborn placenta gDNA for sample_Y10A_a

description: replicate 1


title: Newborn cord blood gDNA for sample_X6_a

description: replicate 1


title: Newborn cord blood gDNA for sample_Y10A_a

description: replicate 1


title: Newborn placenta gDNA for sample_X18_b

description: replicate 2


title: wild-type liver_ZT16_rep 2

description:
6033102053-F
technical replicate 2

source_name: wild-type liver_ZT16


title: genomic DNA from cord blood sample 15CB-351B

description:
Cord Blood DNA
15CB-351B

source_name: cord blood sample 15CB-351B


title: wild-type liver_ZT20_rep 1

description:
6033102053-G
technical replicate 1


title: Newborn placenta gDNA for sample_X24_b

description: replicate 2


title: Newborn placenta gDNA for sample_X24_a

description: replicate 1


title: wild-type liver_ZT12_rep 2

description:
6033102053-D
technical replicate 2

source_name: wild-type liver_ZT12


title: wild-type liver_ZT16_rep 1

description:
6033102053-E
technical replicate 1


title: genomic DNA from cord blood sample 14CB-349B

description:
Cord Blood DNA
14CB-349B

source_name: cord blood sample 14CB-349B


title: genomic DNA from cord blood sample 11CB-295B

description:
Cord Blood DNA
11CB-295B

source_name: cord blood sample 11CB-295B


title: genomic DNA from cord blood sample 12CB-299B

description:
Cord Blood DNA
12CB-299B

source_name: cord blood sample 12CB-299B


title: wild-type liver_ZT12_rep 1

description:
6033102053-C
technical replicate 1


title: Newborn cord blood gDNA for sample_X24_a

description: replicate 1

source_name: Cord Blood


title: Newborn cord blood gDNA for sample_X24_b

description: replicate 2


title: wild-type liver_ZT8_rep 1

description:
6033102053-A
technical replicate 1

source_name: wild-type liver_ZT8


title: genomic DNA from cord blood sample 10CB-290B

description:
Cord Blood DNA
10CB-290B

source_name: cord blood sample 10CB-290B


title: TEPM-6h LPS-rep3

city: Brisbane

first: Kate

last: Schroder

state: QLD

address: University of Queensland, St Lucia

institute: Institute for Molecular Bioscience

description: TEPM-6h LPS-rep3

hyb_protocol: Samples were hybridised according to Agilent's One-colour Microarray-Based Gene Expression Analysis (Quick Amp Labelling) protocol, V5.7 March 2008.

scan_protocol: Samples were scanned according to Agilent's One-colour Microarray-Based Gene Expression Analysis (Quick Amp Labelling) protocol, V5.7 March 2008, using an Agilent Microarray Scanner G2565BA.

data_processing: Features (including processed signal and flags) were extracted using the Feature Extraction 9.5.3 (Agilent Technologies) software, with default settings and no background subtraction. Processed signal intensities were quantile normalized in R using the Affymetrix package in Bioconductor.

source_name: Mouse thioglycollate-elicited peritoneal macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 6h

label_protocol: Labelling was performed using the Agilent Quick-Amp Labelling Kit (one colour) according to manufacturer's instructions.

growth_protocol: BMM were derived from femurs of 6-8 week-old, male C57Bl/6 mice. Femurs were flushed with medium and bone marrow cells were plated out in complete medium (RPMI 1640 containing 10% FCS, 20U/ml penicillin, 20 µg/ml streptomycin and 2mM L-glutamine) supplemented with 104U/ml (100ng/ml) recombinant human CSF-1 (Chiron) on bacteriological plastic plates (Bibby Sterilin) for 7 days, with refeeding on day 5 and reseeding on day 6 at 1x105 cells/cm2. TEPM were elicited by injecting 6-8 week-old male, mice with 1ml sterile thioglycollate broth (10% in pyrogen-free water, Becton Dickinson) intraperitoneally. 5 days post-injection, peritoneal cells were collected by PBS lavage, plated on tissue culture plastic as for BMM in media without CSF-1 and stimulated the following day. >90% TEPM were F4/80+ macrophages, as assessed by surface staining and flow cytometry (not shown). All cells were cultured at 37˚C with 5% CO2.

extract_protocol: Total RNA was prepared using the Qiagen RNeasy Mini kit with on-column DNaseI treatment, according to the manufacturer’s instructions.

treatment_protocol: BMM and TEPM were treated for various times with lipopolysaccharide (LPS) from Salmonella minnesota (Sigma-Aldrich), at a final concentration of 10 ng/ml.

value: peritoneal

value: macrophages

tag: treatment

value: LPS

tag: treatment time

value: 6 hours


title: genomic DNA from cord blood sample 9CB-273B

description:
Cord Blood DNA
9CB-273B

source_name: cord blood sample 9CB-273B


title: wild-type liver_ZT4_rep 2

description:
6033102043-H
technical replicate 2

source_name: wild-type liver_ZT4


title: genomic DNA from cord blood sample 13CB-307B

description:
Cord Blood DNA
13CB-307B

source_name: cord blood sample 13CB-307B


title: TEPM-2h LPS-rep3

description: TEPM-2h LPS-rep3

source_name: Mouse thioglycollate-elicited peritoneal macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 2h

value: 2 hours


title: TEPM-23h LPS-rep3

description: TEPM-23h LPS-rep3

source_name: Mouse thioglycollate-elicited peritoneal macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 24h

value: 24 hours


title: TEPM-0h LPS-rep3

description: TEPM-0h LPS-rep3

source_name: Mouse thioglycollate-elicited peritoneal macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 0h

value: untreated

value: 0 hours


title: TEPM-22h LPS-rep2

description: TEPM-22h LPS-rep2


title: wild-type liver_ZT4_rep 1

description:
6033102043-G
technical replicate 1


title: genomic DNA from cord blood sample 8CB-211B

description:
Cord Blood DNA
8CB-211B

source_name: cord blood sample 8CB-211B

value: Cord Blood


title: Newborn placenta gDNA for sample_X5_b

description: replicate 2

source_name: Placenta

value: Placenta


title: genomic DNA from cord blood sample 7CB-184B

description:
Cord Blood DNA
7CB-184B

source_name: cord blood sample 7CB-184B


title: Newborn placenta gDNA for sample_X5_a

description: replicate 1


title: Newborn cord blood gDNA for sample_X5_b

description: replicate 2


title: TEPM-6h LPS-rep2

description: TEPM-6h LPS-rep2


title: wild-type liver_ZT0_rep 2

description:
6033102043-F
technical replicate 2

source_name: wild-type liver_ZT0


title: wild-type liver_ZT8_rep 2

description:
6033102053-B
technical replicate 2


title: TEPM-2h LPS-rep2

description: TEPM-2h LPS-rep2


title: Reverb alpha/beta DKO liver_ZT20_rep 2

description:
6033102043-D
technical replicate 2

source_name: Reverb alpha/beta DKO liver_ZT20

value: Reverbalpha/beta Alb Cre+

value: Reverb alpha/beta DKO


title: genomic DNA from cord blood sample 6CB-178B

description:
Cord Blood DNA
6CB-178B

source_name: cord blood sample 6CB-178B


title: wild-type liver_ZT0_rep 1

description:
6033102043-E
technical replicate 1

value: Reverbalpha/beta Alb Cre-


title: TEPM-0h LPS-rep2

description: TEPM-0h LPS-rep2


title: Reverb alpha/beta DKO liver_ZT20_rep 1

description:
6033102043-C
technical replicate 1


title: TEPM-21h LPS-rep1

description: TEPM-21h LPS-rep1


title: genomic DNA from cord blood sample 3CB-C24B

description:
Cord Blood DNA
3CB-C24B

source_name: cord blood sample 3CB-C24B


title: Reverb alpha/beta DKO liver_ZT16_rep 2

description:
6033102043-B
technical replicate 2

source_name: Reverb alpha/beta DKO liver_ZT16


title: genomic DNA from cord blood sample 4CB-C30B

description:
Cord Blood DNA
4CB-C30B

source_name: cord blood sample 4CB-C30B


title: genomic DNA from cord blood sample 5CB-159B

description:
Cord Blood DNA
5CB-159B

source_name: cord blood sample 5CB-159B


title: Newborn cord blood gDNA for sample_X5_a

description: replicate 1

source_name: Cord Blood


title: TEPM-2h LPS-rep1

description: TEPM-2h LPS-rep1


title: Reverb alpha/beta DKO liver_ZT12_rep 2

description:
6033102040-H
technical replicate 2

source_name: Reverb alpha/beta DKO liver_ZT12


title: TEPM-6h LPS-rep1

description: TEPM-6h LPS-rep1

source_name: Mouse thioglycollate-elicited peritoneal macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 6h


title: genomic DNA from cord blood sample 1CB-C11B

description:
Cord Blood DNA
1CB-C11B

source_name: cord blood sample 1CB-C11B


title: BMM-6h LPS-rep3

description: BMM-6h LPS-rep3

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 6h

value: bone marrow


title: genomic DNA from cord blood sample 2CB-C18B

description:
Cord Blood DNA
2CB-C18B

source_name: cord blood sample 2CB-C18B


title: BMM-24h LPS-rep3

description: BMM-24h LPS-rep3

source_name: Mouse bone marrow-derived macrophages stimulated with 10ng/ml S. minnesota lipopolysaccharide for 24h

value: male


title: Reverb alpha/beta DKO liver_ZT8_rep 2

description:
6033102040-F
technical replicate 2

source_name: Reverb alpha/beta DKO liver_ZT8

value: 20 week-old