title: G1E-ER-GATA-1 - Control siRNA - Replicate 3 of 3

city: Madison

first: Andrew

last: DeVilbiss

state: WI

address: 1111 Highland Ave, WIMR 4028

department: Cell and Regenerative Biology

institute: UW-Madison

description: Control 3

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer (HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Sureprint G3 Mouse GE 8x60 Microarray (GPL13912), 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), both containing 0.005% Triton X-102Slides were air dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the 8x60K G3 one color Microarray format. Dye channel is green, scan area 61x21.65 mm, scan resolution 3 um, Tiff is 20 bit.

data_processing: Agilent Feature Extraction software used to generate gProcessed Signals.  Data was processed using Edge3 one color limma differential expression analysis. FDR = 10%

source_name: G1E-ER-GATA-1 - Control siRNA

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

growth_protocol: G1E-ER-GATA-1 cells were maintained at a density of 0.5x10^6 cells / ml in IMDM (Gibco) containing 15% FBS (Gemini) 1% penicillin-streptomycin (Gemini), 2 U/ml erythropoietin, 120 nM monothioglycerol (Sigma), 0.6% conditioned medium from a Kit ligand-producing CHO cell line, and 1mg/ml puromycin (Gemini).

extract_protocol: Total RNA from 1 million G1E-ER-GATA-1 cells was isolated using Trizol (Invitrogen). RNA was purified using Rneasy Micro Kit (Qiagen), per manufacture instructions.

treatment_protocol: 3x10^6 cells were transfected at 0 h and 24 h with 240nmol siRNA (non-targeting or Mi2ß-specific) using an Amaxa Nucleofector II system, along with Lonza kit R. At 24 h, cells were treated with 1mm ß-estradiol. Cells were harvested for RNA extraction at 48 h.

tag: cell line

tag: genotype/variation

value: control

value: 24 h ß-estradiol treatment


title: SECONDTMAF_CON_sample_17_

status: Public on Jul 04 2013

type: RNA

city: Medford

first: Heather

middle: C

last: Wick

state: MA

address: 161 College Ave

department: Department of Computer Science

country: USA

institute: Tufts University

description: gene expression data from normal term fetus

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  To obtain detection calls consistent with those produced by Affymetrix 5.0 software, we used the mas5calls function from the Bioconductor affy package.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: AF cell free mRNA from second trimester fetus of lean mother

label_protocol: Samples were labeled using the Encore Biotin Module (NuGEN, San Carlos, CA)

extract_protocol: RNA was extracted from 5-30 mL AF supernatant.All samples were processed using the Qiagen Circulating Nucleic Acid kit with an on-column DNase digestion step to remove genomic DNA. The RNA was then purified and concentrated with the RNeasy MinElute Clean up kit and eluted in RNasefree water. RNA was converted to cDNA and amplified using the Ovation Pico WTA kit V2 and then purified with the QIAquick PCR Purification kit.

tag: gestational age

tag: fetal sex

value: F

tag: maternal bmi


title: SECONDTMAF_OB_sample_6_

description: gene expression data from  fetus with TTTS

source_name: AF cell free mRNA from second trimester fetus of obese mother

value: M


title: SECONDTMAF_CON_sample_15_


title: SECONDTMAF_OB_sample_2_


title: SECONDTMAF_OB_sample_7_


title: SECONDTMAF_OB_sample_9_


title: G1E-ER-GATA-1 - Mi2ß siRNA - Replicate 3 of 3

description: siMi2ß 3

organism: Mus musculus

source_name: G1E-ER-GATA-1 - Mi2ß siRNA

value: Mi2ß knockdown

tag: treatment


title: G1E-ER-GATA-1 - Control siRNA - Replicate 2 of 3

description: Control 2


title: SECONDTMAF_CON_sample_4_


title: G1E-ER-GATA-1 - Mi2ß siRNA - Replicate 1 of 3

description: siMi2ß 1


title: SECONDTMAF_OB_sample_3_


title: G1E-ER-GATA-1 - Mi2ß siRNA - Replicate 2 of 3

description: siMi2ß 2


title: SECONDTMAF_OB_sample_5_


title: SECONDTMAF_CON_sample_5_

description: gene expression data from normal second trimester fetus


title: SECONDTMAF_CON_sample_20_


title: SECONDTMAF_OB_sample_1_


title: SECONDTMAF_CON_sample_11_


title: A549_Nrf2 siRNA_biological rep2

city: Worcester

first: George

last: Acquaah-Mensah

address: 19 Foster Street

institute: MASS COLLEGE OF PHARM HEALTH SCIENCES

description: Gene expression data from A549 cells transfected with siRNA targeting Nrf2 mRNA

hyb_protocol: Approximately 12.5 g of fragmented cRNA was used in a 250- l hybridization mixture containing herring sperm DNA (0.1 mg/ml; Promega Corp., Madison, WI), plus bacterial and phage cRNA controls (1.5 pmol of BioB, 5 pmol of BioC, 25 pmol of BioD, and 100 pmol of Cre) to serve as internal controls for hybridization efficiency as directed by the manufacturer (Affymetrix). Aliquots (200 l) of the mixture were hybridized onto the array for 18 h at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix)

scan_protocol: Each array was scanned with the GeneArray scanner (Agilent Technologies, Palo Alto, CA) to obtain image and signal intensities.

data_processing: R/Bioconductor using RMA

source_name: Human lung adenocarcinoma cells_Nrf2 siRNA transfected

label_protocol: Briefly, double-stranded cDNA was synthesized from 15 g of total RNA with SuperScript Choice System (Invitrogen) by using oligo(dT)24 primers with a T7 RNA polymerase promoter site added to its 3 end (Genset Corp., La Jolla, CA). The isolated cDNA was then labeled to generate biotinylated cRNA in vitro and amplified using the BioArray T7 RNA polymerase labeling kit (Enzo, Farmingdale, NY).

growth_protocol: A549 cells were cultured in Dulbecco's Modified Eagle Medium with high glucose, 10% FBS and 1% penicillin/ streptomycin

extract_protocol: Total RNA was isolated using TRIZOL reagent. RNA was further purified using RNeasy kit from Qiagen, quantified. Quality of RNA was evaluated using Bio-analyzer.

treatment_protocol: For transfection, cells were plated in 10cm tissue culture dishes. Next day, medium was replaced with fresh growth media without antibiotics. Cells were transfected with NS siRNA(25nM) or Nrf2 siRNA(25nM) using Lipofectamine 2000 transfection reagent. Ninty six hours post transfection, cells were harvested and total RNA was isolated.

tag: cell type

value: Lung adenocarcinoma


title: A549_NS siRNA_biological rep3

description: Gene expression data from A549 cells transfected with non-targeting NS siRNA (control siRNA)

source_name: Human lung adenocarcinoma cells_Non targeting (NS) siRNA transfected


title: SECONDTMAF_CON_sample_19_


title: A549_Mock_biological rep3

description: Gene expression data from A549 cells treated with Transfection reagent alone

source_name: Human lung adenocarcinoma cells_mock transfected


title: A549_Nrf2 siRNA_biological rep3


title: A549_Nrf2 siRNA_biological rep1


title: A549_NS siRNA_biological rep1


title: A549_Mock_biological rep2


title: A549_Mock_biological rep1


title: G1E-ER-GATA-1 - Control siRNA - Replicate 1 of 3

description: Control 1


title: Bone marrow 72 clone HIGH

city: Toulouse

first: Nicolas

last: Espagnolle

address: Bâtiment INCERE 4 bis, avenue Hubert Curien

country: France

institute: STROMALab, Université de Toulouse, CNRS  ERL5311, EFS, INP-ENVT, Inserm U1031, UPS, Toulouse, France

description:
MoPur72 HIGH
Gene expression data from human cultivated bone marrow-derived MSC during 28 days.

hyb_protocol: Hybridized on GeneChip HuGene 1.0 ST oligonucleotide microarrays (Affymetrix).

scan_protocol: GeneChip scanner 3000 and software AGCC.

data_processing: Expression signal values and P-values were obtained for each probe set by use of Partek Genomics suite (Partek) by the Robust Multichip Averaging algorithm in normalization. Principal component and gene expression analysis involved use of MeV.

source_name: MSC clone after 28 days of culture, CD146High

label_protocol: Biotinylated cRNA was amplified by the small sample labelling protocol (two cycle amplification kit, Affymetrix).

growth_protocol: MSC non-clonal or clonal were cultivated with aMEM (minimum essential medium) + 10% FCS (fetal calf serum) + 10µg/ml ciprofloxacin during 21 and 28 days, respectively.

extract_protocol: Use of RNeasy kit (Qiagen). RNA purity and integrity were checked by use of Bioanalyzer 2100 (Agilent).

treatment_protocol: No treatment.

value: cultivated bone marrow-derived mesenchymal stem cells

tag: surface cd146

value: high

tag: donor


title: Bone marrow 122 clone HIGH

description:
MoPur122 HIGH
Gene expression data from human cultivated bone marrow-derived MSC during 28 days.


title: Day5_MN+iCdx2+FGF_rep3

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: ES to Motor Neuron differentiation, Day5 motor neurons caudalized with iCdx2 and FGF

hyb_protocol: RNA was hybridized to Affymetrix Mouse Genome 430 2.0 microarrays.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000.

data_processing: Data analysis was carried out using the affylmGUI BioConductor package. GCRMA normalization was performed across all arrays, followed by linear model fitting using Limma. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple hypothesis testing using Benjamini & Hochberg’s method and setting thresholds of p<0.001 and a fold-change of at least 2.

label_protocol: RNA was amplified using NuGen Ovation amplification and labeling kit according to manufacturer’s instructions

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described.  Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x10^5 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0).  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). On Day 3, cultures were treated with Doxycycline (Dox)  (2 µg/ml) for 6 to 8 hours. Cultures were collected, washed with PBS, and treated with 100 nM RA, 100 ng/ml bFGF (PeproTech), and 100 nM Hh agonist and medium was changed on Day 5. For ChIP experiments, the same conditions were used but scaled to seed 1x10^7 cells on Day 0.

extract_protocol: RNA was extracted with Qiagen RNAeasy at different time points following manufacturer’s instructions.

treatment_protocol: Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). 2ug/ml Doxycycline (Sigma) and 100 ng/ml bFGF (PeproTech) were added to the culture medium on Day 3  when required.

tag: cell-line

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible Cdx2-V5 construct

tag: cell-treatment

value: +RA +Hh +Dox +FGF

tag: time


title: Bone marrow 44 clone LOW

description:
MoPur 44 LOW
Gene expression data from human cultivated bone marrow-derived MSC during 28 days.

source_name: MSC clone after 28 days of culture, CD146Low

value: low


title: Bone marrow 122 clone LOW

description:
MoPur 122 LOW
Gene expression data from human cultivated bone marrow-derived MSC during 28 days.


title: Bone marrow 44 clone HIGH

description:
MoPur44 HIGH
Gene expression data from human cultivated bone marrow-derived MSC during 28 days.


title: Bone marrow 72 clone LOW

description:
MoPur72 LOW
Gene expression data from human cultivated bone marrow-derived MSC during 28 days.


title: Bone marrow 122 non-clonal

description:
MoPur122 NC
Gene expression data from human cultivated bone marrow-derived MSC during 21 days.

source_name: MSC non-clonal after 21 days of culture


title: Bone marrow 100 clone HIGH

description:
MoPur100 HIGH
Gene expression data from human cultivated bone marrow-derived MSC during 28 days.


title: Bone marrow 100 non-clonal

description:
MoPur100 NC
Gene expression data from human cultivated bone marrow-derived MSC during 21 days.


title: Day5_MN+iCdx2+FGF_rep2

source_name: ES to Motor Neuron differentiation, Day5 motor neurons caudalized with iCdx2 and FGF


title: Bone marrow 100 clone LOW

description:
MoPur 100 LOW
Gene expression data from human cultivated bone marrow-derived MSC during 28 days.


title: Bone marrow 44 non-clonal

description:
MoPur44 NC
Gene expression data from human cultivated bone marrow-derived MSC during 21 days.


title: Day5_MN_rep3

description: ES to Motor Neuron differentiation, Day5 motor neurons

value: +RA +Hh

value: motor neurons


title: Day5_MN+iCdx2+FGF_rep1

value: motor neurons caudalized with iCdx2 and FGF


title: Day0_rep1

description: ES to Motor Neuron differentiation, Day0

value: ES cells


title: Day5_MN_rep1

source_name: ES to Motor Neuron differentiation, Day5 motor neurons


title: Bone marrow 72 non-clonal

description:
MoPur72 NC
Gene expression data from human cultivated bone marrow-derived MSC during 21 days.


title: Day0_rep3

source_name: ES to Motor Neuron differentiation, Day0


title: Day5_MN_rep2


title: Day0_rep2


title: A549_NS siRNA_biological rep2

description: Gene expression data from A549 cells transfected with non-targeting NS siRNA (control siRNA)


title: HBG3_Day7_H3K4me3_r1

type: genomic

description: H3K4me3 ChIP-chip timeseries during ES to motor neuron differentiation Day7

hyb_protocol: Labeled DNA samples were co-hybridized to custom Agilent DNA microarrays using the Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent, 5188-5220) at 65°C for approximately 16 hours.  Arrays were washed according to previously published protocols (http://jura.wi.mit.edu/young_public/hESregulation/ChIP.html).

scan_protocol: Arrays were scanned at dual PMT intensities (10% and 100%) at a 5um resolution using an Agilent microarray scanner. Data from the two array scans were combined and extracted using the Agilent Feature Extraction software.

data_processing: Feature extraction was performed with Agilent Feature Extraction software. Background subtracted values were normalized with (1) median normalization, (2) line fitting normalization, (3) quantile normalization; all normalization code was implemented in SQL as part of our in-house microarray database.  Median normalization accounts for differences in the amount of dye hybridized between the two channels.  This normalization multiplied IP intensities by median(control)/median(IP) such that the median intensity of the two channels is the same. Line fitting normalization is similar to Loess normalization but with a simpler model; it assumes that the bulk of the data should fall along the line y=x.  Line fitting performed linear regression on the IP values as a function of the control and then rotated the datapoints such that the resulting line had slope one and intercept zero; this transformation is performed in log space. Finally, in order to allow comparison of probe intensities across time-points, arrays were quantile normalized.

molecule: genomic DNA

source_name: H3K4me3 ChIP DNA from ES to motor neuron differentiation Day7

label_protocol: Amplified DNA was labeled with a BioPrime CGH Genomic Labeling System (Invitrogen, 18095-011)

growth_protocol: ES cells were grown on ES Medium (DMEM, 15% FBS, Non-essential amino acids, Glutamine, Pen/Strept, 2-mercaptoethanol and LIF) on feeder cells for amplification or on Gelatin for differentiation and experiments.  Motor neuron differentiation was done as described (Wichterle & Peljto, Curr Protoc Stem Cell Biol, 2009). Briefly, ES cells were tripsinized  and allowed to form aggregates in ANDFK medium (Advanced DMEM/F12,  Neurobasal Medium, Knockout-SR, of Pen/Strep, L-Glutamine, and 2-mercaptoethanol. Day 0 is the day of trypsinization. At Day 2, RA and Hh agonist are added.

extract_protocol: ChIP protocols were adapted from http://jura.wi.mit.edu/young_public/hESregulation/ChIP.html.  Briefly, approximately 3x10e7 cells taken from each developmental time point were cross-linked using formaldehyde and snap-frozen with liquid nitrogen.  Cells were thawed on ice, resuspended in 5ml lysis buffer 1 (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and mixed on a rotating platform at 4°C for 5 minutes.  Samples were spun down for 3 minutes at 3000rpm, resuspended in 5ml lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and mixed on a rotating platform for 5 minutes at room temperature.  Samples were spun down once more, resuspended in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and sonicated using a Misonix 3000 model sonicator to sheer cross-linked DNA to an average fragment size of approximately 500bp.  Triton X-100 was then added to the lysate after sonication to final concentrations of 1% and the lysate spun down to pellet cell debris.  The resulting whole-cell extract supernatant was incubated on a rotating mixer overnight at 4°C with 100 μL of Dynal Protein G magnetic beads that had been preincubated the previous 24 hours with 10 μg of the appropriate antibody in a PBS/BSA solution.  After approximately 16 hours of bead-lysate incubation, beads were collected with a Dynal magnet.  ChIP samples probing for transcription factor binding were washed with the following regimen, mixing on a rotating mixer at 4°C for 5 minutes per buffer: low-salt buffer (20 mM Tris at pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), high-salt buffer (20 mM Tris at pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10 mM Tris at pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% deoxycholate, 1% NP-40), and TE containing 50 mM NaCl.  ChIP samples probing for histone and chromatin marks were washed 4 times with RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and then once with TE containing 50 mM NaCl, again mixing on a rotating mixer at 4°C for 5 minutes per buffer.  After the final bead wash, samples were spun down to collect and discard excess wash solution, and bound antibody-protein-DNA fragment complexes were eluted from the beads by incubation in elution buffer at 65°C with occasional vortexing.  Cross-links were reversed by overnight incubation at 65°C.  Samples were digested with RNase A and Proteinase K to remove proteins and contaminating nucleic acids, and the DNA fragments precipitated with cold EtOH.  Resulting purified DNA fragments were amplified via ligation-mediated (LM) PCR.

tag: chip antibody

source_name: H3 ChIP DNA from ES to motor neuron differentiation Day7


title: HBG3_Day4_H3K27me3_r2

description: H3K27me3 ChIP-chip timeseries during ES to motor neuron differentiation Day4

source_name: H3K27me3 ChIP DNA from ES to motor neuron differentiation Day4

source_name: H3 ChIP DNA from ES to motor neuron differentiation Day4


title: HBG3_Day7_H3K79me2_r2

description: H3K79me2 ChIP-chip timeseries during ES to motor neuron differentiation Day7

source_name: H3K79me2 ChIP DNA from ES to motor neuron differentiation Day7


title: HBG3_Day2+RA_H3K79me2_r1

description: H3K79me2 ChIP-chip timeseries during ES to motor neuron differentiation Day2+8hrs RA

source_name: H3K79me2 ChIP DNA from ES to motor neuron differentiation Day2+8hrs RA

tag: agent

value: RA

source_name: H3 ChIP DNA from ES to motor neuron differentiation Day2+8hrs RA


title: HBG3_Day7_H3K4me3_r2


title: HBG3_Day4_H3K27me3_r1


title: HBG3_Day3_H3K4me3_r1

description: H3K4me3 ChIP-chip timeseries during ES to motor neuron differentiation Day3

source_name: H3K4me3 ChIP DNA from ES to motor neuron differentiation Day3

source_name: H3 ChIP DNA from ES to motor neuron differentiation Day3


title: Day4_iI_Dox_2

description: Gene expression data from Day 4, ES differentiation +48hr Dox, Hb9-GFP-sorted

hyb_protocol: RNA was hybridized to Affymetrix Mouse Gene 1.0 ST microarrays.

data_processing: Data analysis was carried out using the oneChannelGUI BioConductor package (Sanges, et al. Bioinformatics, 2007). RMA-sketch normalization was performed across all arrays. Differentially expressed genes were defined by ranking all probesets by the moderated t-statistic-derived p-value (adjusted for multiple testing using Benjamini & Hochberg’s method) and setting a threshold of p<0.001.

source_name: Day 4, ES differentiation +48hr Dox

label_protocol: RNA was amplified using NuGen Applause bundle  amplification and labeling kit according to manufacturer’s instructions.

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM ?-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described.  Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x105 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x107 cells on Day 0. Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

treatment_protocol: Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 µM all-trans-Retinoic acid (RA, Sigma) and 0.5 µM agonist of hedgehog signaling (SAG, Calbiochem). Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible Isl1-V5 construct


title: HBG3_Day2+RA_H3K27me3_r2

description: H3K27me3 ChIP-chip timeseries during ES to motor neuron differentiation Day2+8hrs RA

source_name: H3K27me3 ChIP DNA from ES to motor neuron differentiation Day2+8hrs RA


title: Day4_iNIP_Dox_3

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible Ngn2.Isl1.Phox2a-V5 construct


title: HBG3_Day7_H3K27me3_r1

description: H3K27me3 ChIP-chip timeseries during ES to motor neuron differentiation Day7

source_name: H3K27me3 ChIP DNA from ES to motor neuron differentiation Day7


title: HBG3_Day2_H3K4me3_r2

description: H3K4me3 ChIP-chip timeseries during ES to motor neuron differentiation Day2

source_name: H3K4me3 ChIP DNA from ES to motor neuron differentiation Day2

source_name: H3 ChIP DNA from ES to motor neuron differentiation Day2


title: HBG3_Day2_H3K27me3_r1

description: H3K27me3 ChIP-chip timeseries during ES to motor neuron differentiation Day2

source_name: H3K27me3 ChIP DNA from ES to motor neuron differentiation Day2


title: HBG3_Day2_H3K79me2_r2

description: H3K79me2 ChIP-chip timeseries during ES to motor neuron differentiation Day2

source_name: H3K79me2 ChIP DNA from ES to motor neuron differentiation Day2


title: HBG3_Day4_H3K4me3_r2

description: H3K4me3 ChIP-chip timeseries during ES to motor neuron differentiation Day4

source_name: H3K4me3 ChIP DNA from ES to motor neuron differentiation Day4


title: Day4_iI_Dox_3


title: Day4_iNIP_Dox_1


title: Theileria_annulata_infected_Bos_taurus_TBL20_control_rep3

city: Glasgow

first: William

last: Weir

address: Room 220, Henry Wellcome Building, Garscube Campus, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

country: United Kingdom

institute: University of Glasgow

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 without any treatment, this is the 3rd of 3 replicates

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Bos taurus

source_name: Theileria annulata infected bovine cells, no treatment

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: The control cell line was BL20, an uninfected bovine lymphosarcoma (Olobo and Black, 1989. Vet. Immunol. Immunopathol. 20, 165-172) and the parasite infected cell line (TBL20), was derived previously from BL20 by in vitro infection with T. annulata (strain Hissar) (Shiels et al., 1986. Vet. Parasitol. 21, 1-10.). Cells were cultured by standard procedures in RPMI with 20% foetal calf serum (Swan et al., 1999. Mol. Biochem. Parasitol. 101, 117-129). Cultures were seeded with 250,000 cells/ml and maintained by feeding with fresh medium every two days.

extract_protocol: Total RNA was extracted using Triazol (ref) and this was cleaned up using an RNeasy Mini kit (Qiagen Inc., CA, USA) . RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (ref)

treatment_protocol: Buparvaquone (BW720c) was used at 50ng/ml to kill the parasite. The drug was added to cultures 4 hours after setting up at 250,000 cells/ml. Cell numbers were estimated each day by Trypan Blue exclusion and cultures fed, if required, by 2-fold dilution in fresh medium and drug to maintain cells in exponential growth over the 48 time course of the experiment.

tag: infection status

value: Theileria annulata infected

tag: treatment time-point


title: HBG3_Day4_H3K79me2_r2

description: H3K79me2 ChIP-chip timeseries during ES to motor neuron differentiation Day4

source_name: H3K79me2 ChIP DNA from ES to motor neuron differentiation Day4


title: HBG3_Day4_H3K4me3_r1


title: HBG3_Day3_H3K27me3_r1

description: H3K27me3 ChIP-chip timeseries during ES to motor neuron differentiation Day3

source_name: H3K27me3 ChIP DNA from ES to motor neuron differentiation Day3


title: Day4_iNIP_Dox_2


title: HBG3_Day2+RA_H3K4me3_r1

description: H3K4me3 ChIP-chip timeseries during ES to motor neuron differentiation Day2+8hrs RA

source_name: H3K4me3 ChIP DNA from ES to motor neuron differentiation Day2+8hrs RA


title: HBG3_Day2_H3K27me3_r2


title: Day4_iI_Dox_1


title: HBG3_Day2+RA_H3K27me3_r1


title: HBG3_Day2+RA_H3K4me3_r2


title: HBG3_Day0_H3K4me3_r1

description: H3K4me3 ChIP-chip timeseries during ES to motor neuron differentiation Day0

source_name: H3K4me3 ChIP DNA from ES to motor neuron differentiation Day0

source_name: H3 ChIP DNA from ES to motor neuron differentiation Day0


title: HBG3_Day3_H3K79me2_r2

description: H3K79me2 ChIP-chip timeseries during ES to motor neuron differentiation Day3

source_name: H3K79me2 ChIP DNA from ES to motor neuron differentiation Day3


title: HBG3_Day2_H3K4me3_r1


title: Theileria_annulata_infected_Bos_taurus_TBL20_control_rep2

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 without any treatment, this is the 2nd of 3 replicates


title: Theileria_annulata_infected_Bos_taurus_TBL20_control_rep1

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 without any treatment, this is the 1st of 3 replicates


title: Day5_GFP_RA_Hh_3

description: Gene expression data from Day 5, ES to MN differentiation +RA+Hh, Hb9-GFP-sorted

growth_protocol: ES cells were cultured over a layer of Mitomycin-C treated fibroblast resistant to Neomycin (Fisher) in EmbryoMax D-MEM (Fisher) supplemented with 10% ES-FBS (Invitrogen), L-Glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U/ml LIF. Motor neuron differentiation of ES cells was performed as previously described.  Briefly, ES cells were trypsinized (Invitrogen) and seeded at 5x105 cells/ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout-SR, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 2 and Day 5 of differentiation.  Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 uM all-trans-Retinoic acid (RA, Sigma) and 0.5 uM agonist of hedgehog signaling (SAG, Calbiochem). For ChIP experiments, the same conditions were used but scaled to seed 1x107 cells on Day 0. Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

extract_protocol: RNA was extracted with Qiagen RNAeasy at different time points following manufacturer's instructions.

treatment_protocol: Patterning of embryoid bodies was induced by supplementing media on Day 2 with 1 uM all-trans-Retinoic acid (RA, Sigma) and 0.5 uM agonist of hedgehog signaling (SAG, Calbiochem). Doxycycline (Sigma) was added to the culture medium at 3ug/ml when required.

value: Ainv15 (ATCC SCRC-1029) with Dox-inducible Ngn2.Isl1.Lhx3-V5 construct


title: Day5_GFP_RA_Hh_2

source_name: Day 5, ES to MN differentiation +RA+Hh, Hb9-GFP-sorted


title: Theileria_annulata_infected_Bos_taurus_TBL20_BW720c_24h_rep3

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 24 hours post BW720c treatment, this is the 3rd of 3 replicates

source_name: Theileria annulata infected bovine cells, 24 hours post BW720c stimulation

value: 24 hours


title: Day3_Dox_3

description: Gene expression data from Day 3, ES differentiation +24hr Dox

source_name: Day 3, ES differentiation +24hr Dox


title: HBG3_Day0_H3K27me3_r3

description: H3K27me3 ChIP-chip timeseries during ES to motor neuron differentiation Day0

source_name: H3K27me3 ChIP DNA from ES to motor neuron differentiation Day0


title: Day4_GFP_Dox_1

description: Gene expression data from Day 4, ES differentiation +48hr Dox, Hb9-GFP-sorted


title: Day4_GFP_Dox_2

source_name: Day 4, ES differentiation +48hr Dox, Hb9-GFP-sorted


title: Theileria_annulata_infected_Bos_taurus_TBL20_BW720c_48h_rep3

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 48 hours post BW720c treatment, this is the 3rd of 3 replicates

source_name: Theileria annulata infected bovine cells, 48 hours post BW720c stimulation

value: 48 hours


title: Day3_Dox_2


title: Day4_GFP_Dox_RA_1

description: Gene expression data from Day 4, ES differentiation +48hr Dox +RA, Hb9-GFP-sorted


title: Day5_GFP_RA_Hh_1


title: Theileria_annulata_infected_Bos_taurus_TBL20_BW720c_24h_rep2

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 24 hours post BW720c treatment, this is the 2nd of 3 replicates


title: Day4_GFP_Dox_RA_3

source_name: Day 4, ES differentiation +48hr Dox +RA, Hb9-GFP-sorted


title: Day4_GFP_Dox_RA_2


title: Theileria_annulata_infected_Bos_taurus_TBL20_BW720c_48h_rep2

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 48 hours post BW720c treatment, this is the 2nd of 3 replicates


title: Day3_Dox_1


title: HBG3_Day0_H3K79me2_r2

description: H3K79me2 ChIP-chip timeseries during ES to motor neuron differentiation Day0

source_name: H3K79me2 ChIP DNA from ES to motor neuron differentiation Day0


title: Theileria_annulata_infected_Bos_taurus_TBL20_BW720c_24h_rep1

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 24 hours post BW720c treatment, this is the 1st of 3 replicates


title: Day3_control_2

description: Gene expression data from Day 3, ES differentiation (no treatment)


title: Theileria_annulata_infected_Bos_taurus_TBL20_BW720c_48h_rep1

description: This sample is of the Theileria annulata transformed bovine lymphosarcoma cell line TBL20 48 hours post BW720c treatment, this is the 1st of 3 replicates


title: HBG3_Day0_H3K4me3_r3

description: H3K4me3 ChIP-chip timeseries during ES to motor neuron differentiation Day0


title: Day3_control_3

source_name: Day 3, ES differentiation (no treatment)


title: Day3_control_1


title: sample 9, hESC derived hepatoblast culture, cAMP treated, replicate 3

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol (GeneChip Scanner 7G)

data_processing: The data were summarized and quantile normalised using the ExonRMA16 normalisation in Genespring (version 11.5.1) followed by logging (base 2). Summarization was based upon the Affymetrix hg19 2010-09-03 version 1 (na31) build for the HuGeneST v1.0 chip.

source_name: cultured cells

label_protocol: 300 ng of total RNA was used as input for the Ambion WT Expression Kit followed by fragmentation and labeling of 2.75ug of cDNA according to the Affymetrix WT protocol.

extract_protocol: RNA was prepared from the RNAqueous Micro Kit (Ambion) and treated with DNase.

value: hESC derived hepatoblast culture

value: cAMP


title: sample 8, hESC derived hepatoblast culture, cAMP treated, replicate 2


title: Bos_taurus_BL20_control_rep3

description: This sample is of the bovine lymphosarcoma cell line BL20 without any treatment, this is the 3rd of 3 replicates

source_name: Bovine cells, no treatment

value: uninfected


title: LGXSM-33

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

scan_protocol: Finally, the plate was read on Luminex set for specified bead regions with the following parameters: 100 uL sample size, 5,000–25,000 DD gate, 45 sec time out and 100 bead events per bead region.

data_processing:
The average signal values were noted and subtracted from the background signal and finally normalized with a housekeeping gene by dividing the average signal value of the target gene with the average signal value of the reference gene [BioRad Bio-Plex Manager v5.0].
Please note that 8-9 replicates were performed per each sample. Each sample data table represents averaged (across the replicate samples) data and non-averaged data (from each replicate) is provided as a Series supplementary file (*setI.txt contains data from Panel 321347 and *setII.txt from panel 321389).

label: Streptavidin phycoerythrin

source_name: Non-healer_Knee joint

growth_protocol: Knee joint sections were taken from mice which underwent full-thicknees articular cartilage repair at 8 weeks old. They were raised on normal diet and standard procedures.

extract_protocol: The quantification of mRNAs using the Affymetrix QuantiGene 2.0 Plex Assay kit.  An appropriate volume of working bead mix was prepared scaled for 96-well plate format: 18.5 uL nuclease-free water, 33.3 uL lysis mixture, 2 uL blocking reagent, 0.2 uL proteinase K, 1 uL capture beads and 5 uL probe set.  The working bead mix was vortexed for 10 sec and 60 uL of it was dispensed into each well of the hybridization plate followed by addition of 40 uL of tissue homogenate to each well.  The plate was sealed using a pressure seal and placed on an inverted plate lid placed onto the VorTemp 56 shaking incubator and incubated for 18-22 h at 54C at 600 rpm.  Post-incubation, the contents of the hybridization plate were transferred to a magnetic separation plate after centrifugation at 240X g for 60 sec and mixing the contents a few times with a pipette.  The magnetic separation plate was inserted into the hand-held magnetic plate washer and washed the plate three times using 100 uL of wash buffer per well.  Then 100 uL of pre-amplifier working reagent (36 uL of 2.0 pre-amplifier in 12 mL of amplifier diluent) was dispensed into each well of the magnetic separation plate, sealed and incubated at 50C for 1 h while shaking at 600 rpm.  After incubation, the plate was washed as above and 100 uL of amplifier working reagent per well and again incubated at 50C for 60 min at 600 rpm.  Then the plate was washed again and 100 uL of label probe working reagent was added to each well and the sealed plate was placed into VorTemp and incubated at 50C for 60 min at 600 shaking rpm.  After 60 min, the washing procedure was repeated as above, 100 uL of SAPE working reagent  was pipetted into each well.  The plate was foiled, removed from plate washer and placed on a shaking platform at room temperature with shaking at 800 rpm for 60 sec followed by shaking at 600 rpm for 30 min.  The plate was washed with 130 uL of SAPE wash buffer in each assay well, sealed the plate, removed from plate washer, wrapped in aluminum foil and allowed to shake at 800 rpm for 3 min at room temperature.

treatment_protocol: Samples were from mice with different genetic background with varying degree of healing capacity.

tag: strain

tag: healing capacity

value: Non-healer

tag: tissue

value: knee joint

tag: tissue type

tag: molecule source

value: tissue lysate containing RNA and microRNA


title: sample 6, hESC derived hepatoblast culture, untreated, replicate 3


title: LGXSM-6

source_name: Healer_Knee joint

value: Healer


title: sample 7, hESC derived hepatoblast culture, cAMP treated, replicate 1


title: Bos_taurus_BL20_control_rep2

description: This sample is of the bovine lymphosarcoma cell line BL20 without any treatment, this is the 2nd of 3 replicates

tag: cell line


title: HBG3_Day0_H3K27me3_r1


title: LGXSM-35

source_name: Intermediate healer_Knee joint

value: Intermediate healer


title: LGXSM-5


title: sample 4, hESC derived hepatoblast culture, untreated, replicate 1


title: Wt 48h x alcApkcA ΔcnaA 48h Replicate 2

city: Ribeirao Preto

first: Neil

last: Brown

address: Av. do Cafe

country: Brazil

institute: USP

description:
252953510042_GE2-v5_95_Feb07_1_3
Biological replicate 2 of 3

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. After data were processed using TIGR platform. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test).

organism: Aspergillus nidulans

source_name: total RNA from Wt grown 48h; labeled with Cyanine-3

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SEB-treated samples) for 2 hours at 40 oC.

growth_protocol: A. nidulans strains (Wt, ΔcnaA and alcApkcAΔcnaA) were grown on minimal medium with glycerol 2% threonine 100mM during 24 or 48 hours at 37 oC.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

tag: growth condition

value: Wt grown on glycerol 2% threonine 100mM along 48h

source_name: total RNA from alcApkcA ΔcnaA grown 48h; labeled with Cyanine-5

value: alcApkcA ΔcnaA grown on glycerol 2% threonine 100mM along 48h


title: Bos_taurus_BL20_BW720c_48h_rep3

description: This sample is of the bovine lymphosarcoma cell line BL20, 48 hours post BW720c treatment, this is the 3rd of 3 replicates

source_name: Bovine cells, 48 hours post BW720c stimulation

tag: treatment


title: Bos_taurus_BL20_BW720c_48h_rep1

description: This sample is of the bovine lymphosarcoma cell line BL20, 48 hours post BW720c treatment, this is the 1st of 3 replicates


title: Bos_taurus_BL20_BW720c_48h_rep2

description: This sample is of the bovine lymphosarcoma cell line BL20, 48 hours post BW720c treatment, this is the 2nd of 3 replicates


title: sample 1, primary hepatocyte, replicate 1

tag: cell type

value: primary hepatocyte


title: Wt 48h x ΔcnaA 48h Replicate 3

description:
252953510042_GE2-v5_95_Feb07_1_1
Biological replicate 3 of 3

source_name: total RNA from ΔcnaA grown 48h; labeled with Cyanine-5

value: ΔcnaA grown on glycerol 2% threonine 100mM along 48h


title: Bos_taurus_BL20_BW720c_24h_rep2

description: This sample is of the bovine lymphosarcoma cell line BL20, 24 hours post BW720c treatment, this is the 2nd of 3 replicates

source_name: Bovine cells, 24 hours post BW720c stimulation


title: Bos_taurus_BL20_BW720c_24h_rep3

description: This sample is of the bovine lymphosarcoma cell line BL20, 24 hours post BW720c treatment, this is the 3rd of 3 replicates


title: sample 3, primary hepatocyte, replicate 3


title: Wt 48h x alcApkcA ΔcnaA 48h Replicate 3

description:
252953510042_GE2-v5_95_Feb07_1_4
Biological replicate 3 of 3


title: Bos_taurus_BL20_control_rep1

description: This sample is of the bovine lymphosarcoma cell line BL20 without any treatment, this is the 1st of 3 replicates


title: sample 2, primary hepatocyte , replicate 2


title: Wt 48h x alcApkcA ΔcnaA 48h Replicate 1

description:
252953510042_GE2-v5_95_Feb07_1_2
Biological replicate 1 of 3


title: MRL

value: MRL/MpJ


title: LG

value: LG/J


title: SM

value: SM/J


title: Rep2

status: Public on Jul 03 2013

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

description: Biological replicate 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed with Agilent Gene Expression Wash Buffers 1 and 2.

scan_protocol: Scanned on an Axon 4200 AL scanner (Axon Instruments) Images were quantified using GenePix Pro 6.0

data_processing: Background subtraction with 'normexp' method. Lowess normalization of processed Cy3 signal/processed Cy5 signal. R software was used with limma package.

organism: Pectobacterium atrosepticum SCRI1043

source_name: Bacterial cells

label_protocol: 10 µg of total RNA and 2,5 µg random hexamers were incubated in 70°C for 10 min, then reversed transcribed at 37°C for 4 h in the presence of 400 U reverse transcriptase (Promega); 7.5 mM DTT; 1.25 mM dATP/dTTP/dGTP; 0.5 mM dCTP and 2.5 mM Cy3 or Cy5 (GE healthcare).

growth_protocol: Exponential phase, incubation 24h, 15 °C, 150 rpm

extract_protocol: Total RNA extracted using Summers method (Summers, W.C. (1970). A simple method for extraction of RNA of E.coli utilizing DEPC. Anal Biochem 33, 459-463.)

treatment_protocol: Incubation in hrp inducing minimal medium supplemented with 10% v/v tuber extract

tag: genotype

value: wild-type

value: VasH knock-out


title: Rep3

description: Biological replicate 3


title: Wt 48h x ΔcnaA 48h Replicate 2

description:
252953510041_GE2-v5_95_Feb07_1_4
Biological replicate 2 of 3


title: B6


title: Rep1

description: Biological replicate 1


title: Bos_taurus_BL20_BW720c_24h_rep1

description: This sample is of the bovine lymphosarcoma cell line BL20, 24 hours post BW720c treatment, this is the 1st of 3 replicates

value: 24 hours


title: Wt 24h x alcApkcA ΔcnaA 24h Replicate 1

description:
252953510033_GE2-v5_95_Feb07_1_4
Biological replicate 1 of 3

source_name: total RNA from Wt grown 24h; labeled with Cyanine-3

value: Wt grown on glycerol 2% threonine 100mM along 24h

source_name: total RNA from alcApkcA ΔcnaA grown 24h; labeled with Cyanine-5

value: alcApkcA ΔcnaA grown on glycerol 2% threonine 100mM along 24h


title: kdpe cra grown OD1 DMEM

city: Dallas

first: Jacqueline

last: Njoroge

state: Tx

address: 5323 Harry hines

institute: UTSW

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: All data processed using GCOS v1.4

organism: Escherichia coli 8624

source_name: kdpE cra mutant grown in DMEM to OD1.0

label_protocol: standard Affymetrix protocol

growth_protocol: All strains grown in DMEM

extract_protocol: Ambion RiboPure RNA isolation protocol

value: kdpE cra mutant


title: Wt 48h x ΔcnaA 48h Replicate 1

description:
252953510041_GE2-v5_95_Feb07_1_3
Biological replicate 1 of 3


title: Wt 24h x ΔcnaA 24h Replicate 1

description:
252953510033_GE2-v5_95_Feb07_1_1
Biological replicate 1 of 3

source_name: total RNA from ΔcnaA grown 24h; labeled with Cyanine-5

value: ΔcnaA grown on glycerol 2% threonine 100mM along 24h


title: Wt 24h x ΔcnaA 24h Replicate 3

description:
252953510033_GE2-v5_95_Feb07_1_3
Biological replicate 3 of 3


title: Latissimus dorsi_t=o_Y1 vs Latissimus dorsi_t=2_Y2

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: US22502676_251485056422_S01_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner version G2505B, protocol according to Agilent scanner and feature extraction version A.7.5.1

data_processing: The R-package LIMMA was used for background correction according to the Edward method and within array Lowess and between array quantile normalization according to Smyth and Speed.

source_name: Y1, Latissimus Dorsi t=0

label_protocol: RNA labeling protocol available via www.agilent.com

extract_protocol: RNA isolation protocol using Trizol according to Invitrogen

value: Latissimus Dorsi

source_name: Y2, Latissimus Dorsi t=2


title: Diaphragm_t=o_C1 vs Diaphragm_t=2_C2

description: US22502676_251485056422_S01_GE2-v5_95_Feb07_1_1.txt

source_name: C1, Diaphragm t=0

value: Diaphragm

source_name: C2, Diaphragm, t=2


title: Diaphragm_t=2_A2 vs Diaphragm_ t=0_A1

description: US22502676_251485044850_S01_GE2-v5_95_Feb07_1_2.txt

source_name: A2, Diaphragm t=2

source_name: A1, Diaphragm, t=0


title: Wt 24h x alcApkcA ΔcnaA 24h Replicate 2

description:
252953510041_GE2-v5_95_Feb07_1_1
Biological replicate 2 of 3


title: wt grown OD1 DMEM

source_name: wt grown in DMEM to OD1.0

value: wt


title: Latissimus dorsi_t=o_Z1 vs Latissimus dorsi_t=2_Z2

description: US22502676_251485056423_S01_GE2-v5_95_Feb07_1_1.txt

source_name: Z1, Latissimus Dorsi t=0

source_name: Z2, Latissimus Dorsi t=2


title: Diaphragm_t=o_D1 vs Diaphragm_t=2_D2

description: US22502676_251485056422_S01_GE2-v5_95_Feb07_1_2.txt

source_name: D1, Diaphragm t=0

source_name: D2, Diaphragm, t=2


title: Wt 24h x ΔcnaA 24h Replicate 2

description:
252953510033_GE2-v5_95_Feb07_1_2
Biological replicate 2 of 3


title: Wt 24h x alcApkcA ΔcnaA 24h Replicate 3

description:
252953510041_GE2-v5_95_Feb07_1_2
Biological replicate 3 of 3


title: Latissimus dorsi_t=o_X1 vs Latissimus dorsi_t=2_X2

description: US22502676_251485056422_S01_GE2-v5_95_Feb07_1_3.txt

source_name: X1, Latissimus Dorsi t=0

source_name: X2, Latissimus Dorsi t=2


title: Diaphragm_t=2_B2 vs Diaphragm_ t=0_B1

description: US22502676_251485044850_S01_GE2-v5_95_Feb07_1_4.txt

source_name: B2, Diaphragm t=2

source_name: B1, Diaphragm, t=0


title: Diaphragm_t=o_A1 vs Diaphragm_t=2_A2

description: US22502676_251485044850_S01_GE2-v5_95_Feb07_1_1.txt

source_name: A1, Diaphragm t=0

source_name: A2, Diaphragm, t=2


title: Mite extract on human skin equivalents, rep 3

city: Dayton

first: Michael

last: Markey

state: OH

address: 3640 Colonel Glenn Hwy.

department: Biochemistry and Molecular Biology

institute: Wright State Unviersity

description:
12_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to mite extract.

hyb_protocol: The Affymetrix GeneChip WT Terminal Labeling Kit was used with the manufacturer's suggested protocol (WT Labeling and Hybridization User Manual for use with the Ambion WT Expression Kit, Revision 7, 2012, Affymetrix).

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

data_processing: Data analysis was carried out in AltAnalyze version 2.0. Probesets with DABG p-values above 0.5 or non-log expression below 1 were removed from the analysis. Gene expression levels were determined using constitutive probesets. Gene annotation was derived from the current version of Ensembl or release 54 in a handful of cases where the Affymetrix probe set does not correlate to a current identifier (these were pseudogenes in each case). Replicates were assigned to groups and pairwise comparisons were performed for live mites vs. controls and extract vs. controls. Gene ontology (GO) over-representation analysis was performed using GO-Elite v.1 Beta. Maximum raw p-value was set at 0.05. Minimum fold change was 2.0. GO terms and pathway rankings were pruned by z-score with a cutoff of 1.96. Minimum number of changed genes in a term was set at 3. Two-thousand (2000) ORA permutations were performed, and the primary relational gene database was Ensembl. The RMA data was generated within ALtAnalyze v.2.0 (http://www.altanalyze.org).

source_name: human skin equivalents, mite extract

label_protocol: 50 ng total RNA was used as input for the Ambion WT Expression Kit (Life Technologies). These were hybridized to the Affymetrix Human Gene 1.0 ST arrays according to manufacturer's protocols.

growth_protocol: EpiDerm EFT-400 full-thickness HSEs and medium were purchased from MatTek (Ashland, MA).

extract_protocol: The aqueous phase from Trizol purification was transferred to EZNA RNA purification columns (Omega Bio-Tek, Norcross, GA) and purified using the manufacturer's protocol.  Purified RNA was DNase treated to remove any contaminating genomic DNA using Turbo DNA-Free (Life Technologies). RNA was quantified by spectrophotometry and on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All samples had RIN numbers > 8.0.

treatment_protocol: One set of HSEs (n=5) were inoculated on their surfaces with several hundred live scabies mites that had been washed and surface-sterilized with 70% ethanol. A second set (n=5) was inoculated on the surface with 100 ug of soluble scabies extract protein. A third set (n=4) remained non-inoculated and served as controls. HSEs were maintained for 48 h in a 37C incubator with 5-7% CO2. At the conclusion of the challenge, the surface of the HSE was washed, it was lifted from its support and cut into pieces which were  submerged in 1.5 mL of RNAlater solution (Ambion Life Technologies, Grand Island, NY). Samples were stored at -80C until processed for gene expression analysis.

value: human skin equivalent

value: mite extract


title: Live mites on human skin equivalents, rep 2

description:
6_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to live mites.

source_name: human skin equivalents, live mites

value: live mites


title: Diaphragm_t=o_B1 vs Diaphragm_t=2_B2

description: US22502676_251485044850_S01_GE2-v5_95_Feb07_1_3.txt

source_name: B1, Diaphragm t=0

source_name: B2, Diaphragm, t=2


title: Mite extract on human skin equivalents, rep 5

description:
14_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to mite extract.


title: Mite extract on human skin equivalents, rep 1

description:
10_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to mite extract.


title: Live mites on human skin equivalents, rep 3

description:
7_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to live mites.


title: Mite extract on human skin equivalents, rep 4

description:
13_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to mite extract.


title: Untreated human skin equivalent control, rep 4

description:
4_(HuGene-1_0-st-v1).CEL
Gene expression data from untreated human skin equivalents.

source_name: human skin equivalents, untreated


title: Live mites on human skin equivalents, rep 4

description:
8_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to live mites.


title: Live mites on human skin equivalents, rep 5

description:
9_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to live mites.


title: Untreated human skin equivalent control, rep 2

description:
2_(HuGene-1_0-st-v1).CEL
Gene expression data from untreated human skin equivalents.


title: Untreated human skin equivalent control, rep 3

description:
3_(HuGene-1_0-st-v1).CEL
Gene expression data from untreated human skin equivalents.


title: cra grown OD1 DMEM

source_name: cra mutant grown in DMEM to OD1.0

value: cra mutant


title: Live mites on human skin equivalents, rep 1

description:
5_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to live mites.


title: DEC1.KO.CD3CD28.rep3

city: London

first: MARC

last: MARTINEZ-LLORDELLA

address: 3rd Floor Cheyne Wing, Denmark Hill

department: Liver Science Department

institute: King's College London

hyb_protocol: Hybridization protocol was performed by the Genome Core of the J. David Gladstone Institutes according to the manufacturer's instructions.

scan_protocol: Scanning protocol was performed by the Genome Core of the J. David Gladstone Institutes according to the manufacturer's instructions.

data_processing: RMA normalization

source_name: naïve T cells from spleen and lymph nodes

label_protocol: Labeling protocol was performed by the Genome Core of the J. David Gladstone Institutes according to the manufacturer's instructions.

growth_protocol: Mouse naïve CD4+ T cells were isolated by FACS sorter and seeded into a 24-well plates at a density of 1x10^6 cells per ml of DMEM media supplemented with 10% Fetal Bovine Serum.

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

treatment_protocol: The cells were activated with latex beads conjugates to antibodies specific for anti-CD3 or to both anti-CD3 and anti-CD28.

value: DEC1 knock-out

value: spleen and lymph nodes

value: CD4+CD62LhiCD25- T cells

value: anti-CD3 + anti CD28


title: DEC1.KO.CD3.rep3


title: Untreated human skin equivalent control, rep 1

description:
1_(HuGene-1_0-st-v1).CEL
Gene expression data from untreated human skin equivalents.


title: DEC1.WT.CD3CD28.rep3

value: Wild-Type


title: DEC1.KO.CD3.rep4


title: DEC1.WT.CD3.rep4


title: DEC1.WT.CD3.rep3


title: DEC1.KO.CD3.rep2


title: DEC1.KO.CD3CD28.rep2


title: DEC1.WT.CD3CD28.rep4


title: Mite extract on human skin equivalents, rep 2

description:
11_(HuGene-1_0-st-v1).CEL
Gene expression data from human skin equivalents exposed to mite extract.


title: DEC1.KO.CD3CD28.rep4


title: DEC1.WT.CD3CD28.rep2


title: DEC1.WT.CD3CD28.rep1


title: DEC1.WT.CD3.rep2


title: DEC1.KO.CD3.rep1


title: DEC1.KO.CD3CD28.rep1


title: LUNG_808_Ne_TX91_d02_rep3

city: Bethesda

first: Marlene

last: Brandes

state: MD

address: 9000 Rockville Pike

department: Laboratory of Systems Biology

institute: NIH, NIAID

hyb_protocol: 2ug of the biotinylated sample was used for hybridization. Hybridization conditions were adjusted according to NuGen's Illumina Solution application notes 2, or else the standard Illumina hybridization protocol was followed.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised by quantile normalisation using the GeneSpring GX 10.0 analysis platform (Agilent), log2 transformed and median baseline transformed.

source_name: mouse lung, neutrophil, H1N1 influenza A TX91 (10^6 PFU), 2 days

label_protocol: 5ug of the amplified product was used for UNG-based abasic site abrasion and biotinylation according to NuGen's Illumina Solution application notes 2.

extract_protocol:
Sorted cells were immediately spun down and lysed in TRI Reagent (Ambion) and then placed at -80°C for storage.
Total RNA from sorted cells was isolated with the MagMAX-96 for Microarrays kit (Ambion) using the phase separation procedure in accordance with the prescribed protocol provided with the kit. All RNA samples were treated with DNase I and analyzed for integrity on an Agilent Bioanalyzer. 100ng total RNA was used for amplification with the Ovation RNA Amplification System V2 (NuGEN Technologies).

treatment_protocol:
5- to 8-week-old male C57BL/6 were intranasally infected with different doses of H1N1 influenza A viruses or sham infected under light isoflurane anesthesia. Infectious doses were supplied in a volume of 50ul sterile pharmaceutical-grade physiological saline.
Lungs were harvested at 48h or 72h post infection. Immediately after euthanasia, lungs were perfused in situ via the right cardiac ventricle with PBS/EDTA (10mM) pre-warmed to 37°C and then immediately processed for down-stream applications.
5 cell types were purified from individual lungs by flow sorting after a 30-minute enzymatic digestion step and staining.

tag: age

value: 5-8 weeks

tag: Sex

value: male

value: lung

value: neutrophil

tag: perturbation

value: H1N1 influenza A TX91 (10^6 PFU)

tag: time post-infection

value: 2 days

tag: mouse id


title: LUNG_808_Am_TX91_d02_rep3

source_name: mouse lung, alveolar macrophage, H1N1 influenza A TX91 (10^6 PFU), 2 days

value: alveolar macrophage


title: LUNG_1131_Mo_0.6LD50PR8_d03_rep3

source_name: mouse lung, Ly6Chi mononuclear myeloid cell, H1N1 influenza A PR8 (0.6LD50), 3 days

value: Ly6Chi mononuclear myeloid cell

value: H1N1 influenza A PR8 (0.6LD50)

value: 3 days


title: LUNG_808_Mo_TX91_d02_rep3

source_name: mouse lung, Ly6Chi mononuclear myeloid cell, H1N1 influenza A TX91 (10^6 PFU), 2 days


title: LUNG_1131_Ne_0.6LD50PR8_d03_rep3

source_name: mouse lung, neutrophil, H1N1 influenza A PR8 (0.6LD50), 3 days


title: DEC1.WT.CD3.rep1


title: LUNG_1033_Am_10LD50PR8_d02_rep3

source_name: mouse lung, alveolar macrophage, H1N1 influenza A PR8 (10LD50), 2 days

value: H1N1 influenza A PR8 (10LD50)


title: LUNG_1033_Ly_10LD50PR8_d02_rep3

source_name: mouse lung, lymphocyte (BC, TC, NK), H1N1 influenza A PR8 (10LD50), 2 days

value: lymphocyte (BC, TC, NK)


title: LUNG_1033_Nh_10LD50PR8_d02_rep3

description:
5398599051_E
Outlier, contamination with leukocytes.

source_name: mouse lung, pulmonary CD45neg, H1N1 influenza A PR8 (10LD50), 2 days

value: pulmonary CD45neg


title: sample 5, hESC derived hepatoblast culture, untreated, replicate 2

source_name: cultured cells

value: hESC derived hepatoblast culture

tag: agent


title: LUNG_1131_Nh_0.6LD50PR8_d03_rep3

source_name: mouse lung, pulmonary CD45neg, H1N1 influenza A PR8 (0.6LD50), 3 days


title: LUNG_808_Nh_TX91_d02_rep3

source_name: mouse lung, pulmonary CD45neg, H1N1 influenza A TX91 (10^6 PFU), 2 days


title: LUNG_808_Ly_TX91_d02_rep3

source_name: mouse lung, lymphocyte (BC, TC, NK), H1N1 influenza A TX91 (10^6 PFU), 2 days


title: LUNG_1033_Ne_10LD50PR8_d02_rep3

source_name: mouse lung, neutrophil, H1N1 influenza A PR8 (10LD50), 2 days


title: LUNG_1011_Ne_Sham_d02_rep3

source_name: mouse lung, neutrophil, sham, 2 days

value: sham


title: LUNG_1011_Mo_Sham_d02_rep3

source_name: mouse lung, Ly6Chi mononuclear myeloid cell, sham, 2 days


title: LUNG_1118_Ne_0.6LD50PR8_d03_rep2


title: LUNG_1011_Am_Sham_d02_rep3

source_name: mouse lung, alveolar macrophage, sham, 2 days


title: LUNG_1118_Nh_0.6LD50PR8_d03_rep2


title: LUNG_1011_Nh_Sham_d02_rep3

source_name: mouse lung, pulmonary CD45neg, sham, 2 days


title: LUNG_1033_Mo_10LD50PR8_d02_rep3

source_name: mouse lung, Ly6Chi mononuclear myeloid cell, H1N1 influenza A PR8 (10LD50), 2 days


title: LUNG_1131_Am_0.6LD50PR8_d03_rep3

source_name: mouse lung, alveolar macrophage, H1N1 influenza A PR8 (0.6LD50), 3 days


title: LUNG_826_Mo_10LD50PR8_d02_rep2


title: LUNG_1011_Ly_Sham_d02_rep3

source_name: mouse lung, lymphocyte (BC, TC, NK), sham, 2 days


title: LUNG_1118_Mo_0.6LD50PR8_d03_rep2

source_name: mouse lung, Ly6Chi mononuclear myeloid cell, H1N1 influenza A PR8 (0.6LD50), 3 days


title: LUNG_1118_Ly_0.6LD50PR8_d03_rep2

source_name: mouse lung, lymphocyte (BC, TC, NK), H1N1 influenza A PR8 (0.6LD50), 3 days


title: LUNG_1131_Ly_0.6LD50PR8_d03_rep3


title: LUNG_1118_Am_0.6LD50PR8_d03_rep2


title: LUNG_826_Am_10LD50PR8_d02_rep2

source_name: mouse lung, alveolar macrophage, H1N1 influenza A PR8 (10LD50), 2 days


title: LUNG_946_Am_100LD50PR8_d02_rep3

source_name: mouse lung, alveolar macrophage, H1N1 influenza A PR8 (100LD50), 2 days

value: H1N1 influenza A PR8 (100LD50)


title: LUNG_826_Ly_10LD50PR8_d02_rep2

source_name: mouse lung, lymphocyte (BC, TC, NK), H1N1 influenza A PR8 (10LD50), 2 days


title: LUNG_826_Ne_10LD50PR8_d02_rep2


title: LUNG_1000_Ne_100LD50PR8_d02_rep2

source_name: mouse lung, neutrophil, H1N1 influenza A PR8 (100LD50), 2 days


title: LUNG_829_Am_10LD50PR8_d02_rep1


title: LUNG_1145_Nh_TX91_d02_rep2


title: LUNG_946_Ly_100LD50PR8_d02_rep3

source_name: mouse lung, lymphocyte (BC, TC, NK), H1N1 influenza A PR8 (100LD50), 2 days


title: LUNG_1000_Ly_100LD50PR8_d02_rep2


title: LUNG_1145_Mo_TX91_d02_rep2

source_name: mouse lung, Ly6Chi mononuclear myeloid cell, H1N1 influenza A TX91 (10^6 PFU), 2 days


title: LUNG_946_Nh_100LD50PR8_d02_rep3

source_name: mouse lung, pulmonary CD45neg, H1N1 influenza A PR8 (100LD50), 2 days


title: LUNG_1000_Am_100LD50PR8_d02_rep2


title: LUNG_826_Nh_10LD50PR8_d02_rep2

source_name: mouse lung, pulmonary CD45neg, H1N1 influenza A PR8 (10LD50), 2 days


title: LUNG_1145_Ne_TX91_d02_rep2

source_name: mouse lung, neutrophil, H1N1 influenza A TX91 (10^6 PFU), 2 days


title: LUNG_829_Ly_10LD50PR8_d02_rep1


title: LUNG_1145_Ly_TX91_d02_rep2

source_name: mouse lung, lymphocyte (BC, TC, NK), H1N1 influenza A TX91 (10^6 PFU), 2 days


title: LUNG_946_Mo_100LD50PR8_d02_rep3

source_name: mouse lung, Ly6Chi mononuclear myeloid cell, H1N1 influenza A PR8 (100LD50), 2 days


title: LUNG_946_Ne_100LD50PR8_d02_rep3


title: LUNG_999_Ne_100LD50PR8_d02_rep1


title: LUNG_1000_Mo_100LD50PR8_d02_rep2


title: LUNG_999_Mo_100LD50PR8_d02_rep1


title: LUNG_829_Mo_10LD50PR8_d02_rep1


title: LUNG_829_Ne_10LD50PR8_d02_rep1

source_name: mouse lung, neutrophil, H1N1 influenza A PR8 (10LD50), 2 days


title: LUNG_829_Nh_10LD50PR8_d02_rep1


title: LUNG_1000_Nh_100LD50PR8_d02_rep2


title: LUNG_999_Ly_100LD50PR8_d02_rep1


title: LUNG_999_Nh_100LD50PR8_d02_rep1


title: LUNG1117_Ly_0.6LD50PR8_d03_rep1


title: LUNG_999_Am_100LD50PR8_d02_rep1


title: LUNG_1145_Am_TX91_d02_rep2

source_name: mouse lung, alveolar macrophage, H1N1 influenza A TX91 (10^6 PFU), 2 days


title: LUNG_1117_Mo_0.6LD50PR8_d03_rep1


title: LUNG_1117_Ne_0.6LD50PR8_d03_rep1

source_name: mouse lung, neutrophil, H1N1 influenza A PR8 (0.6LD50), 3 days


title: LUNG_1117_Am_0.6LD50PR8_d03_rep1

source_name: mouse lung, alveolar macrophage, H1N1 influenza A PR8 (0.6LD50), 3 days


title: LUNG_810_Ly_TX91_d02_rep1b

description:
5398599011_E
Technical replicate of 5398599011_C.


title: LUNG_1117_Nh_0.6LD50PR8_d03_rep1

source_name: mouse lung, pulmonary CD45neg, H1N1 influenza A PR8 (0.6LD50), 3 days


title: LUNG_810_Nh_TX91_d02_rep1

source_name: mouse lung, pulmonary CD45neg, H1N1 influenza A TX91 (10^6 PFU), 2 days


title: LUNG_813_Am_Sham_d02_rep2

source_name: mouse lung, alveolar macrophage, sham, 2 days


title: LUNG_813_Ne_Sham_d02_rep2

source_name: mouse lung, neutrophil, sham, 2 days


title: LUNG_810_Mo_TX91_d02_rep1


title: LUNG_PR8D_d02_284_rep6

description:
4818547057_C
100LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (100LD50), 2 days

label_protocol:
Biotinylated cDNA were prepared after amplification with the Ovation RNA Amplification System V2 (NuGEN Technologies).
5ug of the amplified product was used for UNG-based abasic site abrasion and biotinylation according to NuGen's Illumina Solution application notes 2.

extract_protocol: Preserved whole lung pieces were homogenized in Trizol and total RNA was extracted, followed by clean-up and DNase I treatment with the QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol:
5- to 8-week-old male C57BL/6 were intranasally infected with different doses of H1N1 influenza A viruses or sham infected under light isoflurane anesthesia. Infectious doses were supplied in a volume of 50ul sterile pharmaceutical-grade physiological saline.
Lungs were harvested at various time points post infection. Immediately after euthanasia, lungs were perfused in situ via the right cardiac ventricle with PBS/EDTA (10mM) pre-warmed to 37°C and then immediately processed for down-stream applications.
Entire lungs were immediately transferred into 1.5ml RNAlater (Ambion), chopped into small pieces, left at 4°C overnight and then placed at -20°C for prolonged storage.

value: whole lung


title: LUNG_813_Mo_Sham_d02_rep2

source_name: mouse lung, Ly6Chi mononuclear myeloid cell, sham, 2 days

value: 5-8 weeks


title: LUNG_TX91_d02_444_rep6

description:
4818547057_D
TX91

source_name: mouse lung, H1N1 influenza A TX91 (10^6PFU), 2 days

value: male

value: H1N1 influenza A TX91 (10^6PFU)


title: LUNG_810_Ly_TX91_d02_rep1

value: lung


title: LUNG_SHAM__d02_274_rep6

description:
4818547057_A
Sham

source_name: mouse lung, sham, 2 days


title: LUNG_1007_Nh_Sham_Sd02_rep1

source_name: mouse lung, pulmonary CD45neg, sham, 2 days


title: LUNG_PR8C_d02_668_rep7

description:
4818547058_B
10LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (10LD50), 2 days


title: LUNG_1007_Ne_Sham_d02_rep1

value: neutrophil


title: LUNG_PR8D_d02_627_rep7

description:
4818547058_C
100LD50PR8

value: 2 days


title: LUNG_SHAM__d02_746_rep7

description:
4818547058_A
Sham


title: LUNG_ALUM_h06_887_rep5

description:
4818547050_E
162ugALUM

source_name: mouse lung, ALUM (162g), 6 hours

value: ALUM (162g)

value: 6 hours


title: LUNG_TX91_d02_445_rep7

description:
4818547058_D
TX91


title: LUNG_1007_Mo_Sham_d02_rep1

value: Ly6Chi mononuclear myeloid cell


title: LUNG_1007_Am_Sham_d02_rep1

value: alveolar macrophage


title: LUNG_ALUM_h06_886_rep4

description:
4818547050_D
162ugALUM


title: LUNG_PR8C_d02_667_rep6

description:
4818547057_B
10LD50PR8

value: H1N1 influenza A PR8 (10LD50)


title: LUNG_1007_Ly_Sham_d02_rep1

source_name: mouse lung, lymphocyte (BC, TC, NK), sham, 2 days

value: lymphocyte (BC, TC, NK)


title: LUNG_813_Nh_Sham_d02_rep2

value: pulmonary CD45neg


title: LUNG_ALUM_h06_885_rep3

description:
4818547050_C
162ugALUM


title: LUNG_810_Am_TX91-d02_rep1

value: H1N1 influenza A TX91 (10^6 PFU)


title: LUNG_ALUM_h06_883_rep2

description:
4818547050_B
162ugALUM


title: LUNG_ALUM_h06_882_rep1

description:
4818547050_A
162ugALUM


title: LUNG_813_Ly_Sham_d02_rep2

value: sham


title: LUNG_PR8D_d02_280_rep5

description:
4818547047_C
100LD50PR8

value: H1N1 influenza A PR8 (100LD50)


title: LUNG_TX91_d02_441_rep5

description:
4818547047_D
TX91

value: whole lung


title: LUNG_PR8C_d02_620_rep5

description:
4818547047_B
10LD50PR8

value: 5-8 weeks


title: LUNG_PR8B_d03_245_rep7

description:
4818547046_B
0.6LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (0.6LD50), 3 days

value: male

value: H1N1 influenza A PR8 (0.6LD50)

value: 3 days


title: LUNG_PR8D_d03_275_rep7

description:
4818547046_D
100LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (100LD50), 3 days


title: LUNG_SHAM__d02_273_rep3

description:
4818547041_A
Sham


title: LUNG_SHAM__d02_748_rep4

description:
4818547042_A
Sham


title: LUNG_PR8C_d02_669_rep4

description:
4818547042_B
10LD50PR8


title: LUNG_TX91_d02_443_rep3

description:
4818547041_D
TX91

value: H1N1 influenza A TX91 (10^6PFU)


title: LUNG_PR8C_d02_666_rep3

description:
4818547041_B
10LD50PR8

value: 2 days


title: LUNG_TX91_d02_745_rep4

description:
4818547042_D
TX91


title: LUNG_TX91_d03_396_rep7

description:
4818547046_E
TX91

source_name: mouse lung, H1N1 influenza A TX91 (10^6PFU), 3 days


title: LUNG_PR8D_d02_664_rep2

description:
4818547036_C
100LD50PR8


title: LUNG_SHAM__d02_270_rep5

description:
4818547047_A
Sham


title: LUNG_SHAM__d02_271_rep1

description:
4818547034_A
Sham


title: LUNG_PR8D_d02_283_rep3

description:
4818547041_C
100LD50PR8


title: LUNG_TX91_d02_442_rep1

description:
4818547034_D
TX91


title: LUNG_SHAM__d02_752_rep2

description:
4818547036_A
Sham


title: LUNG_PR8C_d02_751_rep2

description:
4818547036_B
10LD50PR8


title: LUNG_PR8C_d03_411_rep7

description:
4818547046_C
10LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (10LD50), 3 days


title: LUNG_PR8C_d02_621_rep1

description:
4818547034_B
10LD50PR8


title: LUNG_TX91_d02_747_rep2

description:
4818547036_D
TX91


title: LUNG_PR8C_d03_412_rep6

description:
4818547004_C
10LD50PR8


title: LUNG_TX91_d10_410_rep7

description:
4293381017_E
TX91

source_name: mouse lung, H1N1 influenza A TX91 (10^6PFU), 10 days

value: 10 days


title: LUNG_PR8D_d03_276_rep6

description:
4818547004_D
100LD50PR8


title: LUNG_PR8D_d02_660_rep4

description:
4818547042_C
100LD50PR8


title: LUNG_PR8D_d02_282_rep1

description:
4818547034_C
100LD50PR8


title: LUNG_SHAM__d03_236_rep7

description:
4818547046_A
Sham

source_name: mouse lung, sham, 3 days


title: LUNG_TX91_d03_397_rep6

description:
4818547004_E
TX91


title: LUNG_SHAM__d03_237_rep6

description:
4818547004_A
Sham


title: LUNG_PR8B_d03_246_rep6

description:
4818547004_B
0.6LD50PR8


title: LUNG_PR8A_d10_562_rep7

description:
4293381017_C
0.2LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (0.2LD50), 10 days

value: H1N1 influenza A PR8 (0.2LD50)


title: LUNG_PR8A_d03_558_rep7

description:
4293381017_D
0.2LD50PR8d3

source_name: mouse lung, H1N1 influenza A PR8 (0.2LD50), 3 days


title: LUNG_PR8B_d10_467_rep7

description:
4293381017_B
0.6LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (0.6LD50), 10 days


title: LUNG_PR8D_d03_279_rep5

description:
4293381001_D
100LD50PR8


title: LUNG_PR8C_d03_415_rep5

description:
4293381001_C
10LD50PR8


title: LUNG_PR8B_d03_249_rep5

description:
4293381001_B
0.6LD50PR8


title: LUNG_SHAM__d10_436_rep7

description:
4293381017_A
Sham

source_name: mouse lung, sham, 10 days


title: Liver-2-acetylaminofluorene-4

first: Nigel

middle: J

last: Gooderham

address: South Kensington Campus

department: Biomolecular Medicine

institute: Imperial College London

description: Hepatic miRNA profile

hyb_protocol: Labelled RNA was hybridized to microarray slides using the Agilent complete labelling and hybridisation kit

scan_protocol: The slides were scanned using an Agilent scanner (G2505B) and the data were extracted using the Agilent Feature Extraction v.10.1 software.

data_processing: For each miRNA the raw data  were threshold to 1, log2 transformed, and normalized to the 75th percentile.  MiRNAs which were not flagged as present in at least 2 samples in any group were filtered out from further analysis

organism: Rattus norvegicus

source_name: Male Fischer Rats liver at 90 days of study

label_protocol: 100ng total RNA was labelled using the Agilent complete labelling and hybridisation kit

growth_protocol: Eight-week old male Fischer (F344) rats were obtained from Harlac Olac (Netherlands) and left to acclimatise for seven days prior to the commencement of the experiment. The animals were examined to ensure that they were physically and behaviourally normal. During the study the rats were kept at five animals per cage and under controlled lighting (12h light cycles), humidity (30-70%), air flow (15 changes per hour), and temperature (22±3 C). The rats were given access to mains water and powdered diet ad libitum. Animals were randomly assigned to cages and treatment groups based on their pre-experimental weight.

extract_protocol: Total RNA was extracted from 100mg of frozen liver sample using Trizol. The extracted RNA was evaluated as suitable for further analysis in it had an 260:280 ratio above two and a RIN number, as determined with on an Agilent bioanalyser, above eight.

treatment_protocol: Animals were dietary treated daily with a carcinogenic dose or the maximum tolerated dose of each chemicals for a period of three months

value: Liver

tag: gender

value: 8 weeks-old

value: Fischer (F344)


title: Liver-Methapyrilene HCl-2

description: Hepatic miRNA profile

tag: strain

value: Methapyrilene HCl


title: Liver-2-acetylaminofluorene-1

description: Hepatic miRNA profile


title: Liver-Methapyrilene HCl-1

description: Hepatic miRNA profile


title: Liver-2-acetylaminofluorene-2

description: Hepatic miRNA profile


title: Liver-Chlorendic Acid-3

description: Hepatic miRNA profile

value: Chlorendic Acid


title: Liver-Methapyrilene HCl-4

description: Hepatic miRNA profile


title: Liver-Chlorendic Acid-4

description: Hepatic miRNA profile


title: Liver-2-acetylaminofluorene-3

description: Hepatic miRNA profile


title: Liver-Methapyrilene HCl-3

description: Hepatic miRNA profile


title: Liver-Chlorendic Acid-2

description: Hepatic miRNA profile


title: Liver-2-acetylaminofluorene-5

description: Hepatic miRNA profile


title: LUNG_SHAM__d10_531_rep6

description:
4270243064_A
Sham


title: Liver-Chlorendic Acid-1

description: Hepatic miRNA profile


title: LUNG_TX91_d03_400_rep5

description:
4293381001_E
TX91


title: LUNG_TX91_d10_544_rep6

description:
4270243064_E
TX91


title: LUNG_PR8B_d10_568_rep6

description:
4270243064_B
0.6LD50PR8


title: LUNG_PR8A_d10_563_rep6

description:
4270243064_C
0.2LD50PR8


title: LUNG_SHAM__d03_265_rep5

description:
4293381001_A
Sham


title: LUNG_PR8A_d03_554_rep5

description:
4270243062_D
0.2LD50PR8d3


title: LUNG_PR8A_d10_552_rep5

description:
4270243062_C
0.2LD50PR8


title: LUNG_TX91_d10_407_rep5

description:
4270243062_E
TX91


title: LUNG_PR8B_d10_462_rep5

description:
4270243062_B
0.6LD50PR8


title: LUNG_PR8A_d03_559_rep6

description:
4270243064_D
0.2LD50PR8d3


title: LUNG_SHAM__d10_252_rep5

description:
4270243062_A
Sham


title: Liver-Monuron-3

description: Hepatic miRNA profile

value: Monuron


title: Liver-Monuron-2

description: Hepatic miRNA profile


title: Liver-Monuron-1

description: Hepatic miRNA profile


title: Liver-Diethylhexylphthalate-1

description: Hepatic miRNA profile

value: Diethylhexylphthalate


title: Liver-Phenobarbital-1

description: Hepatic miRNA profile

value: Phenobarbital


title: Liver-Diethylhexylphthalate-3

description: Hepatic miRNA profile


title: Liver-Phenobarbital-3

description: Hepatic miRNA profile


title: Liver-Phenobarbital-2

description: Hepatic miRNA profile


title: Liver-Monuron-4

description: Hepatic miRNA profile


title: Liver-Diethylhexylphthalate-4

description: Hepatic miRNA profile


title: Liver-Benzophenone-5

description: Hepatic miRNA profile

value: Benzophenone


title: Liver-Benzophenone-4

description: Hepatic miRNA profile


title: Liver-Diethylhexylphthalate-2

description: Hepatic miRNA profile


title: LUNG_SHAM__d10_253_rep4

description:
4270243061_A
Sham

value: 5-8 weeks

value: whole lung

value: sham


title: Liver-Benzophenone-3

description: Hepatic miRNA profile

value: male


title: LUNG_TX91_d10_408_rep4

description:
4270243061_E
TX91

value: H1N1 influenza A TX91 (10^6PFU)


title: LUNG_PR8A_d03_556_rep4

description:
4270243061_D
0.2LD50PR8d3

value: 3 days


title: LUNG_SHAM__d01_482_rep7

description:
4270243056_A
Sham

source_name: mouse lung, sham, 1 day

value: 1 day


title: Liver-Benzophenone-2

description: Hepatic miRNA profile


title: LUNG_PR8B_d01_452_rep7

description:
4270243056_B
0.6LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (0.6LD50), 1 day

value: H1N1 influenza A PR8 (0.6LD50)


title: LUNG_TX91_d01_487_rep7

description:
4270243056_E
TX91

source_name: mouse lung, H1N1 influenza A TX91 (10^6PFU), 1 day


title: LUNG_PR8D_d01_477_rep7

description:
4270243056_D
100LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (100LD50), 1 day

value: H1N1 influenza A PR8 (100LD50)


title: LUNG_PR8C_d03_576_rep4

description:
4270243055_C
10LD50PR8

value: H1N1 influenza A PR8 (10LD50)


title: LUNG_PR8C_d01_472_rep7

description:
4270243056_C
10LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (10LD50), 1 day


title: LUNG_PR8B_d10_463_rep4

description:
4270243061_B
0.6LD50PR8

value: 10 days


title: LUNG_PR8D_d03_581_rep4

description:
4270243055_D
100LD50PR8


title: LUNG_PR8B_d03_567_rep4

description:
4270243055_B
0.6LD50PR8


title: LUNG_SHAM__d03_533_rep4

description:
4270243055_A
Sham


title: LUNG_PR8A_d10_555_rep4

description:
4270243061_C
0.2LD50PR8

value: H1N1 influenza A PR8 (0.2LD50)


title: LUNG_TX91_d03_543_rep4

description:
4270243055_E
TX91


title: Liver-Benzophenone-1

description: Hepatic miRNA profile

value: Liver

value: 8 weeks-old

value: Fischer (F344)


title: Liver-Diethylthiourea-4

description: Hepatic miRNA profile

value: Diethylthiourea


title: Liver-Diethylthiourea-2

description: Hepatic miRNA profile


title: Liver-Diethylthiourea-3

description: Hepatic miRNA profile


title: Liver-CON-5

description: Hepatic miRNA profile

value: control


title: Liver-CON-3

description: Hepatic miRNA profile


title: Liver-CON-4

description: Hepatic miRNA profile


title: Liver-CON-2

description: Hepatic miRNA profile


title: Liver-CON-1

description: Hepatic miRNA profile


title: day14-1000ppm-3

description: Hepatic miRNA profile

source_name: liver

treatment_protocol: Animals were dietary treated with 0, 50, 500 or 1000 ppm Phenobarbital

value: eight-weeks old

tag: phenobarbital dose (ppm)

tag: timepoint


title: Liver-Diethylthiourea-1

description: Hepatic miRNA profile

tag: tissue


title: day 14-1000ppm-2

description: Hepatic miRNA profile


title: day 14-1000ppm-1

description: Hepatic miRNA profile


title: LUNG_PR8A_d03_560_rep3

description:
4270243051_D
0.2LD50PR8d3

value: 5-8 weeks

value: whole lung


title: LUNG_SHAM__d10_535_rep3

description:
4270243051_A
Sham

value: male

value: sham


title: day14-500ppm-3

description: Hepatic miRNA profile


title: LUNG_TX91_d10_545_rep3

description:
4270243051_E
TX91

value: H1N1 influenza A TX91 (10^6PFU)


title: LUNG_PR8D_d03_583_rep3

description:
4270243050_D
100LD50PR8

value: 3 days


title: LUNG_SHAM__d03_539_rep3

description:
4270243050_A
Sham


title: LUNG_PR8C_d03_578_rep3

description:
4270243050_C
10LD50PR8


title: LUNG_PR8B_d03_569_rep3

description:
4270243050_B
0.6LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (0.6LD50), 3 days

value: H1N1 influenza A PR8 (0.6LD50)


title: LUNG_TX91_d03_547_rep3

description:
4270243050_E
TX91


title: LUNG_PR8A_d10_564_rep3

description:
4270243051_C
0.2LD50PR8


title: LUNG_PR8D_d01_584_rep6

description:
4270243049_D
100LD50PR8

value: H1N1 influenza A PR8 (100LD50)

value: 1 day


title: LUNG_PR8B_d10_570_rep3

description:
4270243051_B
0.6LD50PR8

value: 10 days


title: LUNG_TX91_d01_542_rep6

description:
4270243049_E
TX91


title: day14-500ppm-1

description: Hepatic miRNA profile


title: day14-50ppm-3

description: Hepatic miRNA profile


title: day14-50ppm-2

description: Hepatic miRNA profile


title: day14-50ppm-1

description: Hepatic miRNA profile


title: day14-500ppm-2

description: Hepatic miRNA profile


title: day 14-CON-3

description: Hepatic miRNA profile


title: day 14-CON-2

description: Hepatic miRNA profile


title: day 14-CON-1

description: Hepatic miRNA profile


title: LUNG_SHAM__d01_534_rep6

description:
4270243049_A
Sham


title: day 7-1000ppm-1

description: Hepatic miRNA profile


title: day 7-1000ppm-2

description: Hepatic miRNA profile


title: LUNG_PR8C_d01_585_rep6

description:
4270243049_C
10LD50PR8

value: H1N1 influenza A PR8 (10LD50)


title: day 7-500ppm-3

description: Hepatic miRNA profile

value: Liver


title: LUNG_TX91_d01_541_rep5

description:
4270243048_E
TX91


title: LUNG_PR8B_d01_574_rep6

description:
4270243049_B
0.6LD50PR8


title: LUNG_PR8B_d01_573_rep5

description:
4270243048_B
0.6LD50PR8


title: day7-500ppm-2

description: Hepatic miRNA profile


title: day 7-500ppm-1

description: Hepatic miRNA profile


title: LUNG_SHAM__d01_532_rep5

description:
4270243048_A
Sham


title: LUNG_PR8C_d01_577_rep5

description:
4270243048_C
10LD50PR8


title: LUNG_PR8D_d03_277_rep2

description:
4270243046_D
100LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (100LD50), 3 days


title: day7-50ppm-3

description: Hepatic miRNA profile


title: LUNG_TX91_d03_398_rep2

description:
4270243046_E
TX91

source_name: mouse lung, H1N1 influenza A TX91 (10^6PFU), 3 days


title: LUNG_PR8D_d01_582_rep5

description:
4270243048_D
100LD50PR8


title: day7-1000ppm-3

description: Hepatic miRNA profile


title: LUNG_TX91_d10_406_rep2

description:
4270243042_E
TX91


title: LUNG_SHAM__d03_238_rep2

description:
4270243046_A
Sham


title: LUNG_SHAM__d10_250_rep2

description:
4270243042_A
Sham


title: LUNG_PR8C_d03_413_rep2

description:
4270243046_C
10LD50PR8

source_name: mouse lung, H1N1 influenza A PR8 (10LD50), 3 days


title: day7-CON-2

description: Hepatic miRNA profile


title: LUNG_PR8A_d03_553_rep2

description:
4270243042_D
0.2LD50PR8d3

value: H1N1 influenza A PR8 (0.2LD50)


title: LUNG_PR8A_d10_551_rep2

description:
4270243042_C
0.2LD50PR8


title: LUNG_TX91_d10_409_rep1

description:
4270243039_E
TX91

source_name: mouse lung, H1N1 influenza A TX91 (10^6PFU), 10 days


title: day7-CON-1

description: Hepatic miRNA profile

value: Fischer (F344)


title: LUNG_PR8A_d03_557_rep1

description:
4270243039_D
0.2LD50PR8d3


title: day7-50ppm-2

description: Hepatic miRNA profile


title: day 3-1000ppm-3

description: Hepatic miRNA profile


title: LUNG_PR8B_d03_247_rep2

description:
4270243046_B
0.6LD50PR8


title: day7-50ppm-1

description: Hepatic miRNA profile


title: LUNG_PR8A_d10_561_rep1

description:
4270243039_C
0.2LD50PR8


title: day3-1000ppm-2

description: Hepatic miRNA profile


title: day3-1000ppm-1

description: Hepatic miRNA profile


title: day7-CON-3

description: Hepatic miRNA profile


title: day3-500ppm-2

description: Hepatic miRNA profile


title: day3-500ppm-1

description: Hepatic miRNA profile


title: day 3-50ppm-3

description: Hepatic miRNA profile


title: LUNG_PR8B_d10_465_rep1

description:
4270243039_B
0.6LD50PR8


title: LUNG_TX91_d03_399_rep1

description:
4270243038_E
TX91


title: day3-500ppm-3

description: Hepatic miRNA profile


title: LUNG_PR8C_d03_414_rep1

description:
4270243038_C
10LD50PR8


title: LUNG_SHAM__d10_254_rep1

description:
4270243039_A
Sham


title: LUNG_PR8B_d03_248_rep1

description:
4270243038_B
0.6LD50PR8


title: LUNG_TX91_d01_486_rep4

description:
4270243035_E
TX91


title: LUNG_PR8B_d10_458_rep2

description:
4270243037_C
0.6LD50PR8


title: day3-50ppm-1

description: Hepatic miRNA profile


title: day3-CON-3

description: Hepatic miRNA profile


title: LUNG_PR8D_d03_278_rep1

description:
4270243038_D
100LD50PR8


title: LUNG_SHAM__d03_239_rep1

description:
4270243038_A
Sham

source_name: mouse lung, sham, 3 days


title: day3-CON-1

description: Hepatic miRNA profile


title: day1-1000ppm-2

description: Hepatic miRNA profile


title: day 1-1000ppm-3

description: Hepatic miRNA profile


title: day1-500ppm-3

description: Hepatic miRNA profile


title: day 1-1000ppm-1

description: Hepatic miRNA profile


title: LUNG_PR8D_d01_476_rep4

description:
4270243035_D
100LD50PR8


title: day1-500ppm-2

description: Hepatic miRNA profile


title: day 3-50ppm-2

description: Hepatic miRNA profile


title: LUNG_PR8C_d01_471_rep4

description:
4270243035_C
10LD50PR8


title: LUNG_TX91_d01_488_rep3

description:
4270243034_E
TX91


title: LUNG_PR8B_d01_453_rep3

description:
4270243034_B
0.6LD50PR8


title: LUNG_SHAM__d01_481_rep4

description:
4270243035_A
Sham


title: LUNG_PR8D_d01_478_rep3

description:
4270243034_D
100LD50PR8


title: LUNG_PR8C_d01_473_rep3

description:
4270243034_C
10LD50PR8


title: day1-500ppm-1

description: Hepatic miRNA profile


title: LUNG_TX91_d01_489_rep2

description:
4270243030_E
TX91


title: LUNG_PR8B_d01_451_rep4

description:
4270243035_B
0.6LD50PR8


title: day1-50ppm-3

description: Hepatic miRNA profile


title: day1-50ppm-2

description: Hepatic miRNA profile


title: day1-50ppm-1

description: Hepatic miRNA profile


title: LUNG_PR8C_d01_474_rep2

description:
4270243030_C
10LD50PR8


title: LUNG_PR8B_d01_454_rep2

description:
4270243030_B
0.6LD50PR8


title: day1-CON-1

description: Hepatic miRNA profile


title: LUNG_PR8D_d01_479_rep2

description:
4270243030_D
100LD50PR8


title: LUNG_SHAM__d01_484_rep2

description:
4270243030_A
Sham


title: LUNG_TX91_d01_490_rep1

description:
4270243029_E
TX91


title: LUNG_PR8C_d01_475_rep1

description:
4270243029_C
10LD50PR8


title: LUNG_PR8D_d01_480_rep1

description:
4270243029_D
100LD50PR8


title: LUNG_SHAM__d01_483_rep3

description:
4270243034_A
Sham


title: day1-CON-3

description: Hepatic miRNA profile


title: LUNG_PR8B_d01_455_rep1

description:
4270243029_B
0.6LD50PR8


title: LUNG_SHAM__d01_485_rep1

description:
4270243029_A
Sham


title: day1-CON-2

description: Hepatic miRNA profile


title: LUNG 246C_d3PR8 (4225362018_E)

description:
4225362018_E
Amp batch 3 - BioRep2 - Hyb batch 5

hyb_protocol: 1.2ug of the biotinylated sample was used for hybridization. Hybridization conditions were adjusted according to NuGen's Illumina Solution application notes 2, or else the standard Illumina hybridization protocol was followed.

data_processing: The data were log2-transformed and normalised by quantile normalisation with GenePattern.

label: Biotin

source_name: mouse 246 lung, H1N1 influenza A infected, batch C

label_protocol:
Biotinylated cDNA were prepared after amplification with the Ovation RNA Amplification System V2 (NuGEN Technologies).
5ug of the amplified product was used for UNG-based abasic site abrasion and biotinylation according NuGen's Illumina Solution application notes 2.

treatment_protocol:
5- to 8-week-old male C57BL/6 were intranasally infected with 0.6LD50 of the mouse pathogenic H1N1 influenza A virus PR8 under light isoflurane anesthesia. Infectious doses were supplied in a volume of 50ul sterile pharmaceutical-grade physiological saline.
Lungs were harvested at various time points post infection. Immediately after euthanasia, lungs were perfused in situ via the right cardiac ventricle with PBS/EDTA (10mM) pre-warmed to 37°C and then immediately processed for down-stream applications.
Entire lungs were immediately transferred into 1.5ml RNAlater (Ambion), chopped into small pieces, left at 4°C overnight and then placed at -20°C for prolonged storage.

value: H1N1 influenza A 0.6LD50 PR8


title: LUNG 245A_d3PR8 (4225362018_F)

description:
4225362018_F
Amp batch 1 - BioRep1 - Hyb batch 5

source_name: mouse 245 lung, H1N1 influenza A infected, batch A


title: LUNG 247B_d3PR8 (4225362018_D)

description:
4225362018_D
Amp batch 2 - BioRep3 - Hyb batch 5

source_name: mouse 247 lung, H1N1 influenza A infected, batch B


title: LUNG 246A_d3PR8 (4225362018_B)

description:
4225362018_B
Amp batch 1 - BioRep2 - Hyb batch 5

source_name: mouse 246 lung, H1N1 influenza A infected, batch A


title: NOD.Treg.Rep1.Tech1

description:
Gene expression from sorted T cells
NOD_Toe1a_Tregs

hyb_protocol: aRNA was hybridized to 4x44K Mouse Whole Genome Microarrays (Agilent) for 18 hours following the manufacturer’s protocol.

scan_protocol: Microarrays were washed in 0.01x SSC/0.005% Triton X-102 at 40ºC, dried with HEPA filtered compressed nitrogen and scanned on an Agilent Technologies DNA Microarray Scanner at 5um resolution.

data_processing: The scanned images were analyzed with GeneSpring GX Software (Agilent) using default parameters.

source_name: regulatory T cells from NOD mouse. Biological replicate 1. Technical replicate 1.

label_protocol: Total RNA was  labeled using a modified protocol with the ULS aRNA Fluorescent Cy5 labeling kit (Kreatech Diagnostics, The Netherlands) and purified using RNA Clean and Concentrate spin columns according to manufacturer’s protocol (Zymo Research Corporation, Orange CA)

growth_protocol: All Foxp3+ Tregs were freshely sorted using Foxp3.GFP or based on CD25+GITRhi staining. CD4+CD25-GITR- cells were used as Tconv cells. RNA was isolated from ~30,000 cells and used for microarray analysis.

extract_protocol: Spleen and LN cells were used for sorting Tregs.

value: NOD

tag: t cell type

value: Sorted CD4+ regulatory T cells from spleen and lymph nodes


title: NOD.Treg.Rep1.Tech2

source_name: regulatory T cells from NOD mouse. Biological replicate 1. Technical replicate 2.


title: NOD.Treg.Rep2.Tech1

description:
Gene expression from sorted T cells
NOD_Toe1b_Tregs

source_name: regulatory T cells from NOD mouse. Biological replicate 2. Technical replicate 1.


title: NOD.Treg.Rep2.Tech2

source_name: regulatory T cells from NOD mouse. Biological replicate 2. Technical replicate 2.


title: LUNG 245A_d3PR8 (4225362017_D)

description:
4225362017_D
Amp batch 1 - BioRep1 - Hyb batch 5

value: 5-8 weeks


title: LUNG 246B_d3PR8 (4225362017_E)

description:
4225362017_E
Amp batch 2 - BioRep2 - Hyb batch 5

source_name: mouse 246 lung, H1N1 influenza A infected, batch B

value: whole lung


title: NOD.Treg.Rep3.Tech1

description:
Gene expression from sorted T cells
NOD_Toe7_Tregs

source_name: regulatory T cells from NOD mouse. Biological replicate 3. Technical replicate 1.


title: LUNG 245C_d3PR8 (4225362018_C)

description:
4225362018_C
Amp batch 3 - BioRep1 - Hyb batch 5

source_name: mouse 245 lung, H1N1 influenza A infected, batch C

value: male


title: LUNG 247B_d3PR8 (4225362017_F)

description:
4225362017_F
Amp batch 2 - BioRep3 - Hyb batch 5


title: LUNG 247B_d3PR8 (4225362018_A)

description:
4225362018_A
Amp batch 2 - BioRep3 - Hyb batch 5


title: NOD.Treg.Rep3.Tech2

source_name: regulatory T cells from NOD mouse. Biological replicate 3. Technical replicate 2.


title: NOD.Tconv.Rep4.Tech2

description:
Gene expression from sorted T cells
NOD_Toe7_Tconv

source_name: conventional T cells from NOD mouse. Biological replicate 4. Technical replicate 2.

value: Sorted CD4+ conventional T cells from spleen and lymph nodes


title: LUNG 247C_d3PR8 (4225362017_B)

description:
4225362017_B
Amp batch 3 - BioRep3 - Hyb batch 5

source_name: mouse 247 lung, H1N1 influenza A infected, batch C


title: NOD.Tconv.Rep4.Tech1

source_name: conventional T cells from NOD mouse. Biological replicate 4. Technical replicate 1.


title: LUNG 246C_d3PR8 (4225362017_A)

description:
4225362017_A
Amp batch 3 - BioRep2 - Hyb batch 4


title: Lung 245B_d3PR8 (4225362016_D)

description:
4225362016_D
Amp batch 2 - BioRep1 - Hyb batch 4

source_name: mouse 245 lung, H1N1 influenza A infected, batch B


title: 3h Submerged Arabidopsis (c-myc tagged WRKY22/Columbia) Replicate 5

city: Taipei

first: Fu-Chiun

last: Hsu

address: No. 128, Sec. 2, Academia Road, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

description: ChIP-chip c-myc tagged WRKY22/ Columbia (Cy5/Cy3) with anti-c-myc antibody (9E10)

hyb_protocol: The labeled DNA was hybridized to NimbleGen A. thaliana ChIP-chip 385K Minimal Promoter Arrays (NimbleGen).  The hybridization and washing of arrays were performed following the Nimblegen standard operating protocols (www.nimblegen.com).

scan_protocol: Array images were acquired with Axon GenePix 4000B and GenePix 6.0 software (Axon Instruments, Inc., Union City, CA, USA).

data_processing: The images were then converted to scaled Log2-ratio of the probes for peak finding analysis according to the genomic position in NimbleScan software (NimbleGen).  Peaks of enriched DNA fragments were identified and mapped to promoters in the Arabidopsis genome using the default setting in the NimbleScan software (NimbleGen) according to the manufacturer’s description.

organism: Arabidopsis thaliana

source_name: 3h Submerged Arabidopsis (c-myc tagged WRKY22)

label_protocol: One hundred pg of DNA was amplified using the GenomePlex Whole Genome Amplification Kit (Sigma-Aldrich, St. Louis, MO, USA) according to the manufacturer’s instructions.  The amplified DNA was then purified using the QIAquick PCR cleanup kit (Qiagen).  The purified DNA was quantified using a Nanodrop spectrophotometer and labeled with Cy3 (for Columbia) and Cy5 (for WRKY22-18×c-myc in wrky22-ko2) fluorescent dyes.   Labeling experiments were performed at the DNA Microarray Core facility, Institute of Plant and Microbial Biology, Academia Sinica, as described on http://ipmb.sinica.edu.tw/microarray/protocol.htm.

growth_protocol: Transgenic lines expressing c-myc tagged WRKY22 in wrky22-ko2 background plants were generated using a T-DNA insertion containing 1000 bp of upstream promoter sequence and WRKY22 full-length genomic DNA in frame with 18 copies of c-myc sequence at 3’ end in a pMDC110 derived binary vector.  The recombinant plasmid was then mobilized into Agrobacterium tumefaciens strain GV3101 and the resulting GV3101 strain was used to transform wrky22-ko2 plants through floral dipping.  Seeds were sown on plates with 0.55% of phytagel (Sigma-Aldrich, St. Louis, MO, USA) in half-strength MS medium (Duchefa Biochemie BV, Haarlem, Netherlands) containing 0.5% sucrose at pH 5.7, and kept at 4oC in the dark for 3 days to achieve uniform germination.  The plates were then transferred to a growth chamber and placed vertically, and plants were grown at 22ºC under a 16-hour light (81 μmol s-1 m-2)/8-hour dark cycle.  5-day-old seedlings were transplanted onto fresh plates and the plates were placed vertically to prevent roots from growing into medium.  The transplanted seedlings were grown in the growth chamber until they were 14-day-old.

extract_protocol: Protocols describing materials and methods for ChIP have previously been described in detail by Kaufmann et al. (2010).  Briefly, 1.5 g of 14-day-old seedlings was chemically crosslinked by the addition of 1% formaldehyde for 15 minutes at room temperature.  The fixed seedlings were rinsed five times with MC buffer (10 mM sodium phosphate, pH 7, 50 mM NaCl and 0.1 M sucrose) and frozen in liquid nitrogen.  The frozen samples were homogenized, filtered, centrifuged and washed to isolate nuclei.  The nuclear pellets were resuspended, lysed and sonicated to shear crosslinked DNA.  The sonication was carried out with a Bioruptor UCD-200 (Diagenode, Liège, Belgium) until the average size of sheared DNA was approximately 500 bp.  The sonicated chromatin was pre-cleared with protein-A agarose beads for 1 hour and immunoprecipitated with 2 μg of anti-c-myc antibody for 2 hours followed by addition of protein-A agarose beads for 3 hours.  The beads were washed five times with IP buffer (50 mM HEPES, pH 7.5, 150 mM NaCl, 5 mM MgCl2, 10 μM ZnSO4, 1% Triton X-100 and 0.05% SDS).  The bound IP complexes were eluted with elution buffer (0.1 M glycine, 0.5 M NaCl and 0.05% Tween-20, pH 2.8) and neutralized with 1 M Tris, pH 9.0.  The eluantes were digested with proteinase K overnight at 37 oC to remove proteins followed by incubation at 65 oC for at least 6 hours to reverse crosslinking.  The reverse crosslinked DNA was then purified by extraction with phenol:chloroform:isoamyl alcohol and ethanol precipitation in the presence of glycogen.  The DNA pellets were washed with 70 % of ethanol, air dried and resuspended in TE 8.0.

treatment_protocol: Plates with plants on the surface of the medium were placed into half-strength MS liquid medium that was bubbled with 3 % oxygen balanced with nitrogen for 3h.  The liquid MS medium was pretreated with 3% oxygen for one hour before use.

value: submerged for 3h

value: c-myc tagged WRKY22

tag: genetic background

value: Columbia

value: seedling

tag: chip antibody

tag: chip antibody manufacturer

value: The Developmental Studies Hybridoma Bank (DSHB), University of Iowa, USA

source_name: 3h Submerged Arabidopsis (Columbia)

value: wt


title: NOD.Tconv.Rep3.Tech2

description:
Gene expression from sorted T cells
NOD_Toe6_Tconv

source_name: conventional T cells from NOD mouse. Biological replicate 3. Technical replicate 2.


title: Lung 245C_d3PR8 (4225362016_F)

description:
4225362016_F
Amp batch 3 - BioRep1 - Hyb batch 4

value: 3 days


title: Lung 246B_d3PR8 (4225362016_E)

description:
4225362016_E
Amp batch 2 - BioRep2 - Hyb batch 4


title: 3h Submerged Arabidopsis (c-myc tagged WRKY22/Columbia) Replicate 3

tag: treatment

growth_protocol: Seeds were sown on plates with 0.55% of phytagel (Sigma-Aldrich, St. Louis, MO, USA) in half-strength MS medium (Duchefa Biochemie BV, Haarlem, Netherlands) containing 0.5% sucrose at pH 5.7, and kept at 4oC in the dark for 3 days to achieve uniform germination.  The plates were then transferred to a growth chamber and placed vertically, and plants were grown at 22ºC under a 16-hour light (81 μmol s-1 m-2)/8-hour dark cycle.  5-day-old seedlings were transplanted onto fresh plates and the plates were placed vertically to prevent roots from growing into medium.  The transplanted seedlings were grown in the growth chamber until they were 14-day-old.


title: Lung 247C_d3PR8 (4225362016_C)

description:
4225362016_C
Amp batch 3 - BioRep3 - Hyb batch 4