title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 E3

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 E3


title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 F10

status: Public on Jun 28 2016

type: RNA

city: New Haven

first: Andrew

last: Martins

state: Connecticut

address: 100 College Street Rm 1155

department: Immunobiology

country: USA

institute: Yale School of Medicine

data_processing: We convert gene expression data exported from Fluidigm Real-time PCR Analysis software from Ct (Cycle threshold) units to the more convenient Et=40-Ct units. To correct for plate-plate effects, we shifted all detected gene measurements in a plate by a plate-specific global factor, which is chosen such that the median ERCC-0003 level of the shifted data across all samples in the plate becomes the same across all plates. We then do sample-level normalization by utilizing the variation of control mRNA levels across samples within/across plates. This sample-to-sample variation in ERCC levels correlated with that of highly expressed genes), suggesting well-to-well differences in the starting amount of mRNA or other such technical factors at play besides independent measurement errors. To correct for this potential technical variation, we fitted a linear regression model (expressed in the notation of statistical environment R as “Gene-expression ~ Plate + ERCC-0002-expression + ERCC-0003-expression + ERCC-0044-expression”) separately in each condition, and took the fit residuals as the normalized log-expression of the gene. Note that this regression model, which allows plate effects to be different for different genes, is fitted to the already plate-level normalized data discussed above where the same plate effect was assumed for all genes.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 F10

label_protocol: Sort plates containing Ten cell RNA were thawed, and 1.35 uL of STA mix (1.25 uL of a pool of 96 Taqman assays at 0.2x concentration, and 0.1 uL Superscript III/Platinum Taq mix (CellsDirect kit, Life Technologies)) were added to each well. Plates were then sealed with clear film (Bio-rad) and centrifuged at 2000x G for 3 minutes and STA was run on a CFX Connect thermal cycler (Bio-rad) with the following cycling parameters: 50°C for 15 mins, 95°C for 2 minutes, then 18 cycles of 95°C for 15 seconds and 60°C for 4 minutes. Plates were then placed on ice and cold 10 mM Tris pH 8.0, 0.1 mM EDTA buffer was added to each well at 20 uL per well. Samples were then analyzed by qPCR on the Fluidigm Biomark instrument using 96.96 chips according to manufacturer’s instructions (Fluidigm). Briefly, 2.25 uL per well of each amplified, diluted single cell sample was mixed with 2.5 uL Ssofast 2X Probes Supermix (Bio-rad) that had 0.5X ROX reference dye added (from the CellsDirect Kit, Life Technologies), and 0.25 uL sample loading reagent (Fluidigm). Taqman assays (20x concentration) were combined 1:1 with Assay loading reagent (Fluidigm). Sample and assay mixes were then added to the wells of the 96.96 chip for gene expression measurement. The normal speed cycling gene expression protocol was used, with 40 cycles of amplification. Data was exported from Fluidigm Real-time PCR Analysis software version 3.1.3, using Linear (Derivative) Baseline method, a global threshold of 0.01, and a 0.65 quality threshold, parameters which were found to exclude non-specific amplification and reduce plate-plate variation.

growth_protocol: Peripheral blood leukapheresis sampleswas obtained from healthy donors. Mononuclear cells were isolated using Ficoll-Paque PLUS (low endotoxin) gradient centrifugation (GE Healthcare Life Sciences). Monocytes were isolated from mononuclear cells using the Dynabeads Untouched Human Monocytes negative isolation kit (Life Technologies), which utilizes biotinylated monoclonal antibodies towards CD3, CD7, CD16a, CD16b, CD19, CD56, CD123, and CD235a, with streptavidin linked magnetic beads for depletion of non-monocyte cells. Isolated monocytes were frozen in 10% DMSO (Sigma), 40% Human AB serum (Gemini Biosciences) and 50% X-vivo 15 media (Lonza) by the following procedure: isolated monocytes obtained using the Dynabeads isolation kit were resuspended at 20 million/mL in 4°C X-vivo 15 media (Phenol red and gentamycin free), and an equal volume of filtered, 4°C 20%DMSO/80% Human AB serum was added dropwise while mixing the cell suspension. Cells were immediately transferred to cyrovials and frozen in a Nalgene Mr. Frosty cell freezing container (Thermo Scientific) in a -80 freezer for 24 hours, followed by transfer to liquid nitrogen storage. For use, frozen monocyte vials were quickly thawed in a 37°C water bath and resuspended in X-vivo 15 media (phenol red and gentamycin free) that had been pre-equilibrated in a 37°C, 5% CO2 incubator. Cells were plated on tissue-culture treated 6-well dishes (Corning) at 1 million cells/mL in 2 mL per well. Human macrophage-colony stimulating factor (M-CSF, Peprotech or R&D systems) was added to the media at a concentration of 100 ng/mL. On day 3 and day 6 of differentiation, all culture media was removed from the dish and replaced by fresh, 37°C, 5% CO2 incubator equilibrated X-vivo 15 containing 100 ng/mL M-CSF.

extract_protocol: Harvested macrophages were incubated on ice in PBS containing 5% human AB serum for 15 minutes, followed by surface antibody staining for 30 minutes on ice, in the same buffer, with the following antibody cocktail: FITC anti-CD36, clone 5-271 (Biolegend); PE anti-CD163, clone GHI/61 (Biolegend); PerCP anti-CD16, clone 3G8 (Biolegend); PE-Cy7 anti-CD197, clone G043H7 (Biolegend); APC-Cy7 anti-CD206, clone 15-2 (Biolegend); Alexa Fluor 700 anti-CD195, clone HEK/1/85a (Biolegend); Alexa Fluor 647 anti-CD192, clone TG5/CCR2 (Biolegend); Pacific Orange anti-CD14, clone TüK4 (Life Technologies). Following staining, cells were washed once with ice cold PBS, and resuspended in ice cold PBS containing a 1 in 1000 dilution of Pacific Blue Fixable Live/Dead stain (Life Technologies), which is a fluorescent dye reactive with cellular amines. When the cell membrane becomes permeable, the dye gains access to intracellular amines and hence the fluorescence of the cell increases. For sorting, cells were gated upon Forward scatter (FSC)-width versus side scatter(SSC)-area for doublet discrimination, followed by gating on Pacific blue low (membrane intact) cells (versus FSC-area). A 100 μm nozzle was used at 20 PSI pressure and a drop drive frequency of 34.5 kHz. Sorting was performed on a FACSAriaII (Becton Dickinson) and FACSDiva version 6.1.3 software using Single cell precision mode with default parameters (Yield mask = 0, Purity mask = 32, Phase mask = 16). Sort alignment was checked immediately before sorting, by sorting beads onto a covered PCR plate and confirming that the droplets land in the center of several different wells across the plate. Cells (ten cells per well) were deposited into individual wells of a low-profile 96 well PCR plate (Bio-rad) containing 2.5 uL CellsDirect 2x Reaction Mix (Life Technologies), 0.05 uL Ambion SUPERase-In RNAse inhibitor (Life technologies), and 1 uL RNAse-free water. Cells from different treatment groups were sorted into alternating wells across the plate, to avoid positional or “edge” effects across the plate. Each plate contained a no template control well, and a seven point dilution of a pooled RNA sample derived from a combination of RNA isolated from non-treated, IFNγ, and IL-4 treated macrophages, as a reference positive control. Control RNA was isolated using the miRNeasy mini kit (Qiagen). All wells except the positive control wells also contained ERCC RNA reference standards (Life Technologies) spiked in at 1/50,000 final dilution from the stock ERCC mixture.

treatment_protocol: Fresh media on day 6 was also supplemented with 100 ng/mL Interferon (IFN)γ and 100 ng/mL Tumor necrosis factor α (IFNγ and TNFα treated cells), 100 ng/mL Interleukin 4 (IL-4 treated cells), 10 ng/mL IL-10 (IL-10 treated cells) (cytokines from Peprotech), or M-CSF alone (Control). Cells were harvested for analysis 24 hours after treatment.

tag: plateid

tag: treatment time

tag: growth factor

value: MCSF

tag: treatment

value: IFN+TNF

tag: cell number

tag: well


title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 C5

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 C5


title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 B6

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 B6


title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 E7

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 E7


title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 B2

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 B2


title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 A7

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 A7


title: p4dJul9.10cell 24hr MCSF CNT 10 H9

source_name: p4dJul9.10cell 24hr MCSF CNT 10 H9

value: CNT


title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 A11

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 A11


title: p4dJul9.10cell 24hr MCSF CNT 10 H5

source_name: p4dJul9.10cell 24hr MCSF CNT 10 H5


title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 B10

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 B10


title: FM2-0

status: Public on Jul 01 2016

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

country: Japan

institute: Faculty of Medicine, Shimane University

description: Before n-3 PUFA therapy

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

label: Biotin

source_name: Thigh muscle_Before n-3 PUFA therapy

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA.

growth_protocol: Muscle gene expression was examined in a subset of 10 healthy 60-85 year old men with the largest hypertrophy response (change in thigh muscle volume).

extract_protocol: Thigh muscle biopsies were obtained and immediately frozen in liquid nitrogen. Total RNA was isolated from frozen tissue sample by using Trizol (Invitrogen).

treatment_protocol: After baseline studies, subjects were instructed to take four 1-gram pills per day providing a total of 1.86 g eicosapentaenoic acid [20:5 n-3] and 1.50 g docosahexaenoic acid [22:6 n-3] per day for 6 months.

tag: tissue

value: muscle

tag: treatment status

value: Before

tag: gender

value: male

tag: age

value: 60-85 years


title: p4dJul9.10cell 24hr MCSF CNT 10 G4

source_name: p4dJul9.10cell 24hr MCSF CNT 10 G4


title: p4dJul9.10cell 24hr MCSF CNT 10 G8

source_name: p4dJul9.10cell 24hr MCSF CNT 10 G8


title: p4dJul9.10cell 24hr MCSF CNT 10 F7

source_name: p4dJul9.10cell 24hr MCSF CNT 10 F7


title: p4dJul9.10cell 24hr MCSF CNT 10 G12

source_name: p4dJul9.10cell 24hr MCSF CNT 10 G12


title: p4dJul9.10cell 24hr MCSF CNT 10 D9

source_name: p4dJul9.10cell 24hr MCSF CNT 10 D9


title: p4dJul9.10cell 24hr MCSF CNT 10 F3

source_name: p4dJul9.10cell 24hr MCSF CNT 10 F3


title: p4dJul9.10cell 24hr MCSF IFN+TNF 10 A3

source_name: p4dJul9.10cell 24hr MCSF IFN+TNF 10 A3


title: p4dJul9.10cell 24hr MCSF CNT 10 E6

source_name: p4dJul9.10cell 24hr MCSF CNT 10 E6


title: p4dJul9.10cell 24hr MCSF CNT 10 F11

source_name: p4dJul9.10cell 24hr MCSF CNT 10 F11


title: p4dJul9.10cell 24hr MCSF CNT 10 D5

source_name: p4dJul9.10cell 24hr MCSF CNT 10 D5


title: p4dJul9.10cell 24hr MCSF CNT 10 E2

source_name: p4dJul9.10cell 24hr MCSF CNT 10 E2


title: p4dJul9.10cell 24hr MCSF CNT 10 E10

source_name: p4dJul9.10cell 24hr MCSF CNT 10 E10


title: p4dJul9.10cell 24hr MCSF CNT 10 C8

source_name: p4dJul9.10cell 24hr MCSF CNT 10 C8


title: p4dJul9.10cell 24hr MCSF CNT 10 C12

source_name: p4dJul9.10cell 24hr MCSF CNT 10 C12


title: p4dJul9.10cell 24hr MCSF CNT 10 B3

source_name: p4dJul9.10cell 24hr MCSF CNT 10 B3


title: p4dJul9.10cell 24hr MCSF CNT 10 B7

source_name: p4dJul9.10cell 24hr MCSF CNT 10 B7


title: p4dJul9.10cell 24hr MCSF CNT 10 A10

source_name: p4dJul9.10cell 24hr MCSF CNT 10 A10


title: p4dJul9.10cell 24hr MCSF CNT 10 A2

source_name: p4dJul9.10cell 24hr MCSF CNT 10 A2


title: p4dJul9.10cell 24hr MCSF CNT 10 A6

source_name: p4dJul9.10cell 24hr MCSF CNT 10 A6


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 H4

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 H4


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 H8

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 H8


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 G5

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 G5


title: p4dJul9.10cell 24hr MCSF CNT 10 C4

source_name: p4dJul9.10cell 24hr MCSF CNT 10 C4


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 F10

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 F10


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 E3

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 E3


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 E11

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 E11


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 G9

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 G9


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 F6

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 F6


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 H12

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 H12


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 D4

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 D4


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 D8

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 D8


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 F2

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 F2


title: p4dJul9.10cell 24hr MCSF CNT 10 B11

source_name: p4dJul9.10cell 24hr MCSF CNT 10 B11


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 B2

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 B2


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 B6

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 B6


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 D12

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 D12


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 A11

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 A11


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 A3

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 A3


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 B10

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 B10


title: p3dJul9.10cell 24hr MCSF CNT 10 F3

source_name: p3dJul9.10cell 24hr MCSF CNT 10 F3


title: p3dJul9.10cell 24hr MCSF CNT 10 H5

source_name: p3dJul9.10cell 24hr MCSF CNT 10 H5


title: p3dJul9.10cell 24hr MCSF CNT 10 H9

source_name: p3dJul9.10cell 24hr MCSF CNT 10 H9


title: p3dJul9.10cell 24hr MCSF CNT 10 G8

source_name: p3dJul9.10cell 24hr MCSF CNT 10 G8


title: p3dJul9.10cell 24hr MCSF CNT 10 F7

source_name: p3dJul9.10cell 24hr MCSF CNT 10 F7


title: p3dJul9.10cell 24hr MCSF CNT 10 E6

source_name: p3dJul9.10cell 24hr MCSF CNT 10 E6


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 A7

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 A7


title: p3dJul9.10cell 24hr MCSF CNT 10 E10

source_name: p3dJul9.10cell 24hr MCSF CNT 10 E10


title: p3dJul9.10cell 24hr MCSF CNT 10 D9

source_name: p3dJul9.10cell 24hr MCSF CNT 10 D9


title: p3dJul9.10cell 24hr MCSF CNT 10 G12

source_name: p3dJul9.10cell 24hr MCSF CNT 10 G12


title: p3dJul9.10cell 24hr MCSF CNT 10 C4

source_name: p3dJul9.10cell 24hr MCSF CNT 10 C4


title: p3dJul9.10cell 24hr MCSF CNT 10 C12

source_name: p3dJul9.10cell 24hr MCSF CNT 10 C12


title: p3dJul9.10cell 24hr MCSF CNT 10 G4

source_name: p3dJul9.10cell 24hr MCSF CNT 10 G4


title: p3dJul9.10cell 24hr MCSF CNT 10 B7

source_name: p3dJul9.10cell 24hr MCSF CNT 10 B7


title: p3dJul9.10cell 24hr MCSF CNT 10 C8

source_name: p3dJul9.10cell 24hr MCSF CNT 10 C8


title: p3dJul9.10cell 24hr MCSF CNT 10 A10

source_name: p3dJul9.10cell 24hr MCSF CNT 10 A10


title: p3dJul9.10cell 24hr MCSF CNT 10 A2

source_name: p3dJul9.10cell 24hr MCSF CNT 10 A2


title: p3dJul9.10cell 24hr MCSF CNT 10 B11

source_name: p3dJul9.10cell 24hr MCSF CNT 10 B11


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 H8

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 H8


title: p3dJul9.10cell 24hr MCSF CNT 10 F11

source_name: p3dJul9.10cell 24hr MCSF CNT 10 F11


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 H4

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 H4


title: p3dJul9.10cell 24hr MCSF CNT 10 B3

source_name: p3dJul9.10cell 24hr MCSF CNT 10 B3


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 H12

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 H12


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 F10

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 F10


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 F2

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 F2


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 F6

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 F6


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 G5

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 G5


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 E7

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 E7


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 G9

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 G9


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 E11

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 E11


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 D4

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 D4


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 D8

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 D8


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 E3

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 E3


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 C9

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 C9


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 B6

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 B6


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 C5

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 C5


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 B10

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 B10


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 E7

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 E7


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 B2

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 B2


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 A7

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 A7


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 A3

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 A3


title: p2dJul9.10cell 24hr MCSF CNT 10 H9

source_name: p2dJul9.10cell 24hr MCSF CNT 10 H9


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 A11

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 A11


title: p2dJul9.10cell 24hr MCSF CNT 10 H5

source_name: p2dJul9.10cell 24hr MCSF CNT 10 H5


title: p2dJul9.10cell 24hr MCSF CNT 10 G8

source_name: p2dJul9.10cell 24hr MCSF CNT 10 G8


title: p2dJul9.10cell 24hr MCSF IFN+TNF 10 D12

source_name: p2dJul9.10cell 24hr MCSF IFN+TNF 10 D12


title: p2dJul9.10cell 24hr MCSF CNT 10 F3

source_name: p2dJul9.10cell 24hr MCSF CNT 10 F3


title: p2dJul9.10cell 24hr MCSF CNT 10 F7

source_name: p2dJul9.10cell 24hr MCSF CNT 10 F7


title: p2dJul9.10cell 24hr MCSF CNT 10 G12

source_name: p2dJul9.10cell 24hr MCSF CNT 10 G12


title: p2dJul9.10cell 24hr MCSF CNT 10 E6

source_name: p2dJul9.10cell 24hr MCSF CNT 10 E6


title: p2dJul9.10cell 24hr MCSF CNT 10 G4

source_name: p2dJul9.10cell 24hr MCSF CNT 10 G4


title: p2dJul9.10cell 24hr MCSF CNT 10 F11

source_name: p2dJul9.10cell 24hr MCSF CNT 10 F11


title: p2dJul9.10cell 24hr MCSF CNT 10 E2

source_name: p2dJul9.10cell 24hr MCSF CNT 10 E2


title: p2dJul9.10cell 24hr MCSF CNT 10 E10

source_name: p2dJul9.10cell 24hr MCSF CNT 10 E10


title: p3dJul9.10cell 24hr MCSF CNT 10 D5

source_name: p3dJul9.10cell 24hr MCSF CNT 10 D5


title: p2dJul9.10cell 24hr MCSF CNT 10 D9

source_name: p2dJul9.10cell 24hr MCSF CNT 10 D9


title: p2dJul9.10cell 24hr MCSF CNT 10 D5

source_name: p2dJul9.10cell 24hr MCSF CNT 10 D5


title: p2dJul9.10cell 24hr MCSF CNT 10 B3

source_name: p2dJul9.10cell 24hr MCSF CNT 10 B3


title: p2dJul9.10cell 24hr MCSF CNT 10 B7

source_name: p2dJul9.10cell 24hr MCSF CNT 10 B7


title: p2dJul9.10cell 24hr MCSF CNT 10 B11

source_name: p2dJul9.10cell 24hr MCSF CNT 10 B11


title: p2dJul9.10cell 24hr MCSF CNT 10 C8

source_name: p2dJul9.10cell 24hr MCSF CNT 10 C8


title: p2dJul9.10cell 24hr MCSF CNT 10 A6

source_name: p2dJul9.10cell 24hr MCSF CNT 10 A6


title: p2dJul9.10cell 24hr MCSF CNT 10 A2

source_name: p2dJul9.10cell 24hr MCSF CNT 10 A2


title: p2dJul9.10cell 24hr MCSF CNT 10 A10

source_name: p2dJul9.10cell 24hr MCSF CNT 10 A10


title: p2dJul9.10cell 24hr MCSF CNT 10 C12

source_name: p2dJul9.10cell 24hr MCSF CNT 10 C12


title: p2dJul9.10cell 24hr MCSF CNT 10 C4

source_name: p2dJul9.10cell 24hr MCSF CNT 10 C4


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 H8

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 H8


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 H12

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 H12


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 E7

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 E7


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 F10

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 F10


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 F2

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 F2


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 G9

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 G9


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 E3

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 E3


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 F6

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 F6


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 E11

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 E11


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 D8

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 D8


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 C9

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 C9


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 D12

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 D12


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 C5

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 C5


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 B6

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 B6


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 B2

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 B2


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 H4

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 H4


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 A7

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 A7


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 B10

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 B10


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 G5

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 G5


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 D4

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 D4


title: p1dJul9.10cell 24hr MCSF CNT 10 G4

source_name: p1dJul9.10cell 24hr MCSF CNT 10 G4


title: p1dJul9.10cell 24hr MCSF CNT 10 G8

source_name: p1dJul9.10cell 24hr MCSF CNT 10 G8


title: p1dJul9.10cell 24hr MCSF CNT 10 H5

source_name: p1dJul9.10cell 24hr MCSF CNT 10 H5


title: p1dJul9.10cell 24hr MCSF CNT 10 G12

source_name: p1dJul9.10cell 24hr MCSF CNT 10 G12


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 A11

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 A11


title: p1dJul9.10cell 24hr MCSF CNT 10 H9

source_name: p1dJul9.10cell 24hr MCSF CNT 10 H9


title: p1dJul9.10cell 24hr MCSF CNT 10 E2

source_name: p1dJul9.10cell 24hr MCSF CNT 10 E2


title: p1dJul9.10cell 24hr MCSF CNT 10 F11

source_name: p1dJul9.10cell 24hr MCSF CNT 10 F11


title: p1dJul9.10cell 24hr MCSF CNT 10 B7

source_name: p1dJul9.10cell 24hr MCSF CNT 10 B7


title: p1dJul9.10cell 24hr MCSF CNT 10 D9

source_name: p1dJul9.10cell 24hr MCSF CNT 10 D9


title: p1dJul9.10cell 24hr MCSF CNT 10 D5

source_name: p1dJul9.10cell 24hr MCSF CNT 10 D5


title: p1dJul9.10cell 24hr MCSF CNT 10 B3

source_name: p1dJul9.10cell 24hr MCSF CNT 10 B3


title: p1dJul9.10cell 24hr MCSF CNT 10 F3

source_name: p1dJul9.10cell 24hr MCSF CNT 10 F3


title: p1dJul9.10cell 24hr MCSF CNT 10 A2

source_name: p1dJul9.10cell 24hr MCSF CNT 10 A2


title: p1dJul9.10cell 24hr MCSF CNT 10 A6

source_name: p1dJul9.10cell 24hr MCSF CNT 10 A6


title: p1dJul9.10cell 24hr MCSF CNT 10 A10

source_name: p1dJul9.10cell 24hr MCSF CNT 10 A10


title: p5AdJul9 24hr MCSF IFN+TNF H4

status: Public on Jun 17 2016

description: Single human monocyte-dervide macrophage assayed by fluidigm qPCR

data_processing: We convert gene expression data exported from Fluidigm Real-time PCR Analysis software from Ct (Cycle threshold) units to the more convenient Et=40-Ct units. To correct for plate-plate effects, we shifted all detected gene measurements in a plate by a plate-specific global factor, which is chosen such that the median ERCC-0003 level of the shifted data across all samples in the plate becomes the same across all plates.

source_name: Human monocyte derived macrophages

label_protocol: Sort plates containing single cell RNA were thawed, and 1.35 uL of STA mix (1.25 uL of a pool of 96 Taqman assays at 0.2x concentration, and 0.1 uL Superscript III/Platinum Taq mix (CellsDirect kit, Life Technologies)) were added to each well. Plates were then sealed with clear film (Bio-rad) and centrifuged at 2000x G for 3 minutes and STA was run on a CFX Connect thermal cycler (Bio-rad) with the following cycling parameters: 50°C for 15 mins, 95°C for 2 minutes, then 18 cycles of 95°C for 15 seconds and 60°C for 4 minutes. Plates were then placed on ice and cold 10 mM Tris pH 8.0, 0.1 mM EDTA buffer was added to each well at 20 uL per well. Samples were then analyzed by qPCR on the Fluidigm Biomark instrument using 96.96 chips according to manufacturer’s instructions (Fluidigm). Briefly, 2.25 uL per well of each amplified, diluted single cell sample was mixed with 2.5 uL Ssofast 2X Probes Supermix (Bio-rad) that had 0.5X ROX reference dye added (from the CellsDirect Kit, Life Technologies), and 0.25 uL sample loading reagent (Fluidigm). Taqman assays (20x concentration) were combined 1:1 with Assay loading reagent (Fluidigm). Sample and assay mixes were then added to the wells of the 96.96 chip for gene expression measurement. The normal speed cycling gene expression protocol was used, with 40 cycles of amplification. Data was exported from Fluidigm Real-time PCR Analysis software version 3.1.3, using Linear (Derivative) Baseline method, a global threshold of 0.01, and a 0.65 quality threshold, parameters which were found to exclude non-specific amplification and reduce plate-plate variation.

extract_protocol: Harvested macrophages were incubated on ice in PBS containing 5% human AB serum for 15 minutes, followed by surface antibody staining for 30 minutes on ice, in the same buffer, with the following antibody cocktail: FITC anti-CD36, clone 5-271 (Biolegend); PE anti-CD163, clone GHI/61 (Biolegend); PerCP anti-CD16, clone 3G8 (Biolegend); PE-Cy7 anti-CD197, clone G043H7 (Biolegend); APC-Cy7 anti-CD206, clone 15-2 (Biolegend); Alexa Fluor 700 anti-CD195, clone HEK/1/85a (Biolegend); Alexa Fluor 647 anti-CD192, clone TG5/CCR2 (Biolegend); Pacific Orange anti-CD14, clone TüK4 (Life Technologies). Following staining, cells were washed once with ice cold PBS, and resuspended in ice cold PBS containing a 1 in 1000 dilution of Pacific Blue Fixable Live/Dead stain (Life Technologies), which is a fluorescent dye reactive with cellular amines. When the cell membrane becomes permeable, the dye gains access to intracellular amines and hence the fluorescence of the cell increases. For sorting, cells were gated upon Forward scatter (FSC)-width versus side scatter(SSC)-area for doublet discrimination, followed by gating on Pacific blue low (membrane intact) cells (versus FSC-area). A 100 μm nozzle was used at 20 PSI pressure and a drop drive frequency of 34.5 kHz. Sorting was performed on a FACSAriaII (Becton Dickinson) and FACSDiva version 6.1.3 software using Single cell precision mode with default parameters (Yield mask = 0, Purity mask = 32, Phase mask = 16). Sort alignment was checked immediately before sorting, by sorting beads onto a covered PCR plate and confirming that the droplets land in the center of several different wells across the plate. Cells were deposited into individual wells of a low-profile 96 well PCR plate (Bio-rad) containing 2.5 uL CellsDirect 2x Reaction Mix (Life Technologies), 0.05 uL Ambion SUPERase-In RNAse inhibitor (Life technologies), and 1 uL RNAse-free water. Cells from different treatment groups were sorted into alternating wells across the plate, to avoid positional or “edge” effects across the plate. Each plate contained a no template control well, and a seven point dilution of a pooled RNA sample derived from a combination of RNA isolated from non-treated, IFNγ, and IL-4 treated macrophages, as a reference positive control. Control RNA was isolated using the miRNeasy mini kit (Qiagen). All wells except the positive control wells also contained ERCC RNA reference standards (Life Technologies) spiked in at 1/50,000 final dilution from the stock ERCC mixture.


title: p1dJul9.10cell 24hr MCSF CNT 10 E10

source_name: p1dJul9.10cell 24hr MCSF CNT 10 E10


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 C5

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 C5


title: p3dJul9.10cell 24hr MCSF IFN+TNF 10 C9

source_name: p3dJul9.10cell 24hr MCSF IFN+TNF 10 C9


title: p1dJul9.10cell 24hr MCSF CNT 10 E6

source_name: p1dJul9.10cell 24hr MCSF CNT 10 E6


title: p1dJul9.10cell 24hr MCSF IFN+TNF 10 A3

source_name: p1dJul9.10cell 24hr MCSF IFN+TNF 10 A3


title: p1dJul9.10cell 24hr MCSF CNT 10 C12

source_name: p1dJul9.10cell 24hr MCSF CNT 10 C12


title: p1dJul9.10cell 24hr MCSF CNT 10 C4

source_name: p1dJul9.10cell 24hr MCSF CNT 10 C4


title: p1dJul9.10cell 24hr MCSF CNT 10 B11

source_name: p1dJul9.10cell 24hr MCSF CNT 10 B11


title: p1dJul9.10cell 24hr MCSF CNT 10 F7

source_name: p1dJul9.10cell 24hr MCSF CNT 10 F7


title: p1dJul9.10cell 24hr MCSF CNT 10 C8

source_name: p1dJul9.10cell 24hr MCSF CNT 10 C8


title: p5AdJul9 24hr MCSF IFN+TNF G9


title: p5AdJul9 24hr MCSF IFN+TNF F2


title: p5AdJul9 24hr MCSF IFN+TNF F10


title: p3dJul9.10cell 24hr MCSF CNT 10 A6

source_name: p3dJul9.10cell 24hr MCSF CNT 10 A6


title: p5AdJul9 24hr MCSF IFN+TNF E3


title: p5AdJul9 24hr MCSF IFN+TNF D8


title: p5AdJul9 24hr MCSF IFN+TNF E11


title: p5AdJul9 24hr MCSF IFN+TNF E7


title: p5AdJul9 24hr MCSF IFN+TNF D4


title: p5AdJul9 24hr MCSF IFN+TNF H12


title: p5AdJul9 24hr MCSF IFN+TNF G5


title: p5AdJul9 24hr MCSF IFN+TNF C9


title: p5AdJul9 24hr MCSF IFN+TNF F6


title: p5AdJul9 24hr MCSF IFN+TNF C5


title: p5AdJul9 24hr MCSF IFN+TNF B6


title: p5AdJul9 24hr MCSF IFN+TNF D12


title: p5AdJul9 24hr MCSF IFN+TNF B2


title: p5AdJul9 24hr MCSF IFN+TNF B10


title: p3dJul9.10cell 24hr MCSF CNT 10 E2

source_name: p3dJul9.10cell 24hr MCSF CNT 10 E2


title: p5AdJul9 24hr MCSF CNT G12


title: p5AdJul9 24hr MCSF CNT G4


title: p5AdJul9 24hr MCSF IFN+TNF A11


title: p5AdJul9 24hr MCSF CNT F7


title: p5AdJul9 24hr MCSF CNT F3


title: p5AdJul9 24hr MCSF CNT H5


title: p5AdJul9 24hr MCSF CNT G8


title: p5AdJul9 24hr MCSF CNT H9


title: p5AdJul9 24hr MCSF IFN+TNF A7


title: p5AdJul9 24hr MCSF CNT E10


title: p5AdJul9 24hr MCSF CNT E2


title: p5AdJul9 24hr MCSF CNT F11


title: p5AdJul9 24hr MCSF CNT D9


title: p5AdJul9 24hr MCSF CNT C8


title: p5AdJul9 24hr MCSF CNT D5


title: p5AdJul9 24hr MCSF CNT C12


title: p5AdJul9 24hr MCSF CNT C4


title: p5AdJul9 24hr MCSF CNT B11


title: p5AdJul9 24hr MCSF CNT B7


title: p5AdJul9 24hr MCSF CNT B3


title: p5AdJul9 24hr MCSF CNT A6


title: p4dJul9 24hr MCSF IFN+TNF H8


title: p4dJul9 24hr MCSF IFN+TNF F6


title: p4dJul9 24hr MCSF IFN+TNF G5


title: p4dJul9 24hr MCSF IFN+TNF H4


title: p4dJul9 24hr MCSF IFN+TNF G9


title: p5AdJul9 24hr MCSF CNT E6


title: p5AdJul9 24hr MCSF CNT A10


title: p4dJul9 24hr MCSF IFN+TNF E11


title: p4dJul9 24hr MCSF IFN+TNF D8


title: p4dJul9 24hr MCSF IFN+TNF F2


title: p4dJul9 24hr MCSF IFN+TNF E3


title: p4dJul9 24hr MCSF IFN+TNF F10


title: p4dJul9 24hr MCSF IFN+TNF D4


title: p4dJul9 24hr MCSF IFN+TNF D12


title: p4dJul9 24hr MCSF IFN+TNF E7


title: p4dJul9 24hr MCSF IFN+TNF H12


title: p4dJul9 24hr MCSF IFN+TNF B6


title: p4dJul9 24hr MCSF IFN+TNF C5


title: p4dJul9 24hr MCSF IFN+TNF B2


title: p4dJul9 24hr MCSF IFN+TNF C9


title: p4dJul9 24hr MCSF IFN+TNF B10


title: p4dJul9 24hr MCSF CNT G8


title: p4dJul9 24hr MCSF IFN+TNF A11


title: p4dJul9 24hr MCSF CNT G4


title: p4dJul9 24hr MCSF CNT G12


title: p4dJul9 24hr MCSF IFN+TNF A7


title: p4dJul9 24hr MCSF CNT H9


title: p4dJul9 24hr MCSF CNT H5


title: p4dJul9 24hr MCSF CNT F7


title: p4dJul9 24hr MCSF CNT F3


title: p4dJul9 24hr MCSF CNT A10


title: p4dJul9 24hr MCSF CNT A6


title: p4dJul9 24hr MCSF CNT E6


title: p4dJul9 24hr MCSF CNT F11


title: p4dJul9 24hr MCSF CNT E2


title: p2dJul9 24hr MCSF IFN+TNF H8


title: p2dJul9 24hr MCSF IFN+TNF H4


title: p2dJul9 24hr MCSF IFN+TNF G9


title: p2dJul9 24hr MCSF IFN+TNF H12


title: p4dJul9 24hr MCSF CNT B11


title: p4dJul9 24hr MCSF CNT D9


title: p4dJul9 24hr MCSF CNT B7


title: p4dJul9 24hr MCSF CNT D5


title: p4dJul9 24hr MCSF CNT C8


title: p4dJul9 24hr MCSF CNT C12


title: p2dJul9 24hr MCSF IFN+TNF G5


title: p4dJul9 24hr MCSF CNT C4


title: p2dJul9 24hr MCSF IFN+TNF E11


title: p2dJul9 24hr MCSF IFN+TNF D8


title: p2dJul9 24hr MCSF IFN+TNF F2


title: p2dJul9 24hr MCSF IFN+TNF D4


title: p4dJul9 24hr MCSF CNT E10


title: p4dJul9 24hr MCSF CNT B3


title: p2dJul9 24hr MCSF IFN+TNF C9


title: p2dJul9 24hr MCSF IFN+TNF D12


title: p2dJul9 24hr MCSF IFN+TNF E3


title: p2dJul9 24hr MCSF IFN+TNF E7


title: p2dJul9 24hr MCSF IFN+TNF C5


title: p2dJul9 24hr MCSF IFN+TNF B2


title: p2dJul9 24hr MCSF IFN+TNF A7


title: p2dJul9 24hr MCSF IFN+TNF A11


title: p2dJul9 24hr MCSF IFN+TNF B6


title: p2dJul9 24hr MCSF IFN+TNF B10


title: p2dJul9 24hr MCSF CNT H9


title: p2dJul9 24hr MCSF IFN+TNF F10


title: p2dJul9 24hr MCSF CNT H5


title: p2dJul9 24hr MCSF CNT G8


title: p2dJul9 24hr MCSF CNT G12


title: p2dJul9 24hr MCSF CNT G4


title: p2dJul9 24hr MCSF CNT F3


title: p2dJul9 24hr MCSF IFN+TNF F6


title: p2dJul9 24hr MCSF CNT F7


title: p2dJul9 24hr MCSF CNT E10


title: p2dJul9 24hr MCSF CNT D9


title: p2dJul9 24hr MCSF CNT E6


title: p2dJul9 24hr MCSF CNT F11


title: p2dJul9 24hr MCSF CNT D5


title: p2dJul9 24hr MCSF CNT C12


title: p5AdJul9 24hr MCSF IFN+TNF H8


title: p2dJul9 24hr MCSF CNT C8


title: p2dJul9 24hr MCSF CNT C4


title: p2dJul9 24hr MCSF CNT A10


title: p2dJul9 24hr MCSF CNT B7


title: p2dJul9 24hr MCSF CNT B11


title: p2dJul9 24hr MCSF CNT B3


title: p2dJul9 24hr MCSF CNT A6


title: p2dJul9 24hr MCSF CNT E2


title: p1dJul9 24hr MCSF IFN+TNF H8


title: p1dJul9 24hr MCSF IFN+TNF H12


title: p1dJul9 24hr MCSF IFN+TNF G9


title: p1dJul9 24hr MCSF IFN+TNF F6


title: p1dJul9 24hr MCSF IFN+TNF F10


title: p1dJul9 24hr MCSF IFN+TNF H4


title: p1dJul9 24hr MCSF IFN+TNF F2


title: p1dJul9 24hr MCSF IFN+TNF E7


title: p1dJul9 24hr MCSF IFN+TNF E11


title: p1dJul9 24hr MCSF IFN+TNF E3


title: p1dJul9 24hr MCSF IFN+TNF C9


title: p1dJul9 24hr MCSF IFN+TNF D4


title: p1dJul9 24hr MCSF IFN+TNF D12


title: p1dJul9 24hr MCSF IFN+TNF G5


title: p1dJul9 24hr MCSF IFN+TNF D8


title: p1dJul9 24hr MCSF IFN+TNF A7


title: p1dJul9 24hr MCSF IFN+TNF B6


title: p1dJul9 24hr MCSF IFN+TNF C5


title: p1dJul9 24hr MCSF IFN+TNF B2


title: p1dJul9 24hr MCSF CNT H5


title: p1dJul9 24hr MCSF CNT H9


title: p1dJul9 24hr MCSF IFN+TNF A11


title: p1dJul9 24hr MCSF CNT G8


title: p1dJul9 24hr MCSF IFN+TNF B10


title: p1dJul9 24hr MCSF CNT G12


title: p1dJul9 24hr MCSF CNT E10


title: p1dJul9 24hr MCSF CNT E2


title: p1dJul9 24hr MCSF CNT E6


title: p1dJul9 24hr MCSF CNT D9


title: p1dJul9 24hr MCSF CNT D5


title: p1dJul9 24hr MCSF CNT F7


title: p1dJul9 24hr MCSF CNT F11


title: p1dJul9 24hr MCSF CNT C12


title: p1dJul9 24hr MCSF CNT C4


title: p1dJul9 24hr MCSF CNT C8


title: p1dJul9 24hr MCSF CNT F3


title: p1dJul9 24hr MCSF CNT B3


title: p1dJul9 24hr MCSF CNT B11


title: p1dJul9 24hr MCSF CNT A10


title: p1dJul9 24hr MCSF CNT B7


title: 140825_S2_CNT___ reanalysis

type: SRA

description:
Illumina HiSeq 2000
Transcriptome analysis via RNAseq of human blood derived macrophages treated with/without IL-10 for 18 hours.
GSM2135467
Seq18

library_source: transcriptomic

data_processing:
Covert bcl to fastq: CASAVA 1.8.2
Mapping: Tophat 2.0.11, Bowtie 2.2.2
Read counting: featureCounts (SubRead package), using gencode v19 annotation
Differential expression analysis: DESeq2
Genome_build: UCSC Hg19

source_name: Peripheral blood monocyte-derived macrophages

extract_protocol:
Trizol, Zymo Direct-zol spin column
Illumina Truseq Ribozero Stranded HT

treatment_protocol: Fresh media on day 6 was also supplemented with 100 ng/mL Interferon (IFN)γ and 100 ng/mL Tumor necrosis factor α (IFNγ and TNFα treated cells),, or M-CSF alone (Control). Cells were harvested for analysis 18 hours after treatment.

tag: treatment time (hours)

tag: library type

value: RNAseq (Ribozero Stranded Truseq HT)


title: 140825_S2_IFNgTNFa___ reanalysis

description:
Illumina HiSeq 2000
Transcriptome analysis via RNAseq of human blood derived macrophages treated with/without IL-10 for 18 hours.
GSM2135465
Seq16

data_processing:
Covert bcl to fastq: CASAVA 1.8.4
Mapping: Tophat 2.0.11, Bowtie 2.2.4
Read counting: featureCounts (SubRead package), using gencode v19 annotation
Differential expression analysis: DESeq4
Genome_build: UCSC Hg19

value: IFNgTNFa


title: 140825_S1_IFNgTNFa___ reanalysis

description:
Illumina HiSeq 2000
Transcriptome analysis via RNAseq of human blood derived macrophages treated with/without IL-10 for 18 hours.
GSM2135464
Seq13

data_processing:
Covert bcl to fastq: CASAVA 1.8.3
Mapping: Tophat 2.0.11, Bowtie 2.2.3
Read counting: featureCounts (SubRead package), using gencode v19 annotation
Differential expression analysis: DESeq3
Genome_build: UCSC Hg19


title: p1dJul9 24hr MCSF CNT G4


title: 140825_S3_CNT___ reanalysis

description:
Illumina HiSeq 2000
Transcriptome analysis via RNAseq of human blood derived macrophages treated with/without IL-10 for 18 hours.
GSM2135460
Seq5


title: 140825_S1_CNT___ reanalysis

description:
Illumina HiSeq 2000
Transcriptome analysis via RNAseq of human blood derived macrophages treated with/without IL-10 for 18 hours.
GSM2135462
Seq9


title: expt1xx10nMxx2hr

status: Public on Apr 12 2016

description: 10 nM Kdo2-lipid A (Avanti Polar Lipids, Inc.), 2 hour treatment, experiment 1

data_processing:
Base Calling: Illumina RTAv2
Demultiplexing and fastq conversion: bcl2fastq 2.15.0.4
Read mapping: tophat 2.0.11 (https://ccb.jhu.edu/software/tophat/index.shtml), Command parameters:  --library-type fr-firststrand -r  150,  Genome assembly: Mus_musculus/UCSC/mm9
Counting reads mapping to features: Program:featureCounts v1.4.5-p1 (from Subread package http://subread.sourceforge.net); Command:"featureCounts" "-O" "-g" "gene_id" "-T" "8" "-s" "2" "-a" "/gpfs/bio_data/iGenomes/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf" "-o"
count normalization/regularized log transformation: DESeq2
Genome_build: mm9, downloaded from UCSC
Supplementary_files_format_and_content: raw count output from featureCounts and rlog-normalized counts derived from DESeq2

molecule: polyA RNA

organism: Mus musculus

source_name: bone marrow derived marcophages

growth_protocol: Complete Dulbecco’s modified Eagle’s medium (10% FBS, 100 U/ml penicillin, 100 U/ml streptomycin, 2 mM L-Glutamine, 20 mM HEPES) supplemented with 30ng/ml recombinant mouse M-CSF (R&D systems), 6 days differentiation with media added on days 0 and 3.

extract_protocol:
Media was removed and Qiazol (Qiagen) was added to the plate; Poly-A RNA isolated by Qiazol/Zymo Direct-zol kit
RNAseq library prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina. Sequenced on NextSeq 500 system using v1 reagents.

treatment_protocol: Various doses of Kdo2-LipidA added prior to RNA harvest

tag: strain

tag: cell type

value: bone marrow derived marcophages


title: expt2xx0p03nMxx2hr

description: 0.03 nM Kdo2-lipid A (Avanti Polar Lipids, Inc.), 2 hour treatment, experiment 2


title: expt2xx10nMxx1hr

description: 10 nM Kdo2-lipid A (Avanti Polar Lipids, Inc.), 1 hour treatment, experiment 2


title: expt2xx0p03nMxx1hr

description: 0.03 nM Kdo2-lipid A (Avanti Polar Lipids, Inc.), 1 hour treatment, experiment 2


title: expt2xx10nMxx2hr

description: 10 nM Kdo2-lipid A (Avanti Polar Lipids, Inc.), 2 hour treatment, experiment 2


title: expt1xx10nMxx1hr

description: 10 nM Kdo2-lipid A (Avanti Polar Lipids, Inc.), 1 hour treatment, experiment 1


title: expt1xx0p03nMxx2hr

description: 0.03 nM Kdo2-lipid A (Avanti Polar Lipids, Inc.), 2 hour treatment, experiment 1


title: expt1xx0p03nMxx1hr

description: 0.03 nM Kdo2-lipid A (Avanti Polar Lipids, Inc.), 1 hour treatment, experiment 1


title: expt1xx0nMxx0hr

description: Non-treated control, experiment 1


title: p1dJul9 24hr MCSF CNT A6


title: expt2xx0nMxx0hr

description: Non-treated control, experiment 2


title: PWL140-D

status: Public on Feb 26 2016

description: After 15% weight loss

source_name: Subcutaneous adipose tissue

growth_protocol: Subcutaneous adipose tissue gene expression was examined in 9 obese subjects before and after 5-15% weight loss.

extract_protocol: Subcutaneous adipose tissue biopsies were obtained and immediately frozen in liquid nitrogen. Total RNA was isolated from frozen tissue sample by using Qiazol and Rneasy Mini Kit (Qiagen).

treatment_protocol: After baseline studies, subjects, who were randomized to the diet intervention (weight loss) group, were examined after 5, 10, 15% weight loss. Subcutaneous adipose tissue samples were obtained during the hyperinsulinemic-euglycemic clamp procedure.

value: Subcutaneous adipose tissue

tag: condition

value: 15% weight loss


title: PWL171-C

description: After 10% weight loss

value: 10% weight loss


title: PWL158-A

description: Before intervention (weight loss)


title: PWL140-B2

description: After 5% weight loss

value: 5% weight loss


title: PWL136-A

description: Before intervention (weight loss)


title: PWL081-B

description: After 5% weight loss


title: PWL107-A

description: Before intervention (weight loss)


title: PWL171-B

description: After 5% weight loss


title: PWL136-C

description: After 10% weight loss


title: PWL010-A

description: Before intervention (weight loss)


title: PWL136-D

description: After 15% weight loss


title: PWL124-C

description: After 10% weight loss


title: PWL136-B

description: After 5% weight loss


title: PWL158-D

description: After 15% weight loss


title: PWL158-B

description: After 5% weight loss


title: PWL081-C

description: After 10% weight loss


title: PWL140-C

description: After 10% weight loss


title: PWL171-A

description: Before intervention (weight loss)


title: PWL107-B

description: After 5% weight loss


title: PWL171-D

description: After 15% weight loss


title: PWL158-C

description: After 10% weight loss


title: PWL107-D

description: After 15% weight loss


title: PWL124-A

description: Before intervention (weight loss)


title: PWL140-A2

description: Before intervention (weight loss)


title: PWL124-D

description: After 15% weight loss


title: PWL081-A

description: Before intervention (weight loss)


title: PWL107-C

description: After 10% weight loss


title: PWL081-D

description: After 15% weight loss


title: PWL010-D

description: After 15% weight loss


title: PWL124-B

description: After 5% weight loss


title: PWL010-B

description: After 5% weight loss


title: PWL005-D

description: After 15% weight loss


title: PWL005-B

description: After 5% weight loss


title: PWL005-A

description: Before intervention (weight loss)


title: PWL010-C

description: After 10% weight loss


title: PWL005-C

description: After 10% weight loss


title: U937T_EVI1-HA_E10 -tet 12h

status: Public on Aug 30 2015

city: Wien

first: Gerwin

last: Heller

address: Währinger Gürtel 18-20

department: Medicine I

country: Austria

institute: Medical University of Vienna

hyb_protocol: RNA quality control, sample labelling and hybridization to Affymetrix HG-U133 plus 2.0 microarrays were performed according to Affymetrix guidelines at the Center of Excellence for Fluorescent Bioanalytics (KFB; Regensburg, Germany).

data_processing: Robust Multi-array Analysis was used for background correction, quantile normalization and median polish summarization of probe levels.

source_name: U937T_EVI1-HA_E10 -tet 12h

growth_protocol: U937T_EVI1-HA clones E10 and E14, U937T_vec clone P2, and U937T cells were cultured in RPMI 1640 containing 10% fetal bovine serum, 0.5 μg/ml puromycin, 1 μg/ml tetracycline and 500 μg/ml hygromycin (E10, E14, P2 only) in a humidified incubator at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using the RNAeasy kit.

treatment_protocol: To induce EVI1 expression, exponentially growing cells were washed 3 times with  PBS and resuspended in growth media without tetracycline. Control cultures were washed in the same manner but resuspended in media with tetracycline. E10 and E14 cells were harvested after 6, 12, 24, and 48 h in the absence or presence of tetracycline; U937T and P2 cells were harvested after 48 h in the presence or absence of tetracycline.

tag: clone

tag: protocol

value: absence of tetracycline

tag: time point

tag: cell line


title: U937T_EVI1-HA_E10 -tet 24h

scan_protocol: RNA quality control, sample labelling and hybridization to Affymetrix HG-U133 plus 2.0 microarrays were performed according to Affymetrix guidelines at the Center of Excellence for Fluorescent Bioanalytics (KFB; Regensburg, Germany).

source_name: U937T_EVI1-HA_E10 -tet 24h


title: U937T_vec -tet 48h

source_name: U937T_vec -tet 48h

label_protocol: RNA quality control, sample labelling and hybridization to Affymetrix HG-U133 plus 2.0 microarrays were performed according to Affymetrix guidelines at the Center of Excellence for Fluorescent Bioanalytics (KFB; Regensburg, Germany).


title: U937T_EVI1-HA_E10 -tet 6h

source_name: U937T_EVI1-HA_E10 -tet 6h


title: U937T +tet 48h

source_name: U937T +tet 48h

value: presence of tetracycline


title: U937T_EVI1-HA_E10 +tet 6h

source_name: U937T_EVI1-HA_E10 +tet 6h


title: U937T_EVI1-HA_E14 +tet 48h

source_name: U937T_EVI1-HA_E14 +tet 48h


title: U937T_EVI1-HA_E14 -tet 12h

source_name: U937T_EVI1-HA_E14 -tet 12h


title: U937T_EVI1-HA_E10 +tet 48h

source_name: U937T_EVI1-HA_E10 +tet 48h


title: U937T_EVI1-HA_E14 -tet 24h

source_name: U937T_EVI1-HA_E14 -tet 24h


title: Brain tumor 9403904111_R05C01

status: Public on May 21 2015

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description:
Methylation data from ependymal tumor sample.
Location: 1: infratentorial; 2: spinal; 3: supratentorial.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Data analysis was performed using the open source statistical programming language R (R Core Team, 2014; http://www.R-project.org/). Raw data files generated by the iScan array scanner were read and preprocessed using the capabilities of the Bioconductor (Version 2.9) package minfi (Version 1.12; Aryee et al., 2014 (PMID 24478339)). With the minfi package using function 'preprocessIllumina', the same preprocessing steps, i.e., background subtraction and normalization using control probes, as in Illumina's GenomeStudio software were performed.

label: biotin/DNP

molecule: genomic DNA

source_name: brain tumor, ST-EPN-RELA

label_protocol: Illumina protocol.

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride. DNA was isolated from formalin-fixed and paraffin-embedded (FFPE)  tissue using the blackPREP FFPE DNA Kit (Analytik Jena, Jena, Germany) according to the manufacturer's instructions.

value: ependymal tumor

tag: tumor type

value: primary

tag: molecular subtype

value: ST-EPN-RELA

tag: material

value: frozen

tag: location

tag: who grade


title: U937T_EVI1-HA_E10 +tet 24h

source_name: U937T_EVI1-HA_E10 +tet 24h


title: U937T_EVI1-HA_E10 -tet 48h

source_name: U937T_EVI1-HA_E10 -tet 48h


title: Brain tumor 6752625106_R05C02

source_name: brain tumor, PF-EPN-B

tag: tissue

value: PF-EPN-B


title: Brain tumor 9370847051_R05C02

source_name: brain tumor, ST-SE, WHO grade 2

value: ST-SE


title: U937T_EVI1-HA_E14 +tet 24h

source_name: U937T_EVI1-HA_E14 +tet 24h


title: Brain tumor 9407210090_R05C02

source_name: brain tumor, ST-SE, WHO grade 1


title: U937T -tet 48h

source_name: U937T -tet 48h


title: U937T_EVI1-HA_E14 +tet 12h

source_name: U937T_EVI1-HA_E14 +tet 12h


title: U937T_EVI1-HA_E14 +tet 6h

source_name: U937T_EVI1-HA_E14 +tet 6h


title: U937T_vec +tet 48h

source_name: U937T_vec +tet 48h


title: U937T_EVI1-HA_E14 -tet 48h

source_name: U937T_EVI1-HA_E14 -tet 48h


title: Brain tumor 6752625106_R02C01


title: Brain tumor 8622007106_R02C02

source_name: brain tumor, PF-EPN-A

value: PF-EPN-A


title: U937T_EVI1-HA_E14 -tet 6h

source_name: U937T_EVI1-HA_E14 -tet 6h


title: Brain tumor 9370847051_R05C01


title: U937T_EVI1-HA_E10 +tet 12h

source_name: U937T_EVI1-HA_E10 +tet 12h


title: Brain tumor 6929806038_R04C01

source_name: brain tumor, supratentorial, ST-SE, WHO grade 2


title: Brain tumor 9370847051_R06C01


title: Brain tumor 6929806024_R01C01


title: Brain tumor 6929806038_R04C02


title: Brain tumor 6929689149_R02C02


title: Brain tumor 6929806046_R06C01


title: Brain tumor 8622007203_R03C02


title: Brain tumor 8622007189_R02C01


title: Brain tumor 8622007189_R01C01


title: Brain tumor 8622007203_R05C02


title: Brain tumor 6929806046_R04C02


title: 140825_S3_IFNgTNFa___ reanalysis

description:
Illumina HiSeq 2000
Transcriptome analysis via RNAseq of human blood derived macrophages treated with/without IL-10 for 18 hours.
GSM2135466
Seq17

data_processing:
Covert bcl to fastq: CASAVA 1.8.5
Mapping: Tophat 2.0.11, Bowtie 2.2.5
Read counting: featureCounts (SubRead package), using gencode v19 annotation
Differential expression analysis: DESeq5
Genome_build: UCSC Hg19

source_name: Peripheral blood monocyte-derived macrophages

tag: treatment


title: Brain tumor 8622007203_R04C02


title: Brain tumor 8622007189_R06C01


title: Brain tumor 9003865058_R01C01


title: Brain tumor 9533774066_R01C02

source_name: brain tumor, supratentorial, ST-SE, WHO grade 1


title: Brain tumor 9422491130_R04C02

source_name: brain tumor, spinal, SP-SE, WHO grade 2

value: SP-SE


title: Brain tumor 9406922161_R05C02

source_name: brain tumor, spinal, SP-SE, WHO grade 1


title: Brain tumor 9533774066_R03C02


title: Brain tumor 9373550164_R01C01


title: Brain tumor 9373550164_R06C02


title: Brain tumor 9533774057_R02C02


title: Brain tumor 8622007203_R06C02


title: Brain tumor 9376561024_R05C02


title: Brain tumor 9422491130_R02C02

source_name: brain tumor, SP-EPN, WHO grade 2

value: SP-EPN


title: Brain tumor 8622007189_R03C01


title: Brain tumor 9422491130_R03C02


title: Brain tumor 9407201029_R06C01


title: Brain tumor 9305216209_R05C02


title: Brain tumor 9422491130_R06C02


title: Brain tumor 9379086132_R06C01


title: Brain tumor 9533774066_R01C01


title: Brain tumor 9407201028_R06C02


title: Brain tumor 9407201027_R03C01


title: Brain tumor 9407201027_R05C01


title: Brain tumor 9426020065_R06C02

source_name: brain tumor, spinal, SP-EPN, WHO grade 2


title: Brain tumor 9406922161_R05C01


title: Brain tumor 9426020065_R05C02


title: Brain tumor 9407201027_R02C01


title: Brain tumor 9426020065_R04C02


title: Brain tumor 9422493152_R03C01


title: Brain tumor 9422493152_R04C01

source_name: brain tumor, spinal, SP-EPN


title: Brain tumor 9422493152_R02C01

source_name: brain tumor, spinal, SP-EPN, WHO grade 3


title: Brain tumor 9403904071_R03C01

source_name: brain tumor, infratentorial, PF-SE

value: PF-SE


title: Brain tumor 9373550028_R06C01

source_name: brain tumor, supratentorial, SP-EPN, WHO grade 1


title: Brain tumor 9406921148_R02C02

source_name: brain tumor, PF-SE, WHO grade 1


title: Brain tumor 9406922161_R03C02


title: Brain tumor 9376538149_R02C01


title: Brain tumor 9406922161_R02C02


title: Brain tumor 9407201032_R05C01


title: Brain tumor 9407201032_R01C01


title: Brain tumor 9406921148_R06C01


title: Brain tumor 9305651060_R03C02


title: Brain tumor 9376538149_R03C01


title: Brain tumor 9426020065_R03C02


title: Brain tumor 9373551023_R06C02


title: Brain tumor 9376538149_R04C01

source_name: brain tumor, PF-SE, WHO grade 2


title: Brain tumor 9406921148_R01C02


title: Brain tumor 9406921148_R03C02


title: Brain tumor 9407201032_R02C01

source_name: brain tumor, PF-SE, WHO grade 3


title: Brain tumor 9426020064_R01C02

source_name: brain tumor, infratentorial, PF-SE, WHO grade 2


title: Brain tumor 9426020065_R05C01


title: Brain tumor 9968646156_R05C01


title: Brain tumor 9533774066_R04C01

source_name: brain tumor, infratentorial, PF-SE, WHO grade 1


title: Brain tumor 9533774066_R06C01


title: Brain tumor 9533774066_R02C02


title: Brain tumor 9406922161_R06C02


title: Brain tumor 9533774066_R04C02


title: Brain tumor 9407201032_R06C01


title: Brain tumor 9533774057_R06C02


title: Brain tumor 9533774106_R01C01


title: Brain tumor 9426020064_R04C01


title: Brain tumor 9533774101_R05C02


title: Brain tumor 9534104006_R03C02


title: Brain tumor 6929689149_R06C01


title: Brain tumor 9305651146_R06C01

source_name: brain tumor, SP-MPE, WHO grade 1

value: SP-MPE


title: Brain tumor 9297949046_R02C02


title: Brain tumor 6752625107_R03C02

source_name: brain tumor, SP-MPE


title: Brain tumor 9305216209_R02C01


title: Brain tumor 9305651095_R03C01


title: Brain tumor 9407201027_R04C01

source_name: brain tumor, SP-MPE, WHO grade 2


title: Brain tumor 9305651037_R04C01


title: Brain tumor 9305651037_R05C01


title: Brain tumor 9007225086_R01C01


title: Brain tumor 9007225163_R06C01


title: Brain tumor 9007225064_R01C02


title: Brain tumor 9407201027_R06C01


title: Brain tumor 9007225086_R01C02


title: Brain tumor 9420867124_R04C02


title: Brain tumor 9305216209_R06C01


title: Brain tumor 9533774066_R02C01


title: Brain tumor 9533774106_R04C01


title: Brain tumor 8622007068_R02C01


title: Brain tumor 9533774057_R04C02

source_name: brain tumor, spinal, SP-MPE, WHO grade 1


title: Brain tumor 9533774066_R06C02


title: Brain tumor 8622007120_R02C01


title: Brain tumor 9533774066_R05C01


title: Brain tumor 6752625106_R01C01


title: Brain tumor 9373550131_R06C02

source_name: brain tumor, ST-EPN-YAP1, WHO grade 3


title: Brain tumor 9533774057_R05C02


title: Brain tumor 9533774057_R01C02


title: Brain tumor 9305216209_R05C01


title: Brain tumor 6929806048_R06C01

source_name: brain tumor, supratentorial, ST-EPN-YAP1, WHO grade 3


title: Brain tumor 9968646139_R04C02


title: Brain tumor 9305651027_R03C01


title: Brain tumor 6929689149_R03C02

source_name: brain tumor, supratentorial, ST-EPN-YAP1, WHO grade 2


title: Brain tumor 6929806046_R03C01


title: Brain tumor 6026818091_R02C01

source_name: brain tumor, infratentorial, ST-EPN-YAP1, WHO grade 2


title: Brain tumor 9969477003_R01C02


title: Brain tumor 9373550028_R05C01


title: Brain tumor 9968646155_R01C01


title: Brain tumor 9296930076_R05C01


title: Brain tumor 6752625107_R04C02

source_name: brain tumor, supratentorial, ST-EPN-RELA, WHO grade 2


title: Brain tumor 9340996058_R06C01

source_name: brain tumor, ST-EPN-RELA, WHO grade 3


title: Brain tumor 9374342010_R01C01


title: Brain tumor 9422491056_R01C01


title: Brain tumor 6026818094_R05C02

source_name: brain tumor, ST-EPN-RELA


title: Brain tumor 6026818101_R02C01


title: Brain tumor 9305651053_R01C02

source_name: brain tumor, ST-EPN-RELA, WHO grade 2


title: Brain tumor 9533774057_R03C02


title: Brain tumor 6026818110_R02C01


title: Brain tumor 6752625135_R06C02


title: Brain tumor 9533774066_R05C02

source_name: brain tumor, supratentorial, SP-MPE, WHO grade 1


title: Brain tumor 6929806046_R01C01

source_name: brain tumor, supratentorial, ST-EPN-RELA, WHO grade 3


title: Brain tumor 6929806024_R04C02


title: Brain tumor 6752625107_R05C02


title: Brain tumor 6929806038_R02C01


title: Brain tumor 6929806046_R02C01


title: Brain tumor 6929689149_R01C01


title: Brain tumor 9305651016_R04C01


title: Brain tumor 6929806048_R05C02


title: Brain tumor 6929806038_R03C01


title: Brain tumor 6929806038_R01C01


title: Brain tumor 6929806046_R01C02


title: Brain tumor 9422493133_R04C02


title: Brain tumor 9426021175_R06C01


title: Brain tumor 6752625107_R01C02


title: Brain tumor 6929806048_R04C01


title: Brain tumor 6929806038_R06C02


title: Brain tumor 6929806046_R05C02


title: Brain tumor 6929806046_R04C01


title: Brain tumor 6929806038_R05C01


title: Brain tumor 6929689149_R03C01


title: Brain tumor 6929806046_R03C02


title: Brain tumor 7310440009_R06C01


title: Brain tumor 9426020061_R01C02


title: Brain tumor 6929806048_R02C02


title: Brain tumor 6929806048_R05C01


title: Brain tumor 6285641012_R03C02


title: Brain tumor 6752625106_R01C02


title: Brain tumor 6929806024_R06C02


title: Brain tumor 8622007106_R05C02


title: Brain tumor 6929806048_R04C02


title: Brain tumor 9305651013_R01C01


title: Brain tumor 9305651016_R01C01


title: Brain tumor 9305651027_R02C01


title: Brain tumor 9305651005_R02C01


title: Brain tumor 9426020061_R01C01


title: Brain tumor 9305651016_R05C02


title: Brain tumor 9305651003_R06C02


title: Brain tumor 9296930066_R01C02


title: Brain tumor 9296930066_R01C01


title: Brain tumor 9296930089_R06C01


title: Brain tumor 9296930047_R04C02


title: Brain tumor 9373550034_R03C01


title: Brain tumor 9373550018_R01C02


title: Brain tumor 9296930076_R03C01


title: Brain tumor 9296930066_R03C01


title: Brain tumor 9296930089_R04C01


title: Brain tumor 9296930066_R02C01


title: Brain tumor 9305651013_R02C02


title: Brain tumor 9296930076_R01C02


title: Brain tumor 9296930076_R04C02


title: Brain tumor 9296930089_R03C01


title: Brain tumor 9296930047_R05C02


title: Brain tumor 9296930076_R02C01


title: Brain tumor 9373550035_R06C01


title: Brain tumor 9296930052_R01C02


title: Brain tumor 9305651027_R05C01


title: Brain tumor 9296930052_R05C01


title: Brain tumor 9296930076_R05C02


title: Brain tumor 9373550028_R02C02


title: Brain tumor 9296930066_R03C02


title: Brain tumor 9296930076_R02C02


title: Brain tumor 9305651003_R02C01


title: Brain tumor 9296930066_R04C02


title: Brain tumor 9296930047_R01C01


title: Brain tumor 9296930066_R02C02


title: Brain tumor 9296930052_R03C01


title: Brain tumor 9296930089_R03C02


title: Brain tumor 9296930047_R04C01


title: Brain tumor 9373550018_R02C02


title: Brain tumor 9296930089_R02C02


title: Brain tumor 9533774046_R04C02

source_name: brain tumor, infratentorial, ST-EPN-RELA, WHO grade 3


title: Brain tumor 9373550034_R02C01


title: Brain tumor 9373550034_R05C02


title: Brain tumor 9296930089_R01C01


title: Brain tumor 9373550035_R02C02


title: Brain tumor 9296930052_R04C01


title: Brain tumor 9373550018_R01C01


title: Brain tumor 9420867087_R04C02

source_name: brain tumor, SP-EPN, WHO grade 1


title: Brain tumor 9373550131_R01C01


title: Brain tumor 9296930052_R01C01


title: Brain tumor 9407201032_R04C02

source_name: brain tumor, PF-EPN-B


title: Brain tumor 6026818101_R06C01


title: Brain tumor 6026818094_R04C01

source_name: brain tumor, infratentorial, PF-EPN-B, WHO grade 2


title: Brain tumor 9340996050_R04C02


title: Brain tumor 9968646096_R05C02

source_name: brain tumor, infratentorial, PF-EPN-B, WHO grade 3


title: Brain tumor 6026818101_R01C02


title: Brain tumor 9426020064_R05C01


title: Brain tumor 6752625135_R01C01


title: Brain tumor 6285641010_R02C01


title: Brain tumor 9968646098_R06C01


title: Brain tumor 6026818091_R01C01


title: Brain tumor 9968646096_R04C02


title: Brain tumor 6026818094_R03C01


title: Brain tumor 9968646156_R03C01


title: Brain tumor 9968646096_R06C02


title: Brain tumor 6026818091_R05C01


title: Brain tumor 9968646155_R06C02


title: Brain tumor 6285641010_R03C01


title: Brain tumor 9426020065_R03C01


title: Brain tumor 6752625133_R06C02


title: Brain tumor 7310440009_R03C01

source_name: brain tumor, infratentorial, PF-EPN-B


title: Brain tumor 9968646155_R05C01


title: Brain tumor 6026818091_R03C02


title: Brain tumor 9968646098_R03C02


title: Brain tumor 9968646156_R03C02


title: Brain tumor 9968646156_R02C02


title: Brain tumor 6929689149_R04C02


title: Brain tumor 9553932012_R04C02


title: Brain tumor 9968646139_R02C02


title: Brain tumor 6026818094_R04C02


title: Brain tumor 9420867124_R01C02


title: Brain tumor 9426020065_R06C01


title: Brain tumor 9553932028_R02C01


title: Brain tumor 9533774106_R05C02


title: Brain tumor 9769100071_R04C02


title: Brain tumor 9533774046_R03C02


title: Brain tumor 9533774101_R01C01


title: Brain tumor 6969568124_R02C01


title: Brain tumor 6026818091_R03C01


title: Brain tumor 9426020061_R06C02


title: Brain tumor 9533774102_R01C01


title: Brain tumor 9533774102_R02C02


title: Brain tumor 9305651003_R04C01


title: Brain tumor 9305651013_R01C02


title: Brain tumor 9533774102_R06C01


title: Brain tumor 9373550018_R06C01

source_name: brain tumor, supratentorial, PF-EPN-B, WHO grade 2


title: Brain tumor 9533774102_R05C01


title: Brain tumor 9533774101_R03C02


title: Brain tumor 9533774102_R04C02


title: Brain tumor 9968646096_R05C01

source_name: brain tumor, infratentorial, PF-EPN-A, WHO grade 3


title: Brain tumor 9533774101_R03C01


title: Brain tumor 9533774046_R05C02


title: Brain tumor 9968646156_R05C02


title: Brain tumor 9968646098_R05C02


title: Brain tumor 9968646155_R03C02


title: Brain tumor 9969477098_R03C01

source_name: brain tumor, infratentorial, PF-EPN-A


title: Brain tumor 9968646156_R06C01


title: Brain tumor 9968646156_R02C01


title: Brain tumor 9968646098_R05C01


title: Brain tumor 9968646156_R01C01


title: Brain tumor 9968646156_R04C02


title: Brain tumor 9829119072_R04C01


title: Brain tumor 9403904109_R05C02


title: Brain tumor 9968646155_R04C02


title: Brain tumor 9297949046_R04C02

source_name: brain tumor, PF-EPN-A, WHO grade 3


title: Brain tumor 9403904109_R01C01


title: Brain tumor 6752625107_R01C01

source_name: brain tumor, infratentorial, PF-EPN-A, WHO grade 2


title: Brain tumor 9403904071_R05C01


title: Brain tumor 6026818110_R04C01

source_name: brain tumor, PF-EPN-A


title: Brain tumor 9403904109_R04C01


title: Brain tumor 9379082092_R02C02


title: Brain tumor 9407201032_R03C01


title: Brain tumor 6026818101_R02C02


title: Brain tumor 9379086117_R04C02


title: Brain tumor 9406921039_R04C01


title: Brain tumor 9969477098_R02C01


title: Brain tumor 9297949139_R04C02


title: Brain tumor 9407201032_R04C01


title: Brain tumor 6026818101_R05C01


title: Brain tumor 6026818101_R04C02


title: Brain tumor 6026818110_R06C01


title: Brain tumor 9373551108_R06C02


title: Brain tumor 6026818101_R03C02


title: Brain tumor 9969477023_R02C01


title: Brain tumor 6026818091_R06C02


title: Brain tumor 6026818110_R03C02


title: Brain tumor 6026818101_R06C02


title: Brain tumor 6026818094_R02C01


title: Brain tumor 9426020061_R04C02


title: Brain tumor 9969477022_R06C02


title: Brain tumor 9969477058_R04C02


title: Brain tumor 6026818101_R01C01


title: Brain tumor 9968646139_R05C02


title: Brain tumor 6026818101_R04C01


title: Brain tumor 6026818110_R01C02


title: Brain tumor 6752625135_R02C02


title: Brain tumor 9426020064_R03C02


title: Brain tumor 6929689149_R04C01


title: Brain tumor 6026818110_R04C02


title: Brain tumor 6026818110_R01C01


title: Brain tumor 7310440009_R04C02


title: Brain tumor 9969477023_R01C01


title: Brain tumor 6026818094_R03C02


title: Brain tumor 9968646160_R04C01


title: Brain tumor 9420867124_R06C02


title: Brain tumor 9422493133_R06C02


title: Brain tumor 9426020065_R02C01


title: Brain tumor 9420867125_R04C01


title: Brain tumor 6026818091_R04C02


title: Brain tumor 6026818091_R05C02


title: Brain tumor 9426020064_R06C01


title: Brain tumor 9426020064_R04C02


title: Brain tumor 9969477059_R04C02


title: Brain tumor 6285641012_R01C02


title: Brain tumor 6026818091_R01C02


title: Brain tumor 9420867124_R05C01


title: Brain tumor 9426020061_R03C02


title: Brain tumor 9968646163_R01C02


title: Brain tumor 9426020064_R06C02


title: Brain tumor 9420867125_R01C01


title: Brain tumor 9426020065_R04C01


title: Brain tumor 9426020064_R01C01


title: Brain tumor 9426020064_R05C02


title: Brain tumor 8622007106_R04C02


title: Brain tumor 6026818091_R06C01


title: Brain tumor 9403904125_R02C01


title: Brain tumor 9403904071_R03C02


title: Brain tumor 9403904125_R02C02


title: Brain tumor 6929689149_R05C01


title: Brain tumor 9403904125_R04C01


title: Brain tumor 9426020065_R01C02


title: Brain tumor 8622007106_R01C02


title: Brain tumor 6026818110_R06C02


title: Brain tumor 9426020065_R01C01


title: Brain tumor 9403904125_R06C01


title: Brain tumor 9403904111_R06C02


title: Brain tumor 9403904111_R04C02


title: Brain tumor 6026818110_R05C02


title: Brain tumor 9968646160_R03C01


title: Brain tumor 9968646163_R04C01


title: Brain tumor 9969477061_R05C01

source_name: brain tumor, PF-EPN-A, WHO grade 2


title: Brain tumor 9403904111_R01C02


title: Brain tumor 9969477061_R04C02


title: Brain tumor 9969477061_R03C02


title: Brain tumor 9968646160_R01C01


title: Brain tumor 9969477063_R04C01


title: Brain tumor 6285641012_R05C02

source_name: brain tumor, PF-EPN-B, WHO grade 3


title: Brain tumor 9968646160_R02C02


title: Brain tumor 9969477055_R04C02


title: Brain tumor 9969477057_R05C02


title: Brain tumor 9969477063_R01C01


title: Brain tumor 9969477059_R06C02


title: Brain tumor 9403904111_R02C02


title: Brain tumor 9969477055_R01C02


title: Brain tumor 9968646163_R02C02


title: Brain tumor 9969477055_R05C02


title: Brain tumor 9968646160_R06C01


title: Brain tumor 9968646159_R03C01


title: Brain tumor 9968646160_R05C01


title: Brain tumor 9969477059_R05C02


title: Brain tumor 9968646160_R02C01


title: Brain tumor 9968646159_R02C01


title: Brain tumor 9968646163_R01C01


title: Brain tumor 9968646159_R04C01


title: Brain tumor 9968646160_R05C02


title: Brain tumor 9969477058_R02C02


title: Brain tumor 9968646159_R01C02


title: Brain tumor 9968646160_R03C02


title: Brain tumor 9968646159_R05C02


title: Brain tumor 9829119124_R06C02


title: Brain tumor 9968646163_R06C01


title: Brain tumor 9969477061_R01C01


title: Brain tumor 9969477058_R06C01


title: Brain tumor 9829119124_R03C02


title: Brain tumor 9420867124_R05C02

source_name: brain tumor, PF-SE, WHO grade 3


title: Brain tumor 9968646159_R04C02


title: Brain tumor 9741950021_R04C01


title: Brain tumor 9969477061_R03C01


title: Brain tumor 9968646159_R01C01


title: Brain tumor 9969477061_R05C02


title: Brain tumor 9969477105_R06C02


title: Brain tumor 9969477105_R03C02


title: Brain tumor 9969477109_R05C01


title: Brain tumor 9969477109_R04C01


title: Brain tumor 9969477105_R04C02


title: Brain tumor 9968646163_R02C01


title: Brain tumor 9969477105_R01C01


title: Brain tumor 9969477105_R03C01


title: Brain tumor 9969477105_R02C01


title: Brain tumor 9969477105_R05C01


title: Brain tumor 9969477105_R04C01


title: Brain tumor 9968646160_R04C02


title: Brain tumor 9969477106_R01C01


title: Brain tumor 9969477105_R02C02


title: Brain tumor 9373551020_R05C01

source_name: brain tumor, supratentorial, PF-EPN-A, WHO grade 3


title: Brain tumor 9533774107_R01C01


title: Brain tumor 9533774107_R02C01


title: Brain tumor 9533774102_R04C01


title: Brain tumor 9533774107_R04C02


title: Brain tumor 9534104006_R06C01


title: Brain tumor 9969477106_R02C01


title: Brain tumor 9297949098_R02C01


title: Brain tumor 9297949078_R05C01


title: Brain tumor 9305651013_R06C02


title: Brain tumor 9969477109_R03C01


title: Brain tumor 9296930094_R04C01


title: Brain tumor 9305651016_R06C02


title: Brain tumor 9969477105_R06C01


title: Brain tumor 9297949078_R03C02


title: Brain tumor 9533774101_R01C02


title: Brain tumor 9305651003_R01C01


title: Brain tumor 9534104006_R03C01


title: Brain tumor 9533774106_R03C01


title: Brain tumor 9533774106_R03C02


title: Brain tumor 9969477109_R01C01


title: Brain tumor 9534104006_R04C01


title: Brain tumor 9533774107_R01C02


title: Brain tumor 9533774106_R01C02


title: Brain tumor 9533774102_R01C02


title: Brain tumor 9769100071_R03C01


title: Brain tumor 9829119072_R05C01


title: Brain tumor 9305651005_R01C01


title: Brain tumor 9305651003_R03C01


title: Brain tumor 9305651027_R04C02


title: Brain tumor 9534104006_R02C01


title: Brain tumor 9305651003_R05C02


title: Brain tumor 9533774101_R04C01


title: Brain tumor 9305651003_R06C01


title: Brain tumor 9769100071_R01C01


title: Brain tumor 9533774107_R06C01


title: Brain tumor 9534104006_R05C02


title: Brain tumor 9533774106_R02C01


title: Brain tumor 9533774101_R04C02


title: Brain tumor 9533774102_R05C02


title: Brain tumor 9533774107_R03C02


title: Brain tumor 9305651003_R04C02


title: Brain tumor 9305651005_R05C02


title: Brain tumor 9305651027_R03C02


title: Brain tumor 9305651013_R06C01


title: Brain tumor 9297949098_R01C01


title: Brain tumor 9297949078_R04C02


title: Brain tumor 9305651005_R04C02


title: Brain tumor 9305651005_R01C02


title: Brain tumor 9305651003_R03C02


title: Brain tumor 9305651003_R05C01


title: Brain tumor 9305651016_R01C02


title: Brain tumor 9297949098_R03C01


title: Brain tumor 9769100071_R06C01


title: Brain tumor 9297949078_R01C02


title: Brain tumor 9305651016_R05C01


title: Brain tumor 9296930094_R03C01


title: Brain tumor 9305651005_R05C01


title: Brain tumor 9297949098_R04C01


title: Brain tumor 9305651027_R06C01


title: Brain tumor 9305651016_R06C01


title: Brain tumor 9534104006_R01C01


title: Brain tumor 9533774101_R02C02


title: Brain tumor 9297949078_R06C02


title: Brain tumor 9296930094_R06C01


title: Brain tumor 9305651005_R06C02


title: Brain tumor 9297949078_R06C01


title: Brain tumor 9305651013_R04C01


title: Brain tumor 9305651027_R02C02


title: Brain tumor 9969477105_R01C02


title: Brain tumor 9296930094_R02C01


title: Brain tumor 9296930094_R05C01


title: Brain tumor 9305651005_R03C01


title: Brain tumor 9296930066_R06C02

source_name: brain tumor, supratentorial, PF-EPN-A, WHO grade 2


title: Brain tumor 9305651016_R02C02


title: Brain tumor 9829119072_R01C02


title: Brain tumor 9533774101_R05C01


title: Brain tumor 9533774101_R06C01


title: Brain tumor 9533774102_R02C01


title: Brain tumor 9533774107_R02C02


title: Brain tumor 9533774101_R02C01


title: Brain tumor 9533774046_R06C02


title: Brain tumor 9533774101_R06C02


title: Brain tumor 9533774106_R05C01


title: Brain tumor 9305651005_R02C02


title: Brain tumor 9769100071_R03C02


title: Brain tumor 9533774107_R03C01


title: Brain tumor 9305651016_R03C02


title: Brain tumor 9297949078_R05C02


title: Brain tumor 9305651003_R02C02


title: Brain tumor 9305651013_R02C01


title: Brain tumor 9305651013_R03C01


title: Brain tumor 9305651005_R04C01


title: OV35-Post

status: Public on Jan 09 2015

description: After weight gain

source_name: Subcutaneous adipose tissue

growth_protocol: Obese men and women participated in this study. Intrahepatic triglyceride (IHTG) content was used to identify subjects who were either MNO (IHTG<5.6%) or MAO (IHTG>10%).

extract_protocol: Adipose tissue biopsies were obtained and immediately frozen in liquid nitrogen. Total RNA was isolated from frozen tissue sample by using QIAzol and Rneasy Mini kit (Qiagen).

treatment_protocol: After baseline studies, subjects were instructed to consume 1000 kcal/day more than their estimated basaline total energy requirement, until they gained ~6%.

value: Subcutaneous adipose

tag: metabolic status

value: MNO


title: OV48-Pre

description: Before weight gain


title: OV59-Pre

description: Before weight gain


title: OV23-Pre

description: Before weight gain


title: OV23-Post

description: After weight gain


title: OV32-Post

description: After weight gain


title: OV48-Post

description: After weight gain


title: OV35-Pre

description: Before weight gain


title: OV22-Post

description: After weight gain


title: OV32-Pre

description: Before weight gain


title: OV13-Pre

description: Before weight gain


title: OV31-Pre

description: Before weight gain


title: OV59-Post

description: After weight gain


title: OV04-Post

description: After weight gain


title: OV08-Pre

description: Before weight gain


title: Brain tumor 9969477061_R06C01


title: OV08-Post

description: After weight gain


title: OV13-Post

description: After weight gain


title: OV04-Pre

description: Before weight gain


title: OV05-Pre

description: Before weight gain


title: OV52-Pre

description: Before weight gain

value: MAO


title: OV75-Post

description: After weight gain


title: OV65-Pre

description: Before weight gain


title: OV75-Pre

description: Before weight gain


title: OV31-Post

description: After weight gain


title: OV65-Post

description: After weight gain


title: OV05-Post

description: After weight gain


title: OV22-Pre

description: Before weight gain


title: OV46-Pre

description: Before weight gain


title: OV43-Pre

description: Before weight gain


title: OV46-Post

description: After weight gain


title: OV43-Post

description: After weight gain


title: OV17-Pre

description: Before weight gain


title: OV12-Post

description: After weight gain


title: OV12-Pre

description: Before weight gain


title: Control-3

status: Public on Nov 05 2014

description:
sample name: 939
replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation (background was also subtracted).

label: biotin

source_name: Liver, scrambled control ASO

label_protocol: RNA transcripts were amplified by T7 linear amplification (MessageAmp TotalPrep amplification kit; ABI-Ambion).

growth_protocol: C57BL/6J male mice were fed chow providing 60% of calories from fatty acids (D12492, Research Diets Inc) starting at 6 weeks of age.

extract_protocol: Total liver mRNA was extracted with RNA Bee (Isotex Diagnostics, Friendswood, TX) based on the manufacturer's instructions.

treatment_protocol: Mice received intraperitoneal injections of antisense oligonucleotide (ASO) directed against Mogat1 or a scrambled control ASO (25 mg/kg body weight; ISIS Pharmaceuticals, Carlsbad, CA) twice a week for three weeks. Treatments were initiated after 14 weeks of high fat diet feeding.

tag: gender

value: Male

tag: age

value: 25 weeks

tag: chow

value: HFD


title: Mogat1-ASO-1

description:
sample name: 931
replicate 1

source_name: Liver, antisense oligonucleotide (ASO) directed against Mogat1

tag: strain


title: OV17-Post

description: After weight gain


title: Mogat1-ASO-2

description:
sample name: 935
replicate 2


title: Control-4

description:
sample name: 942
replicate 4


title: Control-2

description:
sample name: 937
replicate 2


title: Control-1

description:
sample name: 930
replicate 1


title: Mogat1-ASO-4

description:
sample name: 940
replicate 4


title: OV52-Post

description: After weight gain


title: H2073

status: Public on Nov 26 2012

hyb_protocol: Accordingto NimbleGen protocols and performed by Nimblegen Service Laboratory (Reykjavik, Iceland)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.5 MeDIP-chip data extraction.

source_name: Input H2073

label_protocol: Input DNA was labeled with Cy3 and MeDIP DNA was labeled with Cy5 by Nimblegen Service Laboratory (Reykjavik, Iceland)

extract_protocol: DNA isolation was performed by proteinase K digestion followed by standard phenol/chloroform extraction and ethanol precipitation. MeDIP was performed according to NimbleGen´s Sample preparation protocol using Eurogentech´s anti 5-methylcytosine antibody. Enrichment of methylated DNA fragments was tested by qRT-PCR comparing H19 and GAPDH levels.

tag: medip antibody

value: Anti-5-mythylcytidine antibody from Eurogentech (BI-MECY-0100)


title: H1993

scan_protocol: Accordingto NimbleGen protocols and performed by Nimblegen Service Laboratory (Reykjavik, Iceland)

source_name: Input H1993


title: Tumor101

source_name: Input Tumor1

extract_protocol: DNA isolation was performed by proteinase K digestion followed by standard phenol/chloroform extraction and ethanol precipitation. MeDIP was performed according to NimbleGen´s "Sample preparation protocol" using Eurogentech´s anti 5-methylcytosine antibody. Enrichment of methylated DNA fragments was tested by qRT-PCR comparing H19 and GAPDH levels.

tag: sample type

value: input

source_name: IP Tumor1

tag: antibody

tag: antibody manufacturer

value: Eurogentech

tag: antibody catalog #

value: NSCLC tumor


title: Normal101

source_name: Input Normal1

source_name: IP Normal1

value: non-malignant lung tissue sample


title: Tumor97

source_name: Input Tumor97

source_name: IP Tumor97


title: A549

source_name: Input A549

tag: cell line

source_name: IP A549


title: Tumor85

source_name: Input Tumor85

source_name: IP Tumor85


title: Tumor87

source_name: Input Tumor87

source_name: IP Tumor87


title: Tumor94

source_name: Input Tumor94

source_name: IP Tumor94


title: Mogat1-ASO-3

description:
sample name: 936
replicate 3

source_name: Liver, antisense oligonucleotide (ASO) directed against Mogat1


title: Tumor89

source_name: Input Tumor89

source_name: IP Tumor89


title: Tumor82

source_name: Input Tumor82

source_name: IP Tumor82


title: Tumor98

source_name: Input Tumor98

source_name: IP Tumor98


title: Tumor83

source_name: Input Tumor83

source_name: IP Tumor83


title: Tumor92

source_name: Input Tumor92

source_name: IP Tumor92


title: Tumor79

source_name: Input Tumor79

source_name: IP Tumor79


title: Tumor84

source_name: Input Tumor84

source_name: IP Tumor84


title: Tumor9

source_name: Input Tumor9

source_name: IP Tumor9


title: Tumor91

source_name: Input Tumor91

source_name: IP Tumor91


title: Tumor81

source_name: Input Tumor81

source_name: IP Tumor81


title: Tumor88

source_name: Input Tumor88

source_name: IP Tumor88


title: Tumor96

source_name: Input Tumor96

source_name: IP Tumor96


title: Tumor99

source_name: Input Tumor99

source_name: IP Tumor99


title: Tumor95

source_name: Input Tumor95

source_name: IP Tumor95


title: Tumor86

source_name: Input Tumor86

source_name: IP Tumor86


title: Tumor90

source_name: Input Tumor90

source_name: IP Tumor90


title: Tumor78

source_name: Input Tumor78

source_name: IP Tumor78


title: Tumor93

source_name: Input Tumor93

source_name: IP Tumor93


title: Tumor75

source_name: Input Tumor75

source_name: IP Tumor75


title: Tumor80

source_name: Input Tumor80

source_name: IP Tumor80


title: Tumor76

source_name: Input Tumor76

source_name: IP Tumor76


title: Tumor77

source_name: Input Tumor77

source_name: IP Tumor77


title: Tumor8

source_name: Input Tumor8

source_name: IP Tumor8


title: Tumor74

source_name: Input Tumor74

source_name: IP Tumor74


title: Tumor72

source_name: Input Tumor72

source_name: IP Tumor72


title: Tumor73

source_name: Input Tumor73

source_name: IP Tumor73


title: Tumor70

source_name: Input Tumor70

source_name: IP Tumor70


title: Tumor64

source_name: Input Tumor64

source_name: IP Tumor64


title: Tumor7

source_name: Input Tumor7

source_name: IP Tumor7


title: Tumor6

source_name: Input Tumor6

source_name: IP Tumor6


title: Tumor67

source_name: Input Tumor67

source_name: IP Tumor67


title: Tumor68

source_name: Input Tumor68

source_name: IP Tumor68


title: Tumor63

source_name: Input Tumor63

source_name: IP Tumor63


title: Tumor62

source_name: Input Tumor62

source_name: IP Tumor62


title: Tumor57

source_name: Input Tumor57

source_name: IP Tumor57


title: Tumor69

source_name: Input Tumor69

source_name: IP Tumor69


title: Tumor56

source_name: Input Tumor56

source_name: IP Tumor56


title: Tumor59

source_name: Input Tumor59

source_name: IP Tumor59


title: Tumor50

source_name: Input Tumor50

source_name: IP Tumor50


title: Tumor52

source_name: Input Tumor52

source_name: IP Tumor52


title: Tumor71

source_name: Input Tumor71

source_name: IP Tumor71


title: Tumor61

source_name: Input Tumor61

source_name: IP Tumor61


title: Tumor51

source_name: Input Tumor51

source_name: IP Tumor51


title: Tumor66

source_name: Input Tumor66

source_name: IP Tumor66


title: Tumor54

source_name: Input Tumor54

source_name: IP Tumor54


title: Tumor5

source_name: Input Tumor5

source_name: IP Tumor5


title: Tumor60

source_name: Input Tumor60

source_name: IP Tumor60


title: Tumor53

source_name: Input Tumor53

source_name: IP Tumor53


title: Tumor65

source_name: Input Tumor65

source_name: IP Tumor65


title: Tumor55

source_name: Input Tumor55

source_name: IP Tumor55


title: Tumor46

source_name: Input Tumor46

source_name: IP Tumor46


title: Tumor44

source_name: Input Tumor44

source_name: IP Tumor44


title: Tumor47

source_name: Input Tumor47

source_name: IP Tumor47


title: Tumor38

source_name: Input Tumor38

source_name: IP Tumor38


title: Tumor32

source_name: Input Tumor32

source_name: IP Tumor32


title: Tumor48

source_name: Input Tumor48

source_name: IP Tumor48


title: Tumor40

source_name: Input Tumor40

source_name: IP Tumor40


title: Tumor4

source_name: Input Tumor4

source_name: IP Tumor4


title: Tumor41

source_name: Input Tumor41

source_name: IP Tumor41


title: Tumor34

source_name: Input Tumor34

source_name: IP Tumor34


title: Tumor43

source_name: Input Tumor43

source_name: IP Tumor43


title: Tumor45

source_name: Input Tumor45

source_name: IP Tumor45


title: Tumor49

source_name: Input Tumor49

source_name: IP Tumor49


title: Tumor39

source_name: Input Tumor39

source_name: IP Tumor39


title: Tumor35

source_name: Input Tumor35

source_name: IP Tumor35


title: Tumor37

source_name: Input Tumor37

source_name: IP Tumor37


title: Tumor28

source_name: Input Tumor28

source_name: IP Tumor28


title: Tumor36

source_name: Input Tumor36

source_name: IP Tumor36


title: Tumor31

source_name: Input Tumor31

source_name: IP Tumor31


title: Tumor33

source_name: Input Tumor33

source_name: IP Tumor33


title: Tumor29

source_name: Input Tumor29

source_name: IP Tumor29


title: Tumor3

source_name: Input Tumor3

source_name: IP Tumor3


title: Tumor30

source_name: Input Tumor30

source_name: IP Tumor30


title: Tumor58

source_name: Input Tumor58

source_name: IP Tumor58


title: Tumor23

source_name: Input Tumor23

source_name: IP Tumor23


title: Tumor27

source_name: Input Tumor27

source_name: IP Tumor27


title: Tumor42

source_name: Input Tumor42

source_name: IP Tumor42


title: Tumor26

source_name: Input Tumor26

source_name: IP Tumor26


title: Tumor24

source_name: Input Tumor24

source_name: IP Tumor24


title: Tumor22

source_name: Input Tumor22

source_name: IP Tumor22


title: Tumor25

source_name: Input Tumor25

source_name: IP Tumor25


title: Tumor16

source_name: Input Tumor16

source_name: IP Tumor16


title: Tumor21

source_name: Input Tumor21

source_name: IP Tumor21


title: Tumor17

source_name: Input Tumor17

source_name: IP Tumor17


title: Tumor15

source_name: Input Tumor15

source_name: IP Tumor15


title: Tumor18

source_name: Input Tumor18

source_name: IP Tumor18


title: Tumor100

source_name: Input Tumor100

source_name: IP Tumor100


title: Normal99

source_name: Input Normal99

source_name: IP Normal99


title: Tumor13

source_name: Input Tumor13

source_name: IP Tumor13


title: Tumor14

source_name: Input Tumor14

source_name: IP Tumor14


title: Tumor19

source_name: Input Tumor19

source_name: IP Tumor19


title: Normal98

source_name: Input Normal98

source_name: IP Normal98


title: Normal96

source_name: Input Normal96

source_name: IP Normal96


title: Tumor1

source_name: Input Tumor1

source_name: IP Tumor1


title: Normal92

source_name: Input Normal92

source_name: IP Normal92


title: Tumor11

source_name: Input Tumor11

source_name: IP Tumor11


title: Normal97

source_name: Input Normal97

source_name: IP Normal97


title: Tumor12

source_name: Input Tumor12

source_name: IP Tumor12


title: Tumor10

source_name: Input Tumor10

source_name: IP Tumor10


title: Normal95

source_name: Input Normal95

source_name: IP Normal95


title: Tumor20

source_name: Input Tumor20

source_name: IP Tumor20


title: Normal93

source_name: Input Normal93

source_name: IP Normal93


title: Normal94

source_name: Input Normal94

source_name: IP Normal94


title: Normal85

source_name: Input Normal85

source_name: IP Normal85


title: Normal90

source_name: Input Normal90

source_name: IP Normal90


title: Tumor2

source_name: Input Tumor2

source_name: IP Tumor2


title: Normal89

source_name: Input Normal89

source_name: IP Normal89


title: Normal9

source_name: Input Normal9

source_name: IP Normal9


title: Normal87

source_name: Input Normal87

source_name: IP Normal87


title: Normal86

source_name: Input Normal86

source_name: IP Normal86


title: Normal91

source_name: Input Normal91

source_name: IP Normal91


title: Normal82

source_name: Input Normal82

source_name: IP Normal82


title: Normal81

source_name: Input Normal81

source_name: IP Normal81


title: Normal8

source_name: Input Normal8

source_name: IP Normal8


title: Normal79

source_name: Input Normal79

source_name: IP Normal79


title: Normal84

source_name: Input Normal84

source_name: IP Normal84


title: Normal73

source_name: Input Normal73

source_name: IP Normal73


title: Normal88

source_name: Input Normal88

source_name: IP Normal88


title: Normal70

source_name: Input Normal70

source_name: IP Normal70


title: Normal78

source_name: Input Normal78

source_name: IP Normal78


title: Normal83

source_name: Input Normal83

source_name: IP Normal83


title: Normal71

source_name: Input Normal71

source_name: IP Normal71


title: Normal60

source_name: Input Normal60

source_name: IP Normal60


title: Normal7

source_name: Input Normal7

source_name: IP Normal7


title: Normal67

source_name: Input Normal67

source_name: IP Normal67


title: Normal77

source_name: Input Normal77

source_name: IP Normal77


title: Normal74

source_name: Input Normal74

source_name: IP Normal74


title: Normal68

source_name: Input Normal68

source_name: IP Normal68


title: Normal75

source_name: Input Normal75

source_name: IP Normal75


title: Normal76

source_name: Input Normal76

source_name: IP Normal76


title: Normal80

source_name: Input Normal80

source_name: IP Normal80


title: Normal63

source_name: Input Normal63

source_name: IP Normal63


title: Normal65

source_name: Input Normal65

source_name: IP Normal65


title: Normal62

source_name: Input Normal62

source_name: IP Normal62


title: Normal69

source_name: Input Normal69

source_name: IP Normal69


title: Normal66

source_name: Input Normal66

source_name: IP Normal66


title: Normal59

source_name: Input Normal59

source_name: IP Normal59


title: Normal64

source_name: Input Normal64

source_name: IP Normal64


title: Normal72

source_name: Input Normal72

source_name: IP Normal72


title: Normal57

source_name: Input Normal57

source_name: IP Normal57


title: Normal6

source_name: Input Normal6

source_name: IP Normal6


title: Normal58

source_name: Input Normal58

source_name: IP Normal58


title: Normal61

source_name: Input Normal61

source_name: IP Normal61


title: Normal55

source_name: Input Normal55

source_name: IP Normal55


title: Normal56

source_name: Input Normal56

source_name: IP Normal56


title: Normal54

source_name: Input Normal54

source_name: IP Normal54


title: Normal53

source_name: Input Normal53

source_name: IP Normal53


title: H2073 AT2

description: Aza-dC/TSA treated

hyb_protocol: Each sample was hybridized to Affymetrix HG-U133_plus_2.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.

scan_protocol: Washing and staining of microarrays were performed on Affymetrix Fluidics Station 450 and scanned on Affymetrix GeneChip scanner 3000.

data_processing: Data were collected using Affymetrix AGCC software. Basic statistical analysis was performed with Flexarray software as follows: Background correction (MAS5.0), array normalization (quantile normalization), probe set summarization technique (Tukey biweight [MAS5.0])

source_name: NSCLC cell line H2073

label_protocol: RNA (200ng) was reverse transcribed using random hexamer primer, amplified and terminal labeled with biotin using Affymetrix Whole Transcript Sense Target Labeling kit according to manufacturer’s protocol.

growth_protocol: Cells were cultured using RPMI1640 supplemented with 10% FCS and incubated at 37 °C and 5% CO2.

extract_protocol: RNA was isolated using Trizol followed by clean up using Qiagen's RNAeasy mini spin colomn according to manufacturer's instuctions.

treatment_protocol: 2x10^5 A549 cells/ml were treated either with 0.5 µM Aza-dC for 6 days or with the combination of 0.5 µM Aza-dC for 6 days and 100 ng/ml TSA for additional 24 hours.

value: NSCLC cell line H2073

value: Aza-dC/TSA treated


title: Normal5

source_name: Input Normal5

source_name: IP Normal5


title: Normal47

source_name: Input Normal47

source_name: IP Normal47


title: H2073 AT1

description: Aza-dC/TSA treated


title: H2073 A2

description: Aza-dC treated

value: Aza-dC treated


title: H2073 A1

description: Aza-dC treated


title: Normal50

source_name: Input Normal50

source_name: IP Normal50


title: Normal39

source_name: Input Normal39

source_name: IP Normal39


title: H2073 C2

description: untreated

value: untreated


title: Normal46

source_name: Input Normal46

source_name: IP Normal46


title: Normal41

source_name: Input Normal41

source_name: IP Normal41


title: Normal51

source_name: Input Normal51

source_name: IP Normal51


title: Normal40

source_name: Input Normal40

source_name: IP Normal40


title: Normal48

source_name: Input Normal48

source_name: IP Normal48


title: Normal52

source_name: Input Normal52

source_name: IP Normal52


title: Normal45

source_name: Input Normal45

source_name: IP Normal45


title: Normal44

source_name: Input Normal44

source_name: IP Normal44


title: Normal43

source_name: Input Normal43

source_name: IP Normal43


title: Normal32

source_name: Input Normal32

source_name: IP Normal32


title: Normal36

source_name: Input Normal36

source_name: IP Normal36


title: Normal49

source_name: Input Normal49

source_name: IP Normal49


title: Normal33

source_name: Input Normal33

source_name: IP Normal33


title: Normal4

source_name: Input Normal4

source_name: IP Normal4


title: H2073 C1

description: untreated

source_name: NSCLC cell line H2073


title: Normal37

source_name: Input Normal37

source_name: IP Normal37


title: Normal42

source_name: Input Normal42

source_name: IP Normal42


title: Normal38

source_name: Input Normal38

source_name: IP Normal38


title: Normal35

source_name: Input Normal35

source_name: IP Normal35


title: H1993 A2

description: Aza-dC treated

source_name: NSCLC cell line H1993

value: NSCLC cell line H1993


title: H1993 AT2

description: Aza-dC/TSA treated


title: Normal31

source_name: Input Normal31

source_name: IP Normal31


title: H1993 AT1

description: Aza-dC/TSA treated


title: Normal28

source_name: Input Normal28

source_name: IP Normal28


title: Normal29

source_name: Input Normal29

source_name: IP Normal29


title: Normal3

source_name: Input Normal3

source_name: IP Normal3


title: H1993 C2

description: untreated


title: A549 AT1

description: Aza-dC/TSA treated

source_name: NSCLC cell line A549

value: NSCLC cell line A549


title: H1993 C1

description: untreated


title: A549 C2

description: untreated


title: H1993 A1

description: Aza-dC treated


title: A549 AT2

description: Aza-dC/TSA treated


title: A549 A2

description: Aza-dC treated


title: A549 C1

description: untreated


title: A549 A1

description: Aza-dC treated


title: A549 Ctrl2_vs_A2

status: Public on Mar 13 2012

hyb_protocol: Microarray analysis was performed as recommended by LC Sciences

scan_protocol: Axon GenePix 4000B Microarray Scanner.

data_processing: Data Process Software: ArrayPro, Global Normalization

source_name: A549 cell line

label_protocol: Small RNA enrichment and Cy3/Cy5 labeling performed by DNAVision (Belgium)

growth_protocol: A549 grown in RPMI1640 medium supplemented with 10% FCS and Refobacin @ 37°C and 5% CO2

extract_protocol: RNA extracted using Trizol reagent

treatment_protocol: 2x10^5 cells/ml were treated either with 0.5 µM Aza-dC for 6 days or with the combination of 0.5 µM Aza-dC for 6 days and 100 ng/ml TSA for additional 24 hours


title: A549 Ctrl1_vs_A1


title: A549 Ctrl2_vs_AT2


title: Normal24

source_name: Input Normal24

source_name: IP Normal24


title: Normal26

source_name: Input Normal26

source_name: IP Normal26


title: Normal22

source_name: Input Normal22

source_name: IP Normal22


title: Normal14

source_name: Input Normal14

source_name: IP Normal14


title: Normal20

source_name: Input Normal20

source_name: IP Normal20


title: Normal27

source_name: Input Normal27

source_name: IP Normal27


title: Normal30

source_name: Input Normal30

source_name: IP Normal30


title: NMN3

status: Public on Dec 05 2011

description: Chip-B

data_processing: The average of redundant genes were calculated in raw microarray results and data were subjected to Z score transformation, and Z ratio were calculated.  False discovery rates for the differences in expression levels between two conditions (RC vs HFDa or HFDb vs NMN) were calculated using the Rank Product Analysis.  All data were analyzed by the R statistical software package.

source_name: Liver, HFD+NMN treatment

label_protocol: Biotinylated cRNA were prepared for Illumina arrays

growth_protocol: Mice were maintained on a regular chow or high fat diet.

extract_protocol: Total RNA was isolated from frozen liver samples with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: For NMN treatment, NMN was intraperitoneally given to HFD-mice for seven days.

value: female

value: liver


title: Normal25

source_name: Input Normal25

source_name: IP Normal25


title: Normal17

source_name: Input Normal17

source_name: IP Normal17


title: Normal2

source_name: Input Normal2

source_name: IP Normal2


title: Normal11

source_name: Input Normal11

source_name: IP Normal11


title: Normal34

source_name: Input Normal34

source_name: IP Normal34


title: Normal15

source_name: Input Normal15

source_name: IP Normal15


title: NMN2

description: Chip-B


title: Normal12

source_name: Input Normal12

source_name: IP Normal12


title: Normal21

source_name: Input Normal21

source_name: IP Normal21


title: HFD4b

description: Chip-B

source_name: Liver, high fat diet (HFD)


title: HFD2b

description: Chip-B


title: Normal10

source_name: Input Normal10

source_name: IP Normal10


title: Normal16

source_name: Input Normal16

source_name: IP Normal16


title: Normal18

source_name: Input Normal18

source_name: IP Normal18


title: Normal23

source_name: Input Normal23

source_name: IP Normal23


title: RC4

description: Chip-A

source_name: Liver, regular chow-fed


title: Normal19

source_name: Input Normal19

source_name: IP Normal19


title: Normal100

source_name: Input Normal100

source_name: IP Normal100


title: Normal13

source_name: Input Normal13

source_name: IP Normal13


title: HFD2a

description: Chip-A


title: HFD3a

description: Chip-A


title: Normal1

source_name: Input Normal1

source_name: IP Normal1


title: HFD1a

description: Chip-A

source_name: Liver, high fat diet (HFD)


title: NMN4

description: Chip-B

source_name: Liver, HFD+NMN treatment


title: RC3

description: Chip-A


title: HFD1b

description: Chip-B


title: RC2

description: Chip-A


title: RC1

description: Chip-A


title: HFD3b

description: Chip-B


title: A549 Ctrl1_vs_AT1

source_name: A549 cell line


title: D6

status: Public on Feb 04 2011

description: c-jun knock out

hyb_protocol: Each sample was hybridized to Affymetrix mouse Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.

source_name: B-lymphoid

extract_protocol: RNA was isolated using Trizol followed by clean up using Qiagen´s RNAeasy mini spin colomn according to manufacturer's instuctions.

value: SW129/C57BL/6J  cells

tag: genotype/variation

value: c-jun knock out

tag: cell type

value: B-lymphoid


title: RO36

description: wild type

value: wild type


title: RO37

description: wild type


title: F4

description: wild type


title: D1

description: c-jun knock out


title: RO38

description: c-jun knock out


title: RO35

description: c-jun knock out


title: NMN1

description: Chip-B


title: F2

description: wild type


title: HFD4a

description: Chip-A