title: Cord_blood_MAIT

description: DNA methylation from Cord blood MAIT

source_name: Cord blood MAIT

growth_protocol: Mononuclear cells were prepared from CB using Ficoll solution and washed extensively with PBS. MAIT cells were purified as 3C10+ cells with biotinylated monoclonal antibody 3C10 using two consecutive magnetic-activated cell sorting (MACS) columns. The purity of the 3C10+ cells after the second column was >96% from donor 1, >88% from donor 2, and >78% from donor 3, as determined by FACS analysis.


title: ST-1 embryonic stem cells [3-1] (methylation)

status: Public on Mar 14 2017

type: genomic

city: Shanghai

first: Hongying

last: Sha

state: Shanghai

address: 220 Handan Rd, WuJiaoChang, Yangpu Qu

country: China

institute: Fudan University

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

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

data_processing: BeadStudio software v3.2

molecule: genomic DNA

organism: Homo sapiens

source_name: embryonic stem cells

label_protocol: Standard Illumina Protocol

growth_protocol: In vitro culture at  5% CO2,37℃

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

treatment_protocol: All embryonic stem cells were cultured onto inactived feeder cells  and classical media for humanembryonic stem cells.  Human embryonic fibroblast cells were cultured under 10% fetal  bovine serum  in DMEM/f12.

tag: tissue

value: from inner cell mass of ST blastocyst


title: KO19M

type: RNA

city: Columbus

first: Bhawana

last: Dikshit

state: OH

address: 500 W 12th Avenue

country: USA

institute: Ohio State University

description: Gene expression data from liver of Wildtype and Knockout mice

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix) •Heat 650C for 5 minutes, 990C for 5 minutes, 450C for 5 minutes centrifuge top speed for 5 minutes. •Hybridize 16 hours at 450 at 60rpm•Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mice liver tissue at 12 weeks of age

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mice liver tissue collected at 12 weeks of age

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

treatment_protocol: Mice were euthanized at 12 weeks of age and liver tissue was snap frozen in liquid nitrogen for RNA extraction

tag: strain

value: Mouse C57BL6/J

value: Liver

tag: genotype


title: reMAIT_day_7-10_Middle

city: Koto-ku

first: Toutai

last: MITUYAMA

state: Tokyo

department: Artificial Intelligence Research Team

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: DNA methylation from reMAIT at 7-10 days after the beginning of induction

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

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

data_processing: Data normalization was performed using Illumina GenomeStudio Methylation Molude.

label: Biotin

source_name: reMAIT, day 7-10, Middle

label_protocol: Extracted genomics DNA (1 micro gram) from each sample was subjected to bisulfite conversion using EZ DNA Methylation Kit (Zymo Research, CA, USA).

growth_protocol: MAIT-derived iPSCs were cultured on OP9, and CD34+ CD43+ cells were isolated. These CD34+ CD43+ precursor cells were furthered cultured on OP9/DL1 for re-differentiation into MAITs.

extract_protocol: Genomic DNA was extracted from each sample using Wizard Genomic DNA Purification Kit (Promega, Tokyo, Japan).

value: cord blood

tag: timecourse


title: WT38F


title: Immature_T_cells_CD4+_CD8+_day_50_Late

description: DNA methylation from immature with CD4- and CD8- at 54 days after the beginning of differentiation

source_name: Immature T-cells, CD4+, CD8+, day 50, Late

growth_protocol: CD34+ cells were isolated from CB using CD34 MicroBead Kit (Miltenyi Biotech)

value: 54 day


title: WT23M


title: reMAIT_day_30_Late

description: Micro RNA expression from reMAIT at 20 days after the beginning of induction

hyb_protocol: The hybridization procedure was performed according to the “miRNA Complete Labeling and Hyb Kit” protocol using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies). Briefly, Cy3-labeled RNA in hybridization buffer was hybridized overnight (20 hours, 55 °C) to Agilent Human microRNA Microarrays 8x60K v19 (Design ID 046064) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 5 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 5 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: reMAIT, day 30, Late

label_protocol: Sample labeling was performed as detailed in the “miRNA Microarray System with miRNA Complete Labeling and Hyb Kit” protocol (version 2.4, part number G4170-90011). Briefly, 90 ng total RNA of sample hES d0 Pool and 100 ng total RNA of all other samples  was used for the labeling step using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies).

extract_protocol: RNA was prepared using the RNAeasy column purification (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were harvested with TRIzol (Sigma, Aldrich).

value: 20 day


title: WT17 M


title: Immature_T_cells_CD34+_day_0_Start

description: DNA methylation from immature T-cells with CD34+ at day 0 after the beginning of differentiation

source_name: Immature T-cells, CD34+, day 0, Start

value: 0 day


title: reMAIT_day_10_Middle

description: Micro RNA expression from reMAIT at 7-10 days after the beginning of induction

source_name: reMAIT, day 10, Middle


title: PB1T-1 embryonic stem cells [1-2] (methylation)

value: from inner cell mass of PB1T blastocyst


title: reMAIT_day_4_Early

description: Micro RNA expression from reMAIT at 4 days after the beginning of induction

source_name: reMAIT, day 4, Early

value: 4 day


title: Subject 29, Meal B (1000 kcal), Postprandial (2h)

city: Bern

first: Doreen

last: Gille

address: Schwarzenburgstrasse 161

country: Switzerland

institute: Agroscope

description: Blood cell transcriptome 2h after ingestion of 1000 kcal of a high fat meal

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16h at 45°C on Human Genome Array HG-U219. Arrays were washed and stained in the Affymetrix Fluidics Station of GeneAtlas™.

scan_protocol: GeneChips were scanned using the GeneAtlas™ Imaging Station.

data_processing: Data was processed by RMA, using the rma() function in the affy package (version 1.38.1) for R (version 3.0.1), to yield log-transformed expression values that were used for all subsequent analysis.

label_protocol: Biotinylated cRNA were prepared according to the GeneAtlas™ 3'IVT Express Kit protocol from Affymetrix.

extract_protocol: Total RNA was extracted using PAXgene Blood RNA Kit (Qiagen AG) according to the manufacturer’s recommendations.Total RNA was purified and concentrated with RNeasy MinElute Cleanup Kit (Qiagen AG). Next step included the depletion of globin mRNA with the GLOBINclear™ hybridization capture technology (Ambion, USA) according to recommendations of manufacturer.

treatment_protocol: Human subjects ingested 500, 1'000, 1'500 kcal of a high-fat meal in a randomized cross-over design. Blood was collected for RNA extraction before ingestion at 0h as well as postprandially at 2h, 4h, and 6h.

value: Whole blood

tag: metabolic status

value: Obese


title: Subject 29, Meal B (1000 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1000 kcal of a high fat meal


title: ST-1 embryonic stem cells [3-2] (methylation)


title: Immature_T_cells_CD4-_CD8-_day_40_Middle

description: Micro RNA expression from immature T-cells with CD4- and CD8- at 40 days after the beginning of differentiation

source_name: Immature T-cells, CD4-, CD8-, day 40, Middle

value: 40 day


title: PB1T-2 embryonic stem cells [2-1] (methylation)


title: Immature_T_cells_CD4+_CD8+_day_59_Late

description: Micro RNA expression from immature with CD4- and CD8- at 59 days after the beginning of differentiation

source_name: Immature T-cells, CD4+, CD8+, day 59, Late

value: 59 day


title: V3034 infected spleen at 72hr-replicate 3

city: Bethesda

first: Paridhi

last: Gupta

state: MD

address: 4301 Jones bridge road

institute: USUHS

hyb_protocol: Microarray slides were first hybridized with the cDNA overnight at 42°C in MAUI microarray hybridization chambers (Biomicro systems Inc.) followed by stringent washes. Slides hybridized with cDNA were then end labeled with Cy5/Cy3 dyes containing dendrimers at 65°C for 5 hours in MAUI microarray hybridization chambers followed by stringent washes.

scan_protocol: The slides were scanned using the Axon GenePix 4000B scanner with a 10-micron resolution

data_processing: Only the spots with spot size of 10μm to 300μm, ≤80% signal saturation, minimum fluorescent intensity of 150 and signal ≥2SD (standard deviation) above background in both Cy3 and Cy5 channels were selected for data analysis; Loess normalization using GenePix Pro 5.1 software

source_name: Uninfected mouse spleen

label_protocol: cDNA synthesized from 1.5µg of total RNA was labeled using 3DNA Array 900 expression array detection kit from Genisphere Inc. as per the manufacturer's protocol.

extract_protocol: Total RNA was extracted using trizol method followed by removal of DNA contamination using the RNeasy mini kit (Qiagen Inc.) as per manufacturr's protocol.

treatment_protocol: Animals were infected with 1000pfu of the virus in 25µl volume and the uninfected animals were injected with 25µl saline in the left rear food pad.

tag: age

value: 6-10 weeks old

tag: gender

value: male

source_name: V3034 infected mouse spleen


title: V3034 infected spleen at 96hr-replicate 1


title: V3034 infected spleen at 96hr-replicate 3


title: V3034 infected spleen at 96hr-replicate 2


title: Subject 29, Meal A (500 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 500 kcal of a high fat meal


title: Subject 29, Meal A (500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 500 kcal of a high fat meal


title: Immature_T_cells_CD34+_day_0_Start

description: Micro RNA expression from immature T-cells with CD34+ at day 0 after the beginning of differentiation


title: Subject 29, Meal A (500 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 500 kcal of a high fat meal


title: reMAIT_day_20_Late

description: DNA methylation from reMAIT at 36 days after the beginning of induction

source_name: reMAIT, day 20, Late

value: 36 day


title: Immature_T_cells_CD4-_CD8-_day_21_Early

description: Micro RNA expression from immature T-cells with CD4- and CD8- at 21 days after the beginning of differentiation

source_name: Immature T-cells, CD4-, CD8-, day 21, Early

value: 21 day


title: Subject 29, Meal A (500 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 500 kcal of a high fat meal


title: V3034 infected spleen at 72hr-replicate 1


title: Subject 28, Meal C (1500 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 1500 kcal of a high fat meal


title: Subject 28, Meal C (1500 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 1500 kcal of a high fat meal


title: Subject 28, Meal B (1000 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 1000 kcal of a high fat meal


title: Subject 28, Meal C (1500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1500 kcal of a high fat meal


title: Subject 28, Meal B (1000 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 1000 kcal of a high fat meal


title: Subject 28, Meal C (1500 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 1500 kcal of a high fat meal


title: Subject 28, Meal B (1000 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 1000 kcal of a high fat meal


title: V3034 infected spleen at 48hr-replicate 3


title: Subject 28, Meal B (1000 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1000 kcal of a high fat meal


title: V3034 infected spleen at 72hr-replicate 2


title: V3034 infected brain at 96hr-replicate 2

source_name: Uninfected mouse brain

source_name: V3034 infected mouse brain


title: V3034 infected spleen at 48hr-replicate 2


title: V3034 infected brain at 96hr-replicate 1


title: V3034 infected brain at 96hr-replicate 3


title: Subject 29, Meal B (1000 kcal), Postprandial (6h)


title: V3034 infected spleen at 48hr-replicate 1


title: V3034 infected brain at 72hr-replicate 3


title: Subject 28, Meal A (500 kcal), Postprandial (6h)


title: V3034 infected brain at 72hr-replicate 2


title: V3034 infected brain at 72hr-replicate 1


title: V3034 infected brain at 48hr-replicate 2


title: V3034 infected brain at 48hr-replicate 1


title: V3000 infected spleen at 96hr-replicate 3

source_name: V3000 infected mouse spleen


title: V3000 infected spleen at 96hr-replicate 2


title: V3000 infected spleen at 72hr-replicate 2


title: V3000 infected spleen at 96hr-replicate 1


title: Subject 28, Meal A (500 kcal), Postprandial (4h)


title: V3000 infected spleen at 72hr-replicate 1


title: Subject 25, Meal C (1500 kcal), Postprandial (4h)


title: Subject 28, Meal A (500 kcal), Fasting (0h)


title: Subject 28, Meal A (500 kcal), Postprandial (2h)


title: Subject 25, Meal B (1000 kcal), Postprandial (6h)


title: Subject 29, Meal B (1000 kcal), Postprandial (4h)


title: Subject 25, Meal C (1500 kcal), Postprandial (6h)


title: Subject 25, Meal C (1500 kcal), Postprandial (2h)


title: V3000 infected spleen at 48hr-replicate 2


title: Subject 25, Meal A (500 kcal), Postprandial (6h)


title: Subject 25, Meal B (1000 kcal), Postprandial (4h)


title: Subject 25, Meal C (1500 kcal), Fasting (0h)


title: Subject 25, Meal A (500 kcal), Postprandial (4h)


title: Subject 25, Meal B (1000 kcal), Postprandial (2h)


title: Subject 25, Meal A (500 kcal), Fasting (0h)


title: V3000 infected spleen at 48hr-replicate 1


title: V3000 infected spleen at 72hr-replicate 3


title: Subject 25, Meal B (1000 kcal), Fasting (0h)


title: Subject 25, Meal A (500 kcal), Postprandial (2h)


title: V3000 infected spleen at 48hr-replicate 3


title: V3000 infected brain at 96hr-replicate 1

source_name: V3000 infected mouse brain


title: V3000 infected brain at 96hr-replicate 2


title: V3000 infected brain at 96hr-replicate 3


title: reMAIT_day_0_Start

description: Micro RNA expression from reMAIT at 0 days after the beginning of induction

source_name: reMAIT, day 0, Start


title: Subject 24, Meal C (1500 kcal), Postprandial (6h)


title: Subject 24, Meal C (1500 kcal), Postprandial (2h)


title: V3000 infected brain at 72hr-replicate 3


title: V3000 infected brain at 72hr-replicate 2


title: V3000 infected brain at 72hr-replicate 1


title: V3000 infected brain at 48hr-replicate 1


title: V3000 infected brain at 48hr-replicate 2


title: Subject 24, Meal C (1500 kcal), Postprandial (4h)


title: V3000 infected brain at 48hr-replicate 3


title: V3034 infected brain at 48hr-replicate 3


title: Subject 24, Meal C (1500 kcal), Fasting (0h)


title: Subject 24, Meal B (1000 kcal), Postprandial (4h)


title: Subject 24, Meal A (500 kcal), Postprandial (2h)


title: Subject 24, Meal B (1000 kcal), Fasting (0h)


title: Subject 24, Meal A (500 kcal), Fasting (0h)


title: Subject 23, Meal C (1500 kcal), Postprandial (4h)


title: Subject 23, Meal C (1500 kcal), Postprandial (6h)


title: Subject 24, Meal A (500 kcal), Postprandial (6h)


title: Subject 23, Meal B (1000 kcal), Postprandial (6h)


title: Subject 24, Meal A (500 kcal), Postprandial (4h)


title: Subject 23, Meal C (1500 kcal), Fasting (0h)


title: Subject 23, Meal C (1500 kcal), Postprandial (2h)


title: Subject 24, Meal B (1000 kcal), Postprandial (6h)


title: Subject 24, Meal B (1000 kcal), Postprandial (2h)


title: Subject 23, Meal B (1000 kcal), Fasting (0h)


title: skeletalmuscle_LF_RFIpl_rep1_55

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

country: France

institute: INRA

description: Gene expression in pig skeletal muscle with high residual feed intake fed with low fat diet

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb hybridization chambers containing 600 ng of Cy3-labeled cRNA sample per hybridization. Hybridization reactions were performed at 65°C for 17 h using Agilent’s Gene Expression Hybridization Kit

scan_protocol: After washing, microarrays were scanned at 3 µm/pixel resolution using the Agilent DNA Microarray Scanner G2505C, and images were analyzed with Agilent Feature Extraction Software (Version 10.7.3.1, protocol GE1_107_Sep09)

data_processing: All analyses were then performed using the R software version 2.10.0 (R Development Core Team, 2008). Raw spots intensities were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3), and data were normalized by median centering, i.e. subtracting the median value across all probes from all raw values for each sample to obtain experimentally consolidated gene expression values. Normalized data were submitted to an analysis of variance using the fixed effects of genetic line breed (RFIpl or RFIneg), diet effect (HF or LF) and the interaction between line and diet.

organism: Sus scrofa

source_name: skeletalmuscle, low fat diet,high-RFI

label_protocol: Total RNA (150 ng) from each sample was labeled with Cy3 dye using the low RNA input linear amplification kit (Agilent Technologies, Les Ulis, France) following the manufacturer’s instructions. Briefly, a two-step procedure was used to generate fluorescent complementary RNA (cRNA) by using T7 RNA polymerase. Samples were then purified with an RNeasy mini elute kit (Qiagen, Hilden, Germany)

growth_protocol: The low-RFI (RFIneg) and high-RFI (RFIpl) pigs were fed ad libitum with high fat ,high fiber (HF) diet or low fat, low fiber (LF) diet.

extract_protocol: For total RNA extraction, samples of frozen tissues (80 to 100 mg each) were homogenized in Trizol reagent (Invitrogen, Cergy-Pontoise, France) using a Precellys homogenizer (Ozyme,Saint-Quentin-en-Yvelines) and were then treated as previously described (Vincent et al., 2012). RNA was finally purified using a silica-membrane technology under vacuum (Nucleospin 8 RNA kit, Macherey Nagel, Hoerdt, France)

value: Longissimus skeletal muscle

value: RFIpl

tag: feed condition

value: LF


title: skeletalmuscle_LF_RFIpl_rep1_2


title: Subject 23, Meal A (500 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 500 kcal of a high fat meal


title: skeletalmuscle_LF_RFIpl_rep1_22


title: skeletalmuscle_LF_RFIpl_rep1_15


title: Subject 23, Meal B (1000 kcal), Postprandial (2h)


title: Subject 23, Meal A (500 kcal), Postprandial (4h)


title: skeletalmuscle_LF_RFIpl_rep1_35


title: Subject 23, Meal B (1000 kcal), Postprandial (4h)


title: skeletalmuscle_LF_RFIpl_rep1_48


title: skeletalmuscle_LF_RFIpl_rep1_10


title: Subject 23, Meal A (500 kcal), Postprandial (2h)


title: skeletalmuscle_LF_RFIpl_rep1_7


title: Subject 22, Meal C (1500 kcal), Postprandial (6h)


title: skeletalmuscle_LF_RFIpl_rep1_13


title: Subject 23, Meal A (500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 500 kcal of a high fat meal


title: skeletalmuscle_LF_RFIpl_rep1_30


title: skeletalmuscle_LF_RFIpl_rep1_44


title: skeletalmuscle_LF_RFIneg_rep1_50

description: Gene expression in pig skeletal muscle with low residual feed intake fed with low fat diet

source_name: skeletalmuscle, low fat diet,low-RFI

value: RFIneg


title: Subject 22, Meal C (1500 kcal), Postprandial (4h)


title: skeletalmuscle_LF_RFIneg_rep1_38


title: Subject 22, Meal C (1500 kcal), Fasting (0h)


title: Subject 22, Meal B (1000 kcal), Postprandial (4h)


title: skeletalmuscle_LF_RFIneg_rep1_33


title: skeletalmuscle_LF_RFIpl_rep1_16


title: Subject 22, Meal B (1000 kcal), Postprandial (6h)


title: Subject 22, Meal B (1000 kcal), Postprandial (2h)


title: Subject 22, Meal C (1500 kcal), Postprandial (2h)


title: Subject 22, Meal B (1000 kcal), Fasting (0h)


title: skeletalmuscle_LF_RFIneg_rep1_11


title: skeletalmuscle_LF_RFIneg_rep1_27


title: skeletalmuscle_LF_RFIneg_rep1_4


title: skeletalmuscle_LF_RFIneg_rep1_6


title: Subject 22, Meal A (500 kcal), Postprandial (4h)


title: skeletalmuscle_LF_RFIneg_rep1_29


title: Subject 22, Meal A (500 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 500 kcal of a high fat meal


title: Subject 22, Meal A (500 kcal), Postprandial (6h)


title: Subject 22, Meal A (500 kcal), Fasting (0h)


title: skeletalmuscle_LF_RFIneg_rep1_54


title: skeletalmuscle_LF_RFIneg_rep1_20


title: skeletalmuscle_LF_RFIneg_rep1_42


title: skeletalmuscle_LF_RFIneg_rep1_23


title: Subject 21, Meal C (1500 kcal), Postprandial (4h)


title: skeletalmuscle_HF_RFIpl_rep1_31

description: Gene expression in pig skeletal muscle with high residual feed intake fed with high fat diet

source_name: skeletalmuscle, high fat diet,high-RFI

value: HF


title: Subject 21, Meal C (1500 kcal), Postprandial (6h)


title: Subject 21, Meal C (1500 kcal), Postprandial (2h)


title: skeletalmuscle_HF_RFIpl_rep1_26


title: Subject 21, Meal B (1000 kcal), Postprandial (6h)


title: Subject 21, Meal B (1000 kcal), Postprandial (2h)


title: skeletalmuscle_HF_RFIpl_rep1_45


title: Subject 21, Meal B (1000 kcal), Postprandial (4h)


title: skeletalmuscle_HF_RFIpl_rep1_41


title: Subject 21, Meal C (1500 kcal), Fasting (0h)


title: skeletalmuscle_HF_RFIpl_rep1_53


title: Subject 21, Meal B (1000 kcal), Fasting (0h)


title: Subject 21, Meal A (500 kcal), Postprandial (4h)


title: skeletalmuscle_HF_RFIpl_rep1_37


title: skeletalmuscle_HF_RFIpl_rep1_14


title: skeletalmuscle_HF_RFIpl_rep1_1


title: Subject 19, Meal C (1500 kcal), Postprandial (6h)

value: Normal weight


title: Subject 21, Meal A (500 kcal), Postprandial (2h)


title: Subject 21, Meal A (500 kcal), Fasting (0h)


title: skeletalmuscle_HF_RFIpl_rep1_19


title: skeletalmuscle_HF_RFIneg_rep1_43

description: Gene expression in pig skeletal muscle with low residual feed intake fed with high fat diet

source_name: skeletalmuscle, high fat diet,low-RFI


title: Subject 21, Meal A (500 kcal), Postprandial (6h)


title: skeletalmuscle_HF_RFIpl_rep1_34


title: skeletalmuscle_HF_RFIpl_rep1_18


title: skeletalmuscle_HF_RFIneg_rep1_28


title: Subject 19, Meal C (1500 kcal), Postprandial (4h)


title: Subject 19, Meal B (1000 kcal), Postprandial (6h)


title: skeletalmuscle_HF_RFIneg_rep1_49


title: Subject 19, Meal B (1000 kcal), Postprandial (4h)


title: skeletalmuscle_HF_RFIpl_rep1_9


title: skeletalmuscle_HF_RFIneg_rep1_12


title: Subject 19, Meal C (1500 kcal), Postprandial (2h)


title: Platelets_thrombin_Total_rep1

city: Stockholm

first: Xinyan

last: Miao

address: Karolinska University Hospital-Solna

department: Medicine

country: Sweden

institute: Karolinska Institutet

description: miRNA expression profile

hyb_protocol: Labeled RNA was hybridized onto Agilent miRNA array (G4470B) for 20 hours at 55°C

scan_protocol: Slides were scanned in an Agilent microarray scanner (G2565BA, Agilent Technologies) using default settings for miRNA microarray v2.0. Images obtained after scanning were processed with Feature Extraction Software 10.7.3.1 (Agilent, Santa Clara, CA)

data_processing:
Processing of the intensity values was done using Cluster 3.0 software whereby data were normalized and median centered. Only normalized miRNAs with less than 25% missing values across the samples were included in the further analysis.
Normalized and median centered intensity values.

source_name: washed platelets from venous peripheral blood

label_protocol: 200 ng of total RNA were dephosphorylated and fluorescence-labeled with Cyanine 3-pCp by using T4 RNA Ligase.

growth_protocol: Venous blood was collected using siliconized vacutainers containing 1/10 volume of 3.8% sodium citrate. The blood was centrifuged at 190 ´g for 20 min at room temperature (RT), and the upper two-thirds of platelet-rich plasma (PRP) was collected. After adding PGE1 (final concentration 1 µM), PRP was re-centrifuged at 190 ´g for 10 min at RT. Again, the top two-thirds of PRP was collect to reduce leukocyte contamination. Platelets were further purified by leukocyte depletion using CD45 Dynabeads. Afterwards, PRP was washed with Tyrode’s HEPES buffer containing 0.1 µM PGE1, and centrifuged at 1000 ´g for 10 min at RT. Platelets were then resuspended in DMEM low glucose medium at 109/ml, and kept on bench for 30 min to allow the recovery of platelet responsiveness.

extract_protocol: RNA extraction of the whole cell lysate of platelets and Ago2-IP supernatant was carried out using TRIzol reagent (Invitrogen) and according to manufacture’s instructions.

treatment_protocol: For total RNA, the purified platelets were treated with vehicle or thrombin (0.1 U/ml) at 37℃ for 30 min, then total RNA was extracted; For Ago2-associated RNA, washed platelets were treated with vehicle or thrombin (0.1 U/ml) for 30 min at 37°C, followed by UV crosslinking, and platelet pellets were lysed. The supernatant was then incubated with Dynabeads® Protein G coupled to anti-Ago2 or the isotypic control IgG for 4 hours at 4℃ with rotation, thereafter, the beads were washed 5 times. The washed beads were then treated with proteinase K, and the supernatant was collected for RNA extraction.

tag: stimulation

value: thrombin stimulation

tag: ip

value: non


title: Platelets_thrombin_Total_rep2

description: miRNA expression profile


title: Platelets_thrombin_Total_rep3

description: miRNA expression profile


title: skeletalmuscle_HF_RFIneg_rep1_40


title: Subject 19, Meal B (1000 kcal), Postprandial (2h)


title: Subject 19, Meal B (1000 kcal), Fasting (0h)


title: Subject 19, Meal C (1500 kcal), Fasting (0h)


title: Subject 19, Meal A (500 kcal), Postprandial (6h)


title: Subject 19, Meal A (500 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 500 kcal of a high fat meal


title: skeletalmuscle_HF_RFIneg_rep1_8


title: Subject 19, Meal A (500 kcal), Fasting (0h)


title: skeletalmuscle_HF_RFIneg_rep1_32


title: skeletalmuscle_HF_RFIneg_rep1_17


title: skeletalmuscle_HF_RFIneg_rep1_25


title: Platelets_resting_Total_rep2

description: miRNA expression profile

value: unstimulation


title: Subject 19, Meal A (500 kcal), Postprandial (2h)

value: Whole blood


title: Subject 18, Meal C (1500 kcal), Postprandial (4h)


title: skeletalmuscle_HF_RFIneg_rep1_39


title: Subject 18, Meal C (1500 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 1500 kcal of a high fat meal


title: skeletalmuscle_HF_RFIneg_rep1_46


title: liver_LF_RFIpl_rep1_2

description: Gene expression in pig liver with high residual feed intake fed with low fat diet

source_name: liver, low fat diet,high-RFI

value: liver


title: liver_LF_RFIpl_rep1_13


title: Subject 18, Meal B (1000 kcal), Postprandial (4h)


title: Platelets_resting_Total_rep1

description: miRNA expression profile


title: skeletalmuscle_HF_RFIneg_rep1_3


title: liver_LF_RFIpl_rep1_22


title: Subject 18, Meal C (1500 kcal), Postprandial (2h)


title: Subject 18, Meal B (1000 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 1000 kcal of a high fat meal


title: Subject 18, Meal B (1000 kcal), Postprandial (2h)


title: liver_LF_RFIpl_rep1_48


title: liver_LF_RFIpl_rep1_15


title: Subject 18, Meal C (1500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1500 kcal of a high fat meal


title: liver_LF_RFIpl_rep1_35


title: liver_LF_RFIpl_rep1_10


title: liver_LF_RFIpl_rep1_7


title: Subject 18, Meal A (500 kcal), Postprandial (4h)


title: liver_LF_RFIpl_rep1_55


title: Subject 18, Meal A (500 kcal), Fasting (0h)


title: liver_LF_RFIpl_rep1_44


title: Subject 18, Meal B (1000 kcal), Fasting (0h)


title: Subject 18, Meal A (500 kcal), Postprandial (6h)


title: liver_LF_RFIpl_rep1_16


title: liver_LF_RFIneg_rep1_27

description: Gene expression in pig liver with low residual feed intake fed with low fat diet

source_name: liver, low fat diet,low-RFI


title: Subject 18, Meal A (500 kcal), Postprandial (2h)


title: Subject 17, Meal C (1500 kcal), Fasting (0h)


title: liver_LF_RFIpl_rep1_30


title: Subject 17, Meal C (1500 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 1500 kcal of a high fat meal


title: Subject 17, Meal C (1500 kcal), Postprandial (6h)


title: Subject 17, Meal B (1000 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 1000 kcal of a high fat meal


title: liver_LF_RFIneg_rep1_50


title: Subject 17, Meal B (1000 kcal), Postprandial (6h)


title: Healthy control [RCJ_NS]

first: Hui

last: Cheng

address: 168 Changhai Road

institute: Changhai Hospital, Second Military Medical University

hyb_protocol: Slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies) in Hybridization Oven (Agilent technologies), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies) with default settings, Dye channel: Green, Scan resolution=3 μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies)

source_name: healthy control_BM-MNCs

label_protocol: Total RNA was labeled by Low Input Quick Amp Labeling Kit, One-Color ( Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit (QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

tag: subject status

value: Healthy control

value: Male

value: Bone marrow

tag: cell type

value: bone marrow-derived mononuclear cells (BM-MNCs)


title: liver_LF_RFIneg_rep1_33


title: Healthy control [GWY_NS]

value: Female


title: Subject 17, Meal B (1000 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 1000 kcal of a high fat meal


title: liver_LF_RFIneg_rep1_4


title: Subject 17, Meal A (500 kcal), Postprandial (2h)


title: Subject 17, Meal A (500 kcal), Postprandial (6h)


title: Healthy control [LPH_NS]


title: Healthy control [LXQ_NS]


title: Healthy control [THM_NS]


title: ALL patients [CC_NS]

source_name: ALL_Leukemia cells

value: ALL patients

value: Leukemia cells


title: Subject 17, Meal B (1000 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1000 kcal of a high fat meal


title: liver_LF_RFIneg_rep1_11


title: liver_LF_RFIneg_rep1_6


title: liver_LF_RFIneg_rep1_29


title: ALL patients [LZW_NS]


title: liver_LF_RFIneg_rep1_23


title: Subject 17, Meal A (500 kcal), Fasting (0h)


title: liver_LF_RFIneg_rep1_38


title: Subject 17, Meal A (500 kcal), Postprandial (4h)


title: liver_LF_RFIneg_rep1_54


title: Healthy control [GSQ_NS]


title: liver_LF_RFIneg_rep1_20


title: Subject 16, Meal C (1500 kcal), Postprandial (6h)


title: liver_LF_RFIneg_rep1_42


title: ALL patients [BSS_NS]


title: Subject 17, Meal C (1500 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 1500 kcal of a high fat meal


title: ALL patients [JAL_NS]


title: Subject 16, Meal C (1500 kcal), Postprandial (2h)


title: ALL patients [CH_NS]


title: ALL patients [WLL_NS]


title: PTEN_LXRKO3_SBN_12

city: AUBIERE

first: silvere

last: BARON

address: 10 avenue Blaise Pascal

department: Endocrine, Signaling and Cancer

institute: Université Clermont Auvergne

hyb_protocol: Following fragmentation and end-labeling, 3 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 2.0 ST arrays interrogating 35240 RefSeq transcripts and ~ 2000 LncRNAs

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm

data_processing:
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2
CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings

source_name: Dorsal prostate

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 250 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

extract_protocol: Total RNA were extract from individual mouse dorsal lobes using Nucleospin RNA Colum (Macherey Nagel) and RNA Integrity were ckeked by Bioanalyzer (Agilent).

value: Dorsal prostate

value: LXRalpha/beta KO PTENpc-/-

tag: prostate histology

value: Carcinoma


title: Subject 16, Meal C (1500 kcal), Fasting (0h)


title: Subject 16, Meal C (1500 kcal), Postprandial (4h)


title: liver_HF_RFIpl_rep1_9

description: Gene expression in pig liver with high residual feed intake fed with high fat diet

source_name: liver, high fat diet,high-RFI

value: RFIpl

value: HF


title: liver_HF_RFIpl_rep1_26


title: AML patients [CCC_NS]

source_name: AML_Leukemia cells

value: AML patients


title: liver_HF_RFIpl_rep1_31


title: PTEN_LXRKO2_SBN_11


title: Subject 16, Meal B (1000 kcal), Postprandial (6h)

value: Normal weight


title: AML patients [YZJ_NS]


title: PTEN3_SBN_9

value: PTENpc-/-


title: Subject 16, Meal B (1000 kcal), Postprandial (4h)

value: Whole blood


title: PTEN_LXRKO1_SBN_10


title: AML patients [WML_NS]


title: liver_HF_RFIpl_rep1_45

value: liver


title: liver_HF_RFIpl_rep1_14


title: Subject 16, Meal B (1000 kcal), Fasting (0h)


title: Cord_blood_MAIT

description: Gene expression from Cord blood MAIT

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K v2 (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 026652_D_F_20100115) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cord blood MAIT

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
Mononuclear cells were prepared from CB using Ficoll solution and washed extensively with PBS. MAIT cells were purified as 3C10+ cells with biotinylated monoclonal antibody 3C10 using two consecutive magnetic-activated cell sorting (MACS) columns. The purity of the 3C10+ cells after the second column was >96% from donor 1, >88% from donor 2, and >78% from donor 3, as determined by FACS analysis.
RNA was prepared using the RNAeasy column purification (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were harvested with TRIzol (Invitrogen, Carlsbad, CA) and proceeded to RNA purification.

value: cord blood


title: AML patients [ZTM_NS]


title: liver_HF_RFIpl_rep1_19


title: AML patients [ZW_NS]

value: Male


title: liver_HF_RFIpl_rep1_53


title: PTEN1_SBN_7


title: PTEN2_SBN_8


title: Subject 16, Meal A (500 kcal), Postprandial (4h)


title: LXRKO2_SBN_28

value: LXRalpha/beta KO

value: no tumor


title: liver_HF_RFIpl_rep1_41


title: Subject 16, Meal A (500 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 500 kcal of a high fat meal


title: LXRKO3_SBN_30


title: Subject 16, Meal A (500 kcal), Postprandial (2h)


title: LXRKO1_SBN_27


title: AML patients [WCM_NS]

value: Bone marrow


title: liver_HF_RFIpl_rep1_37


title: reMAIT_day_20_Late

description: Gene expression from reMAIT at 20 days after the beginning of induction

source_name: reMAIT, day 20, Late

extract_protocol:
MAIT-derived iPSCs were cultured on OP9, and CD34+ CD43+ cells were isolated. These CD34+ CD43+ precursor cells were furthered cultured on OP9/DL1 for re-differentiation into MAITs.
RNA was prepared using the RNAeasy column purification (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: 20 day


title: Subject 16, Meal A (500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 500 kcal of a high fat meal


title: WT3_SBN_26

value: wild-type


title: reMAIT_day_7-10_Middle

description: Gene expression from reMAIT at 7-10 days after the beginning of induction

source_name: reMAIT, day 7-10, Middle


title: WT1_SBN_23

value: Dorsal prostate


title: Subject 15, Meal C (1500 kcal), Postprandial (6h)


title: liver_HF_RFIpl_rep1_1


title: Subject 15, Meal C (1500 kcal), Postprandial (4h)


title: liver_HF_RFIpl_rep1_34


title: reMAIT_day_0_Start

description: Gene expression from reMAIT at 0 days after the beginning of induction

value: 0 day


title: liver_HF_RFIneg_rep1_28

description: Gene expression in pig liver with low residual feed intake fed with high fat diet

source_name: liver, high fat diet,low-RFI

value: RFIneg


title: liver_HF_RFIneg_rep1_49


title: reMAIT_day_4_Early

description: Gene expression from reMAIT at 4 days after the beginning of induction

source_name: reMAIT, day 4, Early

value: 4 day


title: WT-NSC [1112F-03_CPu_a74]

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 3014 Gross Hall

department: Department of Neurobiology & Behavior

institute: University of California, Irvine

hyb_protocol: Following fragmentation, 5.1μg of ss-ccDNA were hybridized for 17hr at 45C GeneChip transcriptome assays 1.0. Genechips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: WT-NSC

label_protocol: Biotinglated ss-ccDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Genechip WT PLUS reagent manual 2013)

growth_protocol: All animals were group housed on a 12h/12h light/dark cycle with access to food and water ad libitum.

extract_protocol: Total RNA was extracted by TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers’ protocols

treatment_protocol: The CPu tissues were collected and stored in liquid nitrogen.

tag: strain background

tag: litter

tag: genotype/variation

value: wild type

tag: Sex

value: Female

value: 12 months

tag: treated with

value: haplotype-matched neural stem cells (NSCs)

value: brain; striatum

tag: rin


title: liver_HF_RFIneg_rep1_43

tag: tissue

value: liver

tag: strain

value: HF


title: Immature_T_cells_CD4+_CD8+_day_59_Late

description: Gene expression from immature with CD4- and CD8- at 59 days after the beginning of differentiation

source_name: Immature T-cells, CD4+, CD8+, day 59, Late

extract_protocol:
CD34+ cells were isolated from CB using CD34 MicroBead Kit (Miltenyi Biotech)
RNA was prepared using the RNAeasy column purification (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: cord blood

tag: timecourse

value: 59 day


title: WT-NSC [1112F-03_CPu_a70]

tag: age


title: Subject 15, Meal B (1000 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 1000 kcal of a high fat meal

value: Whole blood

tag: metabolic status

value: Normal weight


title: Immature_T_cells_CD4-_CD8-_day_40_Middle

description: Gene expression from immature T-cells with CD4- and CD8- at 40 days after the beginning of differentiation

source_name: Immature T-cells, CD4-, CD8-, day 40, Middle

value: 40 day


title: Subject 15, Meal C (1500 kcal), Postprandial (2h)


title: liver_HF_RFIpl_rep1_18

value: RFIpl

tag: feed condition


title: ASO-NSC [1112F-03_CPu_a75]

source_name: ASO-NSC

value: overexpressing human wild-type alpha-synuclein (PDGF-β-ASO line D, ASO)


title: Immature_T_cells_CD4-_CD8-_day_21_Early

description: Gene expression from immature T-cells with CD4- and CD8- at 21 days after the beginning of differentiation

source_name: Immature T-cells, CD4-, CD8-, day 21, Early

value: 21 day


title: ASO-NSC [1112F-03_CPu_a73]


title: Subject 15, Meal C (1500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1500 kcal of a high fat meal


title: Subject 15, Meal B (1000 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 1000 kcal of a high fat meal


title: Immature_T_cells_CD34+_day_0_Start

description: Gene expression from immature T-cells with CD34+ at day 0 after the beginning of differentiation

source_name: Immature T-cells, CD34+, day 0, Start

value: 0 day


title: liver_HF_RFIneg_rep1_12

value: RFIneg


title: ASO-Veh [1112F-03_CPu_a68]

source_name: ASO-Veh

value: saline (Veh)


title: liver_HF_RFIneg_rep1_8


title: liver_HF_RFIneg_rep1_32


title: WT-Veh [1112F-03_CPu_a64]

source_name: WT-Veh

value: wild type

value: Male


title: WT-Veh [1112F-03_CPu_a66]

value: Female

value: 12 months


title: WT-Veh [1112F-03_CPu_a67]

value: brain; striatum


title: liver_HF_RFIneg_rep1_40

value: liver

value: HF


title: liver_HF_RFIneg_rep1_25


title: Subject 15, Meal A (500 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 500 kcal of a high fat meal


title: Subject 15, Meal B (1000 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1000 kcal of a high fat meal


title: Subject 15, Meal B (1000 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 1000 kcal of a high fat meal


title: Subject 15, Meal A (500 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 500 kcal of a high fat meal


title: liver_HF_RFIneg_rep1_3


title: liver_HF_RFIneg_rep1_46


title: liver_HF_RFIneg_rep1_17


title: Subject 15, Meal A (500 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 500 kcal of a high fat meal


title: WT-Veh [1112F-03_CPu_a62]


title: ASO-NSC [1112F-03_CPu_a59]

value: haplotype-matched neural stem cells (NSCs)


title: liver_HF_RFIneg_rep1_39


title: Subject 15, Meal A (500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 500 kcal of a high fat meal

value: Whole blood


title: WT-Veh [1112F-03_CPu_a61]


title: WT-NSC [1112F-03_CPu_a58]


title: Subject 14, Meal C (1500 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 1500 kcal of a high fat meal

value: Normal weight


title: ASO-NSC [1112F-03_CPu_a57]


title: Subject 14, Meal C (1500 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 1500 kcal of a high fat meal


title: Subject 14, Meal C (1500 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 1500 kcal of a high fat meal


title: ASO-NSC [1112F-03_CPu_a56]


title: Subject 14, Meal C (1500 kcal), Fasting (0h)


title: WT-NSC [1112F-03_CPu_a54]


title: WT2_SBN_25

value: Dorsal prostate

tag: genotype

value: wild-type

value: no tumor


title: ASO-Veh [1112F-03_CPu_a47]

value: overexpressing human wild-type alpha-synuclein (PDGF-β-ASO line D, ASO)


title: WT-NSC [1112F-03_CPu_a53]


title: Subject 14, Meal B (1000 kcal), Postprandial (6h)


title: PrEC12 days

city: Osaka

first: Hiroki

last: Shima

address: 3-7-41 Nakatsu YAMAMOTO  Bild. 4F. Kitaku

institute: SHIMA Institution for Quantum Medicine

description: PrEC - 12 days

hyb_protocol: The Cy3-labeled probe using RNA from cells treated with DMSO and the Cy5-labeled probe using RNA from cells treated with DNCB for 4.5 hr were mixed, fragmented, and then suspended in GE hybridization buffer in the Gene Expression Hybridization Kit (Agilent). The probes were applied to Whole Human Genome Oligo array (Agilent), and hybridization (70 degree centigrade, 14 hr) , washing, and scanning by Agilent Microarray Scanner were performed according to the manufacturer’s recommended protocol.

scan_protocol: Scanned on an Agilent Affymetrix 428 Array scanner. The images were processed using Feature Extraction Software (ver9.5.3.1, Agilent), and scanned by Affymetrix 428 Array Scanner.

data_processing:
For each hybridized spot, background intensity was subtracted and normalized by the global LOWESS normalization method.
The log2 ratio of Cy5 to Cy3  fluorescence intensity was assigned as the gene expression value (fold change). Data analysis was performed using the microarray data analysis software, Expressionist (GeneData AG, Basel, Switzerland). Functional analyses were performed and the networks were generated using Ingenuity Pathways Analysis (Ingenuity Systems, CA, USA).

source_name: prostate epithelial cells, RB-treated

label_protocol: Aliquots of 200 ng of total RNAs were labeled with Cy3- or Cy5- UTP using Agilent Quick Amp Labeling Kit (Agilent Technologies Inc.) according to the manufacture’s instructions.

growth_protocol: PrEC (human prostate epithelium cells) were   kept  in PrEGMTM (Lonza, Conshohocken, PA, USA) with PrEGMTM Single QuotsTM (0.4%BEP, 0.1% hydrocortisone, 0.1% HEGF, 0.1% epinephrine, 0.1% transferrn, 0.1% insulin, 0.1% retinoic acid, 0.1% triiodothyronine, 0.1% GA-1000, 50mg/ml and 50μg/ml Anhoterishin-B ) added.

extract_protocol: Total RNA extracted using Isogen kit (NIPPON GENE CO., LTD, Osaka, Japan) from PrEC cells with or without RB on the 7th and 12th day.

treatment_protocol: The culture dish was sandwiched with  far-infrared rays emitter (FIRe, RB),  Another set of culture dish was　not covered with RB, which was used as reference sample. The subculture was done properly at 70-80 % confluency.

tag: cell line

value: PrEC Normal Prostate Epithelium Cells

source_name: prostate epithelial cells, untreated


title: Subject 14, Meal B (1000 kcal), Fasting (0h)


title: ASO-Veh [1112F-03_CPu_a45]


title: Subject 14, Meal B (1000 kcal), Postprandial (2h)


title: ASO-Veh [1112F-03_CPu_a46]


title: PrEC12 days dye-swap

description: PrEC - 12 days (dye-swap)

treatment_protocol: The culture dish was sandwiched with far-infrared rays emitter (FIRe, RB),  Another set of culture dish was　not covered with RB, which was used as reference sample. The subculture was done properly at 70-80 % confluency.

treatment_protocol: The culture dish was sandwiched with FIRe,  Another set of culture dish was　not covered with FIRe, which was used as reference sample. The subculture was done properly at 70-80 % confluency.


title: Subject 14, Meal B (1000 kcal), Postprandial (4h)


title: 12_LPS-HFIP

city: Zurich

first: Beatrice

last: Beck-Schimmer

address: Winterthurerstrasse 190

department: Institute of Physiology

institute: University of Zurich

description: Replicate 12 exposed to LPS and HFIP 8mmol/L over a time period of 6 hrs

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters(protocol GE1_107_Sep09 and Grid: 028004_D_20110708) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: HMVEC (CC-2815)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human microvascular endothelial cells (CC-2815) derived from normal human microvascular blood vessels were purchased from Lonza (Verviers, Belgium) and cultured as described in Urner et. al., Am J Respir Cell Mol Biol. 2011;45(3):617-24.

extract_protocol: Total RNA from HMVEC was extracted using RNeasy (Qiagen) according to the manufacturer's protocol. The quality of the isolated RNA was evaluated using NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and Bioanalyzer 2100 (Agilent, Waldbronn, Germany).

treatment_protocol: Human microvascular endothelial cells (HMVEC, CC-2815) were stimulated with 20mcg/mL LPS from Escherichia coli serotype 055:B5 (Sigma-Aldrich, Buchs, Switzerland) to induce an inflammatory response. Hexafluoro-2-propanol (HFIP; Sigma-Aldrich, Buchs, Switzerland) was added to the cell culture medium containing LPS (Phosphate-buffered saline in controls) for a time period of 6 hours at a concentration of 8mmol/L.

value: Human microvascular endothelial cells (HMVEC)

tag: exposed to

value: LPS 20mcg/mL and HFIP 8mmol/L over a time period of 6 hrs


title: PrEC 7days

description: PrEC - 7days

extract_protocol: Total RNA extracted using Isogen kit (NIPPON GENE CO., LTD, Osaka, Japan) from PrEC cells with or without FIRe on the 7th and 12th day.

treatment_protocol: The culture dish was sandwiched with far-infrared rays emitter (FIRe, RB),  Another set of culture dish was　not covered with FIRe, which was used as reference sample. The subculture was done properly at 70-80 % confluency.


title: ASO-Veh [1112F-03_CPu_a42]

value: saline (Veh)


title: Subject 16, Meal B (1000 kcal), Postprandial (2h)


title: 1_PBS

description: Replicate 1 representing the control incubated over a time period of 6 hrs

tag: cell type

value: PBS (control) over a time period of 6 hrs


title: 6_LPS

description: Replicate 6 exposed to LPS over a time period of 6 hrs

value: LPS 20mcg/mL over a time period of 6 hrs


title: Subject 14, Meal A (500 kcal), Postprandial (2h)


title: 3_PBS

description: Replicate 3 representing the control incubated over a time period of 6 hrs


title: PrEC 7days dye-swap

description: PrEC - 7days (dye-swap)

treatment_protocol: The culture dish was sandwiched with far-infrared rays emitter (FIRe. RB),  Another set of culture dish was　not covered with RB, which was used as reference sample. The subculture was done properly at 70-80 % confluency.

value: Male

treatment_protocol: The culture dish was sandwiched with FIRe,  Another set of culture dish was　not covered with RB, which was used as reference sample. The subculture was done properly at 70-80 % confluency.


title: Subject 14, Meal A (500 kcal), Postprandial (6h)


title: Subject 12, Meal C (1500 kcal), Postprandial (2h)


title: Subject 12, Meal C (1500 kcal), Postprandial (4h)


title: Subject 14, Meal A (500 kcal), Postprandial (4h)


title: 2_PBS

description: Replicate 2 representing the control incubated over a time period of 6 hrs


title: 11_LPS-HFIP

description: Replicate 11 exposed to LPS and HFIP 8mmol/L over a time period of 6 hrs


title: Subject 14, Meal A (500 kcal), Fasting (0h)


title: 4_LPS

description: Replicate 4 exposed to LPS over a time period of 6 hrs


title: 5_LPS

description: Replicate 5 exposed to LPS over a time period of 6 hrs


title: Subject 12, Meal C (1500 kcal), Postprandial (6h)


title: Subject 12, Meal C (1500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1500 kcal of a high fat meal


title: 7_HFIP

description: Replicate 7 exposed to HFIP 8mmol/L over a time period of 6 hrs


title: Subject 12, Meal B (1000 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 1000 kcal of a high fat meal


title: 9_HFIP

description: Replicate 9 exposed to HFIP 8mmol/L over a time period of 6 hrs


title: Prostate - NP5

status: Public on Mar 13 2017

city: Sutton

first: Colin

middle: S

last: Cooper

address: 15 Cotswold Rd

department: Oncogenetics

country: United Kingdom

institute: Institute of Cancer Research

hyb_protocol: Array hybridization was performed according to the manufacturer's instructions (Affymetrix). Arrays were hybridized by rotating them at 60 rpm in the Affymetrix Gene Chip hybridization oven at 45°c for 16 hours. After hybridization, the arrays are washed in the Affymetrix GeneChip Fluidics station FS 450.

scan_protocol: Array scanning was performed according to the manufacturer's instructions (Affymetrix). The arrays are scanned using the Affymetrix Gene Chip scanner 3000 7G system.

data_processing:
Gene-level signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the robust multiarray analysis algorithm8 implemented in the Affymetrix Expression Console software package. The core subset of probes were used. Centre batch effects were adjusted for using the ComBat algorithm9 implemented in the sva R package.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Prostatectomy - Normal

label_protocol: The Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay was used to generate amplified and biotinylated sense-strand DNA targets from the entire expressed genome (1.5 μ g of total RNA) without bias.

extract_protocol:
Trizol
For London (ICR) samples, RNA was extracted from the tissue using TRIzol (Invitrogen Ltd, Paisley, UK) by following the manufacturer’s instructions, and purified using the RNeasy MinElute TM clean up kit (Qiagen Ltd, Crawley, Sussex, UK) according to the manufacturer’s instructions. Cambridge samples were extracted from tissue samples using the Qiagen AllPrep kit (Qiagen Ltd, Crawley, Sussex, UK).

tag: gender

value: Prostate

value: Normal

tag: centre

value: ICR


title: Prostate - AT102

source_name: Fibroblast

value: Fibroblast

value: Edinburgh


title: Subject 12, Meal B (1000 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 1000 kcal of a high fat meal

value: Whole blood

value: Normal weight


title: Prostate - NP1


title: Subject 12, Meal A (500 kcal), Postprandial (2h)

description: Blood cell transcriptome 2h after ingestion of 500 kcal of a high fat meal


title: Prostate - AT103


title: Prostate - AT101


title: Subject 12, Meal B (1000 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 1000 kcal of a high fat meal


title: Prostate - AT104


title: Subject 12, Meal A (500 kcal), Fasting (0h)

description: Blood cell transcriptome before ingestion of 500 kcal of a high fat meal


title: Prostate - NP4


title: Subject 12, Meal B (1000 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 1000 kcal of a high fat meal


title: Prostate - PRC128

source_name: Prostatectomy - Low Tumor

value: Low Tumor


title: Subject 12, Meal A (500 kcal), Postprandial (6h)

description: Blood cell transcriptome 6h after ingestion of 500 kcal of a high fat meal


title: Prostate - AT105


title: Prostate - PRC126

source_name: Prostatectomy - Tumor

value: Tumor


title: Prostate - PRC130


title: Prostate - PRC129


title: Prostate - PRC124


title: Prostate - NP2


title: Prostate - ST1

source_name: Prostatectomy - Stroma

value: Stroma

value: Edel


title: 8_HFIP

description: Replicate 8 exposed to HFIP 8mmol/L over a time period of 6 hrs

value: Human microvascular endothelial cells (HMVEC)


title: Prostate - PRC109


title: Subject 12, Meal A (500 kcal), Postprandial (4h)

description: Blood cell transcriptome 4h after ingestion of 500 kcal of a high fat meal


title: Prostate - PRC123


title: Prostate - PRC125


title: Prostate - PRC127


title: Prostate - PRC122

value: Esplit


title: Prostate - PRC119


title: Prostate - PRC117


title: Prostate - PRC118


title: Prostate - PRC116

value: MixedRearrangement


title: Prostate - PRC112


title: Prostate - PRC106

extract_protocol:
RNAeasyPlus
For London (ICR) samples, RNA was extracted from the tissue using TRIzol (Invitrogen Ltd, Paisley, UK) by following the manufacturer’s instructions, and purified using the RNeasy MinElute TM clean up kit (Qiagen Ltd, Crawley, Sussex, UK) according to the manufacturer’s instructions. Cambridge samples were extracted from tissue samples using the Qiagen AllPrep kit (Qiagen Ltd, Crawley, Sussex, UK).


title: Prostate - PRC114


title: Prostate - PRC105


title: Prostate - PRC115


title: Prostate - PRC111


title: Prostate - ST3


title: Prostate - PRC101


title: Prostate - PRC102


title: Prostate - ST2


title: Prostate - PRC110


title: Prostate - PRC166


title: Prostate - PRC169


title: Prostate - PRC162


title: Prostate - PRC167


title: Prostate - PRC165


title: Prostate - PRC103


title: Prostate - PRC113


title: Prostate - PRC158

value: MixedPloidy


title: Prostate - PRC157


title: Prostate - PRC155


title: Prostate - ST5


title: Prostate - PRC168


title: Prostate - PRC160


title: Prostate - PRC164


title: Prostate - PRC153


title: Prostate - PRC150


title: Prostate - PRC159


title: Prostate - PRC152


title: Prostate - PRC151


title: Prostate - NP19


title: Prostate - NP20


title: Prostate - PRC142


title: Prostate - PRC148


title: Prostate - PRC7


title: Prostate - PRC144


title: Prostate - NP21


title: Prostate - PRC9


title: Prostate - PRC141


title: Prostate - PRC140


title: Prostate - PRC8


title: Prostate - NP17


title: Prostate - PRC145

value: NG


title: Prostate - NP18

value: Male


title: Prostate - PRC5

value: Prostate


title: Prostate - PRC31


title: Prostate - PRC4


title: Prostate - PRC149


title: Prostate - PRC3


title: Prostate - PRC32


title: Prostate - PRC2


title: Prostate - PRC24


title: Prostate - PRC23

value: Normal


title: Prostate - PRC25

value: ICR


title: Prostate - PRC26


title: Prostate - PRC21


title: Prostate - PRC143


title: Prostate - PRC22


title: Prostate - PRC20


title: Prostate - PRC6


title: Prostate - PRC154


title: Prostate - PRC12


title: Prostate - PRC45


title: Prostate - PRC19


title: Prostate - PRC156


title: Prostate - ST4


title: Prostate - PRC17


title: Prostate - PRC10


title: Prostate - PRC39


title: Prostate - PRC13


title: Prostate - PRC16


title: Prostate - PRC11


title: Prostate - PRC146


title: Prostate - PRC36


title: Prostate - PRC34


title: Prostate - PRC28


title: Prostate - PRC147

value: MixedEdel


title: Prostate - PRC18


title: Prostate - PRC35


title: Prostate - PRC27


title: Prostate - PRC1


title: Prostate - PRC15


title: Prostate - PRC42


title: Prostate - PRC29


title: Prostate - PRC163


title: Prostate - PRC30


title: Prostate - PRC40


title: Prostate - PRC38


title: Prostate - PRC161


title: Prostate - PRC14


title: Prostate - NP16


title: Prostate - NP15


title: Prostate - NP11


title: Prostate - NP14


title: Prostate - PRC137


title: Prostate - CI_73_2

extract_protocol:
Qiagen miRNA kit
For London (ICR) samples, RNA was extracted from the tissue using TRIzol (Invitrogen Ltd, Paisley, UK) by following the manufacturer’s instructions, and purified using the RNeasy MinElute TM clean up kit (Qiagen Ltd, Crawley, Sussex, UK) according to the manufacturer’s instructions. Cambridge samples were extracted from tissue samples using the Qiagen AllPrep kit (Qiagen Ltd, Crawley, Sussex, UK).

value: Cambridge


title: Prostate - CI_72_1

value: MixedEsplit


title: Prostate - PRC134


title: Prostate - PRC138


title: Prostate - PRC136


title: Prostate - CI_73_1


title: Prostate - PRC133


title: Prostate - NP8


title: Prostate - CI_69_2

value: RG


title: Prostate - PRC135


title: Prostate - NP10


title: Prostate - CI_69_1

value: Low Tumor


title: Prostate - CI_71_1


title: Prostate - CI_70_1

value: Tumor


title: Prostate - CI_68_1


title: Prostate - CI_67_1


title: Prostate - NP9


title: Prostate - CI_71_2


title: Prostate - CI_65_1


title: Prostate - CI_66_1


title: Prostate - CI_61_1


title: Prostate - CI_63_1


title: Prostate - CI_60_1


title: Prostate - CI_64_1


title: Prostate - NP12


title: Prostate - CI_59_1


title: Prostate - PRC139


title: Prostate - CI_62_1


title: Prostate - CI_55_3


title: Prostate - CI_57_1


title: Prostate - CI_60_2


title: Prostate - CI_56_1

value: Stroma


title: Prostate - CI_54_1

value: Edel


title: Prostate - CI_58_1


title: Prostate - CI_55_2


title: Prostate - CI_51_1


title: Prostate - CI_57_2


title: Prostate - CI_52_1


title: Prostate - CI_55_1


title: Prostate - CI_55_4


title: Prostate - CI_53_1


title: Prostate - CI_56_3


title: Prostate - CI_52_3


title: Prostate - CI_59_2


title: Prostate - CI_49_1


title: Prostate - CI_52_2


title: Prostate - CI_46_3


title: Prostate - CI_47_1


title: Prostate - CI_50_1


title: Prostate - CI_48_1


title: Prostate - CI_56_2


title: Prostate - CI_46_2


title: Prostate - CI_46_1


title: Prostate - CI_50_2


title: Prostate - CI_54_2


title: Prostate - CI_45_1


title: Prostate - CI_46_4


title: Prostate - CI_39_1


title: Prostate - CI_44_2


title: Prostate - CI_40_1


title: Prostate - CI_38_1


title: Prostate - CI_36_1


title: Prostate - CI_44_1


title: Prostate - CI_42_1


title: Prostate - CI_45_2


title: Prostate - CI_39_2


title: Prostate - CI_41_1


title: Prostate - CI_37_2


title: Prostate - CI_29_1


title: Prostate - CI_31_1


title: Prostate - CI_43_1


title: Prostate - CI_35_1


title: Prostate - CI_45_3


title: Prostate - CI_33_1


title: Prostate - CI_32_1


title: Prostate - CI_30_1


title: Prostate - CI_37_1


title: Prostate - CI_29_2


title: Prostate - CI_34_1


title: Prostate - CI_28_1


title: Prostate - CI_29_3


title: Prostate - CI_24_1


title: Prostate - CI_27_1


title: Prostate - CI_23_1


title: Prostate - CI_26_1


title: Prostate - CI_16_3


title: Prostate - CI_21_4


title: Prostate - CI_20_2


title: Prostate - CI_19_1


title: Prostate - CI_21_3


title: Prostate - CI_18_1


title: Prostate - CI_22_1


title: Prostate - CI_17_1


title: Prostate - CI_10_1


title: Prostate - CI_13_1


title: Prostate - CI_20_1


title: Prostate - CI_16_4


title: Prostate - CI_21_2


title: Prostate - CI_39_3


title: Prostate - CI_8_1


title: Prostate - CI_15_1


title: Prostate - CI_14_1


title: Prostate - CI_16_2


title: Prostate - CI_16_1


title: Prostate - CI_21_1


title: Prostate - CI_25_1


title: Prostate - CI_12_1


title: Prostate - CI_11_2


title: Prostate - CI_5_2


title: Prostate - CI_7_1


title: Prostate - CI_9_1


title: Prostate - CI_7_2


title: Prostate - CI_2_1


title: Prostate - CI_11_1


title: Prostate - CI_3_1


title: Prostate - CI_8_2


title: Prostate - CI_6_1


title: Prostate - CI_4_1


title: SKOV3ip.1-SiJMJD1A-Hypoxia-rep3

city: Portland

first: Adam

middle: J

last: Krieg

state: OR

address: 3181 SW Sam Jackson Park Road, L466

department: OB/GYN

institute: Oregon Health & Science University

hyb_protocol: Samples were hybridized using Affymetrix kit materials in the following conditions: 45C , 17hr plus or minus 1hr , 60rpm using GeneChip Hybridization Oven 640. Arrays were washed using protocol FS450_0001

scan_protocol: Chips were scanned using Affymetrix GeneChip Scanner 3000 7G with Autoloader

data_processing:
The exon-arrays were RMA-background corrected, quantile-normalized and gene-level summarized using the Median Polish algorithm (Irizarry et al. 2003). The resulting log (base 2) transformed signal intensities (expression values) were used for downstream analysis.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: SKOV3ip.1_SiRNA to JMJD1A_hypoxia

label_protocol: mRNA was reverse transcribed using the Ambion WT Expression Sense Target Protocol, followed by TdT End labeling with the GeneChip WT Terminal Labeling Kit to incorporate biotin label

growth_protocol: SKOV3ip.1 cells were maintained in RPMI 1640 media, supplemented with 10% FBS

extract_protocol: Total RNA was collected and purified using TriReagent (Sigma) according to manufacturer's protocol, and further purified using QIAGen RNeasy columns. Contaminating salts were removed by desalting column (Princeton separations)

value: SKOV3ip.1 cells

value: ovarian cancer cells

tag: transduced with

value: SiJMJD1A; SiRNA targeting JMJD1A

tag: culture condition

value: hypoxia; 0.5% oxygen


title: Prostate - CI_1_3


title: Prostate - CI_1_1


title: SKOV3ip.1-SiControl-Hypoxia-rep2

source_name: SKOV3ip.1_control SiRNA_hypoxia

value: SiControl2; control SiRNA


title: SKOV3ip.1-SiControl-Hypoxia-rep3


title: SKOV3ip.1-SiJMJD2B-Hypoxia-rep3

source_name: SKOV3ip.1_SiRNA to JMJD2B_hypoxia

value: SiJMJD2B; SiRNA targeting JMJD2B


title: SKOV3ip.1-SiJMJD2B-Hypoxia-rep2


title: Prostate - CI_1_2

value: Male

value: Prostate


title: Prostate - CI_5_1


title: SKOV3ip.1-SiJMJD2B-Hypoxia-rep1


title: SKOV3ip.1-SiControl-Hypoxia-rep1


title: SKOV3ip.1-SiJMJD2B-Normoxia-rep1

source_name: SKOV3ip.1_SiRNA to JMJD2B_normoxia

value: normoxia; 21% oxygen


title: SKOV3ip.1-SiJMJD2B-Normoxia-rep2


title: SKOV3ip.1-SiJMJD1A-Normoxia-rep3

source_name: SKOV3ip.1_SiRNA to JMJD1A_normoxia


title: SKOV3ip.1-SiJMJD1A-Normoxia-rep2


title: SKOV3ip.1-SiControl-Normoxia-rep2

source_name: SKOV3ip.1_control SiRNA_normoxia


title: SKOV3ip.1-SiJMJD1A-Hypoxia-rep2


title: SKOV3ip.1-SiJMJD1A-Hypoxia-rep1


title: SKOV3ip.1-SiJMJD1A-Normoxia-rep1


title: SKOV3ip.1-SiControl-Normoxia-rep1


title: SKOV3ip.1-SiJMJD2B-Normoxia-rep3


title: SKOV3ip.1-SiControl-Normoxia-rep3


title: ID48_Infant8_Sample7

city: Oslo

first: Betty

last: Kalikstad

address: Oslo University Hospital, Institute of Clinical Medicine, Rikshospitalet

country: Norway

institute: 1University of Oslo

hyb_protocol: Human Genome U133 Plus 2.0 arrays were hybridized for 16 h in a 45ºC incubator while being rotated at 60 rpm.

scan_protocol: The arrays were washed and stained with Affymetrix Fluidics Station 450, and finally scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were normalized with the RMA method. All transcripts with an average log2 intensity above 5 were used for further analysis.

source_name: Human blood; Preterm infant born 37.0 or less

label_protocol: From each sample, 100 ng of total RNA were used to prepare biotinylated fragmented cRNA according to the NuGene Ovation WB Reagent User Guide, Version 05.01.07 and FL-Ovation cDNA Biotin Module V2 User Guide, Version 05.13.08 (NuGene Technologies, San Carlos CA, USA). The NuGEN Ovation RNA-Amplification system (NuGen Technologies, San Carlos, CA, USA) for application on Affymetrix arrays was used for RNA labeling. mRNA was amplified in presence of the fetal globin and any possible leftover of α- and β-globin, which is not affected by remaining globin.

treatment_protocol: A 0.3- to 0.5-mL aliquot of whole-blood was added in a 2.0-mL Microfuge tube from Ambion (Austin, TX, USA) containing 1.3 mL RNA-stabilization solution, RNAlater (Austin, TX, USA)To isolate total RNA RiboPure-Blood Kit and GLOBINclear-Human Kit protocol from Ambion (Austin, TX, USA) was used and stored at –80ºC.

tag: pma; postmenstrual age = gestational age + chronicological age = weeks

tag: pna; postnatal age = chronological age; living days

tag: coherent birthweight of the infant

tag: sex; female=1, male=2

tag: current weight by the time point of the sample

tag: clinical and therapeutic description

value: no sepsis, no event of hypoxia or re-oxygenation


title: Fibroblast_KrP_Ventral_Rep2

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

description: Gene expression data from K15 Pthrp nipple-like skin

hyb_protocol: Each sample was hybridized to a Mouse Gene 2.0 ST array using the Affymetrix Hyb Wash Stain kit. (#900720). Arrays were hybridized for 17 hours

scan_protocol: Arrays were scanned using the 3000 7G scanner controlled by Affymetrix GeneChip Command Console. CEL files were generated by AGCC.

data_processing: Cel files were imported into Partek Genomics Suite.  RMA (robust multi-array average) signals were generated using the RMA background correction, Quantile normalization and summarization by Median Polish. RMA data was log base 2 transformed.

source_name: K14 Pthrp Ventral Fibroblast Replicate 2

label_protocol: 100ng of total RNA was labeled using the Ambion WT Expression kit using the standard protocol

growth_protocol: mice: The K14-PTHrP (KrP) transgenic line  was maintained by continual breeding against unrelated C57BL/6 mice WT mice used in this study were littermates of the KrP mice. Ventral skins from 3 female mice were 8 to 12 weeks old were used as the source of cells

extract_protocol:
cell preparation: Primary fibroblasts were isolated by trypsinization and collagenase digestion according to the protocol of Nature Protocols, 3: 799-8-10 and pooled for sorting.
cell sorting: Viable CD140 postive and  CD31, CD45 ,CD117 ,CD49f  negative cells were collected using flow cytometry sorter with FACSDiva software, FACSAria II  sorter. Flow Cytometry analysis was evaluated by FlowJo version X
Total RNA was isolated from sorted cells using RNeasy Mini Kit (Qiagen) with on-column DNase I treatment according to manufacturer’s instruction

tag: strain background

value: K14 Pthrp

tag: tissue

value: ventral skin

value: fibroblast

value: female

tag: age

value: 8-12 weeks


title: Fibroblast_KrP_Ventral_Rep3

description: Gene expression data from K16 Pthrp nipple-like skin

source_name: K14 Pthrp Ventral Fibroblast Replicate 3

tag: genotype


title: Fibroblast_KrP_Ventral_Rep1

description: Gene expression data from K14 Pthrp nipple-like skin

source_name: K14 Pthrp Ventral Fibroblast Replicate 1


title: Fibroblast_WT_Ventral_Rep3

description: Gene expression data from ventral telogen skin of wildtype

source_name: WT Ventral Fibroblast Replicate 3

value: wildtype


title: ID47_Infant8_Sample6

extract_protocol: To isolate total RNA RiboPure-Blood Kit and GLOBINclear-Human Kit protocol from Ambion (Austin, TX, USA) was used and stored at –80ºC.


title: Fibroblast_WT_Ventral_Rep2

source_name: WT Ventral Fibroblast Replicate 2


title: ID40_Infant7_Sample7


title: ID43_Infant8_Sample2


title: ID41_Infant7_Sample8


title: ID45_Infant8_Sample4


title: ID42_Infant8_Sample1


title: ID39_Infant7_Sample6


title: ID38_Infant7_Sample5

value: sepsis, but no event of hypoxia or re-oxygenation


title: ID44_Infant8_Sample3


title: Fibroblast_WT_Ventral_Rep1

source_name: WT Ventral Fibroblast Replicate 1


title: ID34_Infant7_Sample1


title: ID37_Infant7_Sample4


title: ID89_Infant18_Sample1


title: ID35_Infant7_Sample2


title: ID85_Infant15_Sample4


title: ID86_Infant15_Sample5


title: ID36_Infant7_Sample3


title: ID88_Infant17_Sample1


title: ID64_Infant11_Sample1


title: ID82_Infant15_Sample1


title: ID65_Infant11_Sample2


title: ID87_Infant16_Sample1


title: ID63_Infant10_Sample8


title: ID84_Infant15_Sample3


title: ID61_Infant10_Sample6


title: ID46_Infant8_Sample5


title: ID62_Infant10_Sample7


title: MP_rep3

city: Stanford

first: Howard

middle: Y

last: Chang

address: 269 Campus Drive

institute: Stanford University

description: KLRG1lo CD127hi OT1 cells sorted at d8 of Listeria-OVA infection

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: RMA, Genepattern, The Sample data table contains raw expression data post RMA, excluding unlabeled probes or duplicate probes (that showed identical value).

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: Glass slide teasing Flow sorting

treatment_protocol: 2X10^4 OT-I cells were transferred into cogenically matched recipient mice. Mice were i.v. infected with 5000 cfu Listeria-OVA the next day. On day8 of infection cells are purified by Facs Aria sorting.

tag: strain

value: 6 weeks

value: Spleen

tag: phenotypic marker


title: MP_rep2

source_name: KLRG1lo CD127hi OT1 cells sorted at d8 of Listeria-OVA infection


title: ID60_Infant10_Sample5


title: ID56_Infant10_Sample1


title: ID59_Infant10_Sample4


title: ID58_Infant10_Sample3


title: MP_rep1


title: TE_rep2

description: KLRG1hi CD127lo OT1 cells sorted at d8 of Listeria-OVA infection


title: ID53_Infant9_Sample5


title: ID52_Infant9_Sample4


title: ID55_Infant9_Sample7


title: ID57_Infant10_Sample2


title: ID51_Infant9_Sample3


title: ID54_Infant9_Sample6


title: ID49_Infant9_Sample1


title: ID27_Infant5_Sample2


title: ID50_Infant9_Sample2


title: ID28_Infant5_Sample3


title: ID32_Infant6_Sample2


title: ID33_Infant6_Sample3


title: ID30_Infant5_Sample5


title: ID26_Infant5_Sample1


title: ID25_Infant4_Sample8


title: ID107_Infant20_Sample11


title: ID24_Infant4_Sample7


title: ID13_Infant3_Sample2


title: ID18_Infant3_Sample7


title: ID106_Infant20_Sample10


title: ID104_Infant20_Sample8


title: ID16_Infant3_Sample5


title: ID19_Infant3_Sample8


title: ID22_Infant4_Sample5


title: ID105_Infant20_Sample9


title: ID101_Infant20_Sample5


title: ID31_Infant6_Sample1


title: ID21_Infant4_Sample2


title: ID103_Infant20_Sample7


title: ID102_Infant20_Sample6


title: ID11_Infant2_Sample7


title: ID8_Infant2_Sample2


title: ID6_Infant1_Sample7


title: ID95_Infant19_Sample6


title: ID96_Infant19_Sample7


title: ID5_Infant1_Sample6


title: TE_rep3

source_name: KLRG1hi CD127lo OT1 cells sorted at d8 of Listeria-OVA infection


title: ID4_Infant1_Sample5


title: ID94_Infant19_Sample5


title: ID2_Infant1_Sample2


title: ID91_Infant19_Sample2


title: ID10_Infant2_Sample6


title: ID93_Infant19_Sample4


title: ID9_Infant2_Sample5


title: ID92_Infant19_Sample3


title: ID17_Infant3_Sample6


title: ID97_Infant19_Sample8


title: ID81_Infant14_Sample5


title: ID79_Infant14_Sample3


title: ID80_Infant14_Sample4


title: ID70_Infant12_Sample4


title: ID78_Infant14_Sample2


title: ID76_Infant13_Sample3


title: ID72_Infant12_Sample7


title: ID90_Infant19_Sample1


title: ID77_Infant14_Sample1


title: ID73_Infant12_Sample8


title: ID75_Infant13_Sample2


title: ID69_Infant12_Sample5


title: ID71_Infant12_Sample6


title: ID74_Infant13_Sample1


title: ID66_Infant12_Sample1


title: ID99_Infant20_Sample2

value: sample identified originating from the course of sepsis treatment and hypoxia, following re-oxygenation with 100% FiO2


title: ID98_Infant20_Sample1


title: ID68_Infant12_Sample3


title: ID100_Infant20_Sample4

value: sample identified originating from the course of continuous treatment with oxygen >80% and hypoxia, following re-oxygenation with 100% FiO2, but no sepsis


title: ID23_Infant4_Sample6


title: ID83_Infant15_Sample2

value: sample identified originating from continuous oxygen therapy with 30% FiO2 whilst the infant was described as extremely fatigue


title: ID14_Infant3_Sample3


title: ID15_Infant3_Sample4


title: ID12_Infant3_Sample1


title: ID7_Infant2_Sample1


title: ID20_Infant4_Sample1


title: ID67_Infant12_Sample2


title: ID3_Infant1_Sample3


title: ID1_Infant1_Sample1


title: Primary fat from 59F, biological rep2

status: Public on Mar 11 2017

city: Cambridge

first: Max

last: Friesen

address: 455 Main St

institute: Whitehead Institute

description: Primary adipocytes from 59F

hyb_protocol: Arrays were hybridized overnight at 50C, washed and stained.

scan_protocol: Genechips were scanned on a GeneChip Scanner 3000

data_processing: Raw data was normalized by robust multi-array averaging using a custom chip description file from the Michigan Microarray lab.

source_name: Primary fat (59F)

label_protocol: Standard Affymetrix protocol was used

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

value: Primary fat


title: ASC from fat (59F), biological rep2

description: Primary ASCs from 59F

source_name: ASC from fat (59F)

value: ASC


title: ASC from fat (59F), biological rep3

description: Primary ASCs from 59F


title: ASC from fat (59F), biological rep1

description: Primary ASCs from 59F


title: Primary fat from 41F, biological rep2

description: Primary adipocytes from 41F

source_name: Primary fat (41F)


title: Primary fat from 41F, biological rep1

description: Primary adipocytes from 41F


title: ASC-adipocytes with IRF1, biological rep1

description: Gene expression data from ASC-adipocytes expressing IRF1

source_name: ASC-adipocyte with IRF1 virus

value: ASC-adipocyte


title: ASC-adipocyte (59F), biological rep3

description: ASC-adipocytes from 59F

source_name: ASC-adipocyte (59F)


title: ASC-adipocyte (59F), biological rep1

description: ASC-adipocytes from 59F


title: ID29_Infant5_Sample4


title: ASC-adipocytes with rtTA, biological rep3

description: Gene expression data from ASC-adipocytes

source_name: ASC-adipocyte with rtTA virus


title: ASC-adipocyte (59F), biological rep2

description: ASC-adipocytes from 59F


title: ASC-adipocytes with rtTA, biological rep2


status: Public on Mar 12 2017

city: Charlottesville

first: R. Ariel

last: Gomez

state: VA

department: Pediatrics

institute: University of Virginia

description:
Gene expression data fromwild type kidney preglomerular arterioles
C1 is a pool of the 3 wild type samples

hyb_protocol: 2 μg of fragmented and labeled DNA target were hybridized for 16 hr at 45°C on Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip scanner 3000 7G.

data_processing:
All preprocessing and analysis were done using R version 2.15.0.  CEL files were imported using the Affymetrix package, version 1.34.0.  Expression intensities were summarized, normalized, and transformed using Robust Multiarray Average algorithm.
Probesets were annotated using the BioConductor annotation package mogene10sttranscriptcluster.db version 8.0.1, annotate package, version 1.34.0.  Linear models with empirical Bayes moderated standard errors were fit using the BioConductor
limma package version 3.12.1.  False discovery rate was used to correct for multiple testing.

source_name: kidney preglomerular arterioles

label_protocol: Biotinylated cDNA was prepared from 500ng total RNA using the Ambion® WT Expression Kit for Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays and the GeneChip® WT Terminal Labeling and Hybridization kit for use with the Ambion® WT Expression Kit according to the manufacturer's protocols.

growth_protocol: Mice were maintained  under standard vivarium conditions.

extract_protocol: Mice were perfused with iron oxide. The kidney cortex was minced, digested with collagenase and preglomerular arterioles collected by magnetic separation. Total RNA was extracted using Trizol.

value: mixed 129Sv and C57Bl6

value: RBP-J flox/flox;R26R ECFP;Ren1d+/+

value: 3 months

value: 2 males and 1 female


title: Primary fat from 59F, biological rep1

description: Primary adipocytes from 59F


description:
Gene expression data from RBP-J cKO kidney preglomerular arterioles
C2 is a pool of the 4  RBP-J cKO samples

value: RBP-J flox/flox;R26R ECFP;Ren1d+/cre

value: 4 males


title: ASC-adipocytes with IRF1, biological rep2

description: Gene expression data from ASC-adipocytes expressing IRF2


title: ASC-adipocytes with IRF1, biological rep3

description: Gene expression data from ASC-adipocytes expressing IRF3


title: ASC-adipocytes with rtTA, biological rep1


title: 35S:VvMYBA1_Hairy roots_Maccabeu_rep3

city: Verona

first: Erika

last: Cavallini

state: Verona

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

description:
Hairy roots expressing 35S:VvMYBA1 of Vitis vinifera cv Maccabeu, replicate 3
MYBA1_3

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: The in vitro plantlets and the transgenic and wild type hairy roots were grown under light and temperature controlled.

extract_protocol: the  hairy roots were sampled and then frozen in liquid nitrogen. All samples were stored at -80oC. Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: For overexpression of the MYB genes in Vitis vinifera cv Maccabeu hairy roots, each cDNA sequence was transferred into the binary vector pH2GW7 by site-specific recombination. Each construct was then inserted into Agrobacterium tumefaciens A4 by electroporation and used for the grapevine transformation.

tag: cultivar

value: Maccabeu

tag: genotype/variation

value: Hairy roots


title: 35S:VvMYBA7_Hairy roots_Maccabeu_rep2

description:
Hairy roots expressing 35S:VvMYBA7 of Vitis vinifera cv Maccabeu, replicate 2
A08


title: 35S:VvMYBA7_Hairy roots_Maccabeu_rep3

description:
Hairy roots expressing 35S:VvMYBA7 of Vitis vinifera cv Maccabeu, replicate 3
A09


title: 35S:VvMYBA1_Hairy roots_Maccabeu_rep2

description:
Hairy roots expressing 35S:VvMYBA1 of Vitis vinifera cv Maccabeu, replicate 2
MYBA1_2


title: SK-OV-3 cell line_treated with 2.5μM Hu-17_24h

city: Shanghai

first: Jiansheng

last: Liu

address: No.845 LingShan Road, PuDong District

department: Renji Hospital

institute: Shanghai Jiao Tong University,School of Medicine.

description: Gene expression data from SK-OV-3 cells which were treated with 2.5μM Hu-17 for 24h

hyb_protocol: Fragmented and biotin-labeled cRNA was hybridized to affymetrix human U133 plus 2.0 array chip using the Affymetrix hybridization kit. Arrays were incubated in 45°C hybridization oven for 16 hours,rotating at 60rpm.

scan_protocol: Slides were scanned by GeneChip®Scanner 3000.

data_processing: Raw expression data were normalized using robust multi-array averaging (RMA) with quantile normalization.

source_name: SK-OV-3 cell line,treated with 2.5μM Hu-17, 24h

label_protocol: 5 ug of total RNA was used to prepare double-stranded cDNA with the one-cycyle cDNA synthsis kit (Affymetrix,USA). The cDNA was used to synthesize biotin-labeled cRNA with IVT kit (Affymetrix,USA). Biotin-labeled cRNA was fragmented according to affymetrix protocol.

growth_protocol: Ovarian cancer cells SK-OV-3 were cultured in McCoy's 5A medium supplemented with 10% fetal bovine serum on adhered plates.

extract_protocol: Cellular RNA was isolated by Tri-Reagent using the manufaturer's instructions.Qualified total RNA was further purified by RNeasy micro kit and Rnase-Free DNase Set.

treatment_protocol: SK-OV-3 cells were treated with 2.5μM Hu-17 and/or 20μM Cisplatin for 6h, 12h and 24h.

tag: cell type

value: ovarian cancer

tag: cell line


title: SK-OV-3 cell line_treated with 20μM Cisplatin_12h

description: Gene expression data from SK-OV-3 cells which were treated with 20μM Cisplatin for 12h

source_name: SK-OV-3 cell line,treated with 20μM Cisplatin,12h


title: SK-OV-3 cell line_treated with 2.5μM Hu-17 and 20μM Cisplatin_24h

description: Gene expression data from SK-OV-3 cells which were treated with a combination scheme of  2.5μM Hu-17 and 20μM Cisplatin for 24h

source_name: SK-OV-3 cell line,treated with 2.5μM Hu-17 and 20μM Cisplatin, 24h


title: SK-OV-3 cell line_treated with 2.5μM Hu-17 and 20μM Cisplatin_12h

description: Gene expression data from SK-OV-3 cells which were treated with a combination scheme of  2.5μM Hu-17 and 20μM Cisplatin for 12h

source_name: SK-OV-3 cell line,treated with 2.5μM Hu-17 and 20μM Cisplatin,12h


title: 35S:VvMYBA1_Hairy roots_Maccabeu_rep1

description:
Hairy roots expressing 35S:VvMYBA1 of Vitis vinifera cv Maccabeu, replicate 1
MYBA1_1


title: SK-OV-3 cell line_treated with 2.5μM Hu-17_12h

description: Gene expression data from SK-OV-3 cells which were treated with 2.5μM Hu-17 for 12h

source_name: SK-OV-3 cell line,treated with 2.5μM Hu-17,12h


title: SK-OV-3 cell line_treated with vehicle_24h

description: Gene expression data from SK-OV-3 cells which were treated with DMSO for 24h

source_name: SK-OV-3 cell line,treated with vehicle, 24h


title: SK-OV-3 cell line_treated with 2.5μM Hu-17_6h

description: Gene expression data from SK-OV-3 cells which were treated with 2.5μM Hu-17 for 6h

source_name: SK-OV-3 cell line,treated with 2.5μM Hu-17, 6h


title: SK-OV-3 cell line_treated with 20μM Cisplatin_6h

description: Gene expression data from SK-OV-3 cells which were treated with 20μM Cisplatin for 6h

source_name: SK-OV-3 cell line,treated with 20μM Cisplatin, 6h


title: SK-OV-3 cell line_treated with 2.5μM Hu-17 and 20μM Cisplatin_6h

description: Gene expression data from SK-OV-3 cells which were treated with a combination scheme of  2.5μM Hu-17 and 20μM Cisplatin for 6h

source_name: SK-OV-3 cell line,treated with 2.5μM Hu-17 and 20μM Cisplatin, 6h


title: 35S:VvMYBA7_Hairy roots_Maccabeu_rep1

description:
Hairy roots expressing 35S:VvMYBA7 of Vitis vinifera cv Maccabeu, replicate 1
A07


title: 35S:VvMYBA6b_Hairy roots_Maccabeu_rep1

description:
Hairy roots expressing 35S:VvMYBA6b of Vitis vinifera cv Maccabeu, replicate 1
A04


title: 35S:VvMYBA6b_Hairy roots_Maccabeu_rep3

description:
Hairy roots expressing 35S:VvMYBA6b of Vitis vinifera cv Maccabeu, replicate 3
A06


title: SK-OV-3 cell line_treated with vehicle_12h

description: Gene expression data from SK-OV-3 cells which were treated with DMSO for 12h

source_name: SK-OV-3 cell line,treated with vehicle,12h


title: SK-OV-3 cell line_treated with vehicle_6h

description: Gene expression data from SK-OV-3 cells which were treated with DMSO for 6h

source_name: SK-OV-3 cell line,treated with vehicle, 6h


title: PB1T-3 embryonic stem cells [G32]

status: Public on Mar 10 2017

first: Hongying

last: Sha

address: 220 Handan Rd, WuJiaoChang, Yangpu Qu

institute: Fudan University

hyb_protocol: The pre-hybridization of HOA v7 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled aaRNA was hybridize on MOA v2 in duplication (two arrays for each sample) at 50℃ for 16 hour in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (635nm) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by Rosetta Resolver® System (Rosetta Biosoftware, USA). We filtered the spots in which flag=-50 within all arrays and control probes. Probes passed filter were normalized by median scaling to remove systemic effect, then combine the duplicate data by averaging their intensity value.
The pairwised comparison were performed by Rosetta Resolver® System error-weighted modeling to find significant diffrential expressed probes (log2 |Fold change| ≥ 1 and P < 0.05).

source_name: PB1T-3 embryonic stem cells [G32]

label_protocol: aaRNAs were amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion #AM1753, CA, USA) from 1μg total RNA and directed labeled by NHS-CyDye (Cy5, Amershan) to uridine (dUTP).

extract_protocol: RNA extraction by Trizol method. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: All embryonic stem cells were cultured onto inactived feeder cells  and classical media for humanembryonic stem cells.  Human embryonic fibroblast cells were cultured under 10% fetal  bovine serum  in DMEM/f12.

value: from inner cell mass of PB1T blastocyst


title: human adult fibroblast [G12]

source_name: human adult fibroblast [G12]

value: from  head skin of Patients with traumatic brain injury


title: human adult fibroblast [G13]

source_name: human adult fibroblast [G13]


title: 35S:VvMYBA6a_Hairy roots_Maccabeu_rep3

description:
Hairy roots expressing 35S:VvMYBA6a of Vitis vinifera cv Maccabeu, replicate 3
A03


title: IVF-2 embryonic stem cells [G41]

source_name: IVF-2 embryonic stem cells [G41]

value: from inner cell mass of IVF blastocyst


title: ST-4 embryonic stem cells [G21]

source_name: ST-4 embryonic stem cells [G21]

value: from inner cell mass of ST blastocyst


title: PB1T-3 embryonic stem cells [G33]

source_name: PB1T-3 embryonic stem cells [G33]


title: IVF-2 embryonic stem cells [G42]

source_name: IVF-2 embryonic stem cells [G42]


title: PNT-2 embryonic stem cells [9-3]

source_name: PNT-2 embryonic stem cells [9-3]

value: from inner cell mass of PNT blastocyst


title: IVF embryonic stem cells [10-1]

source_name: IVF embryonic stem cells [10-1]


title: 35S:VvMYBA6b_Hairy roots_Maccabeu_rep2

description:
Hairy roots expressing 35S:VvMYBA6b of Vitis vinifera cv Maccabeu, replicate 2
A05


title: ST-4 embryonic stem cells [G22]

source_name: ST-4 embryonic stem cells [G22]


title: PB1T-3 embryonic stem cells [G31]

source_name: PB1T-3 embryonic stem cells [G31]


title: IVF embryonic stem cells [10-3]

source_name: IVF embryonic stem cells [10-3]


title: ST-4 embryonic stem cells [G23]

source_name: ST-4 embryonic stem cells [G23]


title: IVF-2 embryonic stem cells [G43]

source_name: IVF-2 embryonic stem cells [G43]


title: human adult fibroblast [G11]

source_name: human adult fibroblast [G11]


title: 35S:VvMYBA6a_Hairy roots_Maccabeu_rep1

description:
Hairy roots expressing 35S:VvMYBA6a of Vitis vinifera cv Maccabeu, replicate 1
A01


title: SK-OV-3 cell line_treated with 20μM Cisplatin_24h

description: Gene expression data from SK-OV-3 cells which were treated with 20μM Cisplatin for 24h

source_name: SK-OV-3 cell line,treated with 20μM Cisplatin, 24h


title: 35S:VvMYBA6a_Hairy roots_Maccabeu_rep2

description:
Hairy roots expressing 35S:VvMYBA6a of Vitis vinifera cv Maccabeu, replicate 2
A02


title: PNT-1 embryonic stem cells [8-3]

source_name: PNT-1 embryonic stem cells [8-3]


title: PB2T-1 embryonic stem cells [6-3]

source_name: PB2T-1 embryonic stem cells [6-3]

value: from inner cell mass of PB2T blastocyst


title: PNT-2 embryonic stem cells [9-1]

source_name: PNT-2 embryonic stem cells [9-1]


title: PB2T-2 embryonic stem cells [7-1]

source_name: PB2T-2 embryonic stem cells [7-1]


title: PNT-1 embryonic stem cells [8-2]

source_name: PNT-1 embryonic stem cells [8-2]


title: PB2T-2 embryonic stem cells [7-2]

source_name: PB2T-2 embryonic stem cells [7-2]


title: PNT-1 embryonic stem cells [8-1]

source_name: PNT-1 embryonic stem cells [8-1]


title: ST-3 embryonic stem cells [5-3]

source_name: ST-3 embryonic stem cells [5-3]


title: ST-3 embryonic stem cells [5-2]

source_name: ST-3 embryonic stem cells [5-2]


title: ST-3 embryonic stem cells [5-1]

source_name: ST-3 embryonic stem cells [5-1]


title: medial MN, biological rep2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description:
FACS-isolated motor neurons
MMC_145

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), exon level expression were summarized from the corrected intensities and then quantile normalized.
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.mps

source_name: medial MN

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Embryonic day E12 transgenic HB9::GFP mice (line mHB9-Gfp1b (Wichterle et al., Cell 2002))

extract_protocol: Anatomial dissection of lumbar spinal cord columns, preparation of single cell suspensions by  trypsination/trituration, isolation of motor neuron subsets by FACS, flash freezing in dry ice

treatment_protocol: not applicable

value: lumbar spinal cord

value: medial  motor neurons


title: PB2T-1 embryonic stem cells [6-2]

source_name: PB2T-1 embryonic stem cells [6-2]


title: lateral MN, biological rep1

description:
FACS-isolated motor neurons
LMC_141

source_name: lateral MN

value: lateral  motor neurons


title: IVF embryonic stem cells [10-2]

source_name: IVF embryonic stem cells [10-2]


title: PB2T-2 embryonic stem cells [7-3]

source_name: PB2T-2 embryonic stem cells [7-3]


title: lateral MN, biological rep2

description:
FACS-isolated motor neurons
LMC_145


title: medial MN, biological rep1

description:
FACS-isolated motor neurons
MMC_141


title: PNT-2 embryonic stem cells [9-2]

source_name: PNT-2 embryonic stem cells [9-2]


title: lateral MN, biological rep3

description:
FACS-isolated motor neurons
LMC_146


title: ST-2 embryonic stem cells [4-1]

source_name: ST-2 embryonic stem cells [4-1]


title: medial MN, biological rep3

description:
FACS-isolated motor neurons
MMC_146


title: ST-2 embryonic stem cells [4-3]

source_name: ST-2 embryonic stem cells [4-3]


title: PB2T-1 embryonic stem cells [6-1]

source_name: PB2T-1 embryonic stem cells [6-1]