title: Old_CR

city: Nanjing

first: yunlu

last: sheng

state: Jiangsu

address: 300 Guangzhou Road

department: Department of Gerotology

institute: The First Hospital Affiliated to Nanjing Medical University

description: Mice aged 19 months were caged individually and subjected to a calorically restricted diet (60% of the ad libitum diet) for 3 months.

hyb_protocol: The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA microarray scanner (Agilent p/n G2565BA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: calorie restricted (CR)

label_protocol: Total RNA  from each group was linearly amplified and labeled with Cy3-UTP.

growth_protocol: C57BL/6J male mice at different ages were maintained on a 12h light/dark cycle. Mice aged 3months, 12 months,or 19 months were caged individually and fed ad libitum with standard laboratory chow for 4 days. The average calorie intake was estimated from the daily food intake over these 4 days. Then, each age group was weight matched and randomly divided into two groups: fed ad libitum (AL) and calorie restricted (CR). For the next 12 weeks, the AL mice continued to be fed adlibitum. CR was progressive, being initiated at 10% restriction during the first week, changed to 25% during the second week, and to 40% for the remaining 10 weeks. Both groups had unlimited access to water.

extract_protocol: A pool containing equivalent amounts of mixed ventricular tissues for each group was prepared. A total of 6 RNA samples representing 6 individual groups were isolated using TRIzol (Invitrogen) and purified with the RNeasy Mini Kit  (QIAGEN)  according to the manufacturer’s instructions.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: The mice were sacrificed, and blood was withdrawn by cardiac puncture. The hearts were quickly removed, washed, weighed, and sliced into pieces.

value: 22 months old

tag: Sex

value: myocardial tissue


title: PML knock-out, biological rep 1

status: Public on Nov 17 2016

type: RNA

city: Shreveport

first: Martin

last: Sapp

state: LA

address: 1501 Kings Hwy

department: Microbiology and Immunology

country: USA

institute: LSU Health

description:
Gene expresion data from PML protein deficient HaCaT cells
PML-1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays in the Affymetrix GeneChip Hybridization Oven 645.  Arrays were washed and stained in the Affymetrix Fluidics Station 450 using the fluidics protocol FS450_0001.

scan_protocol: GeneChips were scanned in the Affymetrix GeneChip Scanner 3000 7G with Autoloader.

data_processing:
The data intensities were extracted using Affymetrix Expression Console, build 1.4.1.46, using default analysis settings for the MAS5 algorithm (global scaling with a target intensity value of 500). The data files generated by the Affymetrix microarray hybridization platform were analyzed using GeneSifter Analysis Edition by Geospiza software.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.3.1.187

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HaCaT_PML knockout

label_protocol: Biotinylated cRNA were generated, according to the standard Affymetrix protocol, from 200 ng of total RNA (GeneChip 3' IVT Plus Technical Manual, 703210 Rev. 1, Affymetrix).

growth_protocol: HaCaT cells were grown in low glucose DMEM containing 5% FBS and antibiotics. Lentivirus-transduced cells were maintained with continuous puromycin selection.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini RNA isolation kit (Qiagen)

tag: cell line

value: HaCaT

tag: cell type

value: keratinocytes

tag: transduced with

value: lentiviruses expresing shRNA directed against PML


title: Adult_CR

country: China

description: Mice aged 12 months were caged individually and subjected to a calorically restricted diet (60% of the ad libitum diet) for 3 months.

organism: Mus musculus

tag: strain

tag: age

value: 15 months old

value: Male

tag: tissue


title: shLuc

city: Taipei

first: Shu-Chun

last: Teng

address: No.1 Jen Ai Road Section 1

department: Department of Microbiology

country: Taiwan

institute: National Taiwan University

description: Gene expression data cells with shLuc

hyb_protocol: Standard Affymetrix Protocol.

scan_protocol: Standard Affymetrix Protocol, GeneChip Scanner 3000.

data_processing: The data were extracted with Affymetrix Microarray suite (MAS) software

source_name: shLuc

label_protocol: Standard Affymetrix Protocol.

growth_protocol: Breast cancer cell lines MCF7 was maintained in DMEM containing 10% fetal bovine serum (FBS), non-essential amino acid (HyClone), sodium pyruvate (HyClone), and antibiotics (HyClone). The siRNA vector construct targeting  control luciferase and SMYD3 and sequence were generated by usingLentiviral packaging system (National RNAi Core Facility, Institute of Molecular Biology / Genomic Research Center, Academia Sinica, Taiwan, ROC). The shLuc and shSMYD3 knockdown cell lines were selected by incubating them in the feeding medium with inclusion of 1 microgram/ml puromycin for 3 days.

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

value: epithelial

value: mammary gland/breast


title: Old_AL

description: Mice aged 19 months were caged individually and fed ad libitum for 3 months.

source_name: fed ad libitum (AL)


title: Control, biological rep 2

description:
Gene expresion data from wild type HaCaT cell line
HaCaT UN p14

value: lentiviruses expresing scrambled control


title: CD8_Expressing Foxp3_repC

city: Charleston

first: Jessica

last: Heinrichs

state: South Carolina

address: 86 Johnathan Lucas Street

institute: Medical University

hyb_protocol: Biotin labeled samples (3.5 ug) were hybridized to Affymetrix Mouse Gene 2.0 ST arrays according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 using the AFfymetrix HWS Kit in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: CEL files were imported into Affymetrix Expression Console software and data were normalized using the gene-level RMA algorithm to obtain transcript cluster expression values. Transcript clusters corresponding to controls, references, or unknowns were eliminated from the data set by excluding content not categorized as main or rescue, based on Affymetrix annotation.

source_name: murine CD8 T cells treated with IL-2 TGFb and RA, Foxp3 positive

label_protocol: Total RNA (250 ng) was converted to biotinylated second cycle single stranded cDNA using the Affymetrix GeneChip WT Plus Reagent Kit using recommended methodology.

growth_protocol: Resting murine C57BL6-Foxp3-GFP CD4 and CD8 T cells (200,000/ well) stimulated with BALB/c CD11c dendritic cells (20,000/well) in 1640 RPMI media containing 50uM 2-ME, 1% penicillin/streptomycin, 2mM Hepes, and 10% FBS at 37oC degrees in a 5% CO2-humidified incubator

extract_protocol: Total RNA was extracted using Trizol and Qiagen RNeasy Mini Kit. Total RNAs were run on an Agilent 2100 Bioanalyzer to ensure sample quality.

treatment_protocol: Cell were treated for 5 (CD4) to 4 days (CD8) with either IL-2 (5ng/mL) only or IL-2 (5ng/mL), TGFB (5ng/mL), and retinoic acid (40nM) in a 96 well round bottom plate. Cells were then pooled and stained with anti-mouse CD4, CD8, and CD25 molecules (0.5 ug/ 1 x 10e6 cells) for 15 minutes at 4 degrees and sorted for GFP positive (Foxp3 positive) or negatve (Foxp3 negative) expression on an Aria FACS sorter.

tag: background strain

value: CD8 T cell

tag: treatment

value: IL-2, TGFb, and RA

tag: foxp3 expression

value: positive


title: Young_AL

description: Mice aged 3 months were caged individually and fed ad libitum for 3 months.

value: 6 months old


title: CD8_repA

source_name: murine CD8 T cells treated with IL-2, Foxp3 negative

value: negative


title: Control, biological rep 1

description:
Gene expresion data from wild type HaCaT cell line
HaCaT UN p12


title: WT_shH2A.Z

description: Gene expression data of MCF-7 cells with H2A.ZWT overexpression while endogenous H2A.Z knockdown

source_name: WT, shH2A.Z

growth_protocol: Breast cancer cell lines MCF7 was maintained in DMEM containing 10% fetal bovine serum (FBS), non-essential amino acid (HyClone), sodium pyruvate (HyClone), and antibiotics (HyClone). Overexpression plasmids for H2A.Z expression were a gift from Dr. Gaudreau (Svotelis et al., 2010). The mutant construct pWPI-H2A.ZK102Q was generated by mutagenesis PCR. 293T cells were transfected with pWPI constructs and the packaging vectors to produce viruses.  The siRNA vector construct targeting the H2A.Z sequence were generated by usingLentiviral packaging system (National RNAi Core Facility, Institute of Molecular Biology / Genomic Research Center, Academia Sinica, Taiwan, ROC). The H2A.Z knockdown cell lines were selected by incubating them in the feeding medium with inclusion of 1 microgram/ml puromycin for 3 days.


title: Adult_AL

description: Mice aged 12 months were caged individually and fed ad libitum for 3 months.


title: ESC_2

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

description:
Gene expression data from undifferentiated mouse embryonic stem cells (Oct4-Venus+ fraction)
OLV2-1 cell line, Oct4-Venus+ fraction, sorted by FACS

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GCS3000.

data_processing: The data were analyzed with Expression Console Version 1. 1 using Affymetrix default analysis settings. Clustering analysis was performed using Gene Spring GX12 (Digital Biology).

source_name: mouse_embryonic_stem_cell, sorted by FACS

label_protocol: Fragmentation of aRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3’ IVT Express KitUser Manual, 2013, Affymetrix).

growth_protocol: OLV2-1 (Oct4-Venus knock-in mouse embryonic stem cell line)

extract_protocol: Total RNA was purified with the RNeasy Micro Kit according to the manufacturer’s instructions.

treatment_protocol: Oct4-Venus mouse ESCs (OLV2-1) were cultured in SFEBq condition as reported previously (Eiraku M et al., (2008) Cell Stem Cell 3:519-532). To isolate undifferentiated ESCs and epiblast stem cell-like (EpiSC-like) cells, undifferentiated ESCs and SFEBq cell aggregates on day3 were dissociated with 0.25% (v/v) trypsin/imM EDTA, incubated for 1 hour in SFEBq medium to recover surface antigens, washed with 2% FBS (v/v) in PBS, and stained with allophycocyanin-conjugated CD31 antibody (BD pharmingen; 557690) or control Rat IgG2a (BD pharmingen; 557690) for 45 minutes on ice. After staining, cells were washed with 2% FBS (v/v) in PBS and subjected to cell sorting. The Venus+/CD31+ subpopulation of Oct4-Venus mESCs and a Venus+/CD31− population of SFEBq day 3 cell aggregates were defined as mESCs and EpiSC-like cells, respectively. To isolate day7 Oct4-Venus cells, SFEBq day7 cell aggregates were dissociated with PBS containing 1mM EDTA. Venus+ cell fraction was sorted and subjected to cell sorting. PI was used to exclude dead cells. Cell isolation was performed on a FACS AriaII with FACS Diva Software (BD Biosciences).

tag: culture protocol

value: undifferentiated

value: undifferentiated ESCs

tag: fraction

value: Oct4-Venus+ fraction


title: CD4_Expressing Foxp3_repA

source_name: murine CD4 T cells treated with IL-2 TGFb and RA, Foxp3 positive

value: CD4 T cell


title: CD8_Expressing Foxp3_repB


title: PML knock-out, biological rep 2

description:
Gene expresion data from PML protein deficient HaCaT cells
PML-2

value: HaCaT


title: CD8_Expressing Foxp3_repA


title: K102Q_shH2A.Z

description: Gene expression data of MCF-7 cells with H2A.ZK102Q overexpression while endogenous H2A.Z knockdown

source_name: K102Q, shH2A.Z


title: shSMYD3

description: Gene expression data cells with shSMYD3


title: CD4_Expressing Foxp3_repC


title: CD4_repA

source_name: murine CD4 T cells treated with IL-2, Foxp3 negative


title: CD8_repB


title: CD8_repC


title: OSCC_Sample 75

type: genomic

city: Kuala Lumpur

first: Rosnah Binti

last: Zain

state: Kuala Lumpur

address: Jalan Lembah Pantai

department: Faculty of Dentistry

country: Malaysia

institute: University of Malaya

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added to labelled purified samples.  The samples mixture were hybridized at a constant rotation of 20rpm at 65°C for 22 hours.

scan_protocol: After hybridization, the slide was washed with Agilent Wash Buffer 1 and 2 and scanned immediately using an Agilent Microarray scanner.

data_processing:
Data were extracted from scanned images using Feature Extraction Software, version 10.7.3.1 (Agilent Technologies, USA).
The raw data obtained thereafter were uploaded into the CytoSure Interpret software version 4.2.5 (Oxford Gene Technology), normalized and converted into.cgh files.
Data normalization software was used to improve inconsistencies in dye incorporation. The data were segmented using a modified Circular Binary Segmentation (CBS) algorithm
Genomic aberrations were identified by applying log2 intensity ratios of sample to reference (Cy3/Cy5: log2-ratios above 0.3 for duplications and below -0.6 for deletions).

molecule: genomic DNA

label_protocol:
A total of 1.0 ug genomic DNA from patients and controls was labeled with Cy3 and Cy5 dyes respectively using the CytoSure™ Genomic DNA labeling kit (Oxford Gene Technology)
purification protocol: The cy3 and cy5-labelled DNA were then purified using CytoSure™ Clean-up columns (Oxford Gene Technology).

extract_protocol: Total DNA were extracted from the whole tissue Dneasy Blood and Tissue kit (Qiagen,GmBH Germany) following manufacturer's instructions

value: oral squamous cell carcinoma

tag: gender

value: FEMALE

source_name: matched gender gDNA blood (reference control)

value: blood


title: CD4_repB


title: Young_CR

description: Mice aged 3 months were caged individually and subjected to a calorically restricted diet (60% of the ad libitum diet) for 3 months.

value: Male

value: myocardial tissue


title: CD4_Expressing Foxp3_repB


title: hmec

type: SRA

city: Houston

first: Ronak

middle: Y

last: Patel

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: target capture DNA

library_source: genomic

data_processing:
Read mapping and methylation level calling was performed using Bismark (Krueger and Andrews, 2011).
Average level of methylation over each targeted region was computed
Genome_build: hg19
Supplementary_files_format_and_content: Column 1: Chromosome; Column 2: Start position ;  Column 3: End position ; Column 4: Percent methylation;  Column 5: Number of reads methylated in that position; Column 6: Number of reads unmethylated in that position

source_name: Clonetics

growth_protocol: Normal Human Mammary Epithelial Cells (Clonetics), primary human fibroblasts (Asterand), human CD8+ cytotoxic T-cells (Sanguine), and breast cancer cell lines – MCF7, MDA-MB-231, MDA-MB-361, HCC1954, HCC1569, MCF10A (ATCC)—were cultured according to the respective manufacturer protocol. Logarithmically growing cultures were harvested at ~75-90% confluency. Frozen, primary human breast tumor tissue and adjacent normal tissue were obtained with local Institutional Review Board (IRB# PRO11090404) from the University of Pittsburgh’s Health Science Tissue Bank.

extract_protocol:
Frozen samples were pulverized with mortar and pestle under liquid nitrogen conditions. DNA from cell culture, tumor tissue, normal tissue, and buffy coat was isolated using Qiagen’s DNeasy Blood and Tissue kit and bisulfite converted with the EpiTect Bisulfite Kit (Qiagen).
A set of 1000 target regions of around 300bp in length were preselected for targeted bisulfite sequencing. Primer pairs designed to specifically amplify each selected target region were designed by RainDance Technologies. The ThunderStorm BS-seq assay using that set of primer pairs was performed at RainDance Technologies according to the manufacturer’s specification. That assay uses a microfluidic chip to perform multiplex amplification of bisulfite treated DNA using the set of primers designed to amplify the selected set of genomic regions. This step is followed by sequencing of PCR product. Target regions were sequenced on average to 200X coverage.

value: MEC

tag: sample type

value: Normal MEC

tag: subtype


title: OSCC_Sample 74


title: OSCC_Sample 71

value: MALE


title: OSCC_Sample 61


title: OSCC_Sample 69


title: OSCC_Sample 58


title: OSCC_Sample 68


title: OSCC_Sample 72


title: OSCC_Sample 70


title: OSCC_Sample 66


title: OSCC_Sample 54


title: OSCC_Sample 57


title: OSCC_Sample 62


title: OSCC_Sample 60


title: OSCC_Sample 73


title: OSCC_Sample 50


title: OSCC_Sample 56


title: OSCC_Sample 65


title: OSCC_Sample 55


title: OSCC_Sample 52


title: OSCC_Sample 51


title: OSCC_Sample 64


title: OSCC_Sample 59


title: OSCC_Sample 48


title: OSCC_Sample 67


title: OSCC_Sample 53


title: OSCC_Sample 49


title: OSCC_Sample 47

value: male


title: OSCC_Sample 63


title: TCGA14

description: target capture DNA

source_name: TCGA

value: Breast

value: Tumor

value: ER+


title: OSCC_Sample 46


title: Old-AL

hyb_protocol: The Hy3™-labeled samples were hybridized with the miRCURYTM LNA Array (v.18.0) (Exiqon),according to the array manual.

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

label_protocol: Total RNA (1 µg) from each group was labeled using the miRCURY™ Hy3™/Hy5™ Power Labeling Kit (Exiqon, Vedbaek, Denmark) according to the manufacturer’s guideline .

value: 22 months old


title: Old-CR


title: Adult-CR

value: 15 months old


title: Adult-AL


title: Young-AL

value: 6 months old


title: Young-CR


title: OSCC_Sample 44


title: OSCC_Sample 45


title: OSCC_Sample 43


title: OSCC_Sample 41


title: Wild-type control sample #4949

city: Stirling

first: Kevin

last: Petrie

state: Stirling

address: Stirling

department: Biological and Environmental Sciences

country: United Kingdom

institute: University of Stirling

hyb_protocol: The quality and quantity of labeled cRNA was checked and 750 ng of labeled cRNA were hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST arrays using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: The arrays were scanned on a GeneChip Scanner 3000 7G.

data_processing: Raw data from the arrays were normalized and summarized using the RMA algorithm.

label: Biotin

source_name: CD19-positive B-cells isolated from wild-type spleen

label_protocol: All samples were normalized to 200ng and processed according to standard Affymetrix protocols using GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) and WT Expression Kit (Ambion).

extract_protocol: Total RNA was isolated using TRIzol followed by cleanup with the ZR RNA MiniPrep Kit (Zymo Research). The concentration and quality of the total RNA was assessed on an Agilent 2100 BioAnalyzer (Agilent Technologies).

value: wild-type spleen

value: CD19-positive B-cells

tag: genotype

value: wildtype


title: Wild-type control sample #1906


title: HDAC9 TG tumor sample #5282

source_name: CD19-positive B-cells isolated from tumors

value: tumors

value: HDAC9 constitutive expression


title: HDAC9 TG tumor sample #4949


title: OSCC_Sample 42

value: oral squamous cell carcinoma

value: blood


title: OSCC_Sample 38


title: OSCC_Sample 35

value: FEMALE


title: OSCC_Sample 34


title: OSCC_Sample 33


title: HDAC9 TG tumor sample #5513


title: Wild-type control sample #4936


title: OSCC_Sample 37


title: CD4_repC

value: CD4 T cell

value: negative


title: OSCC_Sample 40


title: RNA 24_Cyclo - 6h LPS

city: Maastricht

first: Emiel

last: van der Vorst

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

description: Replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina genomestudio software

source_name: Bone marrow derived macrophage

growth_protocol: Bone marrow was differentiated into bone marrow-derived macrophages using 20% (vol/vol) L929-conditioned medium (LCM) for 8-9 days.

extract_protocol: RNA was isolated using the High Pure RNA Isolation Kit (Roche), according to manufacturer’s instructions

treatment_protocol: Bone marrow derived macrophages were pre-incubated for 24h with 300ug/ml HDL or 4h with 4% cyclodextrin, washed and stimulated with 10ng/ml LPS

value: 9-16 weeks

value: Bone marrow derived macrophage

value: Cyclo - 6h LPS


title: OSCC_Sample 32

value: MALE


title: OSCC_Sample 36


title: OSCC_Sample 39


title: OSCC_Sample 31


title: OSCC_Sample 30


title: Dicer KO T cells rep 2

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description: replicate 2

scan_protocol: Standard Illumina scanning protocol on an Illumina iScan System

data_processing: The data were normalized using the cubic spline algorith implemented in the Illumina® GenomeStudio software

source_name: Mouse thymus

label_protocol: Total RNA was retrotranscribed, amplified and biotinylated with the Illumina Totalprep RNA Amplification kit (Ambion) following manufacturer’s instructions; cRNA was generated after a 14 hours of in vitro transcription.

extract_protocol: Total RNA from sorted cells was isolated with the miRvana kit (Ambion) following manufacturer’s instructions

value: Dicer lox/lox CD4-Cre +/-

value: 4 weeks

tag: sorting strategy

value: HSA low, TCRβ +, CD1d tetramer -


title: RNA 22_Cyclo - 6h LPS

description: Replicate 4


title: OSCC_Sample 26


title: WT T cells rep 1

description: replicate 1

value: Dicer lox/lox CD4-Cre -/-


title: WT T cells rep 2

description: replicate 2


title: RNA 9_PBS - 6h LPS

description: Replicate 2

value: PBS - 6h LPS


title: OSCC_Sample 28


title: OSCC_Sample 23


title: Dicer KO iNKT cells rep 1

description: replicate 1

value: HSA low, TCRβ int, CD1d tetramer +


title: Dicer KO iNKT cells rep 2

description: replicate 2


title: Dicer KO T cells rep 1

description: replicate 1


title: OSCC_Sample 25


title: OSCC_Sample 27


title: Dicer KO T cells rep 3

description: replicate 3


title: OSCC_Sample 21


title: RNA 18_nHDL - 6h LPS

description: Replicate 3

value: nHDL - 6h LPS


title: Dicer KO iNKT cells rep 3

description: replicate 3


title: WT T cells rep 3

description: replicate 3


title: RNA 7_PBS - 6h LPS

description: Replicate 2


title: RNA 16_nHDL - 6h LPS

description: Replicate 3


title: RNA 8_PBS - 6h LPS

description: Replicate 2


title: RNA 23_Cyclo - 6h LPS

description: Replicate 4


title: RNA 17_nHDL - 6h LPS

description: Replicate 3


title: RNA 2_PBS - no LPS

description: Replicate 1

value: PBS - no LPS


title: OSCC_Sample 22

value: oral squamous cell carcinoma


title: OSCC_Sample 24

value: blood


title: RNA 3_PBS - no LPS

description: Replicate 1


title: OSCC_Sample 29

value: FEMALE


title: WT iNKT cells stage 3 rep 3

description: replicate 3

value: HSA low, TCRβ int, CD1d tetramer +, NK1.1 +, CD44 high


title: RNA 1_PBS - no LPS

description: Replicate 1


title: OSCC_Sample 20


title: WT iNKT cells stage 3 rep 2

description: replicate 2


title: WT iNKT cells stage 1+2 rep 2

description: replicate 2

value: HSA low, TCRβ int, CD1d tetramer +, NK1.1 -, CD44 high/low


title: OSCC_Sample 18


title: OSCC_Sample 13


title: WT iNKT cells stage 1+2 rep 1

description: replicate 1


title: WT iNKT cells stage 1+2 rep 3

description: replicate 3


title: OSCC_Sample 16


title: OSCC_Sample 12


title: OSCC_Sample 11


title: OSCC_Sample 15


title: WT iNKT cells stage 3 rep 1

description: replicate 1


title: OSCC_Sample 19


title: OSCC_Sample 1


title: OSCC_Sample 4


title: OSCC_Sample 7


title: OSCC_Sample 14


title: OSCC_Sample 2


title: OSCC_Sample 3


title: OSCC_Sample 17


title: OSCC_Sample 6


title: OSCC_Sample 5


title: OSCC_Sample 10


title: OSCC_Sample 8


title: OSCC_Sample 9


title: SFC831-03-01

status: Public on Nov 16 2016

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

description: single replicate

data_processing: Quality control results were within expected range. The data were normalised using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA triplication donor 831, clone 1

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

value: female

tag: disease state

value: Parkinson's disease

tag: genotype/variation

value: SNCA triplication


title: SFC831-03-05

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA triplication donor 831, clone 5

tag: cell type


title: SFC829-03-06

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 829, clone 6

value: male

value: SNCA A53T


title: SFC831-03-03

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA triplication donor 831, clone 3


title: SFC840-03-05

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 840, clone 5

value: control


title: control cells (3), time point 48h, uninduced

city: Zurich

first: Maria

middle: Elka

last: Gierisch

address: Steinwiesstrasse 32

department: Department of Oncology

country: Switzerland

institute: University Children's Hospital Zurich

description: Gene expression data from A673 cells transduced with shRNA construct against EWS/FLI1 and overexpression construct for 3xflag-EWS/FLI1 K380R, before treatment with doxycycline

hyb_protocol: Hybridization solution was prepared according to Affymetrix´ GeneChip Expression  Analysis Technical Manual. The final concentration of cRNA is 60 ng/μl.  • Spike-in controls: pre-labelled cRNAs (Affymetrix, Cat. No. 900454) were spiked in at  defined concentrations:  o bioB: 1.5 pM  o bioC: 5 pM  o bioD: 25 pM  o cre: 100 pM  • Hybridization was performed for 16-18 hours at 45°C and 60 rpm in a rotating  hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: Command Console V3.2, HuGene-2_0-st

data_processing: RMA

source_name: A673 cells with shRNA construct against EWS/FLI1, expression of 3xflag-EWS/FLI1 K380R , 24h after induction with doxycycline

label_protocol: cDNA synthesis and in vitro-transcription was done with Ambion´s Message Amp II 96  Kit (Cat. No. 1819) according to the manufacturers’ instructions, starting with 1 μg of  total RNA.

growth_protocol: A673 cells were grown in RPMI/10% FBS/ 0.5µg/µl puromycin

extract_protocol: Total RNA was extracted using the RNAeasy kit including the DNAse digestion step

treatment_protocol: Constructs were induced with 0.1ng/µl doxycycline

tag: tumor type

value: Ewing sarcoma


title: SFC856-03-04

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 856, clone 4


title: SFC830-04-08

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 830, clone 8


title: SFC828-03-06

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 828, clone 6


title: SFC830-04-09

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 830, clone 9


title: shRNA directed against EWS/FLI1, expression of 3xflag-EWS/FLI1 48h

description: Gene expression data from A673 cells transduced with shRNA construct against EWS/FLI1 and overexpression construct for 3xflag-EWS/FLI1, 48h after treatment with doxycycline

source_name: A673 cells with shRNA construct against EWS/FLI1, expression of 3xflag-EWS/FLI1 , 48h after induction with doxycyclin


title: SFC180-01-01

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 180, clone 1


title: SFC829-03-04

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 829, clone 4


title: shRNA directed against EWS/FLI1, expression of 3xflag-EWS/FLI1 K380R 48h

description: Gene expression data from A673 cells transduced with shRNA construct against EWS/FLI1 and overexpression construct for 3xflag-EWS/FLI1 K380R, 48h after treatment with doxycycline

source_name: A673 cells with shRNA construct against EWS/FLI1, expression of 3xflag-EWS/FLI1 K380R , 48h after induction with doxycycline


title: SFC840-03-06

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 840, clone 6


title: SFC828-03-04

description: single replicate

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 828, clone 4


title: control cells (2), time point 48h, uninduced

description: Gene expression data from A673 cells transduced with shRNA construct against EWS/FLI1 and overexpression construct for 3xflag-EWS/FLI1, before treatment with doxycycline

source_name: A673 cells with shRNA construct against EWS/FLI1, expression of 3xflag-EWS/FLI1 , before induction with doxycycline


title: shRNA directed against EWS/FLI1, expression of 3xflag-EWS/FLI1 24h

description: Gene expression data from A673 cells transduced with shRNA construct against EWS/FLI1 and overexpression construct for 3xflag-EWS/FLI1, 24h after treatment with doxycycline

source_name: A673 cells with shRNA construct against EWS/FLI1, expression of 3xflag-EWS/FLI1 , 24h after induction with doxycycline


title: shRNA directed against EWS/FLI1, expression of 3xflag-EWS/FLI1 K380R 24h

description: Gene expression data from A673 cells transduced with shRNA construct against EWS/FLI1 and overexpression construct for 3xflag-EWS/FLI1 K380R, 24h after treatment with doxycycline

source_name: A673 cells with shRNA construct against EWS/FLI1, expression of 3xflag-EWS/FLI1 K380R , before doxycyline induction


title: shRNA directed against EWS/FLI1, expression of 3xflag ctr 24h

description: Gene expression data from A673 cells transduced with shRNA construct against EWS/FLI1 and overexpression construct for 3xflag, 24h after treatment with doxycycline

source_name: A673 cells with shRNA construct against EWS/FLI1, expression of 3xflag , 24h after induction with doxycycline


title: NBL036 Old

city: Chapel Hill

first: William

middle: A.

last: Fischer

state: NC

address: 104 Mason Farm Road

department: Division of Pulmonary and Critical Care Medicine

institute: The University of North Carolina School of Medicine

hyb_protocol: According to Nanostring protocol

scan_protocol: According to Nanostring protocol

data_processing: Data were normalized to the geometric mean of Housekeeping genes. Background threshold was set as the mean + 2*standard deviation of the negative controls for each sample. To be included in the analysis a gene had to be greater than background in at least 1 of the 11 samples.

source_name: Nasal Epithelial Biopsy

label_protocol: According to Nanostring protocol

extract_protocol: Nasal biopsies from young (N=6) and older (N=5) subjects were collected into RPMI media at 4°C, pelleted, and resuspended in Trizol (Life Technologies). RNA was extracted with the miRNeasy Mini RNA extraction kit (Qiagen; manufacturer’s protocol altered for extraction with Trizol rather than Qiazol). The biopsy collection protocol was approved by the Institutional Review Board for Biomedical Research of the University of North Carolina at Chapel Hill School of Medicine (IRBs No 09-0716 and 13-2660).

value: nasal epithelium

tag: age group

value: Older


title: ACe022 Young

value: Young


title: ACe023 Young


title: ACe024 Young


title: shRNA directed against EWS/FLI1, expression of 3xflag ctr 48h

description: Gene expression data from A673 cells transduced with shRNA construct against EWS/FLI1 and overexpression construct for 3xflag, 48h after treatment with doxycycline

source_name: A673 cells with shRNA construct against EWS/FLI1, expression of 3xflag , 48h after induction with doxycycline


title: control cells (1), time point 48h, uninduced

description: Gene expression data from A673 cells transduced with shRNA construct against EWS/FLI1 and overexpression construct for 3xflag, before treatment with doxycycline

source_name: A673 cells with shRNA construct against EWS/FLI1, expression of 3xflag , before induction with doxycycline


title: ACe020 Young


title: ACe021 Young


title: ACe004 Old


title: ACe003 Old


title: ACe005 Old


title: C6 glioma cells_diazepam treated_replicate 4

city: Regensburg

first: Barbara

last: Di Benedetto

address: Franz-Joseph-Strauß Allee 11

country: Germany

institute: University of Regensburg

description:
DZP_4
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 4

hyb_protocol: After RNA extraction, RNA quality was assessed using the NanoPhotometer (NanoDrop, Implen, Germany) and agarose gel electrophoresis. 500 ng total RNA was used for in vitro cRNA transcription with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Austin, TX, USA). The hybridization was performed in Illumina chambers at 58°C 17.5 hrs followed by staining with Cy3-streptavidin.

scan_protocol: The BeadChip (Illumina RatRef-12_V1_0_R4) was scanned on a high resolution Illumina BeadArray reader (Software 3.5.49.29917) and processed to the bead summary level.

data_processing: The Illumina GenomeStudio software (Version 1.9.0) was used to extract and normalize the expression data (fluorescence intensities) for the mean intensity of array. The criteria used were a P-value less than 0.05.

organism: Rattus norvegicus

source_name: C6 glioma cells, diazepam treated

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays from 500 ng total RNA.

growth_protocol: Rat C6 glioma cells (provided by Prof. Dr. B. Hamprecht; Faculty of Chemistry and Pharmacy; Eberhard-Karls Universtity, Tübingen, Germany) were cultured and maintained in DMEM containing 4.5 g  glucose/L, 10% fetal calf serum (FCS), 1% penicillin and streptomycin, 1mM sodium pyruvate (all from GIBCO, Invitrogen, Darmstadt, Germany) at 37°C in a humid atmosphere of 5%O2/CO2. For the microarray experiment, confluent cells were collected and seeded into 6-well plates at a density of 2x10^5/well in DMEM with FCS. After 24 hrs, medium was changed to serum-free DMEM before drug treatment 24 hrs later.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For the microarray experiment and its validation by qPCR, cell culture medium was changed to serum-free medium 24 hrs prior to treatment with 25 µM of each drug (desipramine, fluoxetine, haloperidol or diazepam, all from Sigma, Taufkirchen, Germany) for 2 hrs. After treatment, cells were washed with ice-cold PBS, harvested and RNA was prepared using TRI Reagent.

tag: cell line

value: Glioma cell line

tag: cell passage

value: P3 after thawing and re-plating

value: diazepam


title: C6 glioma cells_diazepam treated_replicate 5

description:
DZP_5
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 5


title: C6 glioma cells_diazepam treated_replicate 6

description:
DZP_6
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 6


title: ACe001 Old

tag: tissue


title: Host 166 Young Mock

data_processing: Data were normalized to the geometric mean of all detected genes to account for overall differences in signal between samples, as significant or near-significant differences in housekeeping gene signals were found between groups. Background threshold was set as the mean + 2*standard deviation of the negative controls for each sample. To be included in the analysis a gene had to be greater than background in at least 1 of the 24 samples.

source_name: Nasal Epithelial Cell Culture

growth_protocol: Human primary nasal epithelial cells (hNECs) were cultured and differentiated from nasal epithelial biopsies at air-liquid interface following the protocol described in Muller L, Brighton LE, Carson JL, Fischer WA, 2nd, Jaspers I. Culturing of human nasal epithelial cells at the air liquid interface. Journal of visualized experiments : JoVE. 2013(80). doi: 10.3791/50646. PubMed PMID: 24145828.The biopsy collection protocol was approved by the Institutional Review Board for Biomedical Research of the University of North Carolina at Chapel Hill School of Medicine (IRBs No 09-0716 and 13-2660).

extract_protocol: Total RNA was extracted from cultures using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions except that Trizol (Life Technologies) was used in the initial extracting steps rather than Qiazol.

treatment_protocol: Cultures were infected with 10 TCID50/cell Influenza A H3N2 virus (Influenza A/Washington/897/90) or media alone (Mock; DMEM containing 100U/ml of penicillin, 100ug/ml of streptomycin, 2mM Glutamine, and 0.3% bovine serum albumin) for 1 hour, washed, and maintained in culture for 24 hours post-infection.

value: Nasal Epithelial Cell Culture

tag: treatment

value: Mock


title: Host 146 Young Mock


title: Host 146 Young H3N2


title: C6 glioma cells_haloperidol treated_replicate 6

description:
HAL_6
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 6

source_name: C6 glioma cells, haloperidol treated

value: haloperidol


title: C6 glioma cells_haloperidol treated_replicate 3

description:
HAL_3
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 3


title: C6 glioma cells_haloperidol treated_replicate 2

description:
HAL_2
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 2


title: Host 73 Young H3N2


title: C6 glioma cells_diazepam treated_replicate 1

description:
DZP_1
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 1


title: Host 73 Young Mock


title: C6 glioma cells_haloperidol treated_replicate 1

description:
HAL_1
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 1


title: Host 48 Old Mock


title: Host 48 Old H3N2


title: C6 glioma cells_fluoxetine treated_replicate 5

description:
FLU_5
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 5

source_name: C6 glioma cells, fluoxetine treated

value: fluoxetine


title: Host 47 Young Mock


title: C6 glioma cells_fluoxetine treated_replicate 4

description:
FLU_4
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 4


title: C6 glioma cells_haloperidol treated_replicate 5

description:
HAL_5
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 5


title: C6 glioma cells_haloperidol treated_replicate 4

description:
HAL_4
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 4


title: C6 glioma cells_fluoxetine treated_replicate 3

description:
FLU_3
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 3


title: Host 45 Old H3N2


title: C6 glioma cells_fluoxetine treated_replicate 1

description:
FLU_1
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 1


title: C6 glioma cells_fluoxetine treated_replicate 2

description:
FLU_2
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 2


title: C6 glioma cells_fluoxetine treated_replicate 6

description:
FLU_6
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 6


title: Host 42 Young Mock


title: Host 42 Young H3N2


title: Host 41 Old Mock


title: SFC828-03-04

description:
mTeSR-1 + matrigel
single replicate
humanomniexpress_24v1-0_a

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file and manifest HumanCytoSNP-12v2-1_H provided by Illumina for GPL13829, and humanomniexpress_24v1-0_a or humanomniexpress-24-v1-1-a for GPL19699 as indicated (sheets GPL19699 1-0 and GPL19699 1-1 respectively). Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

value: induced pluripotent stem cell line derived from dermal fibroblasts

value: female


title: SF829

description:
ADMEM + 10% FCS
single replicate
HumanCytoSNP-12v2-1_H

source_name: dermal fibroblasts, SNCA A53T donor 829

value: dermal fibroblasts


title: Host 47 Young H3N2


title: Host 166 Young H3N2


title: SF830

source_name: dermal fibroblasts, SNCA A53T donor 830

value: male


title: C6 glioma cells_desipramine treated_replicate 4

description:
DMI_4
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 4

source_name: C6 glioma cells, desipramine treated

value: desipramine


title: C6 glioma cells_desipramine treated_replicate 6

description:
DMI_6
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 6


title: Host 41 Old H3N2


title: C6 glioma cells_desipramine treated_replicate 5

description:
DMI_5
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 5


title: C6 glioma cells_desipramine treated_replicate 3

description:
DMI_3
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 3


title: ACe019 Young


title: SFC831-03-05

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA triplication donor 831, clone 5

value: SNCA triplication


title: SFC831-03-03

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA triplication donor 831, clone 3


title: SFC840-03-06

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 840, clone 6

value: control


title: C6 glioma cells_desipramine treated_replicate 2

description:
DMI_2
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 2


title: C6 glioma cells_desipramine treated_replicate 1

description:
DMI_1
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 1


title: Host 45 Old Mock


title: C6 glioma cells_unteated_replicate 6

description:
CTL_6
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 6

source_name: C6 glioma cells, unteated

value: unteated


title: SFC831-03-01

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA triplication donor 831, clone 1


title: Host 36 Old H3N2

value: Older


title: Host 40 Old H3N2


title: Host 37 Old Mock


title: Host 37 Old H3N2


title: SFC829-03-06

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 829, clone 6

value: SNCA A53T


title: Host 36 Old Mock


title: C6 glioma cells_unteated_replicate 3

description:
CTL_3
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 3

value: Glioma cell line


title: SFC829-03-04

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 829, clone 4


title: C6 glioma cells_unteated_replicate 2

description:
CTL_2
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 2

value: P3 after thawing and re-plating


title: C6 glioma cells_unteated_replicate 5

description:
CTL_5
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 5


title: Host 35 Old H3N2


title: SFC840-03-05

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 840, clone 5


title: Host 35 Old Mock


title: C6 glioma cells_unteated_replicate 1

description:
CTL_1
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 1


title: SF180

description:
ADMEM + 10% FCS
single replicate
humanomniexpress-24-v1.0

source_name: dermal fibroblasts, control donor 180


title: C6 glioma cells_unteated_replicate 4

description:
CTL_4
Rat glial tumor induced by N-nitrosomethylurea.
Adult
Biological replicate 4


title: SF831

source_name: dermal fibroblasts, SNCA triplication donor 831


title: MOSE_pass28_d1

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

hyb_protocol: 65ºC for 16 hrs in 3.5X SSC, 0.1% SDS, mouse COT1, poli-dA using Telechem (ArrayIt) hyb cassettes. Further details in Urzua et al. (J Cell Physiol. 2006 Mar;206(3):594-602)

scan_protocol: 10 um resolution in a GenePix-B scanner (Axon)

data_processing:
GPR files obtained with GenePix v5.0, normalized with lowess at DNMAD, imputed with KNN at 85%
Lowess normalized log2 ratios of test/reference. Direct (d1, d2 files) indicate test-Cy5 and reference-Cy3. Reverse (r1, r2 files) indicate dye swap replicates, i.e test.Cy3 and reference-Cy5. Log2 data of dye-swap experiments (r1 and r2 headers) in Matrix spreadsheet was already reversed, i.e. multiplied by -1.0.

source_name: ovarian surface epithelium, primary culture, passage 28

label_protocol: First strand direct cDNA labeling with Cy3 or Cy5-dUTP. Further details in Urzua et al. (J Cell Physiol. 2006 Mar;206(3):594-602)

growth_protocol: Isolated ovarian surface epithelial cells were cultured in supplemented DMEM medium with 4% FBS. Further details by Roby et al. (Carcinogenesis 2000 Apr;21(4):585-91).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Ovarian surface epithelial cells were isolated from adult virgin females. Described in detail by Roby et al. (Carcinogenesis 2000 Apr;21(4):585-91).

tag: strain

source_name: whole newborn


title: MOSE_pass25_r1

source_name: ovarian surface epithelium, primary culture, passage 25


title: KF508_Mock_5_1

city: Cambridge

first: Ines

last: de Santiago

state: - Select -

address: Robinson Way

department: CRUK

institute: University of Cambridge

data_processing: The data were normalized using quantile normalisation in R. Differential expression analysis between the two groups (“Mock” vs “Cre”) was carried out using limma and the illuminaArrayPipeline. In addition, the limma function 'duplicateCorrelation' was to estimate the correlation between measurements made on the same technical replicate.

source_name: KF508 with inducible LSL cassette in front of KRASG12D oncogene, Mock treated

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

extract_protocol: Extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: KF508 pancreatic ductal cell line


title: KF508_Mock_5_2


title: KF508_Mock_6_2


title: KF508_Mock_4_2


title: MOSE_pass25_r2


title: KF508_Mock_2_2


title: KF508_Mock_6_1


title: KF508_Mock_2_1


title: MOSE_pass28_d2


title: MOSE_pass25_d1


title: MOSE_pass28_r2


title: MOSE_pass28_r1


title: MOSE_pass25_d2


title: KF508_Mock_3_2


title: KF508_Mock_3_1


title: KF508_Mock_4_1


title: KF508_Mock_1_2


title: SF828

source_name: dermal fibroblasts, SNCA A53T donor 828


title: MOSE_pass23_r1

source_name: ovarian surface epithelium, primary culture, passage 23


title: Host 40 Old Mock

source_name: Nasal Epithelial Cell Culture

value: Nasal Epithelial Cell Culture


title: MOSE_pass23_r2


title: SFC828-03-06

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 828, clone 6


title: MOSE_pass23_d2


title: MOSE_pass23_d1


title: MOSE_pass18_r2

source_name: ovarian surface epithelium, primary culture, passage 18


title: KF508_Cre_6_2

source_name: KF508 with inducible LSL cassette in front of KRASG12D oncogene, Cre treated

value: Cre


title: pDC_CB_16hr_resting_rep1

city: Kaohsiung

first: Yu

middle: Hong

last: Ren

address: No.123, Ta-Pei Road, Niao-Sung district

institute: Kaohsiung Chang Gung Memorial Hospital

description: microRNA after 16 hr in resting pDC (isolated from cord blood from pools of 31 donors )

hyb_protocol: Hybridization buffer (2X) (Agilent Technologies, USA) was added to the labeled mixture at a final volume of 45 ml. The mixture was heated for 5 min at 100°C and immediately cooled to 0°C. Each 45 ml sample was hybridized onto an Agilent human miRNA Microarray R19 (Agilent Technologies, USA) at 55°C for 20 h.

scan_protocol: After hybridization, slides were washed for 5 min in Gene Expression Wash Buffer 1 at room temperature, and then washed for 5 min in Gene Expression Wash Buffer 2 at 37°C. Microarrays were scanned using the Agilent microarray scanner (Agilent Technologies, model G2505C) at 535 nm for Cy3.

data_processing: Feature Extraction (Agilent Technologies) software version 10.7.3.1 was used for image analysis. If both channels produced intensities less than 100 for a given microRNA, that spot was filtered out. For spots with one channel intensity less than 100 and the other 100 or greater, the signal that was less than 100 was set to 100 prior to calculation of the signal ratio. Hierarchical clustering was performed using Genesis software (Graz University of Technology) and Pearson’s correlation was calculated as the distance metric.

source_name: pDC, CB, 16hr, resting, replicate 1

label_protocol: Total RNA (0.1 μg) was dephosphorylated and labeled with pCp-Cy3 using the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies, USA, microRNA Spike- In Apply).

growth_protocol: Leukocytes were then separated into PMNs and mononuclear cells (MNCs) by density gradient centrifugation in Ficoll-Plaqueä (Amersham Pharmacia) at a ratio of 2:1 at 1500 rpm for 30 minutes at 20°C. After centrifugation over a Ficoll cushion, MNCs were washed and counted on a hemocytometer by trypan blue staining. The PMN fraction in MNCs was less than 1% in adult and neonate samples.CD4+ T-cells, CD8+ T-cells, CD14+ monocytes or CD56+ NK cells were separated from MNCs with the IMag Cell Separation Systems (BD Biosciences, San Jose, CA, USA) following the protocol supplied by the manufacturer. In brief, per 2×107 of mononuclear cells pellet was suspended in 100 µl of anti-human CD4, CD8, CD14 or CD56 magnetic particles (BD Biosciences) and incubated at room temperature for 30 min. Then the labeled cells were resuspended in 1X BD IMag™ buffer and the tubes were placed in the BD Imagnet™ (BD Biosciences) for 10 min. With the tube in the BD IMagnet™, the supernatant was removed to discard the undesired leukocytes. To maximize purity, the process was repeated three times. Then the indicated cell fraction was carefully washed and suspended in PBS or medium. For pDCs isolation, dead cells were initially depleted by magnetic negative selection with Dead Cell Removal Kit (Miltenyi. Biotec, Bergisch Gladbach, Germany), then per 5×107 of mononuclear cells pellet was isolated with 50 µl of CD304 (BDCA-4)-microbeads (Miltenyi Biotech) and magnetic columns according to the manufacturer’s instructions. The mDCs were isolated by magnetic positive selection with CD1c (BDCA-1)-microbeads and a magnetic column (Miltenyi Biotech) following the depletion of CD19+ cells. The purity of isolated cells was confirmed by flow cytometry, and all isolated cells demonstrated greater than 90% purity.

extract_protocol: Total RNA was extracted using the TRIzol® Reagent (Invitrogen, USA) according to the manufacturer’s instructions. Purified RNA was quantified at OD260 nm using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitatively analyzed using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano lab-chip kit (Agilent Technologies, USA).PMNs, CD4+ T cells, CD8+ T cells, CD14+ monocytes, and CD56+ NK cells were isolated from healthy adult peripheral or cord blood obtained from pools of five donors each. The BDCA1+ mDCs were obtained from pools of 10 healthy adult peripheral or cord blood donors. The BDCA4+ pDCs were obtained from pools of 19 healthy adult peripheral blood and 31 cord blood donors for its little amount.

treatment_protocol: PMNs, monocytes, and mDCs were stimulated with LPS (100 ng/ml) for 6 h and CD4+ and CD8+ T cells, B-cells, and NK cells were stimulated with PHA (5 ug/ml) for 24 h. The stimulation condition for pDCs was CpG-ODN 2216 (5 ug/ml) for 16 h as previously reported.

value: blood

tag: age

value: neonate

value: pDC

tag: leukocyte subset

tag: stimulation

value: resting


title: KF508_Mock_1_1

value: Mock


title: KF508_Cre_5_2


title: pDC_CB_16hr_stimulate_rep1

description: microRNA after 16 hr in CpG-ODN 2216 pDC (isolated from cord blood from pools of 31 donors )

source_name: pDC, CB, 16hr ,stimulate, replicate 1

value: CpG-ODN


title: MOSE_pass18_r1

tag: gender

value: male

value: female


title: KF508_Cre_6_1


title: KF508_Cre_5_1


title: MOSE_pass18_d2


title: pDC_AD_16hr_resting_rep1

description: microRNA after 16 hr in resting pDC (isolated from healthy adult peripheral  from pools of19 donors )

source_name: pDC, AD ,16hr ,resting,replicate 1

value: adult


title: KF508_Cre_4_2


title: mDC_AD_6hr_stimulate_rep1

description: microRNA after 6 hr in LPS mDC (isolated from healthy adult peripheral  from pools of10 donors )

source_name: mDC, AD, 6hr, stimulate, replicate 1

value: mDC

value: myeloid dendritic cells

value: LPS


title: MOSE_pass14_d2

source_name: ovarian surface epithelium, primary culture, passage 14


title: KF508_Cre_3_1


title: mDC_CB_6hr_stimulate_rep1

description: microRNA after 6 hr in LPS mDC (isolated from cord blood from pools of 10 donors )

source_name: mDC, CB, 6hr, stimulate, replicate 1


title: KF508_Cre_4_1


title: MOSE_pass14_r1


title: mDC_AD_6hr_resting_rep1

description: microRNA after 6 hr in resting mDC (isolated from healthy adult peripheral  from pools of10 donors )

source_name: mDC, AD, 6hr, resting, replicate 1


title: pDC_AD_16hr_stimulate_rep1

description: microRNA after 16 hr in CpG-ODN 2216 pDC (isolated from healthy adult peripheral  from pools of19 donors )

source_name: pDC, AD, 16hr,stimulate, replicate 1


title: KF508_Cre_3_2


title: KF508_Cre_2_2


title: MOSE_pass14_d1

source_name: whole newborn


title: MOSE_pass18_d1


title: MOSE_pass10_r2

source_name: ovarian surface epithelium, primary culture, passage 10


title: CD56_CB_24hr_resting_rep1

description: microRNA after 24 hr in resting CD56  (isolated from cord blood from pools of 5 donors )

source_name: CD56 ,CB, 24hr, resting, replicate 1

value: CD56 natural killer cells


title: mDC_CB_6hr_resting_rep1

description: microRNA after 6 hr in resting mDC  (isolated from cord blood from pools of 10 donors )

source_name: mDC, CB, 6hr, resting, replicate 1


title: MOSE_pass10_r1


title: CD56_CB_24hr_stimulate_rep1

description: microRNA after 24 hr in PHA CD56  (isolated from cord blood from pools of 5 donors )

source_name: CD56, CB, 24hr, stimulate, replicate 1

value: PHA


title: KF508_Cre_2_1

value: KF508 pancreatic ductal cell line


title: KF508_Cre_1_2


title: CD56_AD_24hr_stimulate_rep1

description: microRNA after 24 hr in PHA CD56 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD56, AD, 24hr ,stimulate ,replicate 1


title: CD56_AD_24hr_resting_rep1

description: microRNA after 24 hr in resting CD56 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD56, AD, 24hr, resting, replicate 1


title: MOSE_pass10_d2


title: MOSE_pass7_r1

source_name: ovarian surface epithelium, primary culture, passage 7


title: CD19_CB_24hr_stimulate_rep1

description: microRNA after 24 hr in PHA CD19  (isolated from cord blood from pools of 5 donors )

source_name: CD19, CB, 24hr, stimulate, replicate 1

value: CD19 B cells


title: KF508_Cre_1_1

source_name: KF508 with inducible LSL cassette in front of KRASG12D oncogene, Cre treated

value: Cre


title: CD19_CB_24hr_resting_rep1

description: microRNA after 24 hr in resting CD19  (isolated from cord blood from pools of 5 donors )

source_name: CD19 ,CB, 24hr, resting, replicate 1

value: blood


title: MOSE_pass5_d2

source_name: ovarian surface epithelium, primary culture, passage 5


title: MOSE_pass7_d2


title: MOSE_pass5_r1


title: MOSE_pass10_d1


title: MOSE_pass7_d1


title: CD14_CB_6hr_stimulate_rep1

description: microRNA after 6 hr in LPS CD14  (isolated from cord blood from pools of 5 donors )

source_name: CD14, CB, 6hr, stimulate, replicate 1

value: neonate

value: CD14 monocytes


title: MOSE_pass5_r2


title: CD14_AD_6hr_resting_rep1

description: microRNA after 6 hr in resting CD14 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD14, AD, 6hr, resting, replicate 1

value: resting


title: MOSE_pass2_r2

source_name: ovarian surface epithelium, primary culture, passage 2


title: CD14_CB_6hr_resting_rep1

description: microRNA after 6 hr in resting CD14  (isolated from cord blood from pools of 5 donors )

source_name: CD14, CB, 6hr, resting, replicate 1


title: MOSE_pass5_d1


title: MOSE_pass2_r1


title: CD19_AD_24hr_resting_rep1

description: microRNA after 24 hr in resting CD19 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD19, AD, 24hr, resting, replicate 1


title: CD19_AD_24hr_stimulate_rep1

description: microRNA after 24 hr in PHA CD19 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD19, AD, 24hr ,stimulate ,replicate 1


title: CD14_AD_6hr_stimulate_rep1

description: microRNA after 6 hr in LPS CD14 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD14, AD, 6hr, stimulate, replicate 1


title: MOSE_pass2_d2

source_name: whole newborn


title: CD8_AD_24hr_stimulate_rep1

description: microRNA after 24 hr in PHA CD8 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD8, AD, 24hr ,stimulate ,replicate 1

value: CD8+ T cells


title: CD8_CB_24hr_resting_rep1

description: microRNA after 24 hr in resting CD8  (isolated from cord blood from pools of 5 donors )

source_name: CD8 ,CB, 24hr, resting, replicate 1


title: MOSE_pass2_d1


title: CD4_CB_24hr_stimulate_rep1

description: microRNA after 24 hr in PHA CD4  (isolated from cord blood from pools of 5 donors )

source_name: CD4, CB, 24hr, stimulate, replicate 1

value: CD4+ T cells


title: CD4_CB_24hr_resting_rep1

description: microRNA after 24 hr in resting CD4  (isolated from cord blood from pools of 5 donors )

source_name: CD4 ,CB, 24hr, resting, replicate 1


title: CD8_CB_24hr_stimulate_rep1

description: microRNA after 24 hr in PHA CD8  (isolated from cord blood from pools of 5 donors )

source_name: CD8, CB, 24hr, stimulate, replicate 1


title: 30wkch_1

city: Bangalore

first: Vrushali

middle: Umakant

last: Deshpande

state: Karnataka

address: No. 258/A, Bommasandra Industrial Area,

department: Molecular Immunology

country: India

institute: Thrombosis Research Institute

hyb_protocol: The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking solution (Agilent Technologies, Part Number: 5190-0456) and Hi-RPM Hybridization Buffer (Agilent Technologies, Part Number: 5190-0456) and incubated at 100oC for 5 minutes followed by snap chill on ice for 5 minutes.  The samples were hybridized on the Mouse miRNA 8x60K Arrays. The hybridization was carried out at 55°C for 20 hours .

scan_protocol: After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes. The microarray slide was scanned on a G2600D scanner (Agilent Technologies)

data_processing: Data extraction from Images was done using Agilent Feature Extraction software Version 11.5.1

source_name: MicroRNA expression at 30W kept on Chow diet

label_protocol: The miRNA labeling was performed using miRNA Complete Labeling  Kit (Agilent Technologies, Part Number: 5190-0456). Ligation of one cyanine3 –pCp molecule to the 3’ end of RNA molecule with greater than 90% efficiency that generates fluorescent miRNA.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Invitrogen) according to the manufacturer protocol. Total RNA integrity was assessed using RNA 6000 Nano Lab Chip on the 2100 Bioanalyzer (Agilent, Palo Alto, CA) following the manufacturer’s protocol. Total RNA purity was assessed by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop technologies, Rockland, USA). We considered RNA to be good quality based on the rRNA 28S/18S ratios and RNA integrity number (RIN)

treatment_protocol: Double knockout mice were kept on High fat diet and chow diet for 0, 6, 18 and 30 weeks

value: double knock out Apobtm2Sgy/Ldltm1Her

value: male

tag: diet

value: Chow diet

value: ascending aorta with atherosclerotic lesion


title: CD8_AD_24hr_resting_rep1

description: microRNA after 24 hr in resting CD8 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD8, AD, 24hr, resting, replicate 1

value: adult


title: 30wkch_3


title: PMN_AD_6hr_stimulate_rep1

description: microRNA after 6 hr in LPS PMN (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: PMN, AD, 6hr, stimulate, replicate 1

value: PMN

value: polymorphonuclear

value: LPS


title: PMN_AD_6hr_resting_rep1

description: microRNA after 6 hr in resting PMN (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: PMN, AD, 6hr, resting, replicate 1


title: 18wkhf_2

source_name: MicroRNA expression at 18W kept on High Fat diet

value: high fat diet


title: CD4_AD_24hr_stimulate_rep1

description: microRNA after 24 hr in PHA CD4 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD4, AD, 24hr ,stimulate ,replicate 1

value: PHA


title: PMN_CB_6hr_resting_rep1

description: microRNA after 6 hr in resting PMN (isolated from cord blood from pools of 5 donors )

source_name: PMN, CB, 6hr, resting, replicate 1


title: CD4_AD_24hr_resting_rep1

description: microRNA after 24 hr in resting CD4 (isolated from healthy adult peripheral  from pools of 5 donors )

source_name: CD4, AD, 24hr, resting, replicate 1


title: 18wkch_3

source_name: MicroRNA expression at 18W kept on Chow diet


title: 18wkch_2


title: 18wkch_1


title: 30wkhf_1

source_name: MicroRNA expression at 30W kept on High Fat diet


title: 30wkhf_3

source_name: MicroRNA expression at 30W kept on High fat diet


title: 18wkhf_3

source_name: MicroRNA expression at 18W kept on High fat diet


title: 18wkhf_1


title: PMN_CB_6hr_stimulate_rep1

description: microRNA after 6 hr in LPS PMN ( (isolated from cord blood from pools of 5 donors ) )

source_name: PMN, CB, 6hr, stimulate, replicate 1


title: 30wkhf_2


title: Late_Hep-i(+)_D8_2

status: Public on Nov 15 2016

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

hyb_protocol: For each hybridization, 0.60 ug of Cy3 labeled cRNA were fragmented, and hybridized at 65 °C for 17 hours to an Agilent SurePrint G3 Rat GE 8x60K Microarray (Design ID: 074809).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. We only used features which were flagged as no errors (Detected flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated and population outliers (Compromised and Not Detected flags). Normalization was performed using Agilent GeneSpring version 12.6.1. (per chip: normalization to 75 percentile shift; per gene: normalization to median of all samples).

source_name: Mouse CLiPs at P12 cultured for 8 days with hepatic induction

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA) following the manufacturer's instructions. Briefly, 100 ng of total RNA was reversed transcribed to double-strand cDNA using a poly dT-T7 promoter primer. Primer, template RNA and quality-control transcripts of known concentration and quality were first denatured at 65 °C for 10 min and incubated for 2 hours at 40 °C with 5X first strand Buffer, 0.1 M DTT, 10 mM dNTP mix, and AffinityScript RNase Block Mix. The AffinityScript enzyme was inactivated at 70 °C for 15 min. cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and Cy3 labeled-CTP and incubated at 40 °C for 2 hours. Labeled cRNAs were purified using QIAGEN’s RNeasy mini spin columns and eluted in 30 ul of nuclease-free water. After amplification and labeling, cRNA quantity and cyanine incorporation were determined using a Nanodrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.

extract_protocol: RNA was extracted using microRNeasy kit (Qiagen) following the manufacturer's instruction.

treatment_protocol: For hepatic induction, mouse CLiPs were cultured in the presence or absence of oncostatin M and dexamethasone.

value: Female

tag: hepatic induction

value: yes

tag: passages


title: Late_Hep-i(+)_D8_3

source_name: Mouse CLiPs at P11 cultured for 8 days with hepatic induction


title: 6wkhf_3

source_name: MicroRNA expression at 6W kept on High Fat diet


title: 6wkhf_1


title: Late_Hep-i(-)_D8_2

source_name: Mouse CLiPs at P12 cultured for 8 days without hepatic induction

value: no


title: 30wkch_2

source_name: MicroRNA expression at 30W kept on Chow diet


title: Late_Hep-i(+)_D8_1


title: 6wkch_3

source_name: MicroRNA expression at 6W kept on Chow diet

value: chow diet


title: Late_Hep-i_D0_1

source_name: Mouse CLiPs at P12 before hepatic induction


title: 6wkch_1


title: 0wk_2

source_name: MicroRNA expression at 0W kept on Chow diet


title: Late_Hep-i(-)_D8_1


title: 0wk_1


title: Late_Hep-i_D0_3

source_name: Mouse CLiPs at P11 before hepatic induction


title: 6wkhf_2


title: SCC13 TLR4 cells replicate_no treatment 1

first: Guergana

last: Iotzova-Weiss

address: Gloriastrasse 31

institute: Dermatology Clinic Zurich

description:
gene expression after 24 hours
SCC13 skin tumor cell line stably transfected

hyb_protocol: 600 ng of the obtained Cy3-labeled cRNA was was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Sure Print GE 8x60 K v2 Microarrays (Agilent Technologies)  (G4112A) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent  G2565CA Microarray Scanner System (Scan Control Software 8.5, Agilent) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Normalized Signal Intensity

source_name: TLR4 no LPS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the One-Color Low Input Quick Amp Labeling  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).Quantification and and quality assessment  were done using Nanodrop spectrophotometer  (Witec)  and Agilent 2100 Bioanalyzer (Agilent Technologies) respectively.

growth_protocol: SCC13 cell lines were grown in conventional DMEM medium supplied with 10% fetal calf serum

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to manufacturer's protocol

treatment_protocol: SCC13 tumor cells were stably transfected with control (pUNO, Invivogen) and TLR4 expressing plasmid (pUNO-TLR4GFP, Invivogen) following the manufacturer’s protocol. For the selection of positive clones the transfected cells were further grown in DMEM medium containing blasticidine (10μg/ml) as a selection marker. Afterwards cells were treated with 10μg/ml ultrapure LPS (Sigma) for 24 hours.

tag: transfection agent

value: no treatment replicate 1


title: 6wkch_2

tag: genotype/variation


title: Mouse_P1 CLiP Hep-i(-)_3

source_name: Mouse CLiPs at P1 cultured for 8 days without hepatic induction


title: Mouse_P1 CLiP Hep-i(-)_1


title: Mouse_P1 CLiP Hep-i_D0_3

source_name: Mouse CLiPs at P1 before hepatic induction


title: Mouse_P1 CLiP Hep-i_D0_2


title: Mouse_Fresh_Hep_3

source_name: Freshly isolated hepatocytes


title: Mouse_P1 CLiP Hep-i(+)_2

source_name: Mouse CLiPs at P1 cultured for 8 days with hepatic induction


title: MOSE_pass14_r2

source_name: whole newborn

source_name: ovarian surface epithelium, primary culture, passage 14

value: female


title: Mouse_P1 CLiP Hep-i(-)_2


title: Mouse_Fresh_Hep_2


title: Mouse_P1 CLiP Hep-i(+)_3


title: Late_Hep-i_D0_2


title: Mouse_P1 CLiP Hep-i(+)_1


title: Mouse_P1 CLiP Hep-i_D0_1


title: Mouse_Fresh_Hep_1


title: Chimera_rHep_D14 YAC(+)_2

description: Gene expression of chimera-derived rat hepatocytes cultured, 14 day, YAC(+)

hyb_protocol: For each hybridization, 0.60 ug of Cy3 labeled cRNA were fragmented, and hybridized at 65 °C for 17 hours to an Agilent SurePrint G3 Rat GE 8x60K Microarray (Design ID: 028279).

data_processing: Intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. We only used features which were flagged as no errors (Detected flags) and excluded features which were not positive, not significant, not uniform, not above background, saturated and population outliers (Compromised and Not Detected flags). Normalization was performed using Agilent GeneSpring version 12.6.1. (per chip: normalization to 75 percentile shift; per gene: normalization to median of all samples). There are total of 30,367 probes on Agilent SurePrint G3 Rat GE 8x60K Microarray (Design ID: 028279) without control probes.

source_name: Chimera-derived rat hepatocytes cultured, 14 day, YAC(+)

extract_protocol: RNA was extracted using miRNeasy kit (Qiagen) following the manufacturer's instruction.

treatment_protocol: Primary rat hepatocytes were cultured for 14 days in the presence or absence of YAC. For hepatic induction, CLiPs were cultured in the presence or absence of oncostatin M and dexamethasone.

value: Wistar

tag: time point

value: 14 days

tag: yac stimulation


title: Chimera_rHep_D7 YAC(-)_1

description: Gene expression of chimera-derived rat hepatocytes cultured, 7 day, YAC(-)

source_name: Chimera-derived rat hepatocytes cultured, 7 day, YAC(-)

value: 7 days


title: Chimera_rHep_D7 YAC(-)_2


title: Chimera_rHep_D7 YAC(+)_1

description: Gene expression of chimera-derived rat hepatocytes cultured, 7 day, YAC(+)

source_name: Chimera-derived rat hepatocytes cultured, 7 day, YAC(+)


title: Chimera_rHep_D7 YAC(+)_2


title: Chimera_rHep_D14 YAC(-)_2

description: Gene expression of chimera-derived rat hepatocytes cultured, 14 day, YAC(-)

source_name: Chimera-derived rat hepatocytes cultured, 14 day, YAC(-)


title: Chimera_rHep_D1 YAC(+)_1

description: Gene expression of chimera-derived rat hepatocytes cultured, 1 day, YAC(+)

source_name: Chimera-derived rat hepatocytes cultured, 1 day, YAC(+)

value: 1 day


title: Chimera_rHep_D1 YAC(-)_2

description: Gene expression of chimera-derived rat hepatocytes cultured, 1 day, YAC(-)

source_name: Chimera-derived rat hepatocytes cultured, 1 day, YAC(-)


title: Chimera_rHep_D14 YAC(-)_1


title: Chimera_rHep_D1 YAC(-)_1


title: Chimera_rat fresh Hep_2

description: Gene expression of fresh rat hepatocytes isolated from clone1c-transplanted chimeric mouse liver

source_name: Fresh rat hepatocytes isolated from clone1c-transplanted chimeric mouse liver


title: Chimera_rHep_D14 YAC(+)_1


title: Rat_CLiP Clone1c

description: Gene expression of rat CLiP Clone1c

source_name: Rat CLiP Clone1c


title: Chimera_rat fresh Hep_1


title: Rat_CLiP Clone5c Hep-i(+)

description: Gene expression of rat CLiP Clone5c cultured 8 days with hepatic induction

source_name: Rat CLiP Clone5c cultured 8 days with hepatic induction

value: 8 days


title: Rat_CLiP Clone5b Hep-i(+)

description: Gene expression of rat CLiP Clone5b cultured 8 days with hepatic induction

source_name: Rat CLiP Clone5b cultured 8 days with hepatic induction


title: Rat_CLiP Clone5c Hep-i(-)

description: Gene expression of rat CLiP Clone5c cultured 8 days without hepatic induction

source_name: Rat CLiP Clone5c cultured 8 days without hepatic induction


title: Control_2

first: madavan

last: vasudevan

address: Kasturi Nagar

institute: Theomics International Private Limited

description: WERI RB1 Untreated Replicate 2

hyb_protocol: As per Manufacturer Recommendation

scan_protocol: As per Manufacturer Recommendation

data_processing: Raw signals transformed to 90th Percentile followed by baseline to median normalization for all the replicates

source_name: WERI cell line

label_protocol: As per Manufacturer Recommendation

growth_protocol: Y79 and WERI-Rb1 (Riken cell bank, Japan) were cultured in RPMI 1640 medium and MIO-M1 (kind gift from Dr. G. A. Limb) in Dulbecco's modification of Eagle's medium (DMEM), respectively at 37 °C in a 5% CO2  humidified incubator. RB tumor samples were collected from the freshly enucleated eyeballs, surgically removed as a part of the treatment regimen with written consent from parents/guardian. Normal retina samples were collected from the healthy cadaveric eyes, post corneal transplantation supplied by C U Shah Eye Bank, Medical Research Foundation, Sankara Nethralaya. This study was conducted at Vision Research Foundation, Sankara Nethralaya, India, and was approved by the Vision Research Foundation Institutional Ethics Board (Ethical clearance no: 249B-2011-P). Figure 7 Changes in PC levels upon in vivo assessment of NCL-APT and LNA-NCL-APT. (a) DESI MS images of cryosection from the vehicle control and treatment groups. Images represent the distribution of phosphatidylcholines across the tissue sections. (b) H&E stained images of the tissue sections. Images were presented without alteration, acquired at 10X magnification. Vehicle control 4 mm 4 mm 2 mm 4 mm m/z 782.6 s.c. i.p. NCL-APT s.c. LNA-NCL-APT 100 0 m/z 810.6 H&E stained www.moleculartherapy.org/mtna Nucleolin-aptamer in retinoblastoma Subramanian et al. 9 RB cells were collected in Rosewell Park Memorial Institute (RPMI) media containing 10% FBS, placed on 6-well plate, minced well, passed through 23 gauge needle and the suspended cells were washed and used for assays.

extract_protocol: Trizol Based Total RNA Extraction

treatment_protocol: The effect of NCL-APT on WERI-Rb1 cell lines were studied by treating cells with various concentrations of NCL-APT and LNA-NCL-APT (0.5 to 20 µmol/l) and scrambled aptamer (5 and 20 µmol/l) using MTT assay. The  effective dose or a concentration with lesser cytotoxicity was chosen for further studies.

value: WERI

value: untreated


title: Rat_CLiP Clone5b Hep-i(-)

description: Gene expression of rat CLiP Clone5b cultured 8 days without hepatic induction

source_name: Rat CLiP Clone5b cultured 8 days without hepatic induction


title: Control_1

description: WERI RB1 Untreated Replicate 1


title: Treated_1

description: WERI RBI Nucleolin Treated Replicate 1

value: Nucleolin Treated


title: Treated_2

description: WERI RBI Nucleolin Treated Replicate 2


title: Rat_CLiP Clone5a Hep-i(+)

description: Gene expression of rat CLiP Clone5a cultured 8 days with hepatic induction

source_name: Rat CLiP Clone5a cultured 8 days with hepatic induction


title: Chimera_rHep_D1 YAC(+)_2


title: Rat_CLiP Clone5a Hep-i(-)

description: Gene expression of rat CLiP Clone5a cultured 8 days without hepatic induction

source_name: Rat CLiP Clone5a cultured 8 days without hepatic induction


title: Rat_CLiP Clone4c Hep-i(-)

description: Gene expression of rat CLiP Clone4c cultured 8 days without hepatic induction

source_name: Rat CLiP Clone4c cultured 8 days without hepatic induction


title: Rat_CLiP Clone4c Hep-i(+)

description: Gene expression of rat CLiP Clone4c cultured 8 days with hepatic induction

source_name: Rat CLiP Clone4c cultured 8 days with hepatic induction


title: Rat_CLiP Clone4b Hep-i(-)

description: Gene expression of rat CLiP Clone4b cultured 8 days without hepatic induction

source_name: Rat CLiP Clone4b cultured 8 days without hepatic induction


title: Rat_CLiP Clone4b Hep-i(+)

description: Gene expression of rat CLiP Clone4b cultured 8 days with hepatic induction

source_name: Rat CLiP Clone4b cultured 8 days with hepatic induction


title: Rat_CLiP Clone4a Hep-i(+)

description: Gene expression of rat CLiP Clone4a cultured 8 days with hepatic induction

source_name: Rat CLiP Clone4a cultured 8 days with hepatic induction


title: Rat_CLiP Clone4a Hep-i(-)

description: Gene expression of rat CLiP Clone4a cultured 8 days without hepatic induction

source_name: Rat CLiP Clone4a cultured 8 days without hepatic induction


title: Rat_CLiP Clone3b Hep-i(+)

description: Gene expression of rat CLiP Clone3b cultured 8 days with hepatic induction

source_name: Rat CLiP Clone3b cultured 8 days with hepatic induction


title: Rat_CLiP Clone3c Hep-i(+)

description: Gene expression of rat CLiP Clone3c cultured 8 days with hepatic induction

source_name: Rat CLiP Clone3c cultured 8 days with hepatic induction


title: Late_Hep-i(-)_D8_3

source_name: Mouse CLiPs at P11 cultured for 8 days without hepatic induction


title: Rat_CLiP Clone3a Hep-i(-)

description: Gene expression of rat CLiP Clone3a cultured 8 days without hepatic induction

source_name: Rat CLiP Clone3a cultured 8 days without hepatic induction


title: Rat_CLiP Clone2b Hep-i(+)

description: Gene expression of rat CLiP Clone2b cultured 8 days with hepatic induction

source_name: Rat CLiP Clone2b cultured 8 days with hepatic induction


title: Rat_CLiP Clone3a Hep-i(+)

description: Gene expression of rat CLiP Clone3a cultured 8 days with hepatic induction

source_name: Rat CLiP Clone3a cultured 8 days with hepatic induction


title: Rat_CLiP Clone2a Hep-i(+)

description: Gene expression of rat CLiP Clone2a cultured 8 days with hepatic induction

source_name: Rat CLiP Clone2a cultured 8 days with hepatic induction


title: Rat_CLiP Clone1c Hep-i(+)

description: Gene expression of rat CLiP Clone1c cultured 8 days with hepatic induction

source_name: Rat CLiP Clone1c cultured 8 days with hepatic induction


title: Rat_CLiP Clone2b Hep-i(-)

description: Gene expression of rat CLiP Clone2b cultured 8 days without hepatic induction

source_name: Rat CLiP Clone2b cultured 8 days without hepatic induction


title: Rat_CLiP Clone1b Hep-i(+)

description: Gene expression of rat CLiP Clone1b cultured 8 days with hepatic induction

source_name: Rat CLiP Clone1b cultured 8 days with hepatic induction


title: Rat_CLiP Clone1b Hep-i(-)

description: Gene expression of rat CLiP Clone1b cultured 8 days without hepatic induction

source_name: Rat CLiP Clone1b cultured 8 days without hepatic induction


title: Rat_CLiP Clone3b Hep-i(-)

description: Gene expression of rat CLiP Clone3b cultured 8 days without hepatic induction

source_name: Rat CLiP Clone3b cultured 8 days without hepatic induction


title: Rat_CLiP Clone1a Hep-i(-)

description: Gene expression of rat CLiP Clone1a cultured 8 days without hepatic induction

source_name: Rat CLiP Clone1a cultured 8 days without hepatic induction


title: Rat_P1 CLiP Hep-i(+)_D8_2

description: Gene expression of CLiPs at P1 cultured for 8 days with hepatic induction


title: Rat_CLiP Clone1a Hep-i(+)

description: Gene expression of rat CLiP Clone1a cultured 8 days with hepatic induction

source_name: Rat CLiP Clone1a cultured 8 days with hepatic induction


title: Rat_P1 CLiP Hep-i_D0_2

description: Gene expression of CLiPs at P1 before hepatic induction

source_name: CLiPs at P1 before hepatic induction


title: Rat_Hep_D14_YAC(+)_2

description: Gene expression of hepatocytes cultured for 14 days with YAC

source_name: Hepatocytes cultured, 14 day, YAC(+)


title: Rat_CLiP Clone1c Hep-i(-)

description: Gene expression of rat CLiP Clone1c cultured 8 days without hepatic induction

source_name: Rat CLiP Clone1c cultured 8 days without hepatic induction


title: Rat_CLiP Clone2a Hep-i(-)

description: Gene expression of rat CLiP Clone2a cultured 8 days without hepatic induction

source_name: Rat CLiP Clone2a cultured 8 days without hepatic induction


title: Rat_CLiP Clone3c Hep-i(-)

description: Gene expression of rat CLiP Clone3c cultured 8 days without hepatic induction

source_name: Rat CLiP Clone3c cultured 8 days without hepatic induction


title: Rat_P1 CLiP Hep-i(-)_D8_1

description: Gene expression of CLiPs at P1 cultured for 8 days without hepatic induction


title: Rat_Hep_D7_YAC(+)_2

description: Gene expression of hepatocytes cultured for 7 days with YAC

source_name: Hepatocytes cultured, 7 day, YAC(+)


title: Rat_Hep_D14_YAC(-)_2

description: Gene expression of hepatocytes cultured for 14 days without YAC

source_name: Hepatocytes cultured, 14 day, YAC(-)


title: Rat_P1 CLiP Hep-i(+)_D8_1

source_name: CLiPs at P1 cultured for 8 days with hepatic induction


title: Rat_Hep_D7_YAC(+)_1


title: Rat_Hep_D7_YAC(-)_2

description: Gene expression of hepatocytes cultured for 7 days without YAC

source_name: Hepatocytes cultured, 7 day, YAC(-)


title: Rat_Hep_D7_YAC(-)_1


title: Rat_Hep_D4_YAC(-)_2

description: Gene expression of hepatocytes cultured for 4 days without YAC

source_name: Hepatocytes cultured, 4 day, YAC(-)

value: 4 days


title: Rat_Hep_D4_YAC(-)_1


title: Rat_Hep_D4_YAC(+)_2

description: Gene expression of hepatocytes cultured for 4 days with YAC

source_name: Hepatocytes cultured, 4 day, YAC(+)


title: Rat_Hep_D3_YAC(+)_1

description: Gene expression of hepatocytes cultured for 3 days with YAC

source_name: Hepatocytes cultured, 3 day, YAC(+)

value: 3 days


title: Rat_Hep_D4_YAC(+)_1


title: Rat_Hep_D2_YAC(+)_2

description: Gene expression of hepatocytes cultured for 2 days with YAC

source_name: Hepatocytes cultured, 2 day, YAC(+)

value: 2 days


title: Rat_Hep_D3_YAC(-)_1

description: Gene expression of hepatocytes cultured for 3 days without YAC

source_name: Hepatocytes cultured, 3 day, YAC(-)

value: Female


title: Rat_Hep_D3_YAC(-)_2


title: Rat_Hep_D2_YAC(-)_2

description: Gene expression of hepatocytes cultured for 2 days without YAC

source_name: Hepatocytes cultured, 2 day, YAC(-)


title: Rat_Hep_D3_YAC(+)_2

value: yes


title: Rat_Hep_D1_YAC(+)_2

description: Gene expression of hepatocytes cultured for 1 day with YAC

source_name: Hepatocytes cultured, 1 day, YAC(+)


title: Rat_Hep_D2_YAC(-)_1

value: no


title: Rat_Hep_D1_YAC(-)_2

description: Gene expression of hepatocytes cultured for 1 day without YAC

source_name: Hepatocytes cultured, 1 day, YAC(-)


title: Rat_Fresh_Hep_2

description: Gene expression of freshly isolated hepatocytes

source_name: Freshly isolated hepatocytes


title: Rat_Hep_D1_YAC(+)_1


title: Rat_Fresh_Hep_1


title: SFC856-03-04

description:
mTeSR-1 + matrigel
single replicate
humanomniexpress-24-v1-1-a

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 856, clone 4

tag: cell type

value: control


title: SFC180-01-01

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 180, clone 1


title: Rat_P1 CLiP Hep-i(-)_D8_2

source_name: CLiPs at P1 cultured for 8 days without hepatic induction


title: SFC830-04-09

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 830, clone 9

value: SNCA A53T

value: male


title: SF856

description:
ADMEM + 10% FCS
single replicate
humanomniexpress-24-v1-1-a

source_name: dermal fibroblasts, control donor 856

value: dermal fibroblasts

value: female


title: HMEC_unstimulated_4h_basal

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: The hybridization cocktail  were hybridized to HU133A arrays (Affymetrix, Santa Clara, CA) at 45°C for 16 hours in a rotisserie oven at 60 rpm.  The arrays were washed using non-stringent buffer  at 25°C, followed by stringent buffer at 50°C.

scan_protocol: The arrays were scanned using the GeneArray scanner (Affymetrix).

data_processing: Hybridization intensity was obtained and detection p value and signal were calculated using MAS 5.0 software

source_name: dermal microvascular endothelial cells, unstimulated basal

label_protocol: 5 µg of total RNA was used to generate double-stranded cDNA by reverse transcription using a cDNA synthesis kit (Superscript Choice System; Life Technologies, Inc., Rockville, MD). Labeled cRNA was prepared from the double-stranded cDNA by in vitro transcription using T7 RNA polymerase in the presence of biotin-11-CTP and biotin-16-UTP (Enzo, Farmington, NY). Fifteen µg of cRNA was fragmented and used to prepare the hybridization cocktail.

growth_protocol: Human microvascular endothelial cells (HMECs) were seeded at 3x10˄5 cells  in complete EGM2-MV growth medium on PET transwells of 1 µm pore size to form a confluent layer within 24 h and were then cultured for another 24 h in EGM2-MV medium including 5% FCS but no additional growth factor supplements. HT-29 colon carcinoma cells were seeded in the same growth medium at 4x10˄6 per 30 mm well and conditioned supernatant was collected from 24 to 48 h after cell seeding.

extract_protocol: HMECs were harvested from transwells, total RNA was extracted (Qiagen).

treatment_protocol: HMEC cultures in transwells were left untreated or were stimulated by tumor-conditioned medium from the basal or apical side for 4 hours prior to isolation of total RNA.

value: dermal microvascular endothelial cells


title: Cal-1 JQ1 - 24 hours - mAdbID:128808

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 128808

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 3 Scan_MicronsPerPixelY: 3 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888

data_processing:
Agilent Data Processing Protocol (JQ1)
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization. For JQ1 gene expression profiling, array features were defined as down-regulated or up-regulated following Drug treatment if the Log2 Fold Change was <-0.5 or >+0.5 for at least 2 time points, respectively. When multiple spots for the same gene were present, a representative spot was selected based on the smallest Log2 FC. The Gen2.2 24h JQ1 array was excluded form the final data analysis because of poor data quality.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: Cal-1 DMSO Treated

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was extracted with TRIzol (Invitrogen) and subsequently cleaned-up with RNeasy mini columns (Qiagen).

treatment_protocol:
Agent: DMSO (Dimethyl sulfoxide)
In-vitro treatment: Cells were treated with DMSO.

value: DMSO

tag: cell line

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm) cells

tag: disease state

source_name: Cal-1 JQ1 Treated - 24 hours

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 100 nM
Treatment time: 24 hours
In-vitro treatment: Cells were treated with 100 nM JQ1 for 24 hours.

tag: time

value: 24 hours


title: Gen2.2 JQ1 - 8 hours - mAdbID:128815

description: mAdb experiment ID: 128815

source_name: Gen2.2 DMSO Treated

tag: treatment

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm)

source_name: Gen2.2 JQ1 Treated - 8 hours

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 100 nM
Treatment time: 8 hours
In-vitro treatment: Cells were treated with 100 nM JQ1 for 8 hours.

value: 8 hours


title: Gen2.2 JQ1 - 3 hours - mAdbID:128814

description: mAdb experiment ID: 128814

source_name: Gen2.2 JQ1 Treated - 3 hours

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 100 nM
Treatment time: 3 hours
In-vitro treatment: Cells were treated with 100 nM JQ1 for 3 hours.

value: 3 hours


title: Control lung cancer cells

city: Guangzhou

first: Lei

last: Yang

address: Xinzao, Panyu District,

institute: Guangzhou medical university

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

source_name: lung cancer A549 cells, transfected with empty pEZ-Lv201, G418-resistant cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Cells were cultured at 37 ℃ in 90% humidity and 5% carbon dioxide (CO2) in RPMI-1640 medium (Gibco, life technologies, California, USA) with 10% fetal bovine serum (FBS) and  penicillin (100UI/ mL)/streptomycin(100mg/mL) in Automatic CO2 incubator (SANYO Electric Co., Ltd., Japan ).

tag: tissue

value: Lung epithelial

tag: transfection

value: empty pEZ-Lv201


title: Cal-1 JQ1 - 1 hour - mAdbID:128805

description: mAdb experiment ID: 128805

source_name: Cal-1 JQ1 Treated - 1 hour

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 100 nM
Treatment time: 1 hour
In-vitro treatment: Cells were treated with 100 nM JQ1 for 1 hour.

value: 1 hour


title: SFC830-04-08

source_name: induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 830, clone 8


title: Cal-1 JQ1 - 3 hours - mAdbID:128806

description: mAdb experiment ID: 128806

source_name: Cal-1 JQ1 Treated - 3 hours


title: Rat_P1 CLiP Hep-i_D0_1

description: Gene expression of CLiPs at P1 before hepatic induction

source_name: CLiPs at P1 before hepatic induction

tag: strain

value: Wistar

value: Female


title: Gen2.2 JQ1 - 1 hour - mAdbID:128813

description: mAdb experiment ID: 128813

source_name: Gen2.2 JQ1 Treated - 1 hour


title: Gen2.2 JQ1 - 24 hours - mAdbID:128816

description: mAdb experiment ID: 128816

source_name: Gen2.2 JQ1 Treated - 24 hours


title: Cal-1 JQ1 - 8 hours - mAdbID:128807

description: mAdb experiment ID: 128807

source_name: Cal-1 JQ1 Treated - 8 hours


title: Rat_Hep_D14_YAC(-)_1

source_name: Hepatocytes cultured, 14 day, YAC(-)

value: no

value: 14 days


title: HMEC_stimulated_4h_basal_HT29supernatant

description: stimulation with conditioned medium from HT29 colon carcinoma cells

source_name: dermal microvascular endothelial cells, stimulated basal for 4 h with HT-29 colon carcinoma supernatant


title: FENDRR stably over-expressed lung cancer cells

description: The cDNA of FENDRR was then cloned into the lentiviral expression vector pEZ-Lv201 as defined as pEZ-Lv201-FENDRR.

source_name: lung cancer A549 cells, transfected with pEZ-Lv201-FENDRR, G418-resistant cells