title: B-cell precursors at S1_FBM32_S1_RNA expression


title: B-cell precursors at S1_FBM12_S1_RNA expression

status: Public on Mar 26 2013

type: RNA

city: Seoul

first: Seung-Tae

last: Lee

state: - None -

address: 50 Iron-Dong KanangmGu

department: Laboratory Medicine & Genetics

country: South Korea

institute: Samsung Medical Center

description: Gene expression data of early B-cell precursors from human fetuses ranging in age between 20 and 24 weeks of gestation

hyb_protocol: Following fragmentation, cRNA were hybridized onto GeneChip Human Gene 1.0 ST Array (Affymetrix) according to Affymetrix's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix genechip scanner

data_processing: Data was processed and normalized using the Expression Console software (Affymetrix) with the standard Robust Multi-array Average (RMA) algorithm

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: B-cell precursors at S1

label_protocol: 1 μg of high-quality total RNA was amplified and labeled (NuGen Ovation)

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer's instructions

treatment_protocol: Four stages of B-cell precursors were isolated via flow cytometry sorting

tag: cell type

value: B-cell precursors at S1, predominantly multipotent progenitors and common lymphoid progenitors

tag: tissue

value: fetal bone marrow

tag: subjects

value: fetuses at San Francisco area

tag: age


title: B-cell precursors at S1_FBM16_S1_RNA expression

value: fetuses ranging in age between 20 and 24 weeks of gestation


title: B-cell precursors at S1_FBM24_S1_RNA expression


title: B-cell precursors at S1_FBM20_S1_RNA expression


title: OPT_28-1 month

city: New Haven

first: Robert

middle: D

last: Beech

state: CT

address: 34 Park St

department: Psychiatry

country: USA

institute: Yale University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Peripheral blood

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

extract_protocol: Total RNA was isolated from 10 cc whole blood using the PAXgene Blood RNA Isolation kit (QIAGEN, Valencia, CA) per the manufacturer's instructions, and depleted of globin mRNA message using GLOBINclear hybridization capture technology (Ambion, Austin, TX). Quality control was performed with Agilent Bioanalyser.

tag: treatment group

value: OPT

tag: time point

value: 1 month

tag: responder

value: YES

tag: sex

value: F


title: B-cell precursors at S1_FBM28_S1_RNA expression


title: Li+OPT_27-1 month

value: Li+OPT

value: NO


title: Li+OPT_26-baseline

value: baseline


title: OPT_29-baseline


title: Li+OPT_25-baseline

value: M


title: OPT_31-1 month


title: OPT_32-baseline


title: Li+OPT_28-baseline


title: Li+OPT_26-1 month


title: OPT_30-1 month


title: Px1_A

status: Public on Mar 27 2013

city: London

first: Claude

last: Chelala

state: London

address: Charterhouse square

department: Institute of Cancer

country: United Kingdom

institute: Barts & The London School of Medicine (QMUL)

description:
Gene expression profiling of familial precursor lesions obtained from profilactic pancreatectomy samples before cancer has developed
010pa.cel

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

scan_protocol: The arrays were scanned using GeneChip scanner 3000 7G

data_processing: RMA normalisation

source_name: PanIN lesion family X

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen Life Technologies) according to the manufacturer’s protocol. The quantity and quality of the samples were assessed using Thermo Scientific NanoDrop 1000 spectrophotometer and Agilant 2100 Bioanalyzer, respectively.

tag: disease state

value: PanIN lesion

value: pancreas


title: 24 h Infected replicate 2

city: Charlottetown

first: Fraser

last: Clark

state: PEI

address: 550 University Ave

department: Pathology and Microbiology

country: Canada

institute: University of Prince Edward Island

description:
Biological replicate 2 of 4 for 24 h Infected
MedA (IA) and MedB (IB) columns in .mev files correspond to 'test (Alexa Flour 555)' and 'reference (Alexa Flour 647)' channels, respectively.

hyb_protocol: Labeled aRNA and cDNA were quantified spectrophotometrically (NanoDrop ND-1000) and 140 ng of cDNA and 100 pmol of labeled aRNA were used for microarray hybridization.  Prior to hybridization, labeled aRNA was fragmented using 1 µL 10x Fragmentation solution and incubation for 10 min at 70°C followed by 1 µL of Stop solution (Life Technologies Inc.).  Hybridizations were performed using A2 chambers on a Tecan 400 HS Pro hybridization system (Tecan, NC, USA).  Briefly, microarrays were incubated at 65°C for 10 min, washed twice with hybridization buffer 1 (5x SSC, 0.01% SDS, 0.2% BSA) for 20s at room temperature, incubated at 50°C for 13 min, washed once with buffer 1 for 20s, incubated at 48°C for 13 min, washed once with buffer 1 for 1 min and once with buffer 4 (5x SSC) for 1 min.  The sample was then injected and hybridized to the microarray with sample agitation at 48°C for 16 h.  The microarray was washed with buffer 2 (2x SSC, 0.2% SDS) at 40°C for 1 min and incubated at 40°C for 2 min, washed with buffer 2 at 30°C for 1 min and with buffer 5 at 30°C for 1 min, incubated at 30°C for 2 min, washed with buffer 5 at 23°C for 1 min, and buffer 3 (0.2x SSC) at 23°C for 1 min.  Finally the microarray was incubated at 23°C for 2 min followed by a wash with buffer 3 for 1 min and then dried with nitrogen gas for 3 min.

scan_protocol: Microarrays were imaged using a GenePix 4000B scanner (Molecular Devices, PA, USA) and features were extracted using SpotReader v 1.3.1 (Niles Scientific, CA, USA).

data_processing: Data was analyzed using TM4/MeV v4.8.1 (Saeed et al., 2003).  Two colour gene expression arrays were normalized by LOWESS and flagged using the MIDAS (Microarray Data Analysis Software) v2.2.2 software (Quackenbush, 2002).  The data was used to generate log2 ratios of sample to reference gene intensity so that all arrays could be compared.

label: Alexa Flour 555

organism: Homarus americanus

source_name: 24 h Infected

label_protocol: Alexa Fluor® 555 labeled single strand cDNA was generated from 20 µg high quality sample RNA using 20 µg of RNA using a SuperScript™ Plus Indirect cDNA Labeling System (Life Technologies Inc., Burlington, ON, Canada). Reference aRNA was generated from 5 µg of pooled lobster hepatopancreatic RNA using an Amino Allyl MessageAmp™ II aRNA Amplification kit (Life Technologies Inc.). Reference aRNA was Alexa Fluor® 647  labeled using 12 µg of aRNA and a Superscript™ Plus Indirect cDNA Labeling System (Life Technologies Inc.).

growth_protocol: H. americanus were individually housed in a recirculating artificial sea water system with UV and 1 µm filter.

extract_protocol: Total RNA was extracted using a phenol-chloroform extraction method with the aqueos phase cleaned up using an Rneasy kit following manufacturers instructions.

treatment_protocol: Infected lobster were injected with A. haemophila.

tag: moult status

value: Intermoult

tag: gender

value: male

value: Hepatopancreas

label: Alexa Flour 647

source_name: aRNA reference sample from pooled sample of Homarus americanus hepatopancreatic tissue

tag: sample complexity

value: standard reference pooled sample

value: hepatopancreas


title: OPT_26-1 month


title: Li+OPT_25-1 month


title: OPT_29-1 month


title: OPT_27-1 month


title: OPT_31-baseline


title: OPT_26-baseline


title: OPT_30-baseline


title: OPT_28-baseline


title: OPT_27-baseline


title: OPT_32-1 month


title: OPT_25-1 month


title: Li+OPT_27-baseline


title: Li+OPT_24-1 month


title: B-cell precursors at S2_FBM23_S2_RNA expression

source_name: B-cell precursors at S2

value: B-cell precursors at S2, predominantly pre-B-I cells

value: fetal bone marrow

value: fetuses at San Francisco area


title: OPT_25-baseline

value: OPT


title: OPT_24-baseline

value: YES


title: Li+OPT_24-baseline

value: F


title: Li+OPT_20-1 month

value: Li+OPT

value: 1 month


title: Li+OPT_22-baseline

value: baseline

value: NO


title: OPT_22-baseline


title: Li+OPT_21-baseline


title: OPT_24-1 month


title: Li+OPT_23-1 month

value: M


title: Li+OPT_22-1 month


title: OPT_23-1 month


title: Li+OPT_21-1 month


title: Li+OPT_23-baseline


title: OPT_23-baseline


title: OPT_22-1 month


title: OPT_19-1 month


title: Li+OPT_19-baseline


title: OPT_20-baseline


title: Li+OPT_20-baseline


title: Li+OPT_18-1 month


title: OPT_21-baseline


title: Li+OPT_19-1 month


title: OPT_21-1 month


title: OPT_20-1 month


title: OPT_18-baseline


title: OPT_19-baseline


title: OPT_18-1 month


title: Li+OPT_17-1 month


title: Li+OPT_18-baseline


title: Li+OPT_16-1 month


title: Li+OPT_17-baseline


title: OPT_16-baseline


title: OPT_14-baseline


title: OPT_17-baseline


title: Li+OPT_16-baseline


title: Li+OPT_15-1 month


title: OPT_15-baseline


title: OPT_13-1 month


title: OPT_12-1 month


title: OPT_16-1 month


title: Li+OPT_15-baseline


title: OPT_11-1 month


title: OPT_15-1 month


title: OPT_17-1 month


title: OPT_14-1 month


title: OPT_13-baseline


title: OPT_12-baseline


title: Li+OPT_13-1 month


title: OPT_11-baseline


title: Li+OPT_13-baseline


title: Li+OPT_14-1 month


title: OPT_8-baseline


title: Li+OPT_14-baseline


title: Li+OPT_12-1 month


title: OPT_10-1-month


title: OPT_10-baseline


title: Li+OPT_12-baseline


title: OPT_9-1 month


title: OPT_8-1-month


title: OPT_9-baseline


title: OPT_7-1 month


title: Li+OPT_28-1 month


title: OPT_5-baseline


title: Li+OPT_8-1 month


title: Li+OPT_8-baseline


title: Li+OPT_7-1 month


title: OPT_7-baseline


title: Li+OPT_9-baseline


title: Li+OPT_11-1 month


title: OPT_6-baseline


title: Li+OPT_9-1 month


title: Li+OPT_10-1 month


title: Li+OPT_10-baseline


title: Li+OPT_7-baseline


title: OPT_6-1-month


title: OPT_5-1-month


title: Li+OPT_11-baseline


title: RBC hybridized to spleen, replicate 3

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

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

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

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

organism: Salmo salar

source_name: RBC

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

growth_protocol: Salmon (average weight 100g) was kep in tanks with sea water

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

treatment_protocol: Fish received a single dose of PHZ (Sigma Aldrich, St. Louis, MO, USA) at 6 mg kg-1 body mass in physiological saline (3 mg ml-1, i.p. injection doses of 0.2±0.02 ml). Control fish were injected with 0.2±0.02 ml (adjusted for body mass) physiological saline

value: RBC

source_name: Spleen

value: spleen

tag: sample type

value: reference


title: RBC hybridized to spleen, replicate 4


title: RBC hybridized to spleen, replicate 2


title: RBC hybridized to spleen, replicate 1


title: Li+OPT_4-1 month


title: Li+OPT_4-baseline


title: Li+OPT_5-1 month


title: Li+OPT_6-1 month


title: Li+OPT_6-baseline


title: Li+OPT_2-1 month


title: Li+OPT_3-baseline


title: Li+OPT_5-baseline


title: Li+OPT_3-1 month


title: Saline injected, day 2, fish 8

value: Spleen

tag: treatment

value: Saline injected

tag: time

value: day 2

source_name: Spleen, mixture of all samples


title: OPT_4-1 month


title: Saline injected, day 2, fish 7


title: Saline injected, day 2, fish 6


title: Saline injected, day 2, fish 4


title: Saline injected, day 2, fish 1


title: Saline injected, day 2, fish 26


title: Saline injected, day 2, fish 2


title: OPT_4-baseline


title: OPT_2-baseline


title: OPT_2-1 month


title: Li+OPT_2-baseline


title: Saline injected, day 2, fish 3


title: OPT_3-1 month


title: OPT_1-1 month


title: Li+OPT_1-1 month


title: Saline injected, day 2, fish 22


title: Saline injected, day 2, fish 19


title: PHZ injected, day 4, fish 112

value: PHZ injected

value: day 4


title: Saline injected, day 2, fish 20


title: PHZ injected, day 4, fish 111


title: Saline injected, day 2, fish 24


title: Saline injected, day 2, fish 21


title: Saline injected, day 2, fish 23


title: PHZ injected, day 4, fish 109


title: OPT_1-baseline


title: PHZ injected, day 4, fish 107


title: PHZ injected, day 4, fish 110


title: PHZ injected, day 4, fish 108


title: OPT_3-baseline


title: Li+OPT_1-baseline


title: PHZ injected, day 4, fish 105


title: PHZ injected, day 2, fish 79


title: PHZ injected, day 2, fish 75


title: PHZ injected, day 2, fish 78


title: PHZ injected, day 4, fish 106


title: PHZ injected, day 2, fish 72


title: PHZ injected, day 4, fish 130


title: PHZ injected, day 2, fish 73


title: donor4-10-12h

city: New York

first: David

last: Braun

state: NY

address: 1 Gustave Levy Place

department: Neurology / Computational Biology

institute: Mount Sinai School of Medicine

description: replicate 4, IL-10-treated for 12hrs

hyb_protocol: Standard Illumina hybridization protocol, performed by Yale Center for Genome Analysis

scan_protocol: Standard Illumina scanning protocol, performed by Yale Center for Genome Analysis

data_processing: Data was quantile-normalized in BeadStudio by Yale Center for Genome Analysis (normalized data provided here). Following initial normalization, additional adjustment for between-donor variation was made. For each donor, each gene’s expression value was normalized by that gene’s median expression value in that donor. Low expression genes were filtered out, and the remaining expression data were log2-transformed. Differentially expressed genes (vs. untreated cells) were selected using a two-tail unpaired t-test with a False Discovery Rate-corrected threshold of 0.05

label_protocol: Preparation of labeled cRNA for hybridization onto Illumina BeadChips followed the recommended Illumina protocol using a TotalPrep RNA Amplification kit (Applied Biosystems), performed by the Yale Center for Genome Analysis

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats by Ficoll density gradient centrifugation (Histopaque, Sigma-Aldrich). CD14+ monocytes were then immunomagnetically purified from PBMCs using a MACS CD14 isolation kit (Miltenyi Biotec). CD14+ monocytes were then differentiated into naïve, immature DCs by 5-day incubation in DC growth media [RPMI medium 1640 (Gibco), 10% fetal calf serum (Hyclone), 2mM of L-glutamine, 100 U/ml penicillin (Invitrogen), and 100 U/ml streptomycin (Invitrogen)] supplemented with 500 U/ml hGM-CSF (Peprotech) and 1000 U/ml hIL-4 (Peprotech) at 37°C. DCs were then re-suspended in cytokine-free DC growth media (106 cells/ml) and incubated for 1 day at 37°C. DCs from randomly selected buffy coats were assayed for surface CD11c expression (a dendritic cell marker) as a quality control for cell uniformity. All assayed DCs homogeneously expressed surface CD11c.

extract_protocol: Total RNA was isolated from DCs using a Qiagen Mini RNeasy kit or a Qiagen BioRobot Universal with RNeasy 96 kit, with on-column DNase treatment, according to the manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (NanoDrop)

treatment_protocol: DCs were treated with 10 ng/ml of hIL-6 (Peprotech) or 10 ng/ml of hIL-10 (Peprotech)

value: Monocyte-derived dendritic cell

tag: replicate


title: PHZ injected, day 2, fish 77


title: PHZ injected, day 2, fish 76


title: donor4-6-8h

description: replicate 4, IL-6-treated for 8hrs


title: PHZ injected, day 2, fish 74


title: PHZ injected, day 4, fish 129


title: donor4-6-4h

description: replicate 4, IL-6-treated for 4hrs


title: donor4-U-12h

description: replicate 4, untreated at 12hrs

value: untreated


title: iPSc clone 23 from OX1 fibroblasts

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: iPSc clone 23 from OX1 fibroblasts

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: adult normal human dermal fibroblast-derived induced pluripotent stem cell line

tag: culture

value: mTeSR-1 + matrigel


title: iPSc clone 19 from OX1 fibroblasts

description: single replicate

source_name: iPSc clone 19 from OX1 fibroblasts

tag: cell type


title: donor4-6-12h

description: replicate 4, IL-6-treated for 12hrs


title: iPSc clone 18 from OX1 fibroblasts

description: single replicate

source_name: iPSc clone 18 from OX1 fibroblasts


title: donor4-10-8h

description: replicate 4, IL-10-treated for 8hrs


title: donor4-10-45m

description: replicate 4, IL-10-treated for 45min


title: PHZ injected, day 4, fish 128

tag: tissue


title: donor4-10-4h

description: replicate 4, IL-10-treated for 4hrs


title: donor3-U-12h

description: replicate 3, untreated at 12hrs


title: donor4-U-0

description: replicate 4, untreated at 0min


title: donor4-6-45m

description: replicate 4, IL-6-treated for 45min


title: donor4-6-2h

description: replicate 4, IL-6-treated for 2hrs


title: PHZ injected, day 4, fish 127


title: PHZ injected, day 4, fish 125


title: donor3-6-4h

description: replicate 3, IL-6-treated for 4hrs


title: PHZ injected, day 4, fish 126


title: PHZ injected, day 4, fish 124


title: PHZ injected, day 2, fish 94


title: PHZ injected, day 4, fish 123


title: PHZ injected, day 2, fish 91


title: PHZ injected, day 2, fish 89


title: PHZ injected, day 2, fish 90


title: PHZ injected, day 2, fish 93


title: donor3-10-12h

description: replicate 3, IL-10-treated for 12hrs


title: donor3-6-2h

description: replicate 3, IL-6-treated for 2hrs


title: donor3-10-45m

description: replicate 3, IL-10-treated for 45min


title: donor3-6-12h

description: replicate 3, IL-6-treated for 12hrs


title: PHZ injected, day 2, fish 87


title: PHZ injected, day 2, fish 88


title: Saline injected, day 2, fish 5


title: donor3-10-2h

description: replicate 3, IL-10-treated for 2hrs


title: donor3-U-0

description: replicate 3, untreated at 0min


title: donor2-10-2h

description: replicate 2, IL-10-treated for 2hrs


title: PHZ injected, day 2, fish 92


title: donor3-6-45m

description: replicate 3, IL-6-treated for 45min


title: donor3-10-4h

description: replicate 3, IL-10-treated for 4hrs


title: donor2-6-4h

description: replicate 2, IL-6-treated for 4hrs


title: donor2-6-45m

description: replicate 2, IL-6-treated for 45min


title: donor2-10-12h

description: replicate 2, IL-10-treated for 12hrs


title: donor2-6-2h

description: replicate 2, IL-6-treated for 2hrs


title: donor3-6-8h

description: replicate 3, IL-6-treated for 8hrs


title: donor2-U-12h

description: replicate 2, untreated at 12hrs


title: donor2-10-45m

description: replicate 2, IL-10-treated for 45min


title: donor2-6-12h

description: replicate 2, IL-6-treated for 12hrs


title: Sample 40031

city: Chicago

first: Jun

last: Wang

state: IL

address: 303 E Superior Street

department: Department of Surgery

institute: Northwestern University

hyb_protocol: Total RNA sample labeling and hybridization were performed by Northwestern University Genomics Core Facility

scan_protocol: The raw data were normalized using the robust spline (RSN) algorithm available in the lumi Bioconductor package for R statistical software.  Non-specific filtering was performed by limiting analyses only to those with interquartile range above the median.

source_name: Normal breast rFNA

extract_protocol: Total RNA was extracted from rFNA samples using Trizol reagent (Invitrogen) and purified using RNeasyPlus Micro Kit (Qiagen). RNA was then treated with DNase and checked for integrity using Agilent 2100 Bioanalyze

tag: menopausal status (ms)

value: pre-

tag: er status

value: pos

value: Sample 40031

tag: race

value: C

tag: grade


title: donor2-10-8h

description: replicate 2, IL-10-treated for 8hrs

tag: time point


title: Sample 40055

data_processing: The raw data were normalized using the robust spline (RSN) algorithm available in the lumi Bioconductor package for R statistical software.  Non-specific filtering was performed by limiting analyses only to those with interquartile range above the median.

label_protocol: Total RNA sample labeling and hybridization were performed by Northwestern University Genomics Core Facility

tag: age

value: post-

value: Sample 40055

value: Other


title: donor2-10-4h

description: replicate 2, IL-10-treated for 4hrs


title: donor3-10-8h

description: replicate 3, IL-10-treated for 8hrs


title: donor1-6-4h

description: replicate 1, IL-6-treated for 4hrs


title: donor2-6-8h

description: replicate 2, IL-6-treated for 8hrs


title: Sample 40019

value: Sample 40019


title: donor1-U-12h

description: replicate 1, untreated at 12hrs


title: Sample 40016

value: Sample 40016


title: Sample 40024

value: Sample 40024


title: OX1 fibroblasts [SNP]

type: genomic

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 HumanCytoSNP-12v2-1_H.egt provided by Illumina. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

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

molecule: genomic DNA

source_name: OX1 fibroblasts

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: adult normal human dermal fibroblasts

value: ADMEM + 10% FCS


title: donor2-U-0

description: replicate 2, untreated at 0min


title: donor1-10-2h

description: replicate 1, IL-10-treated for 2hrs


title: iPSc clone 19 from OX1 fibroblasts  [SNP]


title: Sample 40013

value: Sample 40013

value: AA


title: iPSc clone 18 from OX1 fibroblasts  [SNP]


title: donor1-10-12h

description: replicate 1, IL-10-treated for 12hrs

value: Monocyte-derived dendritic cell


title: donor1-6-2h

description: replicate 1, IL-6-treated for 2hrs


title: donor1-6-12h

description: replicate 1, IL-6-treated for 12hrs


title: donor4-10-2h

description: replicate 4, IL-10-treated for 2hrs


title: donor1-10-45m

description: replicate 1, IL-10-treated for 45min


title: donor1-10-8h

description: replicate 1, IL-10-treated for 8hrs


title: Sample 40003

value: Sample 40003


title: Sample 20012

value: neg

value: Sample 20012


title: donor1-6-45m

description: replicate 1, IL-6-treated for 45min


title: Sample 40010

value: pre

value: Sample 40010


title: Sample 40006

value: pre-

value: pos

value: Sample 40006

value: C


title: iPSc clone 23 from OX1 fibroblasts  [SNP]

value: adult normal human dermal fibroblast-derived induced pluripotent stem cell line

value: mTeSR-1 + matrigel


title: donor1-10-4h

description: replicate 1, IL-10-treated for 4hrs


title: Sample 40005

value: post-

value: Sample 40005


title: Sample 40004

value: Sample 40004


title: Sample 40057

hyb_protocol: Total RNA sample labeling and hybridization were performed by Northwestern University Genomics Core Facility.

source_name: normal breast rFNA_postmenopause

extract_protocol: Total RNA was extracted from rFNA samples using Trizol reagent (Invitrogen) and purified using RNeasyPlus Micro Kit (Qiagen). RNA was then treated with DNase and checked for integrity using Agilent 2100 Bioanalyze.

value: postmenopause

value: Random fine needle aspiration (rFNA) sample from normal breasts

value: Sample 40057

value: Other


title: donor1-6-8h

description: replicate 1, IL-6-treated for 8hrs

value: Monocyte-derived dendritic cell


title: Sample 40045

scan_protocol: Total RNA sample labeling and hybridization were performed by Northwestern University Genomics Core Facility.

value: Sample 40045


title: Sample 40056

label_protocol: Total RNA sample labeling and hybridization were performed by Northwestern University Genomics Core Facility.

value: Sample 40056

value: AA


title: donor1-U-0

description: replicate 1, untreated at 0min

value: untreated


title: Sample 40047

value: Sample 40047


title: Sample 40046

value: Sample 40046


title: Sample 40043

value: Sample 40043

value: C


title: Sample 40036

value: Sample 40036


title: Sample 40034

value: Sample 40034


title: Sample 40050

value: Sample 40050


title: Sample 40052

source_name: normal breast rFNA_premenopause_luteal

value: premenopause

tag: menstrual phase (mp)

value: luteal

value: Sample 40052


title: Sample 40066

source_name: normal breast rFNA_premenopause_late follicular

value: pre-menopause

value: late follicular

value: Random fine needle aspiration (rFNA) sample from normal breasts

value: Sample 40066


title: Sample 40053

value: Sample 40053


title: Sample 40029

value: Sample 40029


title: Sample 40044

source_name: normal breast rFNA_premenopause_early follicular

value: early follicular

value: Sample 40044


title: Testis_d60_ko_rep1

city: Beijing

first: min

last: chen

address: No.2, Yuan Ming Yuan West Road

country: China

institute: China Agricultural University

description: Gene expression in 60 day knockout mice testis.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome 4x44k Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: testis, 60 days, plin1 knockout

label_protocol: Total RNA was amplified and Cy3-labeled by the 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 an RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US) following the manufacturer's instructions, and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by an RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: genotype

value: plin1 knockout

value: testis

value: male

value: 60 days

tag: developmental phase

value: mature


title: Sample 40069

value: Sample 40069

value: C


title: Testis_d60_ko_rep2

tag: gender


title: Testis_d60_ko_rep3


title: Sample 40033

value: postmenopause

tag: sample type

value: Sample 40033


title: Testis_d60_wt_rep2

description: Gene expression in 60 day wild type mice testis.

source_name: testis, 60 days, wild type

value: wild type


title: Testis_d40_ko_rep2

description: Gene expression in 40 day knockout mice testis.

source_name: testis, 40 days, plin1 knockout

value: 40 days

value: puberty


title: Testis_d40_ko_rep1


title: Testis_d40_ko_rep3


title: Testis_d40_wt_rep1

description: Gene expression in 40 day wild type mice testis.

source_name: testis, 40 days, wild type


title: Testis_d40_wt_rep2


title: Testis_d40_wt_rep3


title: Testis_d21_ko_rep2

description: Gene expression in 21 day knockout mice testis.

source_name: testis, 21 days, plin1 knockout

value: 21 days

value: meiosis


title: Testis_d60_wt_rep1


title: Testis_d21_ko_rep3


title: Testis_d60_wt_rep3


title: Testis_d21_ko_rep1


title: Testis_d21_wt_rep3

description: Gene expression in 21 day wild type mice testis.

source_name: testis, 21 days, wild type


title: Sample 40037

value: pre-menopause

value: Random fine needle aspiration (rFNA) sample from normal breasts

value: Sample 40037


title: hu-sheep_2 days_small wave_rep3

city: China yangzhou

first: nirong

last: nirong

address: Yangzhou city,yangzhou university  wenhui road

institute: yangzhou nuiversity

description: Gene expression about small wave's dorsal skin in 2 days

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: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Ovis aries

source_name: Dorsal skin,2 days,small wave,replicate3

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), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: breed

value: Hu

value: dorsal skin

tag: days

value: 2 days

tag: wave pattern

value: small wave


title: Testis_d21_wt_rep2

value: testis

value: male


title: hu-sheep_2 days_small wave_rep2

source_name: Dorsal skin,2 days,small wave,replicate2


title: hu-sheep_2 days_large  wave_rep1

description: Gene expression about large wave's dorsal skin in 2 days

source_name: Dorsal skin,2 days,large wave,replicate1

value: large wave


title: Testis_d21_wt_rep1


title: Sample 40042

value: premenopause

value: early follicular

value: Sample 40042

value: AA


title: hu-sheep_2 days_small wave_rep1

source_name: Dorsal skin,2 days,small wave,replicate1


title: hu-sheep_2 days_large wave_rep3

source_name: Dorsal skin,2 days,large wave,replicate3


title: hu-sheep_2 days_large wave_rep2

source_name: Dorsal skin,2 days,large wave,replicate2


title: mU50_wildtype_splenoB

city: Tokyo

first: Yuuichi

last: Soeno

address: 1-9-20 Fujimi, Chiyoda-ku

department: Pathology

country: Japan

institute: The Nippon Dental University

description: Gene expression data from three mice

hyb_protocol: cRNA were hybridized for 16 hr at 45C on GeneChip Microarray (Mouse expression 430 2.0, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were RMA normalized using Expression Console v. 1.1.2800.19935. RMA normalized data were analyzed using GeneSpring software version 7.3.1 (Silicon Genetics Inc.).

source_name: Splenic B-cells from C57BL/6J wildtype mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

growth_protocol: Mice were kept under a 12-h light-dark cycle and were given standard laboratory fodder and water ad libitum.

extract_protocol: Total RNA was extracted from the sample using RNeasy Micro Kit (QIAGEN) according to the manufacturer's instruction.

treatment_protocol: Animals were euthanized by cervical dislocation and the spleen dissected out were placed in Hanks’ balanced salt solution (HBSS) at 4C. A dissected spleen was gently ground by two slide-glasses and collected into a test tube with HBSS. The cell pellet of the splenocytes was treated with 4 ml of ACK lysing buffer (Lonza) for 5 min to lyse out the erythrocytes. After several washing of the cells with HBSS, FITC-conjugated anti-CD45R/B220 antibody (BD Biosciences) was added and reacted for 15 min on ice. Non-reacted antibody was washed out with HBSS, and then the cells were reacted with anti-FITC antibody-coupled magnetic beads (Miltenyi Biotec) for 10 min. After rinsing twice, B-cells were separated using a LS+MACS separation column (Myltenyi Biotec).

tag: strain

value: Spleen


title: mU50_null_splenoB

description: Gene expression data from three mice

source_name: Splenic B-cells from DmU50(HG-b) mice


title: NUID-0000-0100-9131

status: Public on Mar 25 2013

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

description: 91 day, Treated

hyb_protocol: The arrays were washed and stained with the GeneChipÂ® Hybridization Wash and Stain kit (Affymetrix). The washing and staining steps were performed with GeneChipÂ® Fluidics Workstation 450 (Affymetrix).

scan_protocol: Arrays were scanned using a solid-state laser scanner (GeneArrayÂ® Scanner 3000 combined with the GeneChipÂ® autoloader, Affymetrix).

data_processing: The Affymetrix GeneChipÂ® Operating Software (GCOS) was used to generate the primary and secondary raw data files.

source_name: 91 day, Treated

label_protocol: Processing of GeneChipÂ® experiments was conducted as recommended by the manufacturer of the GeneChipÂ® system (Affymetrix). For tissue samples, double stranded cDNA was synthesized with a starting amount of 0.1 Âµg total RNA. For RNA reverse transcription, the GeneChipÂ® 3â€² IVT Express Labelling Assay (lot ID 0904012, Affymetrix) was used in the presence of a T7-(dT)24 DNA oligonucleotide primer (Affymetrix). The cDNA was then transcribed in vitro in the presence of biotinylated ribonucleotides to form biotin-labelled amplified RNA (aRNA). The labelled aRNA was then purified and quantified by UV spectrophotometry at 260 nm and fragmented

growth_protocol: 29-32 days old male B6C3F1/Crl mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divide

extract_protocol: Frozen liver and kidney samples were homogenized in TRIzol reagent (Invitrogen) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen) according to the manufacturer's instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer. RNA was stored at âˆ’80Â°C until GeneChipÂ® experiment analysis.

treatment_protocol: Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days

value: B6C3F1/Crl (C57BL/6 male x C3H/He female)

value: whole liver extract

tag: treatment

value: Phenobarbital

tag: duration

value: 91 days


title: NUID-0000-0100-9085

description: 28 day, Control

source_name: 28 day, Control

tag: tissue

value: Control

value: 28 days


title: NUID-0000-0100-9132

description: 91 day, Treated


title: NUID-0000-0100-9093

description: 91 day, Control

source_name: 91 day, Control


title: NUID-0000-0100-9083

description: 28 day, Control


title: NUID-0000-0100-9135

description: 91 day, Treated


title: NUID-0000-0100-9094

description: 91 day, Control


title: NUID-0000-0100-9133

description: 91 day, Treated


title: NUID-0000-0100-9096

description: 91 day, Control


title: NUID-0000-0100-9084

description: 28 day, Control


title: NUID-0000-0102-2344

description: 28 day, Control


title: NUID-0000-0100-9121

description: 28 day, Treated

source_name: 28 day, Treated


title: NUID-0000-0100-9110

description: 07 day, Treated

source_name: 07 day, Treated

value: 7 days


title: NUID-0000-0100-9120

description: 28 day, Treated


title: NUID-0000-0100-9119

description: 28 day, Treated


title: NUID-0000-0100-9124

description: 28 day, Treated


title: NUID-0000-0100-9130

description: 91 day, Treated


title: NUID-0000-0100-9081

description: 28 day, Control


title: NUID-0000-0100-9113

description: 07 day, Treated


title: NUID-0000-0100-9108

description: 07 day, Treated


title: NUID-0000-0100-9109

description: 07 day, Treated


title: NUID-0000-0100-9095

description: 91 day, Control


title: NUID-0000-0100-9122

description: 28 day, Treated


title: Zebrafish cardiac tissue 21-23 hpf Bmp2b overexpression sample 2

city: Berlin

first: Salim

last: Seyfried

address: Robert-Rössle Str. 10

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description: 25916110322 subarray 1_3

hyb_protocol: 1.5 µg of labeled cRNA were hybridized to Zebrafish (V2) Gene Expression Microarrays (G2519F-019161, 4x44K)

scan_protocol: Spot intensities were recorded on a G2565BA scanner (Agilent Technologies)

data_processing: Scanned images were analyzed after all the Feature Extraction processing steps were completed. In the case of one color, Processsed Signal contains the Multiplicatively Detrended Background Subtracted Signal if the detrending is selected and helps. If the detrending does not help, this column will contain the Background Subtracted Signal.

organism: Danio rerio

source_name: cardiac tissue, pooled from embryo extractions 23 hpf, Bmp2b overexpression

label_protocol: For each sample, 200ng of intact (RIN > 8) total RNA was subjected to a single amplification step and Cy3 labeling reaction.

extract_protocol: Whole hearts were extracted manually from 21-23 hpf embryos as described in Burns and MacRae, 2006. Total RNA was extracted with RNeasy Micro Kit (Qiagen)

treatment_protocol: Tg(hsp70l:bmp2b)fr13 transgenic and WT embryos were raised to 18hpf and heat-shocked for 30 min at 37C. Embryos were then left to recover until 21-23 hpf.

value: whole heart

tag: genotype/variation

value: Bmp2b overexpression


title: NUID-0000-0100-9075

description: 07 day, Control

source_name: 07 day, Control


title: Neuron-glial, control, biological rep 1

city: La tronche

first: didier

last: wion

address: fortuné ferrini

country: France

institute: INSERM

description: gene expression data from mixed neuron-glial cells treated with Vit D versus not treated

hyb_protocol: After fragmentation, biotinylated cDNA were hybridized for 16h at 45 °C on GeneChip® Mouse Gene 1.0 ST Array. Then arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analysed using RMA algorithm with the Affymetrix software Expression Console Suite.

source_name: Primary culture from embryonic mouse brain

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix protocol from 200 ng total RNA using the Ambion® WT Expression Kit and the GeneChip® WT Terminal kit  Labeling and Hybridization

growth_protocol: Primary cultures of NCSs were established from the brain of E17 mouse embryos. And allow to differentiate in the presence of fetal calf serum to generate a mixed neuron-glial cell culture

extract_protocol: Total RNA were extracted from cells with the MirVana isolation kit (AppliedBiosystems)

treatment_protocol: Cells in serum-free medium without growth factors were treated with 1,25 D at 10-8M or with vehicle as control.

value: brain

tag: cell type

value: primary mixed neuron-glial cells culture

value: Not treated (control)


title: hap5 - replicate 4

status: Public on Mar 24 2013

city: Hsinchu

first: Po-Chen

last: Hsu

address: Room 404, Life Science Building I, No. 101, Section 2, Kuang-Fu Road

department: Institute of Molecular and Cellular Biology

country: Taiwan

institute: National Tsing Hua university

description: Geneexpression after 0.5 h of rapamycin treatemnt

hyb_protocol: Total 0.6 ug Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent C_albicans_21 Oligo 8×15K Microarray (Agilent Technologies) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies). Normalization and expression analysis was performed by using GeneSpring GX 11.5 (Agilent Technologies). Genes considered to be significantly regulated in hap5-null mutant were based on an average expression level change of ≥ 2-fold to wild type (average ratio of four independent replicates) and the p-value less than 0.05.

organism: Candida albicans

source_name: hap5-4 rapa

label_protocol: For cRNA synthesis, 0.2 ug total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies) and labeled with Cy3 (CyDye, Agilent Technologies)

growth_protocol: Cell cultures were grown in YPD medium at 30°C overnight and subsequently diluted into fresh YPD medium to an OD600 = 0.5.

extract_protocol: RNA was extracted by the phenol-chloroform method and genomic DNA was removed by TURBO DNase (Ambion, Inc.). Purified RNA was quantified at OD260 using a ND-1000 spectrophotometer (Nanodrop Technology) and qualitated using Bioanalyzer 2100 (Agilent Technology) with RNA 6000 nano labchip kit (Agilent Technologies).

treatment_protocol: After 4.5 h of incubation, cultures were treated with 0.2 ug/ml rapamycin for 0.5 h.

value: 0.2 ug/ml rapamycin for 0.5 h


title: Neuron-glial, control, biological rep 2


title: pDC_ctrl_sample1

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

institute: Renji Hospital, JiaoTong University School of Medicine

description:
human pDC sti ctrl-sample1
the purity of cell >95%

data_processing: SDS 2.3 software (Applied Biosystems) was used to analyze the qRT–PCR data. RNU48 was used for internal normalization because it showed the most consistent expression in our cohort. The relative quantification method, –DCt, was used to calculate miRNA expression relative to that of RNU48. The fold induction for each miRNA sample was calculated using the formula: log2 transformed fold induction =–(DCt stimulated PDC – DCt control PDC).

label: FAM

source_name: human primary pDC isolated from PBMCs

label_protocol: Samples for the TaqMan® Human MicroRNA Arrays (Applied Biosystems, Foster City, CA, USA) were reverse transcribed using Megaplex RT Primers and the TaqMan® MicroRNA Reverse Transcription Kit. The cDNAs were produced in preamplification reactions for 12 cycles using the Megaplex PreAmp Primers and TaqMan® PreAmp Master Mix. We then detected the miRNA expression by real-time polymerase chain reactions (PCRs) with the TaqMan® Universal PCR Master Mix (No AmpErase UNG) and TaqMan® MicroRNA Array. For more detailed protocols, see the website: https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=605479.

extract_protocol: Total RNA was isolated with the mirVana™ miRNA Isolation Kit (Ambion, Texas, USA). The extraction protocol is available in the website: http://www.ambion.com/catalog/CatNum.php?AM1560.

treatment_protocol: We obtained fresh peripheral blood mononuclear cells (PBMCs) from healthy individuals. We isolated PDCs by magnetic-activated cell sorting using the Human Diamond Plasmacytoid Dendritic Cell Isolation Kit (Miltenyi-Biotec, Auburn, CA). The purity of the isolated PDCs was > 95% determined by flow cytometry (FCM). The studies were approved by the Ethics Committee of Renji Hospital. The isolation protocol is available in the website: http://www.miltenyibiotec.com/en/PG_297_566_Diamond_Plasmacytoid_Dendritic_Cell_Isolation_Kit.aspx.  The pDCs were stimulated with 10ug/ml R837 (Invivogen, San Diego, CA, USA) for 4 hours.

value: pDC

tag: agent

value: control


title: NUID-0000-0100-9072

description: 07 day, Control


title: pDC_ctrl_sample2

description:
human pDC sti ctrl-sample2
the purity of cell >95%


title: pDC_sti_sample1

description:
human pDC sti-sample1
the purity of cell >95%

source_name: human primary pDC isolated from PBMCs, stimulated


title: NUID-0000-0100-9100

description: 01 day, Treated

source_name: 01 day, Treated

value: 1 day


title: NUID-0000-0100-9099

description: 01 day, Treated


title: NUID-0000-0100-9097

description: 01 day, Treated


title: NUID-0000-0100-9074

description: 07 day, Control


title: hap5 - replicate 3

source_name: hap5-3 rapa


title: Neuron-glial 1,25(OH)2D3 treated, biological rep 2

value: Vit D treated


title: Zebrafish cardiac tissue 21-23 hpf Bmp2b overexpression sample 1

description: 25916110322 subarray 1_1


title: NUID-0000-0100-9098

description: 01 day, Treated

value: B6C3F1/Crl (C57BL/6 male x C3H/He female)


title: NUID-0000-0100-9101

description: 01 day, Control

source_name: 01 day, Control

value: whole liver extract


title: Neuron-glial 1,25(OH)2D3 treated, biological rep 3


title: Zebrafish cardiac tissue 21-23 hpf WT sample 2

description: 251916110258 subarray 1_3

source_name: cardiac tissue, pooled from embryo extractions 23 hpf, WT

value: wild type


title: NUID-0000-0100-9073

description: 07 day, Control


title: NUID-0000-0100-9071

description: 07 day, Control


title: pDC_sti_sample2

description:
human pDC sti-sample2
the purity of cell >95%


title: Zebrafish cardiac tissue 21-23 hpf WT sample 1

description: 251916110257 subarray 1_2


title: NUID-0000-0100-9111

description: 07 day, Treated

value: Phenobarbital


title: NUID-0000-0100-9069

description: 01 day, Control

value: Control


title: NUID-0000-0100-9112

description: 01 day, Control


title: Neuron-glial, control, biological rep 3


title: Neuron-glial 1,25(OH)2D3 treated, biological rep 1


title: NUID-0000-0100-9092

description: 91 day, Control

value: 91 days


title: NUID-0000-0100-9090

description: 01 day, Control


title: NUID-0000-0100-9102

description: 01 day, Treated


title: hap5 - replicate 2

source_name: hap5-2 rapa


title: Wild type - replicate 4

source_name: WT-4 rapa


title: hap5 - replicate 1

source_name: hap5-1 rapa


title: Wild type - replicate 1

source_name: WT-1 rapa


title: Wild type - replicate 2

source_name: WT-2 rapa


title: MockCy3.subarray4

status: Public on Mar 23 2013

city: Helsinki

first: Tuuli

last: Haikonen

address: Latokartanonkaari 7

department: Department of Agricultural Sciences

country: Finland

institute: University of Helsinki

hyb_protocol: Labeled samples were combined pairwise, fragmented and hybridised to subarrays of tobacco 4x44K 60mer oligo array (Agilent, design ID 021113) according to instructions of Gene expression hybridisation kit (Agilent). During hybridisation, the array was rotated at 10rpm at +65C for 17h. Slide was washed with Gene expression wash buffers 1 and 2 (Agilent) with triton-X102 added.

scan_protocol: The signals were scanned using GenePix 4200 AL microarray scanner and image analysis was done using GenePixPro 6.1 software (both Molecular devices (Axon), Sunnyvale, CA).

data_processing: Fluorescence intensities were normalized using quantile normalization function. Differences in log-intensities were tested with moderated t-test and the resulting p-values were transferred to FDR-values using limma R/Bioconductor package (Smyth, 2004). To annotate the probe targets, probe sequences were blasted against tobacco unigene database (SOL genomics network, http://solgenomics.net/) using BLAST+ command-line applications (National Institutes of Health). The log2 mutant/wt data and additional annotations for all of the Samples combined are linked on the Series record.

organism: Nicotiana tabacum

source_name: Mock Cy3.subarray4

label_protocol: 20μg of the amino-allyl-UTP RNA were labelled with Cy3 or Cy5 (GE Healthcare), and purified (Amino allyl MessageAmp kit, Life Technologies). Incorporation of dyes to samples were assessed with Nanodrop. 825μg of each labeled RNA was used in hybridisation.

growth_protocol: Nicotiana tabacum cv. Samsun nn were grown from seeds and planted in soil prepared by mixing peat (Kekkilä Horticulture Peat, Kekkilä Oyj, Finland) and washed sand at 5:1 ratio (v/v) . Plants were grown in growth rooms (photoperiod 16 h, temperature 18/22°C, relative humidity 70%; light intensity 200 μE m–2s–1; or temperature 20/24°C, relative humidity 40%, light intensity 250 μE m–2s–1), with. fertilizer (N:P:K = 16:9:22, Yara, Espoo, Finland) mixed in water (0.3g/l) and given in every watering.

extract_protocol: Leaf samples were ground with mortal and pestle in liquid nitrogen. RNA was extracted using home-made Trizol (Caldo et al., 2004, Plant Cell 16, 2514–2528) and purifed with LiCl precipitation. Equal amounts of RNA from 6 plants were pooled and further purified with Rneasy plant mini kit (Qiagen, Hilden, Germany) and quality of total RNA was assessed with Bioanalyzer (Agilent). mRNA was captured with oligo(dT)-primers, first and second strands of cDNA synthesized and resulting cDNA transcribed to antisense RNA to incorporate amino allyl-dUTP using Amino allyl MessageAmp kit (Life Technologies, Carlsbad, California). The quality of the resulting RNA was analysed with Bioanalyzer prior to labeling.

treatment_protocol: Tobacco plants were sap-inoculated with sap from healthy, mutPVA or wtPVA-infected N. benthamiana leaves. Samples were collected at 12 days post inoculation from the first systemically infected leaves and frozen in liquid nitrogen.

tag: variety

value: Samsun nn

value: leaf

value: mock-inoculation


title: WTCy3.subarray3

source_name: WT Cy3.subarray3

value: wild type PVA


title: MutCy5.subarray4

value: mutated PVA


title: WTCy5.subarray1


title: MutCy3.subarray2

source_name: Mut Cy3.subarray2


title: FrII_Leukemic_K\L_mice_1

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description: CD45.1−CD45.2+Lin*–Sca-1-Mac1lo/+c-Kit+ cells from K/L leukemic mouse 1

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

data_processing: The data were analyzed using RMA in the bioconducter and normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 8.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All mice were kept in a sterile barrier facility approved by the Beth Israel Deaconess Medical Center Institutional Animal Care and Use Committee.

extract_protocol:
Cells using the markers (CD45.1−CD45.2+Lin*–Sca-1-Mac1lo/+c-Kit+) were collected after sorting and placed on ice in the Trizol solution (GibcoBRL).
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: blood

value: K/L leukemic

tag: age

value: 2-4 months


title: FrII_Leukemic_K\L_mice_3

description: CD45.1−CD45.2+Lin*–Sca-1-Mac1lo/+c-Kit+ cells from K/L leukemic mouse 3


title: MutCy3.subarray1

source_name: Mut Cy3.subarray1


title: MockCy5.subarray3


title: FrII_Leukemic_Sox4_mice_1

description: CD45.1−CD45.2+Lin*–Sca-1-Mac1lo/+c-Kit+ cells from Sox4 overexpressing leukemic mouse 1

value: Sox4 overexpressing leukemic


title: KYSE140 CD90-

city: Hong Kong

first: Stephanie

last: Ma

address: Rm 47, 1/F, Lab Block, Faculty of Medicine Bldg, 21 Sassoon Rd, Pok Fu Lam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: Gene expression.

hyb_protocol: Service by The University of Hong Kong (HKU) Genome Research Centre (protocol attached to the Series).

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling as the normalization method.

source_name: CD90- ESCC

growth_protocol: CD90+ and CD90- cells were sorted from KYSE-140 ESCC cells using the flow cytometry cell sorting technique.

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

tag: cell line

value: esophageal squamous carcinoma cell (ESCC)

tag: cell population


title: empty

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

institute: Tokyo Medical University

description: pcDNA3.1(-) (Life technologies, Tokyo, Japan).

hyb_protocol: Labeled RNA was hybridized to microarray at 60 degrees C for 17hr and washed with miRCURY microarray labeling kit (Exiqon) according to the manufacturer protocol.

scan_protocol: Hybridization signals were detected with a DNA microarray scanner G2505B (Agilent Technologies).

data_processing: The scanned images were analyzed  by using Agilent feature extraction software (v9.1.3.1).

source_name: mouse embryonic fibroblast

label_protocol: Total RNA (2 µg) was labeled with miRCURY microarray labeling kit (Exiqon) according to the manufacturer protocol.

growth_protocol: NIH3T3 cells were cultivated in D-MEM (Life technologies) supplemented with 10% fetal calf serum (Gibco BRL, Rockville, MD).

extract_protocol: Total RNA was extracted with ISOGEN (NIPPONGENE) following the manufacture's protocol.

treatment_protocol: NIH3T3 (2.2×105) cells were seeded in 6 cm plates.  16 hours later, they were transfected by 5 μg of DNA (TLS/CHOP type 2 vector and control vector) according to the FuGENER HD Transfection protocol (Qiagen, Tokyo, Japan).

value: mouse embryonic fibroblast

tag: transfection

value: empty vector


title: FrII_Leukemic_Sox4_mice_2

description: CD45.1−CD45.2+Lin*–Sca-1-Mac1lo/+c-Kit+ cells from Sox4 overexpressing leukemic mouse 2

tag: genotype


title: TLS-CHOP

description: Polymerase chain reaction (PCR) fragments containing the full-length coding regions of TLS-CHOP type2 were cloned into a BamH1/Hind III restriction sites of pcDNA3.1(-) (Life technologies, Tokyo, Japan).

value: TLS-CHOP


title: WTCy5.subarray2


title: FrII_Leukemic_Sox4_mice_3

description: CD45.1−CD45.2+Lin*–Sca-1-Mac1lo/+c-Kit+ cells from Sox4 overexpressing leukemic mouse 3


title: SCC12 only rep2

city: London

first: Hemant

last: Kocher

address: Charterhouse Square

institute: Barts and the London

description:
SCC only 2
gene expression data from replicate 2

hyb_protocol: Protocol EukGE-WS2v4_450

scan_protocol: Scanner ID 50102480, Scanner Type M10

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. We then log2 transformed the scaled data for the following differential expression analysis.

source_name: SCC12 only

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: SCC12 cells were seeded ontop of organotypic gels with HN-CAF (head and neck carcinoma associated fibroblasts). Differential gene expression was analysed between cancer cells not exposed to CAFs or non-invading cancer cells exposed to CAFs.

extract_protocol: Qiagen RNA micro kit

treatment_protocol: Affymetix amplification patterson instiute method)

value: Human squamous cell carcinoma cells


title: FrII_Leukemic_K\L_mice_2

description: CD45.1−CD45.2+Lin*–Sca-1-Mac1lo/+c-Kit+ cells from K/L leukemic mouse 2


title: KYSE140 CD90+

description: Gene expression.

scan_protocol: Service by The University of Hong Kong (HKU) Genome Research Centre (protocol attached to the Series).

source_name: CD90+ ESCC


title: Cancer cell only rep2

description:
c2
Replicate 2

hyb_protocol: Standard illumina hybridisation protocol

scan_protocol: Standard illumina illumina scanning protocol

data_processing: Quality Control and normalization were performed using BeadStudio (Genome Studio expression analysis module, Genome Studio v2011.1, Gene expression module 1.9.0). Statistical analyses were performed using Bioconductor (www.bioconductor.org) packages within the open source R statistical environment (www.r-project.org)

source_name: Capan1 only

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

growth_protocol: Pancreatic stellate cells were embedded within a gel matrix composing collagen type I and Matrigel, and cancer cells were seeded on top. The gel was lifted on to metal grid after 24 hourd and fed from below. Gels were harvested on day 10 and frozen sections obtained. The cancer cell layer on top of the gel was captured by laser microdissection for RNA extraction.

extract_protocol: RNA was extracted from laser captured Capan1 cells by using RNaqeous micro kit according to manufacturer's instruction

value: Well differentiated human pancreatic cancer cells

tag: exposed to

value: pancreatic stellate cell line (PS1)


title: Wild type - replicate 3

source_name: WT-3 rapa

value: 0.2 ug/ml rapamycin for 0.5 h


title: Capan1 exposed to stellate cell rep3

description:
c/ps 3
Replicate 3

source_name: Capan1 exposed to PS1


title: SCC12 only rep1

description:
SCC only 1
gene expression data from replicate 1


title: Cancer cell only rep1

description:
c1
Replicate 1


title: Capan1 exposed to stellate cell rep1

description:
c/ps 1
Replicate 1


title: 2645-486

description: The myxoid liposarcoma-derived cell lines, called 2645/94, were kindly provided from Prof. David Ron (University of Cambridge Institute of Metabolic Science, Cambridge, UK).

hyb_protocol: Labeled RNA was hybridized to Human Whole Genome Microarray kit (Agilent) at 65 degrees C for 24hr rotating at 10 rpm and washed with Gene Expression Hybridization Kit (Agilent) according to the manufacturer protocol (Version 5.7).

scan_protocol: Hybridization signals were detected with a DNA microarray scanner G2505A (Agilent Technologies).

data_processing: The scanned images were analyzed  by using Agilent feature extraction software (v9.5.1.1).

source_name: myxoid liposarcoma cell-line

label_protocol: Total RNA (0.5 µg) was labeled and hybridized by using Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer protocol (Version 5.7).

growth_protocol: The myxoid liposarcoma-derived cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma, St. Louis, MO) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted from liposarcoma cell-line with ISOGEN (NIPPONGENE) following the manufacture's protocol.

treatment_protocol: For miRNA trasnfection, myxoid liposarcoma-derived cells were trasnfected with 250 nM in DMEM without serum using Oligofectamine Reagent (Invitrogen Japan, Tokyo, Japan) and Opti-MEM I (Invitrogen Japan).

value: myxoid liposarcoma cell-line

value: Randamized sequence oligo


title: Capan1 exposed to stellate cell rep2

description:
c/ps 2
Replicate 2


title: SCC12 exposed to CAFs rep1

description:
SCC_CAF 1
gene expression data from replicate 1

source_name: Non-invaded SCC12 cells exposed to CAFs

value: HN-CAF (head and neck carcinoma associated fibroblasts)


title: 2645-Nega

value: miR-486 oligonucleotides


title: FrII_Wildtype_BL6_mice_2

description: Lin*–Sca-1-Mac1lo/+c-Kit+ cells from wild type C57/BL6 mouse 2

source_name: Lin*–Sca-1-Mac1lo/+c-Kit+ (FrII) cells

value: wildtype


title: P0 SCG from Egr3-/-; Bax-/- mouse sample 2

status: Public on Mar 22 2013

last: Quach

state: Illinois

address: 303 E. Chicago Ave.

description:
Replicate 2
SAMPLE 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol (Illumina iScan)

data_processing: The data was processed by subtracting background noise and normalizing with an average normalization parameter using the Gene Expression Module (v.3.2.6)/Illumina BeadStudio software (v.3.1).

label: Biotin

source_name: P0 SCG_Egr3-/-

label_protocol: Biotinylated cRNA was prepared with the TotalPrep RNA Amplification kit.

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen), followed by column purification using the QIAGEN RNeasy mini kit. Integrity of RNA samples was verified using the Agilent 2100 Bioanalyzer.

tag: strain background

value: mixed background of C57BL/6 and 129/SvJ

value: superior cervical ganglion (SCG)


title: P0 SCG from Egr3+/+; Bax-/- mouse sample 2

description:
Replicate 2
SAMPLE 5

source_name: P0 SCG_Egr3+/+


title: P0 SCG from Egr3+/+; Bax-/- mouse sample 3

description:
Replicate 3
SAMPLE 6


title: FrII_Wildtype_BL6_mice_3

description: Lin*–Sca-1-Mac1lo/+c-Kit+ cells from wild type C57/BL6 mouse 3

value: blood

value: 2-4 months


title: SCC12 exposed to CAFs rep2

description:
SCC_CAF 2
gene expression data from replicate 2


title: P0 SCG from Egr3+/+; Bax-/- mouse sample 1

description:
Replicate 1
SAMPLE 4


title: P0 SCG from Egr3-/-; Bax-/- mouse sample 3

description:
Replicate 3
SAMPLE 3


title: Cancer cell only rep3

description:
c3
Replicate 3


title: P0 SCG from Egr3-/-; Bax-/- mouse sample 1

description:
Replicate 1
SAMPLE 1


title: Expt. tMCAO cortex Replicate 4

city: West Point

first: I-Ming

state: PA

address: 770 Sumneytown Pike

department: Genetics and Pharmacogenomics

institute: Merck Research Lab

description: Biological replicate 4 of 4 tMCAO cortex

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: Control sham-operated cortex Pool

label_protocol: 100 ng-input two-round RT/IVT RNA amplification protocol

growth_protocol: Brain tissues were collected from 4 transient middle cerebral artery occlusion (tMCAO) rats and 4 controls at 24 hr.  Selection of optimal time points was primarily based upon the time course of infarct formation (histological data). Brain tissue of 4 mm thick ipsilateral brain section (dissected into cortex and striatum) were collected but only cortex samples were used for expression profiling.

extract_protocol: Total RNA was extracted from brain cortex using Qiagen RNeasy Midi kit as described by the manufacturer. Samples were treated with DNaseI on-column (Qiagen) for 30 minutes. RNA concentration was measured using a NanoDrop ND-1000 and RNA integrity was determined with a 2100 Bioanalyzer.

value: sham

value: Brain - cortex

value: Sprague Dawley

value: middle cerebral artery occlusion


title: FrII_Wildtype_BL6_mice_1

description: Lin*–Sca-1-Mac1lo/+c-Kit+ cells from wild type C57/BL6 mouse 1


title: Expt. tMCAO cortex Replicate 2

description: Biological replicate 2 of 4 tMCAO cortex


title: Expt. tMCAO cortex Replicate 1

description: Biological replicate 1 of 4 tMCAO cortex


title: TCDC pH 4 treated Epithelium 01

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description: RNA pooled from patients 1,2 and 3

hyb_protocol: hybridized to GeneChip Human Exon 1.0 ST Arrays, washed and stained using the Affymetrix GeneChip Hybridization, Wash and Stain Kit and an Affymetrix Fluidics Station 450

scan_protocol: scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols

data_processing: Expression Console (Affymetrix) was used to normalise the data using the RMA defaults for core transcripts only.

source_name: cultured 3D oesophageal epithelium

label_protocol: The Ambion WT Expression Kit was used to amplify the RNA and convert it to cDNA.  The cDNA was then fragmented and biotin-labelled using the Affymetrix GeneChip WT Terminal Labelling Kit

growth_protocol: Monolayers of fibroblasts were then grown in T75 flasks with 20mL of Ham’s F-10 Media (Gibco) with 10% Fetal Calf serum (Biosera), 1% Penicillin-streptomycin antibiotic solution, 0.25% Holo-transferrin (Sigma) and 2.5 ng epidermal growth factor (Sigma).

extract_protocol: RNA was extracted from the fibroblasts using the Qiagen RNeasy Mini Kit (Qiagen).

tag: patient group

value: TCDC pH 4 treated


title: Control sham-operated cortex Replicate 2

description: Biological replicate 2 of 4 sham-operated cortex


title: Control sham-operated cortex Replicate 3

description: Biological replicate 3 of 4 sham-operated cortex


title: Control sham-operated cortex Replicate 1

description: Biological replicate 1 of 4 sham-operated cortex


title: Control Epithelium  01

description: RNA pooled from patients 1,2 and 3

value: control


title: TCDC treated Epithelium 01

description: RNA pooled from patients 1,2 and 3

value: TCDC treated


title: Control sham-operated cortex Replicate 4

description: Biological replicate 4 of 4 sham-operated cortex


title: TCDC pH 4 treated Epithelium 02

description: RNA pooled from patients 1,2 and 3


title: Control Epithelium  02

description: RNA pooled from patients 1,2 and 3


title: TCDC treated Epithelium 02

description: RNA pooled from patients 1,2 and 3


title: Flagellin-treated mouse rep7

city: Lille

first: Jean-Claude

last: SIRARD

address: 1 rue du Pr Calmette

department: Centre d'Infection et d'Immunité de Lille

institute: Institut Pasteur de Lille

description: gene expression data from lung of mouse treated 1h with flagellin

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner.

data_processing: The data were analyzed with GCOS (Affymetrix GeneChip Operating System). We treated data in R using rma function from Affy package.

source_name: mouse lung treated 1h with flagellin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: mice were sacrified and lungs sampled. Lungs were directly put on 2ml of RA1+0.01% beta-mercaptoethanol and homogenized using a polytron.

value: lung

value: 1h with flagellin


title: pH 4 treated Epithelium 01

description: RNA pooled from patients 1,2 and 3

value: pH 4 treated


title: Expt. tMCAO cortex Replicate 3

last: Wang

description: Biological replicate 3 of 4 tMCAO cortex


title: Flagellin-treated mouse rep3


title: Flagellin-treated mouse rep2


title: Flagellin-treated mouse rep6


title: PBS-treated mouse rep7

description: gene expression data from lung of mouse treated 1h with PBS

source_name: mouse lung treated 1h with PBS

value: 1h with PBS


title: Flagellin-treated mouse rep4


title: PBS-treated mouse rep6


title: Flagellin-treated mouse rep1


title: PBS-treated mouse rep5


title: PBS-treated mouse rep4


title: Hcrt_ub2

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

description: Total tissue RNA (unbound) from Replicate 2

hyb_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform

data_processing: GCRMA normalization within biological replicate groups.  Performed with R / Bioconductor.

label_protocol: Affymetrix two cycle amplification kit, starting with 20 ng of total RNA.

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice(see PMID:19013282), followed by Trizol extraction, DNAse treatment, and RNeasy-Minelute Cleanup

value: Dissected diencephalon(Thalamus and Hypothalamus)

value: adult(6-12 weeks)

tag: line

value: Hcrt JD218

value: mixed Fvb and c57/bl6j

tag: rna type

value: unbound(total)

tag: Sex

value: both

tag: number of mice


title: pH 4 treated Epithelium 02

description: RNA pooled from patients 1,2 and 3


title: NLP7:GFP_+N_II vs NLP7:GFP_no_N_II

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

description: ChIP-chip analysis of NLP7 targets

hyb_protocol: Co-hybridization was performed using the NimbleGen 3x720K array design and following manufacturer’s instructions

scan_protocol: Data acquisition was performed according to Roche Nimblegen instructions.

data_processing: Hybridization data were normalized using an ANOVA model to remove technical biases. Data were averaged on the dye-swap to remove tile-specific dye biases. Normalized data were analysed under stringent criteria using Parsimonious Higher-Order Hidden Markov Models (www.jstacs.de/index.php/PHHMM). Adjacent tiles are joined into domains by requiring a minimal run of 400 bp and allowing a maximal gap of 200 bp.

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, DNA recovered after MeDIP and directly from input chromatin was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit following instructions of the manufacturer.

growth_protocol: Seedlings were grown for 10 days on a 3 mM KNO3 liquid medium (3 mM KNO3, 1 mM KH2PO4/K2HPO4, pH 5.8, 0.5 mM CaSO4, 0.5 mM MgCl2, 3 mM MES, pH 5.8, 0.25% (w/v) Sucrose, supplemented with microelements) in long-day photoperiod (16/8h at 250°C/18°C). Plants were then nitrogen-starved for three days by changing the culture medium with a nitrogen free medium in which KNO3 was replaced by KCl. A 10 min-nitrate induction was performed by changing the culture medium for the 3 mM nitrate solution (+N). For the control samples (-N), the nitrogen-free solution was changed for a fresh one.

extract_protocol: Chromatin Immunoprecipitation was performed essentially as described in Gendrel et al. (Nature Methods 2005 vol.2, 213-218) using 3.5 ul of anti-GFP antibody and Dynabeads coupled with Protein A and G (Invitrogen).

treatment_protocol: no treatment

tag: ecotype

value: 13 days

tag: developmental stage

value: whole seedlings

tag: antibody

value: anti-GFP antibody

tag: vendor

value: Ab290, AbCam


title: Hcrt_ip4

description: Trap'd Hypocretin neuron RNA, biological replicate 4

scan_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform

tag: tissue

tag: strain

value: immunoprecipitate(IP)


title: PBS-treated mouse rep2

tag: treatment


title: PBS-treated mouse rep1


title: Hcrt_ub3

description: Total tissue RNA (unbound) from Replicate 3

tag: age


title: Hcrt_ip3

description: Trap'd Hypocretin neuron RNA, biological replicate 3


title: Dox-treated lung Replicate 2

description: Dox-treated lung replicate 2

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45?C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

source_name: Diseased

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

growth_protocol: Lungs were harvested from water- or Dox-treated mice after 7 days at ~12-week of age. IL-1b is induced in Dox-treated mice which showed increased inflammation and emphysema in lung.

extract_protocol: Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

value: Lung

value: BALB/c

tag: transgene

value: doxycyline


title: NLP7:GFP_+N_I vs NLP7:GFP_no_N_I

description: ChIP-chip analysis of NLP7 targets

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, DNA recovered after ChIP was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit following instructions of the manufacturer.

label_protocol: Cy3 and Cy5 labeling were performed using the Nimblegen Dual color DNA labeling kit (Roche NimbleGen) according to manufacturer’s instructions, amplification=yes, DNA recovered after MeDIP and directly from input DNA was amplified using the Sigma GenomePlex Complete Whole Genome Amplification (WGA) Kit following instructions of the manufacturer.

growth_protocol: Seedlings were grown for 10 days on a 3mM KNO3 liquid medium (3 mM KNO3, 1 mM KH2PO4/K2HPO4, pH 5.8, 0.5 mM CaSO4, 0.5 mM MgCl2, 3 mM MES, pH 5.8, 0.25% (w/v) Sucrose, supplemented with microelements) in long-day photoperiod (16/8h at 250°C/18°C). Plants were then nitrogen-starved for three days by changing the culture medium with a nitrogen free medium in which KNO3 was replaced by KCl. A 10 min-nitrate induction was performed by changing the culture medium for the 3 mM nitrate solution (+N). For the control samples (-N), the nitrogen-free solution was changed for a fresh one.


title: Dox-treated lung Replicate 3

description: Dox-treated lung replicate 3


title: PBS-treated mouse rep3

tag: genotype

value: lung


title: Hcrt_ip1

description: Trap'd Hypocretin neuron RNA, biological replicate 1


title: Hcrt_ip2

description: Trap'd Hypocretin neuron RNA, biological replicate 2


title: NLP7:GFP_no_N_I vs NLP7:GFP_+N_I

description: ChIP-chip analysis of NLP7 targets


title: Control water-treated lung Replicate 3

description: Control Water-treated lung Replicate 3

source_name: Control

value: control


title: Dox-treated lung Replicate 5

description: Dox-treated lung replicate 5


title: Dox-treated lung Replicate 4

description: Dox-treated lung replicate 4


title: Hcrt_ub1

description: Total tissue RNA (unbound) from Replicate 1


title: Dox-treated lung Replicate 1

description: Dox-treated lung replicate 1


title: Control water-treated lung Replicate 2

description: Control Water-treated lung Replicate 2


title: NLP7:GFP_no_N_II vs NLP7:GFP_+N_II

description: ChIP-chip analysis of NLP7 targets


title: Control water-treated lung Replicate 1

description: Control Water-treated lung Replicate 1


title: Hcrt_ub4

description: Total tissue RNA (unbound) from Replicate 4


title: smNPC_(hESC)_P20

city: Münster

first: Peter

last: Reinhardt

address: Von-Esmarch-Straße 54

institute: Max Planck Institute for Molecular Biomedicine

hyb_protocol: According to manufacturer's instructions. Hybridization time: 18h

scan_protocol: Illumina iScan system using default settings

data_processing: Cubic Spline normalization with background subtraction in Illumina GenomeStudio. Signal intensities below 10 were arbitrarily trimmed to the value of 10.

source_name: small molecule Neural Precursor Cells, passage 20; derived from HuES6 hESC

label_protocol: Ambion TotalPrep RNA Amplification Kit. RNA in put: 400ng, IVT: 12h

growth_protocol: human pluripotent stem cells were grown on MEF feeder layers in hES medium supplemented with 5ng/ml FGF2. smNPCs were grown on matrigel-coated dishes in N2B27 medium supplemented with 3µM CHIR99021 and 0.5 µM purmorphamine.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion

tag: cell type

value: small molecule Neural Precursor Cells


title: MCF7-PremiR-30a 2

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw miRNA and transcriptome data were background subtracted, normalized, and further analysed by BRB-Array Tools Version 3.8.1.

label_protocol: Standard Illumina labeling protocol

growth_protocol: Breast cancer cell lines (American Type Culture Collection) were grown in standard (10% fetal calf serum, 1% penicillin/streptomycin, 1% sodium pyruvate and 1% glutamine) medium. Supernatant from confluent cells was centrifuged and plated in mammosphere conditions, as previously described (Hernandez-Vargas et al., 2011).

extract_protocol: Total RNA was extracted using TRIzol (Sigma) according to the manufacturer’s instructions.

treatment_protocol: Pre-miR mature microRNA (Pre-miR-30a) sequence (Applied Biosystems) and knock-down (miR-30 family-KD) locked nucleic acid (LNA) (Exiqon) were used for overexpression and inhibition of miR-30a, respectively. miR-159 LNA was used as negative control.

tag: cell line

value: breast cancer


title: hiPSC1

source_name: human induced pluripotent stem cell line iPSC1 at passage 15

growth_protocol: human pluripotent stem cells were grown on MEF feeder layers in hES medium supplemented with 5ng/ml FGF2. pNESCs were grown on matrigel-coated dishes in N2B27 medium supplemented with 3µM CHIR99021 and 0.5 µM purmorphamine.

value: human induced pluripotent stem cells


title: MCF7-miR-30a KD 1

source_name: MCF7-miR-30a KD


title: MCF7-miR-159 3


title: MCF7-PremiR-30a 1


title: Flagellin-treated mouse rep5

value: 1h with flagellin


title: MCF7-miR-30a KD 2


title: hESC_HuES6

source_name: human embryonic stem cell line HuES6 at passage 33

value: human embryonic stem cells


title: MCF7-miR-159 1


title: MCF7-miR-159 4


title: MCF7-miR-159 2


title: Human astrocyte primary culture

city: Kyoto

first: Haruhisa

last: Inoue

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: We used GeneChip® Scanner 3000 7Gt, according to the manufacturer's instructions.

data_processing: Data were analyzed by default analysis settings and global scaling as normalization method of GeneSpring GX7.3.1 software (Agilent)

source_name: Human astrocyte primary culture

label_protocol: We used Ovation Pico WTA System/ Encore Biotin Module kit (NuGENE), according to the manufacturer's instructions.

growth_protocol: human iPS cells were differentiated into neural precursors by SFEBq method with Dorsomorphine 2 uM and SB431542 10 uM. Neural precursors were maturated on Matrigel coat dish for additional 32 days. After neural maturation, neural cells were disseminated on gelatin coated dish and cultivated up to 200 days.

extract_protocol: We used Rneasy (Quiagen) total RNA extraction kit, according to the manufacturer's instructions.

treatment_protocol: Differentiated cultivated cells were scraped in PBS, and collected by centrifugation of 200 G, 5 minutes.

value: primary astrocyte


title: MCF7-miR-30a KD 3


title: iPS-derived astrocyte　Day200

description:
gene expression data from iPSC-derived neural cells
iPSdAstrocyte6

source_name: Mature iPSC-derived astrocytes

value: Mature iPSC-derived astrocytes (iPS cells originated from skin fibroblast)


title: iPS-derived astrocyte　Day90

description:
gene expression data from iPSC-derived neural cells
iPSdAstrocyte5

source_name: Inmature  iPSC-derived astrocytes

value: Inmature iPSC-derived astrocytes (iPS cells originated from skin fibroblast)


title: iPS-derived Neuron

description:
gene expression data from iPSC-derived neural cells
iPSdAstrocyte4

source_name: iPSC-derived neuron

value: iPSC-derived neuron (iPS cells originated from skin fibroblast)


title: iPS cells

source_name: Human iPS cells

value: iPS cells (originated from skin fibroblast)


title: iPS-derived Neural stem cell

description:
gene expression data from iPSC-derived neural cells
iPSdAstrocyte3

source_name: iPSC-derived neural stem cells

value: iPSC-derived neural stem cells (iPS cells originated from skin fibroblast)


title: smNPC_(iPSC1)_P20

source_name: small molecule Neural Precursor Cells, passage 20; derived from iPSC line iPSC1


title: iPSdN_APPE693delta_3_APP1E311

description:
gene expression data from iPSC-derived neural cells
AD3

source_name: iPSC-derived neural cells

growth_protocol: human iPS cells were differentiated into neural precursors by SFEBq method with Dorsomorphine 2 uM and SB431542 10 uM. Neural precursors were maturated on Matrigel coat dish for additional 32 days.

treatment_protocol: Differentiated iPSC-derived neural cells were scraped in PBS, and collected by centrifugation of 200 G, 5 minutes.

value: iPSC-derived neural cells (iPS cells originated from skin fibroblast)

tag: genotype/variation

value: APP E693delta


title: iPSdN_APPE693delta_1_APP1E111

description:
gene expression data from iPSC-derived neural cells
AD1


title: iPSdN_APPE693delta_2_APP1E211

description:
gene expression data from iPSC-derived neural cells
AD2


title: Fibroblast

source_name: Human fibroblast

value: skin fibroblast


title: iPSdN_APPWild_1_N116213

description:
gene expression data from iPSC-derived neural cells
control1

value: APP wild-type


title: MCF7-PremiR-30a 3


title: InVivo_KO_3

city: Rechovot

first: Ram

last: Jaschek

address: P.O Box 26

country: Israel

institute: Weizmann Institute of Science

description:
YG174_MoST
Mature megakaryocytes derived from E14.5 fetal liver and cultured with TPO for 7 days.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Microarrays were scanned using GeneChip scanner 3000 7G.

data_processing: Data was normalized using dChip.

source_name: Mature FL-derived megakaryocytes, Runx1 KO

label_protocol: Purified RNA was reverse-transcribed, amplified and labeled with the Affymetrix GeneChip Whole Transcript Sense Target Labeling kit.

growth_protocol: FL cells were derived from E14.5 embryos and cultured in DMEM medium supplemented with 10% FBS (Gibco, US), 2mM L-glutamine and penicillin/streptomycin and TPO (50ng ml-1) at 37ºC and 10% CO2. After 7 days in culture, mature MKs were isolated by two sequential 2%-4% BSA gradients.

extract_protocol: RNA was isolated using EZ-RNA (Biological Industries, Beit Haemek, Israel) according to the manufacturer's instructions.

tag: strain/background

value: Runx1 knockout

value: mature megakaryocytes


title: iPSdN_APPWild_2_N117322

description:
gene expression data from iPSC-derived neural cells
control2


title: InVivo_WT_2

description:
YG160_MoST
Mature megakaryocytes derived from E14.5 fetal liver and cultured with TPO for 7 days.

source_name: Mature FL-derived megakaryocytes, WT

value: WT


title: InVivo_KO_2

description:
YG161_MoST
Mature megakaryocytes derived from E14.5 fetal liver and cultured with TPO for 7 days.


title: InVivo_WT_3

description:
YG173_MoST
Mature megakaryocytes derived from E14.5 fetal liver and cultured with TPO for 7 days.


title: InVivo_KO_1

description:
YG151_MoST
Mature megakaryocytes derived from E14.5 fetal liver and cultured with TPO for 7 days.


title: iPSdN_APPWild_3_409B2

description:
gene expression data from iPSC-derived neural cells
control3


title: irs_HZ_8336_MST1_32415

city: Houston

first: Peng

last: Yu

state: TX

address: 1 Baylor Plaza

institute: BCM

description: biological rep 4

hyb_protocol: An 80 uL hybridization cocktail containing Affymetrix spike-in controls and the fragmented, labeled cDNA was loaded onto the GeneChip® Mouse Gene 1.0 ST array. The arrays were hybridized for 17 hours at 45°C, with rotation at 60 rpm on the GeneChip® Hybridization Oven 640. The arrays were then washed and stained with a Streptavidin, R-phycoerythrin conjugate stain on the GeneChip® Fluidics Station 450. Signal amplification was assessed using biotinylated antistreptavidin.

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000.

data_processing: The images were analyzed and quality control metrics recorded using Affymetrix Expression Console software version 3.0.

source_name: KO

label_protocol: The Baylor College of Medicine Genomic and RNA Profiling Core Facility used the Ambion WT Expression Kit protocol and reagents to convert total RNA into sense-strand cDNA. The cDNA is then fragmented and labeled using the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671)

growth_protocol: mouse hippocampus dissected at either 4 weeks of age or 9 weeks of age

extract_protocol: tissue was idssected over ice and snap frozen in liquid nitrogen. Tissue was homogenized in PureZOL and RNA was purified using an Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio Rad).

value: 9 weeks

value: Hippocampus


title: irs_HZ_8336_MST1_32417

description: biological rep 4

source_name: WT


title: irs_HZ_8291_MST1_32212

description: biological rep 2


title: irs_HZ_8336_MST1_32412

description: biological rep 3


title: irs_HZ_8336_MST1_32413

description: biological rep 4


title: irs_HZ_8336_MST1_32416

description: biological rep 3


title: irs_HZ_8336_MST1_32414

description: biological rep 3


title: irs_HZ_8291_MST1_32210

description: biological rep 2


title: irs_HZ_8336_MST1_32411

description: biological rep 4


title: irs_HZ_8336_MST1_32410

description: biological rep 3


title: irs_HZ_8291_MST1_32211

description: biological rep 1


title: InVivo_WT_1

description:
YG150_MoST
Mature megakaryocytes derived from E14.5 fetal liver and cultured with TPO for 7 days.


title: irs_HZ_8291_MST1_32208

description: biological rep 2


title: irs_HZ_8291_MST1_32207

description: biological rep 1


title: irs_HZ_8291_MST1_32205

description: biological rep 1


title: TGFb-treated, Rep1

city: Louisville

first: Michele

middle: M

last: Kosiewicz

state: KY

address: 319 Abraham Flexner Way, Rm 405

department: Microbiology & Immunology

institute: University of Louisville

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16h at 45 °C to a GeneChip U74Av2 array. The arrays were washed and stained in an Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using a Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data was analyzed using Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Peritoneal Cavity

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Mice were injected intraperitoneally with 2 ml of 3% thioglycolate 4 days before peritoneal exudate cells (PEC) were harvested from the peritoneum.

extract_protocol: Total RNA was extracted following the manufacturer's instructions.

treatment_protocol: PEC were incubated overnight in serum-free media (RPMI 1640, 2 mM glutamine, 10 mM HEPES, 100 U/ml penicillin G sodium, 100 μg/ml streptomycin sulfate and ITS supplement [1 mg/ml iron-free transferrin, 10 ng/ml linoleic acid, 0.3 ng/ml Na2Se, and 0.2 mg/ml Fe(NO3)3; Collaborative Biomedical Products, Bedford, MA] in the presence of porcine TGFb2 (5ng; R&D Systems) or PBS.  Adherent cells were collected (>95% F4/80+) and placed in Trizol.

value: F4/80+ thioglycolate-elicited peritoneal exudate cells

value: BALB/c

value: 6-8 weeks

tag: gender

value: Female


title: irs_HZ_8267_MST1_32125

description: biological rep 4

value: 4 weeks


title: irs_HZ_8267_MST1_32120

description: biological rep 3


title: irs_HZ_8267_MST1_32122

description: biological rep 3


title: irs_HZ_8267_MST1_32124

description: biological rep 3


title: PBS-treated, Rep1

value: PBS


title: PBS-treated, Rep2


title: TGFb-treated, Rep2


title: irs_HZ_8267_MST1_32121

description: biological rep 4


title: irs_HZ_8253_MST1_32055

description: biological rep 1


title: irs_HZ_8267_MST1_32123

description: biological rep 4


title: irs_HZ_8253_MST1_32056

description: biological rep 2


title: PGK12.1 H3K27me3 Day15_genome tiling

city: Seattle

first: Joel

last: Berletch

state: WA

address: 1959 NE Pacific St.

institute: University of Washington

description: NimbleGen genome tiling array 2007-07-27_MM8_TILE_ChIP_10_HX1 was used.

hyb_protocol: Standard NimbleGen protocol

scan_protocol: Standard NimbleGen protocol

data_processing: Standard deviates of bi-weight mean adjusted log base 2 ratios of Cy5/Cy3 were computed. The supplementary GFF files contain the bi-weight mean adjusted log base 2 ratios in MM8 coordinates

source_name: H3K27me3 ChIP DNA from mouse female PGK12.1 ES cells after 15 days of differentiation

label_protocol: Amplified ChIP or input DNA were labeled by Cy5 or Cy3 respectively using standard NimbleGen protocol.

growth_protocol: ES cells were differentiated by embryoid body formation and removal of LIF for 15 days. Cells were plated in bacterial dishes for 7 days then were replated onto standard cell culture dishes and grown for 8 days. Cells were collected for ChIP.

extract_protocol: 1x10E7 cells were fixed with 1% formaldehyde and lysed in 1 ml of IP buffer (150mM NaCl, 50 mM Tris pH7.5, 5 mM EDTA, 0.5% NP-40, 1.0% Triton X-100). The nuclear pellet was sheared to an average size of 0.5-1 kb by sonication. A 10% of chromatin was saved as the input fraction. ChIP was performed using 5ug antibody . Pull-down chromatin by protein A sepharose beads and input were treated with 0.2M NaCl at 65°C overnight to remove crosslinks. DNA was purified using Qiaquick® PCR purification kit (Qiagen) and amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma) prior to labeling.

treatment_protocol: No treatment

value: Wild type XX

value: PGK12.1 ES cell line

value: Derived from female blastcysts from a 129 female crossed to a (129 X PGK)F1 male.

tag: chip antibody

tag: chip antibody manufacturer

value: Abcam

source_name: ChIP input DNA


title: irs_HZ_8291_MST1_32206

description: biological rep 2


title: irs_HZ_8267_MST1_32119

description: biological rep 4


title: Expt. db/db eWAT Replicate 3

description: Biological replicate 3 of 3 db/db eWAT

source_name: Control 10 Weeks

growth_protocol: Adipose tissues (eWAT) were isolated from the db/db and the lean control (db/+) mice at 10-week of age. The db/db mice are obese, severely hyperglycemic and only modestly hyperinsulinemic at 10 weeks of age.

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

value: 10 weeks

value: eWAT

value: db/+

source_name: db/db 10 week #3

value: db/db


title: PGK12.1 KDM6A_ES_genome tiling

source_name: KDM6A ChIP DNA from mouse female PGK12.1 ES cells

growth_protocol: ES cells were maintained in standard ES medium with 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) on MEF feeders. ES cells were incubated on 1% gelatin coated dishes for 30min to deplete MEF feeders and transferred to fresh gelatin coated plates for culture for experiments and cell collection.

value: αUTX (K. Ge)


title: irs_HZ_8267_MST1_32118

description: biological rep 3


title: Recipient cells, no exosomes replicate1

city: Utrecht

first: Bas

middle: van

last: Balkom

address: Heidelberglaan 100

department: Nephrology and Hypertension

country: Netherlands

institute: UMC Utrecht

description: Gene expression not exposed to exosomes

hyb_protocol: cRNA was hybridized using the Agilent Gene Expression Hybridization Kit (5188-5242) according to the manufacturer's guidelines

scan_protocol: Slides were scanned using an Agilent Microarray Scanner (G2565BA).

data_processing: Image analysis was performed using feauture extraction software version 9.5 (Agilent Technologies). The Agilent GE2-v5_95 protocol was applied (default settings)

source_name: Recipient cells, no exosomes replicate1

label_protocol: Samples were labeled using the Agilent Low RNA Input Linear Amplification Kit Plus (5188-5340) according to the manufacturer's guidelines

growth_protocol: HMEC were cultured for 6h in medium containing HMEC derived exosomes, HMEC derived exosomes depleted of miR-214 or no exosomes

extract_protocol: RNA was isolated using the MirVana isolation kit (Life Technologies) according to the manufacturer's guidelines

value: HMEC endothelial cell


title: irs_HZ_8253_MST1_32054

description: biological rep 2

value: Hippocampus


title: WD44 KDM6A_Day15_genome tiling

source_name: KDM6A ChIP DNA from mouse male WD44 ES cells after 15 days of differentiation

value: Wild type XY

value: WD44 ES cell line

value: Derived from male blastocysts from C57B/6J


title: WD44_KDM6A_ES_genome tiling

source_name: KDM6A ChIP DNA from mouse male WD44 ES cells


title: irs_HZ_8253_MST1_32050

description: biological rep 2


title: Recipient cells with ctrl-miR-214-exosomes replicate2

description: Gene expression after exposure to exosomes


title: irs_HZ_8253_MST1_32052

description: biological rep 2


title: Expt. db/db eWAT Replicate 2

description: Biological replicate 2 of 3 db/db eWAT

source_name: db/db 10 week #2


title: irs_HZ_8253_MST1_32053

description: biological rep 1


title: irs_HZ_8253_MST1_32051

description: biological rep 1


title: Control db/+ eWAT Replicate 3

description: Biological replicate 3 of 3 db/+ eWAT

source_name: db/+ 10 week #3


title: irs_HZ_8291_MST1_32209

description: biological rep 1

value: 9 weeks


title: Con2

city: Munich

first: Karin

last: Weber

address: Veterinärstr. 13

department: Medizinische Kleintierklinik

institute: Zentrum für klinische Tiermedizin

description: miRNA expression profile in the serum of a healthy Doberman Pinscher

hyb_protocol: Microarray analysis was performed using custom-made Agilent miRNA microarrays. Cy3-labeled miRNA was hybridized to the microarrays according the manufacturer’s instructions (User Manual G4170-90011_miRNA_complete_2.3).

scan_protocol: Hybridized and washed slides were scanned at 2 µm resolution with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies).

data_processing: Image processing was performed with Feature Extraction Software 10.7.3.1 (Agilent Technologies).

organism: Canis lupus familiaris

source_name: Serum

label_protocol: Labeling of miRNAs with Cy3-CTP was performed with the miRNA Complete Labeling and Hybridization Kit (Cat.-No. 5190-1934; Agilent Technologies) according the manufacturer’s instructions.

growth_protocol: All dogs were client-owned adult Dobermann Pinschers (Age 7 -11 years) that were presented as patients or for health checks to the clinic of Small Animal Veterinary Medicine, LMU University of Munich, Germany

extract_protocol: Total RNA was isolated from  8 serum samples using Qiazol® Reagent (Qiagen, Hilden Germany) and the miRNeasy Mini Kit (QIAGEN, Valencia, CA, USA) according to the supplementary protocol “Purification of total RNA, including small RNAs, from serum or plasma". Quantity and purity of RNA were measured with a NanoDrop 1000 (PEQLAB Biotechnologie GMBH, Erlangen, Germany).

treatment_protocol: Blood was collected by venipuncture in serum tubes and left to clot for 20 min. The blood was centrifuged at 600g for 5 min and the serum was stored at -80°C until RNA extraction.

tag: sample type

value: serum

tag: disease state

value: healthy


title: Recipient cells with ctrl-miR-214-exosomes replicate1