title: DLD1 2Gy irradiation replicate 3

description: DLD1 cells were cultivated under 3D cell culture and irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 3 of 3.

source_name: Colorectal cancer DLD1 cells cultivated under 3D cell culture conditions, irradiated with 2 Gy


title: Wild type 1

status: Public on Dec 12 2015

type: RNA

city: Jena

first: Abinaya

last: Nathan

address: Beutenberg Str. 11

country: Germany

institute: Leibniz Institute on Aging - FLI

hyb_protocol: cRNA was fragmented and hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array.

scan_protocol: GeneChips were scanned.

data_processing:
The data were analysed using Microsoft Excel and the probe IDs were ranked according to up- or downregulation.
Signal intensity (probe IDs where signal intensity < 30 were eliminated)
Programmatic identifier: GeneChip.CallGEBaseCall.1
Algorithm: ExpressionStat 5.0

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Oviduct E2.5

label_protocol: Biotinylated cRNA was preparedl from 1 ug total RNA

growth_protocol: Female mice were mated with wild type males and the oviducts were harvested at embryonic day 2.5 (E2.5)

extract_protocol: The integrity of each RNA sample was first checked with a RNA 6000 Nano chip. 1 μg total RNA per sample was used for the analysis

treatment_protocol: Oviducts were harvested, washed in PBS and RNA was extracted using the RNEasy Mini kit (Qiagen).

tag: strain

tag: genotype

tag: tissue

value: oviduct


title: s_H3K4_PA1KO_Bcells

type: SRA

city: Copenhagen N

first: Laura

middle: Maarit

last: Pikkupeura

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description: Chromatin IP

library_source: genomic

data_processing:
Sequence reads were aligned to the mm9 mouse genome using the standard Illumina Genome Analyzer Pipeline. Only uniquely mapped reads were retained for further anaylsis.
Wig data files were built using SICER by summing sequence read numbers into 200bp non-overlapping windows, with read position shifted 75bp to represent the DNA fragment center. More details as described in Daniel et al., Science, 2010.
Genome_build: mm9
Supplementary_files_format_and_content: wig, bed files

molecule: genomic DNA

source_name: mouse B cells

growth_protocol: B cells were isolated from spleens of 6- to 14-week old mice by immunomagnetic depletion with α-CD43 beads (Miltenyi Biotech) and stimulated with LPS (25 μg/ml; Sigma), and either α-IgD-dextran (2.5ng/ml; FinaBio) or IL4 (5 ng/ml; Sigma) for 2 days as indicated.

extract_protocol:
2 day stimulated B cells were harvested for chromatin preparation, and ChIP and Illumina sequencing was performed.  Briefly, for histone modification ChIPs, cells were washed and digested with MNase to generate native mononuclesomal chromatin fragments. Chromatin from 10^7 cells was used for each ChIP experiment. DNA was quantified using PicoGreen (Invitrogen) prior to library preparation.
Libraries were prepared by making blut-end DNA with End-It end repair kit (Epicentre #ER81050) according the manufacturer's instructions.  The blunt, phosphorylated ends were treated with Taq DNA polymerase (5U/ul, Invitrogen #18038-042) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~220 bp were band isolated from an agarose gel. The purified DNA quantified using PicoGreen (Invitrogen) and was captured on an Illumina flow cell for cluster generation using Single-Read Cluster Generation Kit v2. Libraries were sequenced on the Genome Analyzer following the SBS Sequencing 36 Cycle Kit v3 protocol.

tag: genotype/variation

tag: antibody


title: P_72_D

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

country: China

institute: Xuzhou Medical University

hyb_protocol: 1650 ng of Cy3-labelled cRNA from each sample was hybridized to Agilent SurePrint G3 Human Exon 4x180K Microarrays according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x180k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data was extracted using GeneSpring GX software and quantile normalized using the limma package in the R program.

organism: Homo sapiens

source_name: Patient 72, diluent challenged

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng total RNA using the Agilent One-Color Microarray-Based Exon Analysis (Low Input Quick Amp Labeling) kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total CD4+ T cells were enriched from PBMCs by MACS negative sorting. Total RNA was extracted using a miRNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: PBMCs from 10 patients with seasonal allergic rhinitis and 10 healthy controls were challenged with diluent and grass pollen extract (ALK-Abelló A/S; 100 μg/mL) for 17 hours.

tag: subject

tag: disease status

value: seasonal allergic rhinitis (SAR)

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: diluent


title: mm9-Bcell-KO-LPS-dex-H3K4me4

description: Chromatin IP


title: DLD1 2Gy irradiation replicate 2

city: Vilnius

first: Vaidotas

last: Stankevicius

state: Lithuania

address: Santariskiu 1

country: Lithuania

institute: National Cancer Institute

description: DLD1 cells were cultivated under 3D cell culture and irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 2 of 3.

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Human Gene Expression (v2) 4x44k Oligonucleotide Microarrays (Agilent) for 17 hours at 65°C  using HS 400 hybridization station (Tecan).

scan_protocol: Microarrays were scanned  using Tecan LS Reloaded scanner

data_processing: Image analysis was performed performed Imagene v9.0 software (BioDiscovery). Raw probe signal values were LOWES normalized

source_name: Colorectal cancer DLD1 cells cultivated under 3D cell culture conditions, without iradiation

label_protocol: 1µg of total RNA was used for cDNA synthesis and amplification using MessageTMAmp aRNA kit (Ambion).  cRNA labeled with Cy3/Cy5 dyes using Arcturus® TURBO labelingTM CyTM3/CyTM5 Kit (Apllied Biosystems).

growth_protocol: Cells were cultured in DMEM (HT29 cell line) or RPMI-1640 (DLD1 cell line) cell culture medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2nM glutamine (Gibco), 100 UI/ml penicillin (ROTH) and 0.1 mg/ml streptomycin (ROTH) at 37°C in a humidified atmosphere containing 5% CO2. For 3D cell culture conditions, cells were plated in 0.5 mg/ml laminin rich extracellular matrix (GeltrexTM, Gibco) and cell culture medium upon a layer of agarose ir a 24-well cell culture plates.

extract_protocol: Total RNA was isolated from harvested cells using GeneJET RNA Purification Kit (ThermoFisher Scientific) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

treatment_protocol: Cell were treated with single (2 Gy or 10 Gy) or fractionated (5x2 Gy) doses of ionizing radiation

tag: cell line

tag: origin

value: Colorectal cancer

value: Control

value: single dose of 2Gy


title: H1299 p300KO siNT 48h #2

city: Chuo-ku

first: Takashi

last: Kohno

state: Tokyo

address: 1-1, Tsukiji 5-chome

country: Japan

institute: National Cancer Center Research Institute

description: Gene expression 48 h after siRNA knockdown

hyb_protocol: cDNA was hybridized to Agilent microarrays (SurePrint G3 Human Gene Expression 8 x 60K Ver.1.0, G4851: 42405 probes) using a Gene Expression Hybridization Kit (Agilent Technologies) for 16 h at 65°C in duplicate.

scan_protocol: After the arrays were washed using the Gene Expression Wash Pack (Agilent Technologies), the data were extracted using an Agilent scanner.

data_processing: The arrays were first analyzed using the Feature Extraction software (Agilent Technologies).

source_name: H1299 p300KO siNT 48h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit.

treatment_protocol: CBP and p300 wild-type H1299 cancer cells, CBP-KO H1299 cells, and p300-KO H1299 cells were transfected with siRNAs (siNT, sip300 D1, siCBP D2) using the Lipofectamine RNAiMAX reagent. After 48 h, total RNA was extracted.

value: Lung


title: mm9-Bcell-WT-LPS-dex-H3K4me4

description: Chromatin IP


title: DLD1 2Gy irradiation replicate 1

description: DLD1 cells were cultivated under 3D cell culture and irradiated with single 2 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.


title: P_12_A

source_name: Patient 12, allergen challenged

value: allergen


title: P_12_D

source_name: Patient 12, diluent challenged


title: HC_24_A

source_name: Healthy control 24, allergen challenged

value: healthy


title: DLD1 10Gy irradiation replicate 1

description: DLD1 cells were cultivated under 3D cell culture and irradiated with single 10 Gy X-ray dose. For differential gene expression analysis non-treated cells served as a control. Biological replicate 1 of 3.

source_name: Colorectal cancer DLD1 cells cultivated under 3D cell culture conditions, irradiated with 10 Gy

value: single dose of 10Gy


title: H1299 p300KO siCBP 48h #2

source_name: H1299 p300KO siCBP 48h


title: Wild type 3


title: HC_24_D

source_name: Healthy control 24, diluent challenged


title: H1299 CBPKO sip300 48h #2

source_name: H1299 CBPKO sip300 48h


title: H1299 CBPKO siNT 48h #2

source_name: H1299 CBPKO siNT 48h


title: H1299 p300KO siNT 48h #1


title: H1299 CBPKO sip300 48h #1


title: MAC (PF-956980) D3

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description:
iMAC treated with LPS for 24 h
MAC_sample  3 in the presence of JAK3 inhibitor (PF-956980)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: Regular BeadStudio processing

label: Cy5 and Cy3

source_name: iMAC treated with LPS for 24 h

label_protocol: Standard Illumina Protocol

growth_protocol: Human monocytes were isolated using MACS CD14 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol

extract_protocol: not provided

value: iMAC


title: H1299 p300KO siCBP 48h #1


title: MAC (PF-956980) D2

description:
iMAC treated with LPS for 24 h
MAC_sample  2 in the presence of JAK3 inhibitor (PF-956980)


title: H1299 siCBP 48h #2

source_name: H1299 siCBP 48h


title: H1299 sip300 48h #2


title: H1299 CBPKO siNT 48h #1


title: U937-has-miR-608 inhibitor-rep3

city: chongqing

first: Wei

last: Gu

address: 10th, Changjiangzhilu

department: the institue of surgery research

institute: the third military medical university

description: Gene expression data from U937 cells transfected by has-miR-608 inhibitor virus for 72h.

hyb_protocol: Following fragmentation, 5.5 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 450.

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

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: U937 cells, transfected by has-miR-608 inhibitor virus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.25 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The U937 cells were purchased from American Type Culture Collection (Rockville, MD). U937  cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% fetal bovine serum (HyClone, Logan, UT, USA) and 1% penicillin/streptomycin (Invitrogen) at 37℃ in a humidified atmosphere consisting of 5% CO2.

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

treatment_protocol: The experimental cells were divided into two groups: a negative control (NC) group consisting of U937 cells infected with a negative control virus, and a microRNA-down (MD) group consisting of U937 cells infected with the miR-608-inhibition virus containing the target gene. Cells under good culture conditions from each experimental group were inoculated into 6-well plates one day prior to viral infection. On the day of infection, lentiviruses were added to each group of cells to perform the infection experiments. Three days after infection, the expression of GFP was observed under a fluorescence microscope, and the proportion of cells with positive fluorescence was higher than 90%. When cells became confluent, they were harvested and examined.


title: H1299 siNT 48h #2

source_name: H1299 siNT 48h


title: U937-has-miR-608 inhibitor-rep2


title: H1299 siCBP 48h #1


title: U937-negative control-rep3

description: Gene expression data from U937 cells transfected by negatiove control virus for 72h.

source_name: U937 cells, transfected by negative control virus


title: U937-has-miR-608 inhibitor-rep1


title: SET2 Sponge

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

institute: Universidad de Oviedo

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Human Gene 2.0 ST Array according to the protocols recommended by the manufacturer (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing: After scanning, raw data (Affymetrix CEL files) were processed with Affymetrix Expression Console using default settings. The full set of exons was used.

source_name: miR125a-transduced SET2 cell line

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

growth_protocol: HEL and SET2 cell lines were grown at 37 ºC, 5% CO2, under standard conditions.

treatment_protocol: Cells were transduced with lentiviral particles, selected with puromycin for 96 h and lysed for RNA extraction.

value: acute myeloid leukemia cell line

value: miR-125a sponge


title: MAC (DMSO) D2

description:
CD14 cells treated with GM-CSF for 96 h
MAC_sample  2

source_name: CD14 cells treated with GM-CSF for 96 h


title: MAC (DMSO) D3

description:
CD14 cells treated with GM-CSF for 96 h
MAC_sample  3


title: H1299 siNT 48h #1


title: H1299 sip300 48h #1


title: SET2 shRNA.IGF1R

source_name: shRNA.IGF1R-transduced SET2 cell line


title: DC (PF-956980) D2

description:
iDC treated with LPS for 24 h
DC_sample  2 in the presence of JAK3 inhibitor (PF-956980)

source_name: iDC treated with LPS for 24 h

value: iDC


title: MAC (PF-956980) D1

description:
iMAC treated with LPS for 24 h
MAC_sample  1 in the presence of JAK3 inhibitor (PF-956980)


title: DC (DMSO) D2

description:
CD14 cells treated with IL4/ GM-CSF for 96 h
DC_sample  2


title: U937-negative control-rep2


title: MAC (DMSO) D1

description:
CD14 cells treated with GM-CSF for 96 h
MAC_sample 1


title: SET2 pLKO

source_name: pLKO-transduced SET2 cell line

value: control


title: HEL Sponge

source_name: miR125a-transduced HEL cell line

value: HEL


title: TG_173

status: Public on Dec 11 2015

city: Freising

first: Nadine

last: Waldschmitt

address: Gregor-Mendel Str. 2

institute: Technische Universität München

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_H5_15_TG

hyb_protocol: Affymetrix GeneChip Mouse Gene 1.1 ST arrays

scan_protocol: scanned on an Affymetrix GeneTitan instrument

data_processing: The probes present on the mouse Gene 1.1 ST arrays represent 21225 Entrez IDs. Arrays were normalized with the Robust Multi-array Average (RMA) method. Only probe sets with normalized signal intensities above 20 on at least five arrays, interquartile range > 0.15 and at least 7 probes per probeset were selected for further analysis. Enriched pathways and gene ontology (GO) groups were identified by using the GeneRanker tool in the Genomatix Genome Analyzer.

label: Ambion WT Expression kit (Life Technologies, Bleiswijk, The Netherlands),

source_name: intestinal epithelial cells from murine distal colon-TG

label_protocol: Ambion WT Expression kit

growth_protocol: 12 weeks old female CHOPIEC Tg/Tg mice and CHOPflox/flox mice as wild-type controls from SPF facility

extract_protocol: Intestinal epithelial cells were isolated by DTT, EDTA treatment followed by percoll gradient centrifugation

treatment_protocol: no treatment

tag: gender

value: female

value: distal colon

value: colonic epithelial cell

value: IEC Tg/Tg

tag: age

value: 12 weeks


title: WT_131

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_H7_16_WT

source_name: intestinal epithelial cells from murine distal colon-WT

value: flox/flox


title: U937-negative control-rep1


title: WT_171

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_G5_13_WT


title: TG_170

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_F7_12_TG


title: WT_145

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_F5_11_WT


title: DC (PF-956980) D1

description:
iDC treated with LPS for 24 h
DC_sample  1 in the presence of JAK3 inhibitor (PF-956980)


title: TG_135

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_D7_08_TG


title: TG_144

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_E7_10_TG


title: DC (PF-956980) D3

description:
iDC treated with LPS for 24 h
DC_sample 3 in the presence of JAK3 inhibitor (PF-956980)


title: WT_172

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_G7_14_WT


title: WT_130

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_D5_07_WT_2


title: DC (DMSO) D1

description:
CD14 cells treated with IL4/ GM-CSF for 96 h
DC_sample 1


title: MO D3

description:
peripheral blood isolated CD14+ cells (monocytes)
CD14_monocyte_samples 3


title: TG_136

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_C7_06_TG


title: HEL shRNA.IGF1R

source_name: shRNA.IGF1R-transduced HEL cell line


title: DC (DMSO) D3

description:
CD14 cells treated with IL4/ GM-CSF for 96 h
DC_sample  3


title: MO D1

description:
peripheral blood isolated CD14+ cells (monocytes)
CD14_monocyte_sample 1


title: TG_129

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_E5_09_TG


title: TG_148

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_B7_04_TG


title: WT_138

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_B5_03_WT


title: MO D2

description:
peripheral blood isolated CD14+ cells (monocytes)
CD14_monocyte_sample 2


title: MEF_Ascl1_FK_rep2

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from mouse embryonic fibroblast transfected with a viral vector for Ascl1, treated with forskolin

hyb_protocol: According to the Affymetrix expression protocol (HWS kit)

data_processing: RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.3.0.187) including median polish and Sketch-Quantile normalization

source_name: Mouse embryonic fibroblast transfected with a viral vector for Ascl1, treated with forskolin

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen)

growth_protocol: Animals per housed under spf conditions

extract_protocol: RNeasy Plus Micro Kit (Qiagen)

treatment_protocol: As described in the paper

value: not determined

value: WT

value: MEF

tag: transfection

value: viral vector for Ascl1

tag: agent

value: forskolin


title: Muscle_WT_Sedentary_21

city: Novato

first: James

last: Flynn

state: CA

address: 8001 Redwood Blvd.

country: USA

institute: Buck Institute for Research on Aging

description: This is a biological replicate of within the sample groupWild-type without endurance exercise

hyb_protocol: 5 μg of Cy3 labeled samples were hybridized to Mus musculus 12x135k, NimbleGen Gene Expression Arrays (Cat.# 05543797001; Roche NimbleGen Inc., Madison, WI), washed and scanned according to manufactures’ protocol.

scan_protocol: NimbleGen Gene Expression Arrays were scanned using a Axon GenePix 4200A scanner (Molecular Devices Inc., Downingtown, PA) with settings of 100 POW and 300-350 photomultiplier (PMT). Pair files were generated for each array using NimbleScan software (Roche NimbleGen Inc., Madison, WI).

data_processing:
Array data was analyzed with Bioconductor software (Bioconductor, Seattle, WA) in which the data was normalized and tests for significantly differentially expressed genes were determined based upon a 5% false discovery rate (FDR). The resulting data was input into Ingenuity Pathway Analysis (Ingenuity® Systems, Redwood City, CA) to determine the over-represented gene categories using strict association.
Pair files were generated for each array using NimbleScan software (Roche NimbleGen Inc., Madison, WI).Normalization strategy for arrays ultilized Loess normalization algorithm for resulting normalized spot intensities.  Microarray-based Ingenuity Pathway Analysis of muscle enrichment of categories which are significantly over-represented expressed genes (Fisher’s exact test, n = 8/group). The gene probes within these categories are plotted as a heat map displaying the normalized within these categories are plotted as a heat map displaying the normalized expression changes within each gene.

source_name: quadriceps femoris Muscle _WT; PolgA+/+_Sedentary

label_protocol: TransPlex Whole Transcriptome Amplification kit (Sigma-Aldrich®, Oakville, ON) was used to amplify cDNA from the muscle RNA samples according to the manufacturer’s instructions. Samples were amplified for 25 cycles using the recommended cycling parameters. All samples were subsequently purified using Qiagen’s QIAquick PCR Purification kit (Qiagen, Mississauga, ON) and processed on Qiagen’s QIAcube (Qiagen, Mississauga, ON) using the standard “Cleanup QIAquick PCR for amplification reactions” (Version 4) protocol.Samples were purified and examined using Nanodrop 2000 (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer DNA 7500 chip (Agilent Technologies, Palo Alto, CA) to ensure proper yield and quality of amplification. To perform the microarray hybridization, 2 μg of cDNA from each sample were labeled using NimbleGen’s One Color Labeling kit (Cat.# 05223555001; Roche NimbleGen Inc., Madison, WI) according to manufacturer’s protocol.

growth_protocol: Heterozygous mice (C57Bl/6J, PolgA+/D257A) for the mitochondrial polymerase gamma knock-in mutation were a kind gift of Dr. Tomas A. Prolla, University of Wisconsin-Madison, USA. We generated homozygous knock-in mtDNA mutator mice (PolG; PolgAD257A/D257A) and littermate wildtype (WT; PolgA+/+) from heterozygous mice-derived colony maintained at the McMaster University Central Animal Facility. Muscle-specific p53 knock-out mice (p53 MKO) were bred by crossing p53 flox mice (Trp53tm1Brn/J) with muscle-creatine kinase Cre recombinase mice (Tg(Ckmm-cre)5Khn/J) purchased from Jackson Laboratories. A triple transgenic homozygous knock-in mtDNA mutator mice with muscle-specific p53 knock-out (PolG-p53 MKO) was generated by crossing heterozygous mice (PolgA+/D257A) with p53 MKO mice. During breeding, all animals were housed three to five per cage in a 12-h light/dark cycle and were fed ad libitum after weaning.

extract_protocol: Tissues were collected at time of euthanasia as previously described. Immediately following cervical dislocation, the chest cavity was exposed and heart was removed rapidly, followed by skeletal muscle (quadriceps femoris). Skeletal muscle (quadriceps femoris) and heart were either: (i) collected in RNase-free cryoviles, immediately immersed in liquid nitrogen, and stored at -80C for later molecular analysis.Total RNA was isolated from ~25 mg of skeletal muscle (quadriceps femoris) using the Qiagen total RNA isolation kit (Qiagen, Mississauga, ON) [11, 13]. RNA samples were treated with RNase-free DNase on Qiagen spin-columns (Qiagen, Mississauga, ON) to remove DNA contamination. RNA integrity and concentration was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) [13]. The average RIN (RNA integrity number) value for all samples was 9.64 ± 0.20 (scale 1 – 10), ensuring a high quality of isolated RNA.

treatment_protocol:
Briefly, at three months of age, mice were housed individually in micro-isolator cages
in a temperature- and humidity- controlled room and maintained on a 12-h light-dark
cycle with food and water ad libitum [13]. PolG mice and PolG-p53 MKO mice were
randomly assigned to sedentary (PolG-SED or PolG-p53 MKO-SED) or forced-endurance (PolG-END or PolG-p53 MKO-END) exercise groups (n = 5-20/group; ♀ = ♂). None of the mice had been previously subjected to a structured exercise regiment. One week of pre-training was allowed to acclimatize mice in endurance exercise groups to the treadmill. Mice in endurance exercise were subjected to forced treadmill exercise (Eco 3/6 treadmill; Columbus Instruments, Columbus, Ohio) three times per week at 15 m/min for 45 min for six months. A 5-min warm-up and cool-down at 8 m/min was also included. PolG mice were age- and sex- matched with sedentary littermate WT mice (n = 20; ♀ = ♂), which served as controls for the study to assess if endurance exercise intervention can molecularly bring PolG mice to normalcy. At eight months of age animals were euthanized, and tissues were collected for molecular analyses.

value: Wild-type

tag: treatment group

value: Sedentary


title: MEF_Ascl1_rep1

description: Gene expression data from mouse embryonic fibroblast transfected with a viral vector for Ascl1

scan_protocol: According to the Affymetrix expression protocol

source_name: Mouse embryonic fibroblast transfected with a viral vector for Ascl1


title: WT_139

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_A7_02_WT


title: TG_140

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_A5_01_TG


title: Muscle_WT_Sedentary_18


title: MEF_Ctrl_rep1

description: Gene expression data from mouse embryonic fibroblast transfected with an empty viral vector

source_name: Mouse embryonic fibroblast transfected with an empty viral vector

value: empty viral vector


title: MEF_Ascl1_rep3


title: MEF_Ascl1_FK_rep3


title: WT_146

description:
Gene expression data from 12 weeks old females with/without transgene CHOP-HA overexpression in the intestinal epithelium
G069_C5_05_WT


title: Muscle_WT_Sedentary_17


title: Muscle_WT_Sedentary_19


title: MEF_Ctrl_rep2


title: MEF_Ascl1_rep2


title: Muscle_WT_Sedentary_20


title: Muscle_WT_Sedentary_24


title: Muscle_WT_Sedentary_15


title: Muscle_WT_Sedentary_13


title: MEF_Ascl1_FK_rep1


title: Muscle_WT_Sedentary_22


title: Muscle_WT_Sedentary_11


title: Muscle_WT_Sedentary_23


title: Muscle_WT_Sedentary_12


title: Muscle_WT_Sedentary_16


title: Muscle_WT_Sedentary_14


title: Muscle_WT_Sedentary_8


title: Muscle_WT_Sedentary_7


title: Muscle_WT_Sedentary_10


title: Muscle_WT_Sedentary_2


title: HEL pLKO

source_name: pLKO-transduced HEL cell line

value: acute myeloid leukemia cell line


title: Muscle_WT_Endurance Exercise_12

description: This is a biological replicate of within the sample group PolG-p53 KO without endurance exercise

source_name: quadriceps femoris Muscle _WT; PolgA+/+_Endurance Exercise

value: Endurance Exercise


title: Muscle_WT_Sedentary_9


title: Muscle_WT_Endurance Exercise_7


title: Muscle_WT_Sedentary_5


title: Muscle_WT_Sedentary_4


title: Muscle_WT_Sedentary_6


title: Muscle_WT_Endurance Exercise_2


title: Muscle_WT_Endurance Exercise_10


title: Muscle_WT_Sedentary_3


title: Muscle_WT_Endurance Exercise_4


title: Muscle_WT_Sedentary_1


title: Muscle_WT_Endurance Exercise_9


title: Muscle_WT_Endurance Exercise_5


title: Muscle_PolG_Sedentary_23

source_name: quadriceps femoris Muscle _PolG-p53 MKO_Sedentary

value: PolG-p53 MKO


title: Muscle_PolG_Sedentary_21


title: Muscle_WT_Endurance Exercise_1


title: Muscle_WT_Endurance Exercise_6


title: Muscle_WT_Endurance Exercise_3


title: Muscle_PolG_Sedentary_19


title: Muscle_PolG_Sedentary_24


title: Muscle_PolG_Sedentary_20


title: Muscle_PolG_Sedentary_22


title: Muscle_PolG_Sedentary_16


title: Muscle_PolG_Sedentary_17


title: Muscle_PolG_Sedentary_15


title: Muscle_PolG_Sedentary_13


title: Muscle_PolG_Sedentary_14


title: Muscle_PolG_Sedentary_18


title: Muscle_PolG_Sedentary_12


title: Muscle_PolG_Sedentary_11


title: hGRB_Liver_Lobe A Replicate 2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression of AAV-hGRβ Liver

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: AAV-hGRβ Liver

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: RNA was prepared using the Qiagen RNeasy midi kit (Qiagen Sciences, Germantown, MD) following the manufacturers instructions.  This included DNase treatment of all samples.

treatment_protocol: C57BL/6 mice were treated with AAV-GFP and AAV-hGRB, respectively.

value: Male

value: liver


title: Muscle_PolG_Sedentary_8


title: Muscle_PolG_Sedentary_10


title: Muscle_PolG_Sedentary_9


title: Muscle_PolG_Sedentary_5


title: GFP_Liver_Lobe A Replicate 1

description: Gene expression of AAV-GFP Liver

source_name: AAV-GFP Liver


title: hGRB_Liver_Lobe A Replicate 3

description: Gene expression of AAV-hGRβ Liver


title: Muscle_PolG_Sedentary_4


title: hGRB_Liver_Lobe A Replicate 1

description: Gene expression of AAV-hGRβ Liver


title: GFP_Liver_Lobe A Replicate 2

description: Gene expression of AAV-GFP Liver


title: GFP_Liver_Lobe A Replicate 3

description: Gene expression of AAV-GFP Liver


title: Muscle_PolG_Sedentary_7


title: 750_B6_Liver_Lobe_A Replicate 4

description: Gene expression of WT Liver

source_name: WT Liver


title: Muscle_PolG_Sedentary_6


title: Muscle_PolG_Sedentary_2


title: Muscle_WT_Endurance Exercise_11


title: Muscle_PolG_Sedentary_3


title: Muscle_PolG_Sedentary_1


title: Muscle_PolG_Endurance Exercise_22

description: This is a biological replicate of within the sample group PolG-p53 KO with Endurance Exercise

source_name: quadriceps femoris Muscle _PolG-p53 MKO_Endurance Exercise


title: Muscle_PolG_Endurance Exercise_23


title: Muscle_PolG_Endurance Exercise_20


title: 750_B6_Liver_Lobe_A Replicate 3

description: Gene expression of WT Liver


title: Muscle_WT_Endurance Exercise_8


title: PBS Replicate 4

description: Gene expression of liver treated with PBS

source_name: Liver treated with PBS

treatment_protocol: GR Liver Knockout mice were treated with AAV-GFP and AAV-hGRB, respectively.

value: GR knockout


title: Muscle_PolG_Endurance Exercise_21


title: PBS Replicate 3


title: hGRB Replicate 4

description: Gene expression of liver treated with AAV-hGRB

source_name: Liver treated with AAV-hGRB


title: hGRB Replicate 3


title: PBS Replicate 1


title: hGRB Replicate 2


title: Muscle_PolG_Endurance Exercise_19


title: Muscle_PolG_Endurance Exercise_18


title: Muscle_PolG_Endurance Exercise_17


title: GFP Replicate 4

description: Gene expression of liver treated with AAV-GFP

source_name: Liver treated with AAV-GFP


title: Muscle_PolG_Endurance Exercise_13


title: Muscle_PolG_Endurance Exercise_11


title: Muscle_PolG_Endurance Exercise_15


title: 750_B6_Liver_Lobe_A Replicate 2

description: Gene expression of WT Liver


title: PBS Replicate 2


title: GFP Replicate 3


title: Muscle_PolG_Endurance Exercise_14


title: Muscle_PolG_Endurance Exercise_16


title: hGRB Replicate 1


title: Muscle_PolG_Endurance Exercise_12


title: GFP Replicate 1


title: GFP Replicate 2


title: Muscle_PolG_Endurance Exercise_9


title: Muscle_PolG_Endurance Exercise_10


title: Muscle_PolG_Endurance Exercise_8


title: MDMA-10/25D-3

city: Atlanta

first: William

last: Lewis

state: Georgia

address: 101 Woodruff Circle

department: Pathology

institute: Emory University

hyb_protocol: Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001)following their standard operating protocol.

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol

data_processing: Each sample was processed utilizing NimbleScan software default values, including analysis of the 635/532 ratio utilizing a 500bp sliding window KS test according to manufacturer instructions.

source_name: Methylated Genomic DNA

label_protocol: DNA labeling was completed using NimbleGen Dual-Color DNA labeling Kit (Cat # 06370250001) following their standard operating protocol.

extract_protocol: DNA was extracted  using a MagNAPure DNA Extraction System (Roche), quantiated, sonicated and enriched using the MethylCollector Ultra Kit (Active Motif) following the manufacturer's protocol. Both methylated and input DNA was amplified using whole genome amplification (Sigma-Aldrich).

value: MDMA for 10 days followed by 25 days Saline

source_name: Total Genomic DNA


title: MDMA-10/25D-4


title: MDMA-10/25D-2


title: MDMA-10/25D-1


title: PBS_DEX Replicate 4

description: Gene expression of liver from GR knockout mouse with dexamethasone treatment treatment

source_name: Liver from GR knockout mouse, dexamethasone treated

treatment_protocol: Wild type and GR Liver Knockout mice were treated with Dexamethasone (DEX) or vehicle.


title: PBS_DEX Replicate 1


title: Muscle_PolG_Endurance Exercise_7


title: PBS_DEX Replicate 2


title: Muscle_PolG_Endurance Exercise_3


title: PBS_CTL Replicate 3

description: Gene expression of liver from GR knockout mouse with no treatment

source_name: Liver from GR knockout mouse, no treatment


title: Arabidopsis Col-0, control treatment, biological rep1

city: Olomouc

first: Maria

last: Majeska Cudejkova

address: Slechtitelu 27

department: Centre of Region Hana for Biotechnological and Agricultural Research

country: Czech Republic

institute: Palacky University

description:
Gene expression data from Arabidopsis senescent leaves
7_Arabidopsis Col-0  DMSO ctrl-1

hyb_protocol: Biotin-tagged cDNA was subsequently used for hybridization with the Arabidopsis Gene 1.0 ST Array (Affymetrix, Inc., Santa Clara, CA). GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with R/Bioconductor oligo package with default settings and RMA normalization method. All statistical analyses were performed by methods in limma package, moderated t-test and Benjamini-Hochberg correction were applied.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0 senescent leaves

label_protocol: Double-stranded cDNA was prepared and amplified using the WT expression kit (Ambion, Life Technologies Ltd, UK). The resulting cDNA was then fragmented by the combined action of uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 with the WT terminal labeling kit (Affymetrix, Inc., Santa Clara, CA) to yield biotin-tagged cDNA.

growth_protocol: The plants were grown in soil for 3 weeks, after which leaves of similar size and chlorophyll content were cut and immediately treated with the appropriate cytokinin.

extract_protocol: Total RNA was isolated from Arabidopsis leaves using the RNAqueous total RNA isolation kit (Ambion, Life Technologies Ltd, UK) according to the manufacturer's recommendations. In addition, samples were treated with DNase I to remove contaminant genomic DNA.

treatment_protocol: 10-15 detached leaves were immersed in 1 x MS medium supplemented with 10 µM of the chosen cytokinin; this amount represented one sample. Three biological replicates were performed for each cytokinin treatment and the control group. Control samples were treated with 0.05% DMSO in MS medium. After incubation for 48 hours in the dark, detached leaves were frozen in liquid nitrogen and used for RNA isolation.

value: leaf

tag: ecotype


title: PBS_CTL Replicate 1

tag: strain


title: Muscle_PolG_Endurance Exercise_5

tag: genotype


title: WT_Dex Replicate 3

description: Gene expression of liver from WT mouse with dexamethasone treatment

source_name: Liver from WT mouse, dexamethasone treated

tag: tissue

value: wildtype


title: PBS_DEX Replicate 3


title: MDMA-35D-3

value: MDMA for 35 days


title: Arabidopsis Col-0, control treatment, biological rep2

description:
Gene expression data from Arabidopsis senescent leaves
8_Arabidopsis Col-0 DMSO ctrl-2


title: PBS_CTL Replicate 2


title: Muscle_PolG_Endurance Exercise_6


title: TQ MF 180K-CGH replicate 1

city: New York

first: Richard

middle: H

last: Baker

state: NY

address: 79th at Central Park West

department: Sackler Institute for Comparative Genomics

institute: American Museum of Natural History

hyb_protocol: Agilent array-based CGH protocol with hybridization for 24 h at 65oC

scan_protocol: Scanned using an Agilent G2505C microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Features were excluded from further analysis if the majority of pixels were saturated or the median pixel intensity was less than two times the background. Intensity scores were normalized using the linear normalization methodology. Normalized average log2(female intensity/male intensity) for two replicates of each probe. Transcripts were assembled de novo using Trinity and then multiple probes (indicated by decimal number) designed per transcript. These values were normalized so that the maximum number of probes had a log2(f/m) ratio of 0, the expected value given the nature of the array.

organism: Teleopsis quinqueguttata

label_protocol: Each DNA sample was fractionated by restriction digestion with AluI and RsaI for 2 h at 37oC. 3 µg of each sample was then labeled with either Cy-3 or Cy-5

growth_protocol: Each sample consisted of 4 or 5 male or female adult flies that were taken from population cages maintained at the University of Maryland, College Park, derived from flies originally collected at Gombak, penisular Malaysia

extract_protocol: Genomic DNA was extracted from macerated fly bodies after removing eyes and digestive tract with Qiagen DNeasy kits using the insect sample protocol

treatment_protocol: All samples were treated with RNAse

value: female

tag: population

value: Gombak

value: male


title: MDMA-35D-2


title: TQ MF 180K-CGH replicate 4


title: MDMA-35D-1


title: Muscle_PolG_Endurance Exercise_2


title: Saline-35D-4

value: Saline for 35 days


title: WT_Dex Replicate 4


title: PBS_CTL Replicate 4


title: Saline-35D-3


title: Arabidopsis Col-0, control treatment, biological rep3

description:
Gene expression data from Arabidopsis senescent leaves
9_Arabidopsis Col-0 DMSO ctrl-3


title: WT_Dex Replicate 2


title: TQ MF 180K-CGH replicate 3


title: Arabidopsis Col-0, treatment with compound 3, biological rep3

description:
Gene expression data from Arabidopsis senescent leaves
21_Arabidopsis Col-0 Compound 3-3


title: Muscle_PolG_Endurance Exercise_4


title: Saline-35D-2


title: WT_Dex Replicate 1


title: Saline-35D-1


title: Muscle_PolG_Endurance Exercise_1


title: MDMA-10D-1

value: MDMA for 10 days


title: MDMA-10D-3


title: MDMA-10D-2


title: Saline-10D-2

value: Saline for 10 days


title: Saline-10D-3


title: Saline-10D-1


title: MDMA-10D-4


title: Saline-10D-4


title: WT_Control Replicate 3

description: Gene expression of liver from WT mouse with no treatment

source_name: Liver from WT mouse, no treatment


title: WT_Control Replicate 4


title: Arabidopsis Col-0, treatment with compound 3, biological rep1

description:
Gene expression data from Arabidopsis senescent leaves
19_Arabidopsis Col-0 Compound 3-1


title: WT_Control Replicate 1


title: Arabidopsis Col-0, treatment with compound 6, biological rep3

description:
Gene expression data from Arabidopsis senescent leaves
18_Arabidopsis Col-0 Compound 6-3


title: WT_Control Replicate 2


title: Wnt1-Cre;Erk2 E14.5 Conditional Knockout Mouse Model Palate 4, Batch 2

city: Oklahoma City

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

description: Whole genome transcriptome profile of palate mesenchyme, collected at E14.5 from mice with a conditional inactivation of Erk2 in the cranial neural crest.

hyb_protocol: Standard Affymetrix hybridization protocol was used.

scan_protocol: Standard Affymetrix scanning protocol was used.

data_processing: Within each developmental timepoint, samples were processed by GCRMA normalization and log2-scaled expression values were generated through the WebArray tool (URL: http://www.webarraydb.org/webarray/index.html) with default options. p-values for significance testing were adjusted using the SPLOSH (Spacings LOESS Histogram) method as implemented by WebArray. For samples at timepoint E14.5, two batches of samples were produced at different times. Batch status is indicated in the sample title. The ComBat method in the R/bioconductor package sva  (Johnson, WE, Rabinovic, A, and Li, C (2007). Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics 8(1):118-127.) was used to reduce the batch effect differentiating samples from these two batches prior to normalization. Although both E13.5 and E14.5 data are included in the sample matrix, data from each timepoint were analyzed separately for the discovery of differentially expressed transcripts. Data values from E13.5 are not normalized to be comparable to data values from E14.5.

source_name: E14.5 Wnt1-Cre;Erk2 Conditional Knockout Mouse Model palate mesenchyme

label_protocol: Standard Affymetrix cRNA labeling protocol was used.

growth_protocol: Standard IACUC protocols were used

extract_protocol: Embryo was harvested at E13.5 or E14.5 as indicated on sample. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from palate mesenchyme tissue.

treatment_protocol: Mice were maintained under standard IACUC protocols.

value: Erk2 fl/fl; Wnt1-Cre

value: palate mesenchyme

value: Not determined


title: Erk2 E14.5 Wild-Type Mouse Model Palate 2, Batch 1

description: Whole genome transcriptome profile of palate mesenchyme, collected at E14.5 from control mice .

source_name: E14.5 Erk2 Wildtype Mouse Model Palate Mesenchyme

value: Erk2 fl/fl


title: Wnt1-Cre;Erk2 E14.5 Conditional Knockout Mouse Model Palate 5, Batch 2


title: Arabidopsis Col-0, treatment with compound 6, biological rep2

description:
Gene expression data from Arabidopsis senescent leaves
17_Arabidopsis Col-0 Compound 6-2


title: Erk2 E14.5 Wild-Type Mouse Model Palate 5, Batch 2


title: Erk2 E14.5 Wild-Type Mouse Model Palate 4, Batch 2


title: Wnt1-Cre;Erk2 E14.5 Conditional Knockout Mouse Model Palate 2, Batch 1


title: Arabidopsis Col-0, treatment with compound 6, biological rep1

description:
Gene expression data from Arabidopsis senescent leaves
16_Arabidopsis Col-0 Compound 6-1


title: Erk2 E14.5 Wild-Type Mouse Model Palate 3, Batch 2


title: Erk2 E14.5 Wild-Type Mouse Model Palate 1, Batch 1


title: Wnt1-Cre;Erk2 Conditional Knockout Mouse Model Palate 2

description: Whole genome transcriptome profile of palate mesenchyme, collected at E13.5 from mice with a conditional inactivation of Erk2 in the cranial neural crest.

source_name: E13.5 Wnt1-Cre;Erk2 Conditional Knockout Mouse Model palate mesenchyme


title: Erk2 Wild-Type Mouse Model Palate 1

description: Whole genome transcriptome profile of palate mesenchyme, collected at E13.5 from control mice .

source_name: E13.5 Erk2 Wildtype Mouse Model Palate Mesenchyme


title: Erk2 Wild-Type Mouse Model Palate 2


title: Erk2 Wild-Type Mouse Model Palate 3


title: Wnt1-Cre;Erk2 Conditional Knockout Mouse Model Palate 3


title: Wnt1-Cre;Erk2 E14.5 Conditional Knockout Mouse Model Palate 3, Batch 2


title: Wnt1-Cre;Erk2 Conditional Knockout Mouse Model Palate 1


title: Wnt1-Cre;Erk2 E14.5 Conditional Knockout Mouse Model Palate 1, Batch 1


title: 73MP-P

city: Palo Alto

first: Rajini

last: Haraksingh

address: 3165 Porter Drive, Room 2270

institute: Stanford University

description: aCGH of hearing loss cases and controls on NimbleGen 2.1M CNV platform

hyb_protocol: 34 μg of test and control DNA were mixed together and hybridized to an array for 60-72 hrs. The arrays were washed using the NimbleGen Wash kit.

scan_protocol: The arrays were scanned using the MS 200 scanner (Roche NimbleGen) in two channels: 532nm and 635nm.

data_processing:
Images were processed using NimbleScan 2.6 with default parameters (Roche NimbleGen).
Log2-transformed raw data are reported in the EXP_chipID_532 and REF_chipID_635 columns of segMNT.txt.
The NimbleScan 2.6 segMNT algorithm with default parameters (Roche NimbleGen) was used to derive Log R Ratios (reported in the RATIO_CORRECTED column of segMNT.txt)

source_name: Genomic DNA isolated from peripheral blood of patient with non-syndromic hereditary hearing loss

label_protocol: Genomic DNA from each sample was labeled with cy3 dye and genomic DNA from a control pool of seven female individuals (Promega) was labeled using cy5 dye according to the NimbleGen CGH protocol.

extract_protocol: Genomic DNA was isolated from peripheral blood using standard methods.

treatment_protocol: DNA extracted directly from blood

value: Male

tag: phenotype

value: non-syndromic hereditary hearing loss

source_name: Genomic DNA isolated from a pool of seven healthy females. Purchased from Promega

treatment_protocol: DNA was purchased from Promega - Pool of seven female human genomes

value: Female


title: KO_KCl_3

city: Hong Kong

first: Nancy

middle: Y.

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

description: RMA expression value derived from Affymetrix Expression Console Software on Exon level

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 2.0 ST Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Expression data was further processed via Affymetrix Expression Console Software and R scripts

source_name: Cdk5 KO mice

label_protocol: not provided

growth_protocol: Primary cortical neurons were prepared from embryonic day (E) 18  Cdk5 WT or KO mice and maintained in Neurobasal medium with 2% B27 supplement.

extract_protocol: RNA was extracted using the QIAGEN RNA extraction kit according to the manufacturer’s instructions.

treatment_protocol: Cultured cortical neurons at 5 days in vitro (DIV) were treated with 50 mM KCl or NaCl and RNA was collected for further analysis

value: Cortical neuron

value: Cdk5 KO


title: Mouse Medulloblastoma, sample 4

city: Philadelphia

first: Jessica

middle: Mei Y.

last: Ng

state: PA

address: Colket Translational Research Bldg (Rm 4059) 3501 Civic Center Blvd

department: Pathology and Laboratory Medicine

institute: The Children's Hopsital of Philadelphia

description: Mouse model of medulloblastoma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The CEL files were processed using the RMA method (http://www.ncbi.nlm.nih.gov/pubmed/12582260) and a custom library provided by the BRAINARRAY project, version 18.0.0 (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/18.0.0/entrezg.asp).

source_name: Brain tumor

label_protocol: Biotinylated cRNA were prepared according to the MessageAmp Premier Amplification Kit protocol using 200 ng of total RNA as input (MessageAmp Premier Ampification Kit Manual, Revision G, Ambion).

growth_protocol: Snf5F/F/p53L/L/GFAP-Cre mice transgenic mice for AT/RT samples, and Ptc1+/- p53+/- (n = 2) and Ptc1+/- p53-/- (n = 3) transgenic mice for medulloblastoma samples

extract_protocol: Total RNA was isolated using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit.

treatment_protocol: Mice were sacrifced by cervical dislocation after intraperitoneal injection with ketamine and xylazine. Following dissection, brain tissues were isolated for RNA extraction

tag: tumor type

value: medulloblastoma


title: KO_NaCl_3

institute: Hong Kong University of Science and Technology


title: KO_KCl_1


title: Mouse Brain AT/RT, sample 2

description: Mouse model of AT/RT brain tumor

value: AT/RT


title: Mouse Medulloblastoma, sample 5

description: Mouse model of medulloblastoma


title: Mouse Brain AT/RT, sample 1

description: Mouse model of AT/RT brain tumor


title: KO_KCl_2


title: Mouse Medulloblastoma, sample 3

description: Mouse model of medulloblastoma


title: KO_NaCl_2


title: Mouse Brain AT/RT, sample 3

description: Mouse model of AT/RT brain tumor


title: Mouse Brain AT/RT, sample 4

description: Mouse model of AT/RT brain tumor


title: Mouse Brain AT/RT, sample 5

description: Mouse model of AT/RT brain tumor


title: Mouse Medulloblastoma, sample 1

description: Mouse model of medulloblastoma


title: Mouse Medulloblastoma, sample 2

description: Mouse model of medulloblastoma


title: WT_KCl_3

source_name: Cdk5 WT mice

value: wildtype


title: KO_NaCl_1


title: WT_NaCl_1


title: WT_KCl_2


title: WT_tumor_23672

city: Saint Louis

first: Katherine

last: Weilbaecher

state: Missouri

address: 660 South Euclid Avenue

department: Department of Medicine

institute: Washington University in St. Louis

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

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

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

source_name: Wildtype mouse

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen Ovation PicoSL WTA System V2 system. 50ng of total RNA was used to generate biotinylated cDNA, according to the standard NuGen WT-Ovation Pico RNA Amplification kit.

growth_protocol: PyMT-BO-1-GFP-Luc cells or CD206hi TAMs directly FACS-sorted from tumor tissue and used for RNA extraction, without cell culture or treatment.

extract_protocol: Total RNA was extracted by Nucleospin RNA II Kit according to the manufacturer's instructions.

value: PyMT-BO1-GFP-Luc tumor cells

value: Wildtype


title: WT_NaCl_3


title: WT_NaCl_2


title: WT_tumor_23671


title: Human MCF-7 cells treated with MELK-T1 during 72 hours 16041

city: Beerse

first: Steven

last: Osselaer

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica NV

hyb_protocol: Target hybridization was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933).

scan_protocol: Plate scan was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933). Images were analyzed using the GeneChip® Command Console Software (AGCC), (Affymetrix).

data_processing: The data were analyzed with R version 3.0.1 using RMA algorithm for preprocessing (affy_1.38.1) and Entrez based alternative CDF version 15.1.0 for probeset annotation

label_protocol: All microarray related steps for target preparation including  amplification of total RNA and  labeling were carried out as described in the GeneChip®3’ IVT, Express Kit User Manual , (Affymetrix 2004).

growth_protocol: MCF-7 cells were cultured in high-glucose DMEM (LifeTechnologies) supplemented with 10% FBS (LifeTechnologies).

extract_protocol: Cells were lysed using RLT buffer (Qiagen) and RNA extracted with the RNeasy 96 kit (p/n 74181 Qiagen).

treatment_protocol: MCF-7 cells were incubated with 10 µM of MELK-T1 for 48 h. DMSO was used as negative control.

tag: time (hours)


title: Human MCF-7 cells treated with MELK-T1 during 72 hours 16022


title: Human MCF-7 cells treated with MELK-T1 during 72 hours 16016


title: MCF7_VEC_plastic_48h

city: Liège

first: Erik

last: Maquoi

address: Tour de Pathologie, B23 Sart-Tilman

institute: University of Liège

description: Gene expression data from MCF-7 cells stably expressing pcDNA3.1/Zeo vector.

hyb_protocol: cRNA was hybridized to Affymetrix U133A 2.0 GeneChip array according to the manufacturer protocol

scan_protocol: The arrays were scanned in an Affymetrix/Hewlett-Packard GeneChip Scanner 3000-7G

data_processing: The data were processed through the MAS5.0 algorithm included in Affymetrix® Expression Console™ Software.

source_name: MCF-7 human breast adenocarcinoma cell line

label_protocol: Double-stranded cDNA was synthesized from 100 ng of total RNA primed with a poly-(dT)–T7 oligonucleotide. The cDNA was used in an in vitro transcription reaction in the presence of T7 RNA polymerase and biotin-labeled modified nucleotides during 16 hours at 40°C. Biotinylated cRNA was purified and fragmented (35-200 nucleotides).

growth_protocol: Cells were passaged in DMEM medium (Invitrogen) supplemented with heat-inactivated fetal bovine serum (Invitrogen), 2mM L-glutamine (Invitrogen) and penicillin-streptomycin (Invitrogen). Cells were routinely cultured in 37°C with 5% CO2. For the monolayer cultures, cells were seeded in 12-well plates, 20000 cells/well, in 1 ml of medium supplemented with 5.5% serum. For the 3D environment, cells were suspended in neutralized native rat tail type I collagen gels, 200000 cells/800 µl gel in 12-well plates and incubated 30 min at 37°C to allow polymerization of the collagen fibers. After polymerization, 1 ml of medium supplemented with 10% serum was added to each well, resulting in a final serum concentration of 5.5%. The culture medium was refreshed after 48 hours and cells were allowed to grow for 24, 48 and 72 hours. Four independent replicates were prepared for each treatment-time combination.

extract_protocol: RNA was extracted with TRIzol reagent (Invitrogen), followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: MCF-7 cells stably transfected with either an empty pcDNA3.1/Zeo expression vector (Invitrogen) or human MMP-14 cDNA subcloned in pcDNA3.1/Zeo were cultured 48 hours in 100 mm platic culture plates.


title: KOM_tumor_23674

source_name: b3KOM mouse

tag: cell type


title: Arabidopsis Col-0, treatment with compound 3, biological rep2

description:
Gene expression data from Arabidopsis senescent leaves
20_Arabidopsis Col-0 Compound 3-2

value: leaf


title: Human MCF-7 cells treated with MELK-T1 during 48 hours 16002

tag: treatment


title: MCF7_MT1_plastic_48h

description: Gene expression data from MCF-7 cells stably expressing pcDNA3.1-MMP-14/Zeo vector.

tag: cell line


title: mMAC_donor 3

city: Badalona, Barcelona

last: Ballestar

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

description:
mMAC D3
iMAC treated with LPS for 24 h

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing: Regular BeadStudio processing; the non_normalized.txt contains unmethylated and methylated signal intensities

source_name: iMAC treated with LPS for 24 h

label_protocol: Standard Illumina Protocol

extract_protocol: sample preparation protocol: Human monocytes were isolated using MACS CD14 microbeads (Milteny) from peripheral blood mononuclear cells using the manufacturer's protocol

tag: donor id

value: donor 3

value: activated/mature MACs

tag: treated with

value: LPS for 24 h


title: MDMA-10/25D-4

hyb_protocol: Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001) following their standard operating protocol.

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol.

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

source_name: Total RNA from MDMA-10/25D Left Ventricle

label_protocol: DNA labeling was completed using NimbleGen labeling Kit following their standard operating protocol.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc.) and cDNA was synthesized using Superscript Double-Stranded cDNA Synthesis kit (Invitrogen/Life Technologies).  cDNA quality was determined using a Spectramax 190 plate reader ( ) for A260 and A280 absorbance determination along with gel electrophoresis.

value: MDMA for 10 days followed by 25 days Saline


title: Human MCF-7 cells treated with MELK-T1 during 48 hours 15995


title: iMAC_donor 1

description:
iMAC D1
CD14 cells treated with GM-CSF for 96 h

source_name: CD14 cells treated with GM-CSF for 96 h

value: donor 1

value: immature MACs

value: GM-CSF for 96 h


title: Human MCF-7 cells treated with DMSO during 72 hours 16036

value: DMSO


title: mDC_donor 3

description:
mDC D3
iDC treated with LPS for 24 h

source_name: iDC treated with LPS for 24 h

value: activated/mature DCs


title: Human MCF-7 cells treated with MELK-T1 during 48 hours 15979


title: WT_CD206hi_23667

value: CD206hi tumor-associated macrophages


title: KOM_tumor_23673


title: MDMA-10/25D-2


title: mMAC_donor 2

description:
mMAC D2
iMAC treated with LPS for 24 h

value: donor 2


title: WT_CD206hi_ 23666


title: MDMA-10/25D-3


title: MDMA-10/25D-1


title: Human MCF-7 cells treated with DMSO during 72 hours 16034


title: mMAC_donor 1

description:
mMAC D1
iMAC treated with LPS for 24 h


title: Human MCF-7 cells treated with DMSO during 72 hours 16031


title: WT_KCl_1

value: Cortical neuron


title: iMAC_donor 2

description:
iMAC D2
CD14 cells treated with GM-CSF for 96 h


title: KOM_CD206hi_23670


title: KOM_CD206hi_23669


title: MDMA-35D-3

source_name: Total RNA from MDMA-35D Left Ventricle

value: MDMA for 35 days


title: MDMA-35D-4


title: Human MCF-7 cells treated with DMSO during 72 hours 16023


title: Human MCF-7 cells treated with DMSO during 72 hours 16017


title: mDC_donor 1

description:
mDC D1
iDC treated with LPS for 24 h


title: iDC_donor 3

description:
iDC D3
CD14 cells treated with IL4/ GM-CSF for 96 h

value: immature DCs

value: IL4/ GM-CSF for 96 h


title: KOM_CD206hi_ 23668


title: Human MCF-7 cells treated with DMSO during 48 hours 16004


title: Human MCF-7 cells treated with DMSO during 48 hours 16007


title: Human MCF-7 cells treated with DMSO during 48 hours 15988


title: MDMA-35D-2


title: Human MCF-7 cells treated with DMSO during 72 hours 16020


title: Saline-35D-2

source_name: Total RNA from Saline-35D Left Ventricle

value: Saline for 35 days


title: MDMA-35D-1


title: Saline-35D-4


title: mDC_donor 2

description:
mDC D2
iDC treated with LPS for 24 h


title: Saline-35D-3


title: Saline-35D-1


title: Human MCF-7 cells treated with DMSO during 48 hours 15986


title: MDMA-10D-4

source_name: Total RNA from MDMA-10D Left Ventricle

value: MDMA for 10 days


title: Human MCF-7 cells treated with DMSO during 48 hours 15984


title: CD14_monocyte_donor 2

description:
MO D2
peripheral blood isolated CD14+ cells (monocytes)


title: WT_CD206hi_23675

value: Wildtype


title: iDC_donor 1

description:
iDC D1
CD14 cells treated with IL4/ GM-CSF for 96 h


title: iDC_donor 2

description:
iDC D2
CD14 cells treated with IL4/ GM-CSF for 96 h


title: CD14_monocyte_donor 1

description:
MO D1
peripheral blood isolated CD14+ cells (monocytes)


title: CD14_monocyte_donor 3

description:
MO D3
peripheral blood isolated CD14+ cells (monocytes)

value: donor 3


title: Human MCF-7 cells treated with DMSO during 48 hours 15980


title: iMAC_donor 3

description:
iMAC D3
CD14 cells treated with GM-CSF for 96 h


title: MDMA-10D-3


title: MDMA-10D-1


title: MDMA-10D-2


title: Saline-10D-4

source_name: Total RNA from Saline-10D Left Ventricle

value: Saline for 10 days


title: SB MF 180K-CGH replicate 3

organism: Sphyracephala beccarii

growth_protocol: Each sample consisted of 4 or 5 male or female adult flies that were taken from population cages maintained at the University of Maryland, College Park, derived from flies originally collected near Pietermaritzburg, South Africa

tag: gender

value: female

value: Pietermaritzburg

value: male


title: SB MF 180K-CGH replicate 1


title: Saline-10D-2


title: Saline-10D-3


title: ExVivoBlood_IL-4 rep1

status: Public on Dec 10 2015

city: Sendai

first: Masayuki

last: Asano

state: Miyagi

address: Seiryo-machi 1-1, Aoba-ku

department: Department of Dermatology

institute: Tohoku University Graduate School of Medicine

description: Gene expression with sRANKL treatment

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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 (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20100115) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peripheral Blood, sRANKL, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: CD14+ cells were isolated from the peripheral blood mononuclear cells of healthy donors using magnetic-activated cell sorting beads (CD14 microbeads, Miltenyi Biotec, CA) according to the manufacturer’s protocol. CD14+ monocytes (2 x 105 /ml) were cultured in complete medium containing 100 ng/ml of recombinant human M-CSF for 5 days. On the fifth day, the monocyte-derived M2 macrophages (M2MF) were treated  with or without IL-4 (20 ng/ml, Peprotech London, UK) for 6 hours.

value: whole blood

value: monocyte-derived M2 macrophages

tag: age


title: CD4+Tcells_CTRL_Patient 4

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

hyb_protocol: Labeled cRNA was then hybridized for 17 hours at 65°C on Whole Human Genome Microarray 4x44 K slides, (Agilent Technologies, Santa Clara, CA). After hybridization the slides were washed according to manufacturer’s protocols.

scan_protocol: The slides were scanned using the High-Resolution Microarray C Scanner (Agilent Technologies).

data_processing:
Data extraction was performed using Agilent Feature Extraction software.
A p-value cut-off of 0.05 and a fold-change cut-off of 2 were applied to identify differentially expressed genes able to discriminate between the study groups.

label_protocol: Labeled cRNA was generated using the Low Input Quick Amp Labeling (LIQA) kit (Agilent Technologies, Santa Clara, CA).

extract_protocol: CD4+ T cells were isolated from PBMCs using a CD4+ isolation kit (Miltenyi Biotech, Auburn, CA) according to the manufacturer's instructions. Total RNA was extracted with the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). The concentration of total RNA was measured using NANODROP® spectrophotometer ND-1000 (Thermo Scientific, Waltham, MA, US) and RNA integrity was measured using the Agilent 2100 BIOANALYZER® (Agilent Technologies Deutschland GmbH, Waldbronn, Germany) along with the Agilent® RNA 6000 Nano Kit.

value: CD4+ T cells isolated from total PBMC

tag: disease state

value: Control

value: Tacrolimus


title: CD4+Tcells_CTRL_Patient 5


title: ExVivoBlood_IL-4 rep2

description: Gene expression with sRANKL treatment

source_name: Peripheral Blood, sRANKL, replicate 2

value: IL-4 (20 ng/ml, Peprotech London, UK) for 6 hours.


title: CD4+Tcells_CTRL_Patient 1


title: CD4+Tcells_CTRL_Patient 3


title: CD4+Tcells_CAMR_patient 3

source_name: CD4+Tcells_chronic antibody mediated rejection

value: chronic antibody mediated rejection


title: ExVivoBlood_control rep1

description: Gene expression without sRANKL treatment

source_name: Peripheral Blood, control, replicate 1

value: control


title: CD4+Tcells_CAMR_patient 1


title: CD4+Tcells_CAMR_patient 4


title: Saline-10D-1


title: CD4+Tcells_CTRL_Patient 2


title: Naïve_CD11b+ CDC

city: La Jolla

first: Monica

last: Macal

address: 9500 Gilman Dr 0322

institute: UC San Diego

description: pooled from 5-8 mice/group

hyb_protocol: Following fragmentation, 15ug cRNA were hybridized to mouse genechip 430 2.0 for 16hr 45C

scan_protocol: Genechips were scanned using the GCS3000 scanner

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. The trimmed mean target intensity of each array where MAS5 has been median scaled to value of 100

source_name: spleen

label_protocol: Biotinylated cRNA amplified (2-Target Labeling Assay) from 20ng total RNA were prepared according to the standard Affymetrix protocol available (Technical Manual Affymetrix 2006)

extract_protocol: Qiagen Rneasy mini kits were used for isolation of total RNA

treatment_protocol: Splenic mononuclear cells were enriched by negative magnetic bead depletion of T and B cells.  Enriched cells were then FACS purified for pDC, CD11b+ cDC, and CD8+ cDC by BD FACS ARIA sort

tag: cell  type

value: Naïve CD11b+ CDC

value: 6-8 week adult


title: PBMC_CTRL_Patient 10

source_name: PBMC_Transplanted stable recipient

extract_protocol: PBMC were isolated by density separation over a Ficoll-PaqueTM (GE healthcare, Uppsala, Sweden) gradient (460g for 30 min) and were washed three times with PBS pH 7.4/1 mM EDTA (Sigma, Milan, Italy). Cells were counted and their viability was evaluated by trypan blue exclusion (>90% PBMC were viable).Total RNA was extracted from a minimum of 106 PBMCs using the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany). The concentration of total RNA was measured using NANODROP® spectrophotometer ND-1000 (Thermo Scientific, Waltham, MA, US) and RNA integrity was measured using the Agilent 2100 BIOANALYZER® (Agilent Technologies Deutschland GmbH, Waldbronn, Germany) along with the Agilent® RNA 6000 Nano Kit.

value: PBMC

value: Female


title: PBMC_CTRL_Patient 5


title: PBMC_CTRL_Patient 9


title: Naïve_CD8+ CDC

description: pooled from 5-8 mice/group

value: Naïve CD8+ CDC


title: PBMC_CTRL_Patient 4

value: Male


title: Naïve_PDC

description: pooled from 5-8 mice/group

value: Naïve PDC

value: female


title: ExVivoBlood_control rep2

source_name: Peripheral Blood, control, replicate 2

value: male


title: PBMC_CTRL_Patient 6


title: CD4+Tcells_CAMR_patient 2


title: SB MF 180K-CGH replicate 4

value: Pietermaritzburg


title: CD4+Tcells_CAMR_patient 5

value: Cyclosporine


title: PBMC_CTRL_Patient 2


title: PBMC_CAMR_Patient 9

source_name: PBMC_chronic antibody mediated rejection


title: PBMC_CAMR_Patient 10


title: PBMC_CTRL_Patient 1


title: pam48 (mterf6-1), biological rep3

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ATH1 Genome Array in a Hyridisation Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with Flexarry and RMA as normalization method.

source_name: pam48 (mterf6-1), biological rep3

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: A. thaliana plants were grown on potting soil (Stender) under controlled greenhouse conditions (daylight was supplemented with illumination from HQI Powerstar 400W/D, providing a total fluence of ~120 µmol photons m-2 s-1 on leaf surfaces and a 16/8 h light/dark cycle). Wuxal Super fertilizer (8% N, 8% P2O5, and 6% K2O; MANNA) was used according to the manufacturer’s instructions.

extract_protocol: Rneasy plant mini kit (QIAGEN) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Leaves of the same age of plants from the 8-leaf-rosette stage were harvested and frozen directly in liquid N2.

tag: ecotype

value: pam48 (mterf6-1)


title: PBMC_CAMR_Patient 8


title: pam48 (mterf6-1), biological rep2

source_name: pam48 (mterf6-1), biological rep2


title: PBMC_CTRL_Patient 3


title: PBMC_CAMR_Patient 5


title: pam48 (mterf6-1), biological rep1

source_name: pam48 (mterf6-1), biological rep1


title: Adult control cerebellum [AC3 miRNA]

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

country: United Kingdom

institute: Barts & The London School of Medicine & Dentistry

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in GenomeStudio

source_name: Adult control cerebellum AC3 (BioChain #A911104)

label_protocol: Cy3 Standard illumina prorocol

extract_protocol: RNA was extracted with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: Adult control cerebellum

tag: Sex

value: M


title: Adult control frontal lobe [AC2 miRNA]

source_name: Adult control frontal lobe AC2 (BioChain #A803159)

value: Adult control frontal lobe


title: Adult control cerebellum [AC1 miRNA]

source_name: Adult control cerebellum AC1 (BioChain #A510131)


title: Adult control cerebellum [AC4 miRNA]

source_name: Adult control cerebellum AC4 (BioChain #508112)


title: Adult control frontal lobe [AC7 miRNA]

source_name: Adult control frontal lobe AC7 (BioChain #A803160)


title: Adult control frontal lobe [AC6 miRNA]

source_name: Adult control frontal lobe AC6 (BioChain #A507293)


title: Adult control frontal lobe [AC5 miRNA]

source_name: Adult control frontal lobe AC5 (BioChain #B210079


title: wild type Col-0, biological rep1

source_name: wild type Col-0, biological rep1

tag: genotype

value: wild type


title: PBMC_CAMR_Patient 2

value: chronic antibody mediated rejection

value: Tacrolimus


title: Choroid plexus papilloma [P3 miRNA]

source_name: Paediartric brain tumour P4

tag: tissue

value: Choroid plexus papilloma

tag: grade

value: I

value: F

value: nd


title: wild type Col-0, biological rep3

source_name: wild type Col-0, biological rep3


title: wild type Col-0, biological rep2

source_name: wild type Col-0, biological rep2


title: PBMC_CAMR_Patient 7

value: PBMC

value: Male


title: PBMC_CAMR_Patient 4


title: PBMC_CAMR_Patient 6

value: Female


title: Choroid plexus papilloma [P2 miRNA]

source_name: Paediartric brain tumour P2


title: PBMC_CAMR_Patient 1


title: Choroid plexus papilloma [P4 miRNA]

source_name: Paediartric brain tumour P3


title: PBMC_CAMR_Patient 3

source_name: PBMC_chronic antibody mediated rejection


title: U87MG-miR338-5p

city: Brno

first: Andrej

last: Besse

address: Kamenice 5

institute: Masaryk University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The whole-genome expression data, Affymetrix raw data (.cel files), were normalized using the robust multichip average (RMA) algorithm from ‘oligo’ Bioconductor package in R version 3.0.1.

label_protocol: standard Affymetrix protocol

growth_protocol: GBM primary cell lines A172, T98G and U87MG were obtained from ATCC and cultivated in culture medium DMEM (Sigma Aldrich, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% nonessential amino acids, 2 mM L-glutamine, 4.5 g/l D-glucose, 110 mg/l sodium pyruvate, 100 µg/ml streptomycin and 100 U/ml penicillin (all Gibco, CA, USA). Cells were cultivated at 37°C in humidified atmosphere containing 5% CO2.

extract_protocol: mirVana miRNA Isolation Kit, with phenol

treatment_protocol: cell were transfected with pre-miR338-5p or with negative control

value: glioblastoma multiforme (GBM) cell line

tag: transfected with


title: Atypical teratoid/rhabdoid tumour [R4 miRNA]

source_name: Paediartric brain tumour R4

value: Atypical teratoid/rhabdoid tumour

value: IV

value: 9 months


title: Atypical teratoid/rhabdoid tumour [R5 miRNA]

source_name: Paediartric brain tumour R5

value: 2 months


title: Atypical teratoid/rhabdoid tumour [R3 miRNA]

source_name: Paediartric brain tumour R3


title: Atypical teratoid/rhabdoid tumour [R2 miRNA]

source_name: Paediartric brain tumour R2

value: 7 months


title: Atypical teratoid/rhabdoid tumour [R1 miRNA]

source_name: Paediartric brain tumour R1

value: M


title: Choroid plexus papilloma [P1 miRNA]

source_name: Paediartric brain tumour P1

value: 10 months


title: Medulloblastoma [M9 miRNA]

source_name: Paediartric brain tumour M9

value: Medulloblastoma


title: U87MG-Negative control

source_name: GBM_negative control

value: negative control


title: T98G-Negative control


title: Medulloblastoma [M6 miRNA]

source_name: Paediartric brain tumour M6


title: T98G-miR338-5p


title: Medulloblastoma [M8 miRNA]

source_name: Paediartric brain tumour M8


title: Medulloblastoma [M3 miRNA]

source_name: Paediartric brain tumour M3

value: 6 months


title: A172-miR338-5p


title: Medulloblastoma [M7 miRNA]

source_name: Paediartric brain tumour M7


title: bone marrow derived macs_media_only_2

city: New Haven

first: Raymond

middle: Morris

last: Johnson

state: CT

department: Med/Infectious Diseases

institute: Yale University

hyb_protocol: Standard hybridization cocktail, hybed 17 hours at 45C.

scan_protocol: Standard wash and stain controlled by GCOS

data_processing: Cel Files generated by GCOS, imported into Partek (ver. 6.2) and RMA signals were generated for only the core probe sets (28,853).   RMA signals were generated for the core probe sets using the RMA background correction, quantile normalization and summarization by Median Polish.  Summarized signals for each probe set were log2 transformed.

source_name: C57BL/6 mouse femur

label_protocol: Standard Affymetrix WT labeling and control kit starting with 100ng of total RNA.

growth_protocol: RPMI 1640 medium supplemented with 10 mM Hepes, 10% characterized FBS, 5x10-5M 2-ME, 25 uM gentamicin)

extract_protocol: RNAeasy Kit with optional RNAse-free DNAse step (Qiagen)

treatment_protocol: Monolayers treated with conditioned RPMI media 33%(v/v) from Chlamydia-specific CD4 T cell clone incubated with infected  epithelial monolayer supplemented to a final IFN-gamma concentration of 4 ng/ml versus RPMI media (no treatment control)

value: Media (no treatment)

tag: strain

value: femur bone marrow

value: GM-CSF bone marrow derived macrophages


title: bone marrow derived macs_media_only_4


title: Medulloblastoma [M1 miRNA]

source_name: Paediartric brain tumour M1


title: A172-Negative control


title: Neurons_siRbfox1&3_rep3

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description:
Hippocampal culture treated AraC, co-culture, and siRNAs
siRbfox1&3_Rep3

hyb_protocol: Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix).

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G.

data_processing:
Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
probe group file: mjay.pgf
meta-probeset file: mjay.clf

source_name: Hippocampal culture, AraC treated, co-cultured, Rbfox1 and Rbfox3 siRNAs

label_protocol: Samples were labeled using GeneChip Terminal Labeling Kit (Affymetrix).

growth_protocol: The mouse neurons were cultured as decribed by Ho et al. (PMID: 24784359).

extract_protocol: Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction.

treatment_protocol: Cultures were treated with AraC at 3 DIV and co-cultured with cortical culture at 6 DIV. SiRNAs were added at 10 DIV and incubated for 4 days.

value: Hippocampal culture

value: 14 DIV

value: AraC and co-culture

tag: sirna

value: Rbfox1 and Rbfox3


title: LLC1 3D cell culture replicate 1

city: Vilnius

first: Vaidotas

last: Stankevicius

address: Santariskiu 1

institute: National Cancer Institute

description: Biological replicate 1 of 3. LLC1 cells were cultivated under 2D or 3D cell culture conditions for 48 hours, total RNA was extracted and amplified and labeled with Cy3 or Cy5, respectively. For differential gene expression analysis cell grown under 2D conditions served as a control.

hyb_protocol: 825 ng of cRNA labeled with Cy3/Cy5 dyes was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized to Whole Mouse Genome 4x44k Oligonucleotide Microarrays (Agilent) for 17 hours at 65°C  using HS 400 hybridization station (Tecan).

scan_protocol: Microarrays were scanned  using Tecan LS Reloaded scanner.

data_processing: Image analysis was performed performed Imagene v9.0 software (BioDiscovery). Raw probe signal values were LOWES normalized.

source_name: Control LLC1 cell line cultivated in 2D cell culture

label_protocol: 1µg of total RNA was used for cDNA synthesis and amplification using MessageTMAmp aRNA kit (Ambion).  cRNA labeled with Cy3/Cy5 dyes using Arcturus® TURBO labelingTM CyTM3/CyTM5 Kit (Apllied Biosystems).

growth_protocol: For 2D cell culture, cells were cultured in DMEM cell culture medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 2nM glutamine (Gibco), 100 UI/ml penicillin (ROTH) and 0.1 mg/ml streptomycin (ROTH) at 37°C in a humidified atmosphere containing 5% CO2. For 3D cell culture, cells were plated in 0.5 mg/ml laminin rich extracellular matrix (GeltrexTM, Gibco) and cell culture medium upon a layer of agarose ir a 24-well cell culture plates.

extract_protocol: Total RNA was isolated from harvested cells using mirVana miRNA Isolation Kit (Ambion) according to manufacturer’s instructions. The quantity and quality of RNA were evaluated using Nanodrop 2000c (Thermo Scientific) and Bioanalyzer (Agilent).

tag: sample type

value: control

tag: growth condition

source_name: LLC1 cell line cultivated in 3D cell culture

value: experimental


title: LLC1 3D cell culture replicate 3

tag: cell line


title: LLC1 3D cell culture replicate 2


title: bone marrow derived macs_media_only_3

tag: treatment

tag: cell type


title: Neurons_siRbfox1&3_rep1

description:
Hippocampal culture treated AraC, co-culture, and siRNAs
siRbfox1&3_Rep1


title: Neurons_control_rep3

description:
Hippocampal culture treated AraC and co-culture
Control_Rep3

source_name: Hippocampal culture, AraC treated, co-cultured

value: No siRNA


title: Medulloblastoma [M5 miRNA]

source_name: Paediartric brain tumour M5

value: IV


title: Neurons_siRbfox1&3_rep2

description:
Hippocampal culture treated AraC, co-culture, and siRNAs
siRbfox1&3_Rep2


title: Ependymoma [E14 miRNA]

source_name: Paediartric brain tumour E14

value: Ependymoma

value: III

value: F


title: Medulloblastoma [M4 miRNA]

source_name: Paediartric brain tumour M4

value: Medulloblastoma

value: M


title: Ependymoma [E13 miRNA]

source_name: Paediartric brain tumour E13

value: II


title: Bm12.4 epithelial cell line_media_only_4

source_name: B6(C)-H2-Ab1bm12/KhEgJ mouse upper reproductive tract

value: Media (no treatment)

value: upper reproductive tract

value: Bm12.4 cells


title: Neurons_control_rep2

description:
Hippocampal culture treated AraC and co-culture
Control_Rep2

value: Hippocampal culture


title: Ependymoma [E9 miRNA]

source_name: Paediartric brain tumour E9


title: Medulloblastoma [M2 miRNA]

source_name: Paediartric brain tumour M2


title: Ependymoma [E12 miRNA]

source_name: Paediartric brain tumour E12


title: Neurons_control_rep1

description:
Hippocampal culture treated AraC and co-culture
Control_Rep1

value: 14 DIV


title: Ependymoma [E5 miRNA]

source_name: Paediartric brain tumour E5


title: Ependymoma [E10 miRNA]

source_name: Paediartric brain tumour E10


title: Ependymoma [E8 miRNA]

source_name: Paediartric brain tumour E8


title: Ependymoma [E7 miRNA]

source_name: Paediartric brain tumour E7


title: Ependymoma [E6 miRNA]

source_name: Paediartric brain tumour E6


title: Ependymoma [E11 miRNA]

source_name: Paediartric brain tumour E11

value: ND

value: nd


title: Ependymoma [E3 miRNA]

source_name: Paediartric brain tumour E3


title: Ependymoma [E4 miRNA]

source_name: Paediartric brain tumour E4


title: bone marrow derived macs_media_only_1

source_name: C57BL/6 mouse femur

value: femur bone marrow

value: GM-CSF bone marrow derived macrophages


title: Ependymoma [E2 miRNA]

source_name: Paediartric brain tumour E2


title: Ependymoma [E1 miRNA]

source_name: Paediartric brain tumour E1


title: Glioblastoma [GBM5 miRNA]

source_name: Paediartric brain tumour GBM5

value: Glioblastoma


title: Glioblastoma [GBM4 miRNA]

source_name: Paediartric brain tumour GBM4

value: IV


title: Bm12.4 epithelial cell line_media_only_3

source_name: B6(C)-H2-Ab1bm12/KhEgJ mouse upper reproductive tract


title: Bm12.4 epithelial cell line_media_only_2


title: C57epi.1 epithelial cell line_media_only_2

source_name: C57BL/6 mouse upper reproductive tract

value: C57epi.1 cells


title: Bm12.4 epithelial cell line_media_only_1


title: C57epi.1 epithelial cell line_media_only_4


title: C57epi.1 epithelial cell line_media_only_1


title: C57epi.1 epithelial cell line_media_only_3


title: Glioblastoma [GBM3 miRNA]

source_name: Paediartric brain tumour GBM3


title: Glioblastoma [GBM1 miRNA]

source_name: Paediartric brain tumour GBM1


title: Glioblastoma [GBM2 miRNA]

source_name: Paediartric brain tumour GBM2


title: Anaplastic astrocytoma [AA2 miRNA]

source_name: Paediartric brain tumour AA2

value: Anaplastic astrocytoma

value: III


title: Anaplastic astrocytoma [AA1 miRNA]

source_name: Paediartric brain tumour AA1


title: Diffuse astrocytoma [DA3 miRNA]

source_name: Paediartric brain tumour DA3

value: Diffuse astrocytoma


title: Pilocytic astrocytoma [PA14 miRNA]

source_name: Paediartric brain tumour PA14

value: Pilocytic astrocytoma

value: I

value: F


title: Pilocytic astrocytoma [PA12 miRNA]

source_name: Paediartric brain tumour PA12


title: Diffuse astrocytoma [DA1 miRNA]

source_name: Paediartric brain tumour DA1

value: II


title: Diffuse astrocytoma [DA2 miRNA]

source_name: Paediartric brain tumour DA2


title: Pilocytic astrocytoma [PA15 miRNA]

source_name: Paediartric brain tumour PA15

value: M


title: bone marrow derived macs_inflammatory_supernatent_4

source_name: C57BL/6 mouse femur

value: Inflammatory supernatant


title: bone marrow derived macs_inflammatory_supernatent_3


title: Bm12.4 epithelial cell line_inflammatory_supernatent_3

value: upper reproductive tract

value: Bm12.4 cells


title: bone marrow derived macs_inflammatory_supernatent_1


title: Pilocytic astrocytoma [PA11 miRNA]

source_name: Paediartric brain tumour PA11


title: Bm12.4 epithelial cell line_inflammatory_supernatent_2


title: Bm12.4 epithelial cell line_inflammatory_supernatent_4


title: Pilocytic astrocytoma [PA9 miRNA]

source_name: Paediartric brain tumour PA9


title: Pilocytic astrocytoma [PA8 miRNA]

source_name: Paediartric brain tumour PA8


title: Pilocytic astrocytoma [PA5 miRNA]

source_name: Paediartric brain tumour PA5


title: Pilocytic astrocytoma [PA6 miRNA]

source_name: Paediartric brain tumour PA6


title: Papillary glioneuronal [PGNT miRNA]

source_name: Paediartric brain tumour PGNT

value: Papillary glioneuronal


title: Pilocytic astrocytoma [PA7 miRNA]

source_name: Paediartric brain tumour PA7


title: Pilocytic astrocytoma [PA13 miRNA]

source_name: Paediartric brain tumour PA13


title: Pilocytic astrocytoma [PA10 miRNA]

source_name: Paediartric brain tumour PA10


title: Bm12.4 epithelial cell line_inflammatory_supernatent_1

source_name: B6(C)-H2-Ab1bm12/KhEgJ mouse upper reproductive tract


title: Pilocytic astrocytoma [PA2 miRNA]

source_name: Paediartric brain tumour PA2


title: bone marrow derived macs_inflammatory_supernatent_2

value: femur bone marrow


title: C57epi.1 epithelial cell line_inflammatory_supernatent_4

source_name: C57BL/6 mouse upper reproductive tract


title: C57epi.1 epithelial cell line_inflammatory_supernatent_3


title: C57epi.1 epithelial cell line_inflammatory_supernatent_1


title: Pilocytic astrocytoma [PA1 miRNA]

source_name: Paediartric brain tumour PA1


title: C57epi.1 epithelial cell line_inflammatory_supernatent_2


title: Pilocytic astrocytoma [PA3 miRNA]

source_name: Paediartric brain tumour PA3


title: D14-5 Tumor microenvironment at Day 14

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R, log2 transformed and filtered for probes with bad detection p-values in all samples.

source_name: tumor microenvironment

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

extract_protocol: Tissues were lysed using Tissue Lyser (Qiagen). RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: 8 weeks

value: Tissue

tag: replicate

value: Day 14 tumor microenvironment


title: BRCA1-unscreened_triple_negative_breast_cancer_sample9

city: GOSSELIES

first: SEBASTIEN

last: TOFFOLI

address: AVENUE GEORGES LEMAITRE 25

institute: IPG

scan_protocol: Agilent Technologies, protocol #G4410-90020, version 3.3. Agilent type C scanner (G2505C - DNA microarray scanner with surescan high-resolution technology) was used with the Agilent Scan Control software (Version A.8.4.1).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used for data extraction.  Agilent Genomic Workbench (Version 7.0) was used to analyse the data (Z-score, threshold 0.2)

source_name: BRCA1-unscreened triple negative breast cancer

tag: gender

value: Female

value: Breast cancer

tag: tumour type

source_name: Pooled gDNA 7 women

tag: reference

value: normal pooled gDNA 7 women

value: Lymphocyte


title: Colonic_macrphages_CTL

city: Atlanta

first: Timothy

middle: L

last: Denning

state: GA

address: 100 Piedmont Ave.

department: Center for Inflammation Immunity & Infection

institute: Georgia State University Institute for Biomedical Sciences

description: Gene expression data from untreated colonic macrophages

hyb_protocol: Fragmented cDNA The fragmented biotinylated targets were placed in hyb cocktail and were hybridized on the Mouse Gene 1.0ST arrays following standard Nugen/Affymetrix Protocols

scan_protocol: Hybridized chips were stained and washed and were scanned with a GeneArray scanner (Affymetrix)

data_processing: RMA

source_name: Untreated lamina propria macrophages

label_protocol: Biotinylated cRNA were prepared with the Nugen's Ovation Biotin System according to the standard Affymetrix protocol from 100 ng total RNA

extract_protocol: Total RNA was extracted from freshly isolated, flow cytometry–sorted lamina propria macrophages (CD45+IAb+CD11b+F4/80+CD103-) using the Qiagen Rneasy kit

value: Mice were provided drinking water for 5 days


title: BRCA1-unscreened_triple_negative_breast_cancer_sample15

hyb_protocol: Agilent Technologies, protocol #G4410-90020, version 3.3


title: D14-3 Tumor microenvironment at Day 14

tag: age


title: BRCA1-unscreened_triple_negative_breast_cancer_sample8

label_protocol: Agilent Technologies, protocol #G4410-90020, version 3.3


title: BRCA1-unscreened_triple_negative_breast_cancer_sample13

extract_protocol: Agilent Technologies, protocol #G4410-90020, version 3.3


title: BRCA1-unscreened_triple_negative_breast_cancer_sample14


title: BRCA1-unscreened_triple_negative_breast_cancer_sample12


title: Colonic_macrphages_DSS

description: Gene expression data from DSS-treated colonic macrophages

source_name: DSS-treated lamina propria macrophages

value: Mice were provided 3% (wt/vol) DSS dissolved in the drinking water for 5 days


title: BRCA1-unscreened_triple_negative_breast_cancer_sample11


title: BRCA1-unscreened_triple_negative_breast_cancer_sample5


title: D14-2 Tumor microenvironment at Day 14


title: D14-1 Tumor microenvironment at Day 14


title: BRCA1-unscreened_triple_negative_breast_cancer_sample10


title: BRCA1-unscreened_triple_negative_breast_cancer_sample7


title: BRCA1-unscreened_triple_negative_breast_cancer_sample4


title: D14-4 Tumor microenvironment at Day 14


title: BRCA1-unscreened_triple_negative_breast_cancer_sample1


title: BRCA1-unscreened_triple_negative_breast_cancer_sample3


title: BRCA1-unscreened_triple_negative_breast_cancer_sample2


title: D4-4 Tumor microenvironment at Day 4

value: Day 4 tumor microenvironment


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample20

source_name: BRCA1-non-mutated triple negative breast cancer


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample19


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample21


title: CD25 DC injected mice,rep3

city: MONTPELLIER

first: Paul

last: CHUCHANA

address: 80 rue Augustin Fliche

country: France

institute: CNRS

description: DC-induced spleen CD25+

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on the Affymetrix® MG-430 PM Array Strip. StripChips were washed and stained on the fluidic station of the Affymetrix GeneAtlas system with HWS kit.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas scanner.

data_processing: Data were generated with Affymetrix Expression Console v 1.2.1 and GCRMA algorithm

source_name: Spleen DBA/1 DC-injected

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneAtlas IVT Express protocol from 100 ng total RNA (GeneAtlas 3'IVT ExpressTechnical Manual, 2010, P/N702833 Rev4 Affymetrix).

growth_protocol: Mice were repetitively injected intraperitonealy with immature dendritic cells (0.5 x 106), day -7, -5 and -3, before their euthanasia. Splenocytes from DC vaccinated mice were recovered by filtration on cell strainer, washed and CD4+ cells were purified by negative selection using Dynabeads. Cells were stained with anti-CD4, anti-CD49b and anti-CD25 conjugated antibodies and cell sorting was performed on FACSAria

extract_protocol: Rneasy Micro-kit was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: We determined the differential transcriptional profile associated with DC-vaccination protocol using the comparative analysis of CD4+ cells isolated from non-injected and DC-injected mice. The transcriptional profile of DC-induced CD25+ and CD49b+ include both the transcriptional profile associated with the cell subset and the DC-vaccination induced transcripts.

value: spleen CD25+

value: DC-induced


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample18


title: BRCA1-unscreened_triple_negative_breast_cancer_sample6


title: D4-3 Tumor microenvironment at Day 4


title: D4-2 Tumor microenvironment at Day 4


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample17


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample14


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample15


title: CD25 DC injected mice,rep2

description: DC-induced spleen CD25+


title: D4-1 Tumor microenvironment at Day 4


title: CTRL 5 Control Tissue

source_name: control tissue

value: control


title: CTRL 4 Control Tissue


title: CTRL 6 Control Tissue


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample16


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample11


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample12


title: CTRL 7 Control Tissue


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample10


title: CD49b DC injected mice,rep2

description: DC-induced spleen CD49b+

value: spleen CD49b+


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample9


title: CD25 DC injected mice,rep1

description: DC-induced spleen CD25+


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample8


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample5


title: CTRL 2 Control Tissue


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample3


title: CD49b DC injected mice,rep1

description: DC-induced spleen CD49b+


title: CTRL 3 Control Tissue


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample13


title: BRCA1-non-mutated_triple_negative_breast_cancer_sample6


title: CD49b DC injected mice,rep3

description: DC-induced spleen CD49b+


title: CD4 DC injected mice,rep2

description: DC-induced spleen CD4+

value: spleen CD4+


title: CD4 Naive mice,rep2

description: ex-vivo spleen CD4+

source_name: Spleen DBA/1 naive

value: naive