title: Treated parasites from time-point T3 replicate 2

city: Pretoria

first: Shaun

last: Reeksting

state: Gauteng

address: Lunnon Rd.

country: South Africa

institute: University of Pretoria

description: biological replicate 2 of 3 4PEHz-treated schizont stage parasites

hyb_protocol: Individual Cy5 labelled cDNA samples (20 pmol) were combined with 20 pmol of the Cy3 labelled reference pool cDNA sample, together with proprietary Agilent)buffer solutions. The tubes were incubated at 60°C for 30 min, after which 25 µL 2× GE hybridization buffer was gently added to ensure no unwanted foaming occurred, and stored on ice. After loading the slide chamber assembly was tightened and placed in a hybridization oven at 65°C for 18 h on rotational speed 10. After this the slides were washed twice in wash buffer 1 (Proprietary, Agilent) for 1 min, followed by washing in preheated (37°C) wash buffer 2 (Proprietary, Agilent) for 1 min

scan_protocol: Slides were dried by centrifugation using an Agilent desktop centrifuge, after which slides were scanned on an Axon GenePix 4000B scanner (Molecular devices). Automated spot detection was performed to ensure correct spot quality, saturation and signal-to-noise ratios.

data_processing: The LIMMA (Smyth et al. 2005 Limma: linear models for microarray data, www.bioconductor.com) and LIMMA-GUI packages were used to analyse the gene expression microarray data. The R computing environment was used to normalised array data using within array global robust spline normalisation and between array Gquantile normalisation. Linear contrast matrices were used to compare treated expression values to untreated control from respective time points. Differentially expressed genes were defined as transcripts with an adjusted P-value (for multiple testing, Smyth et al. 2005) smaller than 0.05, with log2 ratio ≥ 0.75 and log2 ratio ≤ -0.75.

organism: Plasmodium falciparum

source_name: Treated schizont stage parasite cDNA

label_protocol: cDNA (1.5 µg) of each sample, together with 1.5 µg reference pool samples, were dried in vacuo, after which the samples were resuspended in 2.5 µL water (SABAX, Adcock-Ingram). Dyes, prepared in DMSO were diluted in 100 mM freshly prepared Na2CO3 (pH 9.0) and added to resuspended cDNA samples. Excess dye was removed using the QIAquick PCR purification kit (Qiagen) according to the manufacturer’s instructions.

growth_protocol: P. falciparum (3D7) parasites were maintained under aseptic conditions in continuous culture in RMPI 1640 culture medium with 25 mM HEPES, 10 mM glucose, 20 mM sodium bicarbonate, 25 mM hypoxanthine and 0.5% w/v AlbuMAX II (Invitrogen) at pH 7.4. Parasite cultures were maintained at 5% haematocrit using human O+ erythrocytes. Before drug treatments, the synchronicity of the parasite life-stages was controlled by three consecutive D-sorbitol (5% w/v in 1x PBS) treatments, each 8 h apart in early and late ring-stage parasite cultures.

extract_protocol: RNA was isolated from infected erythrocytes using Tri-reagent (Sigma-Aldrich) combined with RNeasy mini kit (Qiagen) using on-column DNase-1 digestion (Qiagen) according to the each respective manufacturer’s instructions. First strand cDNA synthesis was performed by mixing 4 µg RNA, 250 pmol OligodT primer (dT23VN) and 775 pmol random nonamer (N9) using Superscript III (Invitrogen) according to the manufacturer’s instructions. The synthesised cDNA was subjected to a clean-up procedure using the PCR Clean-up kit (Macherey-Nagel) as recommended by the manufacturer. A cDNA reference pool comprising of all the time points was created by combining 1.5 µg cDNA from each of the 24 samples, this was mixed and split into 24 aliquots.

treatment_protocol: Early ring stage parasites (defined as 0 hours post invasion, HPI) were treated with 20 µM 4PEHz, equivalent to 2 x IC50. After 24 h, the media was replaced with fresh media, maintaining drug pressure for the 4PEHz treatments. Infected erythrocytes were harvested at three different time points each 12 h apart (t1 = 12 HPI, t2 = 24 HPI and t3 = 36 HPI) by removing 10 mL culture from the flasks and washing the harvested infected erythrocytes twice with 10 pellet volumes of cold 1x PBS

tag: time point

value: time point 3 (36 HPI)

source_name: pooled cDNA from all time points of 4PEHz-treated and untreated cells


title: Treated parasites from time-point T3 replicate 3

status: Public on Feb 28 2014

type: RNA

department: Biochemistry

description: biological replicate 3 of 3 4PEHz-treated schizont stage parasites

molecule: total RNA

tag: strain

tag: treatment


title: DBA patient C

city: Boston

first: Vijay

middle: G

last: Sankaran

state: MA

address: 300 Longwood Avenue

country: USA

institute: Boston Children's Hospital

description: DBA patient C

hyb_protocol: Standard Affymetrix HG-U133A arrays were hybridized with purified RNA samples.

scan_protocol: Signal amplication on Affymetrix Fluidics station 400

data_processing: Microarray data were processed with RMA from the affy package in Bioconductor using custom probeset definitions for NCBI Entrez Genes derived from the method of Dai M et al (PMID: 16284200): HG-U133A Version 16 Custom CDF.

label: biotin

organism: Homo sapiens

source_name: DBA patient C

label_protocol: Standard Affymetrix label protocol

growth_protocol: Primary patient samples that did not involve cell culture.

extract_protocol: Qiagen RNA purification

treatment_protocol: Primary CD34+/CD71(high)/CD45- mononuclear cells of the bone marrow of DBA patients (with RPS19 mutations) and controls were harvested and sorted.

tag: tissue

value: bone marrow

tag: cell type

tag: disease status

value: Diamond-Blackfan anemia (due to RPS19 mutations)


title: CD4 unstimulated 5 days, rep1

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description:
Sample 13
Gene expression data of unstimulated CD4+ AND-TCR transgenic cells following 2 days of culture and 3 days in an antigen-free host.

hyb_protocol: Biotin-labled cRNA was hybridized on Affymetrix Mouse Genome 430.2 arrays in a GeneChip Hybridization oven 645, washed and stain3d with a GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000.

data_processing: Primary CEL files were normalized with the ExpressionFileCreator module implementing RMA and redundant probe sets collapsed with the CollapseDataset module.

organism: Mus musculus

source_name: day 5, CD4, unstimulated

label_protocol: Amplified aRNA (10µg) was processed using the Message Amp II-Biotin Enhanced Kit (Ambion).

growth_protocol: 1-2x10^5 TCR transgenic CD4+ or CD8+ T cells were cultured for 2 days in 96-well untreated round bottom plates or plates precoated with 10 µg/ml anti-CD3 and anti-CD28 mAbs in RPMI supplemented with 10% FCS, 2 mM glutamine, 50µM 2-ME, antibiotics and 5 ng/ml IL7.

extract_protocol: RNAs from AND and OT1 cells sorted from spleen and subcutaneous lymph nodes were isolated as described (Obst et al,. 2007, Proc Natl Acad Sci USA 104, 15460-15465).

treatment_protocol: For samples 13-28, T cells were adoptively transferred into antigen-free or -expressing (dtg-O or -M) hosts.

tag: strain/background

value: CD4+ AND-TCR transgenic T lymphocytes

value: unstimulated in culture

tag: host

value: antigen-free


title: CD8 stimulated 2 days, rep3

description:
Sample 12
Gene expression data of CD8+ OT1-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 mAbs for 2 days of culture.

source_name: day 2, CD8, stimulated

value: CD8+ OT1-TCR transgenic T lymphocytes

value: stimulated with anti-CD3 and anti-CD28 mAbs in culture


title: Control B

description: Control B

source_name: Control B

value: healthy control


title: CD4 transient 5 days, rep2

description:
Sample 16
Gene expression data of CD4+ AND-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 for 2 days of culture and additional 3 days in antigen-free host.

source_name: day 5, CD4, transiently stimulated


title: CD8 unstimulated 2 days, rep3

description:
Sample 9
Gene expression data of unstimulated CD8+ OT1-TCR transgenic cells following 2 days of culture.

source_name: day 2, CD8, unstimulated


title: Control A

description: Control A

source_name: Control A


title: Treated parasites from time-point T3 replicate 1

description: biological replicate 1 of 3 4PEHz-treated schizont stage parasites


title: CD8 stimulated 2 days, rep2

description:
Sample 11
Gene expression data of CD8+ OT1-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 mAbs for 2 days of culture.


title: Control untreated parasites from time-point T3 replicate 3

description: biological replicate 3 of 3 untreated schizont stage parasites

source_name: Untreated schizont stage parasite cDNA

value: untreated


title: Treated parasites from time-point T1 replicate 2

description: biological replicate 2 of 2 4PEHz-treated early rings stage parasites

source_name: Treated early ring stage parasite cDNA

value: time point 1 (12 HPI)


title: CD4 stimulated 2 days, rep3

description:
Sample 6
Gene expression data of CD4+ AND-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 mAbs for 2 days of culture.

source_name: day 2, CD4, stimulated


title: Treated parasites from time-point T2 replicate 2

description: biological replicate 2 of 2 4PEHz-treated trophozoite stage parasites

source_name: Treated trophozoite parasite cDNA

value: time point 2 (24 HPI)


title: CD8 stimulated 2 days, rep1

description:
Sample 10
Gene expression data of CD8+ OT1-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 mAbs for 2 days of culture.


title: Treated parasites from time-point T2 replicate 1

description: biological replicate 1 of 2 4PEHz-treated trophozoite stage parasites


title: Control untreated parasites from time-point T2 replicate 1

description: biological replicate 1 of 2 untreated trophozoite stage parasites

source_name: Untreated trophozoite stage parasite cDNA


title: CD8 unstimulated 2 days, rep1

description:
Sample 7
Gene expression data of unstimulated CD8+ OT1-TCR transgenic cells following 2 days of culture.


title: CD4 stimulated 2 days, rep2

description:
Sample 5
Gene expression data of CD4+ AND-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 mAbs for 2 days of culture.


title: CD8 unstimulated 2 days, rep2

description:
Sample 8
Gene expression data of unstimulated CD8+ OT1-TCR transgenic cells following 2 days of culture.


title: Control untreated parasites from time-point T3 replicate 1

description: biological replicate 1 of 3 untreated schizont stage parasites


title: Control untreated parasites from time-point T2 replicate 2

description: biological replicate 2 of 2 untreated trophozoite stage parasites


title: CD4 stimulated 2 days, rep1

description:
Sample 4
Gene expression data of CD4+ AND-TCR transgenic cells stimulated with anti-CD3 and anti-CD28 mAbs for 2 days of culture.


title: Control untreated parasites from time-point T3 replicate 2

description: biological replicate 2 of 3 untreated schizont stage parasites


title: Mouse pachytene spermatocytes, biological rep 3, chip F

status: Public on Feb 27 2014

city: Shatin

first: Tin-Lap

last: Lee

address: Area 39

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description:
Spcy_F.bar
Affymetrix Mouse Tiling 1.1R Array Set

hyb_protocol: Purified biotin-labelled cDNA was hybrided to the microarray gene for 16 hours at 45C with 60 rpm rotation on Affymetrix Mouse Tiling 1.1R Array Set (14 GeneChips per set). GeneChips were washed and stained in the Afymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G and the images were obtained by the Affymetrix GeneChip Operating Software (GCOS).

data_processing:
Expression data were analyzed with Affymetrix Tiling Analysis Software (TAS) and library files BPMAP files version 35 (available from Affymetrix website http://www.affymetrix.com/)
A BAR file was created for each triplicate.
The resulting BAR files were generated by the Affymetrix TAS using probe analysis parameters: Bandwidth = 75, Test type = One side Upper, Intensities = PM/MM

label: Biotin

source_name: Mouse pachytene spermatocytes

label_protocol: cDNA was synthesized with GeneChip WT Amplified Double-Stranded cDNA Synthesis Kit and amplified with GeneChip WT cDNA Amplification Kit. Amplified double-stranded cDNA was labeled with GeneChip WT Double-Strand DNA Terminal Labeling Kit according to manufacturer's guideline.

growth_protocol: Balb/c mice were on a 12-hour light-dark cycle in a pathogen-free animal facility.

extract_protocol: 15 micrograms of total RNA was extracted for each biological replicate. RNA quality was validated with Bioanalyzer 2100 (Agilent). mRNA was enriched with RiboMinus Human/Mouse Transcriptome Isolation Kit according to manufacturer's protocol.

treatment_protocol: Testes from mice at different ages were harvested and decapsulated. Isolated seminiferous tubules were enzymatic digested and mechanically dissociated to single cells, and undergone differential plating for 2 hours to eliminate Sertoli cells. Cells at different developmental stages were isolated by a preivously described method (Bellvé AR, et al. J Cell Biol 1977; 74:68-85). The purities of three isolated cell types were all above 90%.

value: Balb/c

tag: gender

value: male

tag: age

value: 60 days

value: pachytene spermatocytes


title: Mouse pachytene spermatocytes, biological rep 1, chip F


title: Mouse round spermatids, biological rep 1, chip F

description:
Sptd_F.bar
Affymetrix Mouse Tiling 1.1R Array Set

source_name: Mouse round spermatids

value: round spermatids


title: Mouse pachytene spermatocytes, biological rep 2, chip F


title: Mouse round spermatids, biological rep 2, chip F


title: CD4 unstimulated 2 days, rep3

description:
Sample 3
Gene expression data of unstimulated CD4+ AND-TCR transgenic cells following 2 days of culture.

source_name: day 2, CD4, unstimulated


title: Mouse round spermatids, biological rep 3, chip F


title: CD4 unstimulated 2 days, rep2

description:
Sample 2
Gene expression data of unstimulated CD4+ AND-TCR transgenic cells following 2 days of culture.


title: Mouse round spermatids, biological rep 2, chip G

description:
Sptd_G.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Control untreated parasites from time-point T1 replicate 1

description: biological replicate 1 of 2 untreated early rings stage parasites

source_name: Untreated early ring stage parasite cDNA


title: Mouse type A spermatogonia, biological rep 2, chip F

description:
Spga_F.bar
Affymetrix Mouse Tiling 1.1R Array Set

source_name: Mouse type A spermatogonia

value: 6 days

value: type A spermatogonia


title: Treated parasites from time-point T1 replicate 1

description: biological replicate 1 of 2 4PEHz-treated early rings stage parasites

source_name: pooled cDNA from all time points of 4PEHz-treated and untreated cells


title: Control untreated parasites from time-point T1 replicate 2

description: biological replicate 2 of 2 untreated early rings stage parasites


title: Mouse type A spermatogonia, biological rep 3, chip F


title: CD4 unstimulated 2 days, rep1

description:
Sample 1
Gene expression data of unstimulated CD4+ AND-TCR transgenic cells following 2 days of culture.


title: Mouse round spermatids, biological rep 1, chip G


title: Mouse type A spermatogonia, biological rep 3, chip G

description:
Spga_G.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 3, chip G

description:
Spcy_G.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse round spermatids, biological rep 3, chip G


title: Mouse type A spermatogonia, biological rep 1, chip F


title: Mouse pachytene spermatocytes, biological rep 1, chip G


title: Mouse type A spermatogonia, biological rep 2, chip G


title: U937

type: genomic

city: Montreal

first: Josée

last: Dostie

state: QC

address: 3655 Promenade Sir-William-Osler

country: Canada

institute: McGill University

description: Raw feature file from scanning 5C library on microarray and corresponding normalized data

hyb_protocol: As per the manufacturer’s guidelines, approximately 100 ng of 5C library were individually hybridized to arrays using the NimbleGen CGH Hybridization kit.

scan_protocol: 5C arrays were scanned with a DNA microarray scanner (Agilent Technologies, model G2505) at 5 µm resolution.

data_processing:
Raw data were extracted from the images using the NimbleScan 2.6 software (NimbleGen Systems, Inc.), and specific features were extracted with our 'ArrayQC' software and then normalized using our 'Ifcalculator' software.
420 out of over 350,00 probes: 5C data filtered for noise and normalized for both quantity of DNA hybridized (using a gene desert) and primer pair efficiency (using a BAC library)

molecule: genomic DNA

source_name: 5C library from U937 cell line

label_protocol: The 5C libraries were amplified by PCR with the T7 (TAATACGACTCAACTATAGCC) and 5'-Cy3-labelled T3 (TATTAACCCTCACTAAAGGGA) primers, respectively. Unincorporated primers and other contaminants were removed from the 5C libraries using the MinElute Reaction Cleanup kit (Qiagen®).

growth_protocol: Grown in RPMI 1640 (Gibco) supplemented with 10% FBS (Fisherbrand), and 1% penicillin-streptomycin (Invitrogen™).

extract_protocol: 5C libraries were generated by incubating an individual 3C library with a pool of 5C primers to a final volume of 10ul of annealing buffer (20mM tris-acetate pH 7.9, 50mM potassium acetate, 10mM magnesium acetate, and 1mM dithiothreitol), and to final individual primer concentrations of 20nM. 5C primers were annealed to 3C templates overnight at 48ºC, and ligated the following day by adding 20ul of ligation buffer containing 10 units of Taq DNA ligase (NEB; 25mM Tris-HCl pH 7.6, 31.25mM potassium acetate, 12.5mM magnesium acetate, 1.25mM NAD, 12.5mM dithiothreitol, 0.125% Triton X-100) for 1h at 48ºC. The reactions were terminated by a 10 minute incubation at 65ºC.

tag: cell line

tag: mll state

value: wt

tag: leukemia type

value: ALL


title: NT2D1-24h

source_name: 5C library from NT2D1 cell line

growth_protocol: Cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco) supplemented with 10% FBS (HyClone) in the presence of 1% penicillin–streptomycin (Invitrogen™; 'complete DMEM').

value: EC


title: Mouse round spermatids, biological rep 3, chip H

description:
Sptd_H.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse type A spermatogonia, biological rep 1, chip G


title: Mouse round spermatids, biological rep 2, chip H


title: Mouse round spermatids, biological rep 1, chip H


title: RS4;11

source_name: 5C library from RS4;11 cell line


title: NOMO-1

source_name: 5C library from NOMO-1 cell line

value: AML


title: HL60

source_name: 5C library from HL60 cell line


title: Mouse pachytene spermatocytes, biological rep 2, chip G


title: Karpas-45

source_name: 5C library from Karpas-45 cell line

growth_protocol: Grown in RPMI 1640 (Gibco) supplemented with 20% FBS (Fisherbrand), and 1% penicillin-streptomycin (Invitrogen™).

value: AFX


title: NT2D1-3


title: ML-2

source_name: 5C library from ML-2 cell line


title: MOLT-4

source_name: 5C library from MOLT-4 cell line


title: NT2D1-2


title: Mouse pachytene spermatocytes, biological rep 1, chip H

description:
Spcy_H.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 3, chip H


title: Mouse type A spermatogonia, biological rep 3, chip H

description:
Spga_H.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: NT2D1-1


title: Mouse pachytene spermatocytes, biological rep 2, chip H


title: NALM6-5

source_name: 5C library from NALM6 cell line

growth_protocol: Grown in RPMI 1640 medium (Wisent), supplemented with 10% FBS (HyClone), and 1% penicillin-streptomycin (Gibco).


title: Jurkat

source_name: 5C library from Jurkat cell line

value: Jurkat


title: Mouse type A spermatogonia, biological rep 2, chip H


title: NALM6-3


title: NALM6-1


title: stat phase wt2 (minimal medium)

type: mixed

city: Norwich

first: Arthur

last: Thompson

address: Colney Lane

country: United Kingdom

institute: Institute of Food Research

description: Biologica replicate 2 of 3

hyb_protocol: Hybridisation according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: GenePix 4000A at 10µm resolution

data_processing: Intensity ratios of channel 1 (cDNA) divided by channel 2 (reference gDNA) signals are calculated usiong BlueFuse 3.01 (BlueGnome, Cambridge, UK). Data centering was subsequently performed using the block median

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: S. Typhimurium wt. Biol. Rep. 2

label_protocol: Labelling according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

growth_protocol: Grown aerobically at 370C with shaking at 250rpm in minimal medium MM5.8 (Erikkson et al., 2006 Inf & Imm., 74:1243) to stationary phase overnight

extract_protocol: RNA extracted according to Erikkson et al., 2006 Inf & Imm., 74:1243 and http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

treatment_protocol: Where appropriate 1µm cortisol added.

tag: genotype

source_name: S. Typhimurium 112910a


title: NALM6-4


title: NB4-2

source_name: 5C library from NB4 cell line

growth_protocol: Grown in RPMI 1640 medium (Gibco), supplemented with 10% FBS (Wisent), 1 mM L-glutamine (Invitrogen™), and 1% penicillin-streptomycin (Invitrogen™).


title: Mouse type A spermatogonia, biological rep 1, chip H


title: Mouse round spermatids, biological rep 3, chip I

description:
Sptd_I.bar
Affymetrix Mouse Tiling 1.1R Array Set

source_name: Mouse round spermatids


title: Mouse round spermatids, biological rep 2, chip I


title: Mouse round spermatids, biological rep 1, chip I


title: Mouse pachytene spermatocytes, biological rep 3, chip I

description:
Spcy_I.bar
Affymetrix Mouse Tiling 1.1R Array Set

source_name: Mouse pachytene spermatocytes


title: KOPN8-2

source_name: 5C library from KOPN8 cell line

growth_protocol: Grown in RPMI 1640 (Gibco) supplemented with 10% FBS (Fisherbrand) and 1% penicillin-streptomycin (Invitrogen™)

value: ENL


title: HB1119

source_name: 5C library from HB1119 cell line

growth_protocol: Grown in RPMI 1640 (Wisent) supplemented with 10% FBS (HyClone), 1mM L-glutamine (Gibco) and 10% penicillin-streptomycin (Invitrogen™).


title: ENL-B-2

source_name: 5C library from ENL cell line

growth_protocol: Cultured in alpha-MEM (Minimum Essential Media) containing glutamine, ribonucleosides and deoxyribonucleosides (Gibco, cat. no. 12571-071), 20% fetal bovine serum (FBS; HyClone Premium Serum), 5% human plasma (Stem Cell Technologies peripheral blood, cat. no. PB021F), and a growth factor cocktail containing the following human recombinant factor: 100 ng/ml rhSCF (Gibco, cat. no. PHC2111), 10 ng/ml rhIL-3 (Gibco, cat. no. PHC0034), 5 ng/ml rhIL-7 (Gibco, cat. no. PHC0075), 5 ng/ml rhFLT3 (Gibco, cat. no. PHC9414). The media was not supplemented with antibiotics, and the human plasma was filtered through a 0.22 µM membrane before adding to the media. The growth factor cocktail was prepared as a mixture and stored in PBS containing 0.5% BSA (Sigma, cat. no. A9418-5G) at -20°C.


title: Mouse pachytene spermatocytes, biological rep 2, chip I


title: ENL-A-4


title: ENL-A-3


title: Mouse pachytene spermatocytes, biological rep 1, chip I


title: ENL-B-1


title: ENL-A-1


title: THP1-F-2

source_name: 5C library from THP1 cell line

growth_protocol: Grown in Roswell Park Memorial Institute medium (RPMI 1640; Invitrogen™) containing 10% FBS (HyClone), 50 mM 2-mercaptoethanol (Invitrogen™), 1mM sodium pyruvate (Invitrogen™), 10 mM HEPES (Invitrogen™), and 1% penicillin-streptomycin (Invitrogen™).


title: ENL-A-2


title: THP1-F-1


title: THP1-E-2


title: NB4-1


title: Mouse type A spermatogonia, biological rep 3, chip I

description:
Spga_I.bar
Affymetrix Mouse Tiling 1.1R Array Set

source_name: Mouse type A spermatogonia


title: KOPN8-1


title: DMH_14m_dmh_7

city: Warsaw

first: Hanna

last: Oszkiel

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: WARSAW UNIVERSITY OF LIFE SCIENCES – SGGW  (WULS-SGGW)

description: Experimental rat 7 after 14 months of experiment

hyb_protocol: according to the Agilent manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C US10353831 scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: liver tissue from 1,2-dimethylhydrazine (DMH) treated group

growth_protocol: Animals were divided into two groups: a control group and an experimental group. Rats from both groups were receiving semi-synthetic diets formulated according to the nutritional requirements for laboratory animals and described in National Research Council. The application of the semi-synthetic diet allowed elimination of the additional impact of biologically active compounds contained in commercially available diets. To experimental  diet the following biologically active compounds were added: 6% of salmon fat replacing lard (to increase the level of unsaturated fatty acids), 8% of hydrolysed water extract from small-leaved linden (Tilia cordata) inflorescence (as a source of antioxidant compounds), 8% puree from giant pumpkin (Curcubita macima) (the source of beta-carotene) and 1% of two strains of bacteria with documented probiotic activity: Lactobacillus acidophilus LA-5 and Bifidobacterium animals ssp. lactis. The dry matter content of both diets was the same. All rats in 14 month of experiment were given 1,2-dimethylhydrazine (DMH) by intraperitoneal injection at a dose of 30mg/kg of body weight once a week to induce the process of carcinogenesis.

extract_protocol: Total RNA extracted using RNeasy Lipid Tissue Mini Kit following manufacturer's instructions (Qiagen, USA)

treatment_protocol: not applicable

tag: group

value: experimental

value: liver

tag: duration of the experiment

value: 14 months

source_name: common reference sample compsed of total RNAs isolated from 10-week healthy rats not participating in the experiment, haused for two weeks in the same room with experimental rats

value: common reference


title: ENL-B-4


title: DMH_14m_dmh_5

description: Experimental rat 5 after 14 months of experiment

label_protocol: according to the Agilent manufacturer's protocol


title: DMH_14m_dmh_6

description: Experimental rat 6 after 14 months of experiment


title: THP1-E-1


title: Mouse type A spermatogonia, biological rep 2, chip I

value: Balb/c

value: male


title: Mouse type A spermatogonia, biological rep 1, chip I


title: DMH_14m_dmh_4

description: Experimental rat 4 after 14 months of experiment


title: THP1-D-1


title: THP1-A-1


title: DMH_14m_dmh_1

description: Experimental rat 1 after 14 months of experiment


title: THP1-B-1


title: THP1-C-1


title: AF9-A-2


title: Control_14m_dmh_5

description: Control rat 5 after 14 months of experiment

source_name: liver tissue from control group

value: control


title: AF9-A-1


title: DMH_14m_dmh_2

description: Experimental rat 2 after 14 months of experiment


title: Control_14m_dmh_4

description: Control rat 4 after 14 months of experiment


title: Control_14m_dmh_3

description: Control rat 3 after 14 months of experiment


title: DMH_14m_dmh_3

description: Experimental rat 3 after 14 months of experiment


title: Control_14m_dmh_2

description: Control rat 2 after 14 months of experiment


title: Control_14m_dmh_1

description: Control rat 1 after 14 months of experiment


title: affyexp_wt_glucose_NH4CL_anaerobic_3.CEL

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

institute: University of California San Diego

description: SAMPLE 18

hyb_protocol: cDNA synthesis, fragmentation, end-terminus biotin labeling, and array hybridization were performed as recommended by Affymetrix standard protocol.

data_processing: Raw CEL files were analyzed using robust multi-array average for normalization and calculation of probe intensities. The processed probe signals derived from each microarray were averaged for both the wild type and deletion mutant strains. This was done using the GCRMA package (version 2.13) from Bioconductor in R.

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: All strains used in this study were E. coli K-12 MG1655 and its derivatives. The deletion mutants (Δfnr and ΔarcA) were constructed by a λ red and FLP-mediated site-specific recombination method. Glycerol stocks of E. coli strains were inoculated into M9 minimal medium containing 0.2% (w/v) carbon source (glucose) and 0.1% (w/v) nitrogen source (NH4Cl), and cultured overnight at 37 °C with constant agitation. The cultures were diluted 1:100 into fresh minimal medium and then cultured at 37 °C to an appropriate cell density with constant agitation. For the anaerobic cultures, the minimal medium were flushed with nitrogen and then continuously monitored using a polarographic-dissolved oxygen probe (Cole-Parmer Instruments) to ensure anaerobicity. For nitrate respiration 20 mmol potassium nitrate was added.

extract_protocol: Samples for transcriptome analysis were taken from exponentially growing cells. From the cells treated by RNAprotect Bacteria Reagent (Qiagen), total RNA samples were isolated using RNeasy columns (Qiagen) in accordance with manufacturer’s instruction.

tag: genotype/variation

value: wild type

tag: culture condition

value: anaerobic fermentive condition


title: affyexp_delta-fnr_glucose_NH4CL_anaerobic_2.CEL

description: SAMPLE 14

scan_protocol: cDNA synthesis, fragmentation, end-terminus biotin labeling, and array hybridization were performed as recommended by Affymetrix standard protocol.

value: Δfnr


title: affyexp_delta-fnr_glucose_NH4CL_anaerobic_3.CEL

description: SAMPLE 15

label_protocol: cDNA synthesis, fragmentation, end-terminus biotin labeling, and array hybridization were performed as recommended by Affymetrix standard protocol.


title: affyexp_wt_glucose_NH4CL_anaerobic_1.CEL

description: SAMPLE 16


title: affyexp_wt_glucose_NH4CL_anaerobic_2.CEL

description: SAMPLE 17


title: Resting T-Cells CR-2

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

description: Expression of mRNAs from Resting T-Cells

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55ºC in a hybridization oven  (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for mRNA Microarray.Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 10.7.3.1 and protocol GE1_107_Sep09

data_processing: Data were truncated to 1 and quantiles normalized using GeneSpring Software.Limma package from Bioconductor was used for statistical analysis

source_name: Resting Cells culture #2

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

growth_protocol: Human peripheral blood mononuclear cells were isolated from buffy coats from healthy donors as previously described (Mittelbrunn et al., Nat Commun, 2011) and cultured in RPMI (Sigma) containing 10% fetal bovine serum (FBS; Invitrogen) depleted of bovine exosomes by overnight centrifugation at 100000g)

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) and the miRNeasy® mini kit (Quiagen),

treatment_protocol: When indicated, T lymphoblasts were activated with PMA (50ng ml-1) plus ionomycin (500ng ml-1). Exosomes were isolated from cell supernatants by several centrifugation and filtration steps . Briefly, cells were centrifuged (320g for 5 min) and the supernatant filtered through 0.22 μm membranes. Exosomes were pelleted by ultracentrifugation at 100000g for 60 min at 4ºC (Beckman Coulter Optima L-100 XP).

value: Resting T-Cells

tag: origin

value: Cell

tag: state

value: Resting


title: Activated T-Cell Exosomes EA-2

description: Expression of mRNAs from Exosomes from Activated T-Cells

source_name: Activated Exosomes culture #2

value: Activated T-Cell Exosomes EA-2

value: Exosome

value: Activated


title: Resting T-Cells CR-1

source_name: Resting Cells culture #1


title: Resting T-Cell Exosomes ER-1

description: Expression of mRNAs from Exosomes from Resting T-Cells

source_name: Resting Exosomes culture #1

value: Resting T-Cell Exosomes


title: Resting T-Cell Exosomes ER-2

source_name: Resting Exosomes culture #2


title: affyexp_delta-arcA_glucose_NH4CL_anaerobic_2.CEL

description: SAMPLE 11

value: ΔarcA


title: affyexp_delta-arcA_glucose_NH4CL_anaerobic_3.CEL

description: SAMPLE 12


title: Activated T-Cells CA-1

description: Expression of mRNAs from Activated T-Cells

source_name: Activated Cells culture #1

value: Activated T-Cells


title: Activated T-Cell Exosomes EA-1

source_name: Activated Exosomes culture #1


title: chip-ArcA_ArcA8myc_glucose_NH4CL_anaerobic_3

description: Sample 3

hyb_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

data_processing: The raw data (.pair file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP/mock-IP ratio computation and enriched region identification as implemented in the NimbleScan software package, version 2.4.27 (www.nimblegen.com).

source_name: E. Coli ArcA ChIP DNA anaerobic

extract_protocol: Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 - 1000 bp. For the control (mock-IP), 2 ug of normal mouse IgG was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) then amplified PCR.

treatment_protocol: Cross-linked and sonicated chromatin complex of ArgR-8myc and DNA was immunoprecipitated by rabbit serum containing myc antibody.

value: harboring ArcA-8myc

tag: chip antibody

value: biotin conjugated anti-c-myc antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology

source_name: E. Coli ArcA-8myc ChIP DNA Mock antibody anaerobic

treatment_protocol: Cross-linked and sonicated chromatin complex of ArcA-8myc and DNA was immunoprecipitated by rabbit serum containing myc antibody.

value: HRP-conjugated sheep anti-mouse IgG

value: Amersham Biosciences


title: affyexp_delta-fnr_glucose_NH4CL_anaerobic_1.CEL

description: SAMPLE 13


title: affyexp_delta-arcA_glucose_NH4CL_anaerobic_1.CEL

description: SAMPLE 10


title: affyexp_wt_glucose_NH4Cl_NO3_3.CEL

description: SAMPLE 9

value: wild type

value: nitrate respiratory condition


title: Activated T-Cells CA-2

source_name: Activated Cells culture #2

tag: cell type


title: small unilamellar vesicles, biological rep 5

city: Nashville

first: Kasey

middle: C

last: Vickers

state: TN

address: 2220 Pierce Ave   358 PRB

department: Medicine

institute: Vanderbilt Univ. School of Medicine

data_processing: Ct values were calculated by SDS 1.2 software (Applied Biosystems) and normalized to MammU6 (miRNA) housekeeping Ct values and expressed as 2-(Ct[microRNA]—Ct[U6])

source_name: 1-palmitoyl-2-linoleoyl phosphatidylcholine (PLPC; Avanti Polar Lipids, Alabaster, AL)

growth_protocol: Human coronary artery endothelial cells (HCAEC) and human umbilical vein endothelial cells (HUVEC), passages 3 to 6, were grown in MesoEndo Growth Medium (Cell Applications, Inc. San Diego CA) containing 5% (v/v) serum and plated 24 hours before use in 12 well plates at a density of 1x105 cells per well.

extract_protocol:
The cells were harvested and total RNA was isolated using Qiazol miRNAeasy kits (Qiagen) and quantified by spectrophotometry
Reverse transcription was performed using Human MegaPlex RT Primer pools. cDNA was amplified using human MegaPlex PreAmp Primer Pools and PreAmp Master mix
The amplified samples were loaded into Taqman microRNA arrays Pool A (377 miRNAs) and pool B (373 miRNAs).
Analysed using the 7900 Real Time PCR System (Applied Biosystems)

treatment_protocol: HCAEC were incubated at 37 °C for 16-24 h with SUV (final PLPC concentration 3 mmol/L), lipid-free apoA-I (final concentration 1 mg /ml), rHDL (final apoA-I concentration 1 mg/ml), native HDL (final total protein concentration 1 mg/ml) or PBS.

value: Coronary Artery Endothelial Cells

tag: treatment

value: small unilamellar vesicles


title: chip-Fnr_Fnr8myc_glucose_NH4CL_NO3_3

description: Sample 12

scan_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

source_name: E. Coli Fnr ChIP DNA NO3

treatment_protocol: Cross-linked and sonicated chromatin complex of Fnr-8myc and DNA was immunoprecipitated by rabbit serum containing myc antibody.

value: harboring Fnr-8myc

source_name: E. Coli Fnr-8myc ChIP DNA Mock antibody NO3


title: small unilamellar vesicles, biological rep 4


title: affyexp_wt_glucose_NH4Cl_NO3_2.CEL

description: SAMPLE 8


title: affyexp_delta-fnr_glucose_NH4Cl_NO3_3.CEL

description: SAMPLE 6

value: Δfnr


title: chip-Fnr_Fnr8myc_glucose_NH4CL_anaerobic_3

description: Sample 9

source_name: E. Coli Fnr ChIP DNA anaerobic

label_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

source_name: E. Coli Fnr-8myc ChIP DNA Mock antibody anaerobic


title: affyexp_wt_glucose_NH4Cl_NO3_1.CEL

description: SAMPLE 7


title: chip-Fnr_Fnr8myc_glucose_NH4CL_NO3_2

description: Sample 11


title: chip-ArcA_ArcA8myc_glucose_NH4CL_NO3_2

description: Sample 5

source_name: E. Coli ArcA ChIP DNA NO3

source_name: E. Coli ArcA-8myc ChIP DNA Mock antibody NO3


title: small unilamellar vesicles, biological rep 3


title: small unilamellar vesicles, biological rep 2


title: chip-ArcA_ArcA8myc_glucose_NH4CL_anaerobic_1

description: Sample 1


title: chip-Fnr_Fnr8myc_glucose_NH4CL_anaerobic_1

description: Sample 7


title: affyexp_delta-fnr_glucose_NH4Cl_NO3_1.CEL

description: SAMPLE 4


title: affyexp_delta-arcA_glucose_NH4Cl_NO3_3.CEL

description: SAMPLE 3


title: small unilamellar vesicles, biological rep 1


title: chip-ArcA_ArcA8myc_glucose_NH4CL_NO3_3

description: Sample 6


title: chip-ArcA_ArcA8myc_glucose_NH4CL_anaerobic_2

description: Sample 2


title: chip-Fnr_Fnr8myc_glucose_NH4CL_anaerobic_2

description: Sample 8


title: Native HDL, biological rep 5

source_name: Human plasma

value: Native HDL


title: Native HDL, biological rep 3


title: rHDL, biological rep 3

source_name: Human plasma (apoA-I) & 1-palmitoyl-2-linoleoyl phosphatidylcholine (PLPC; Avanti Polar Lipids, Alabaster, AL)

value: rHDL


title: rHDL, biological rep 5


title: Native HDL, biological rep 2


title: Native HDL, biological rep 1


title: rHDL, biological rep 4


title: Native HDL, biological rep 4


title: affyexp_delta-arcA_glucose_NH4Cl_NO3_1.CEL

description: SAMPLE 1


title: rHDL, biological rep 2


title: affyexp_delta-arcA_glucose_NH4Cl_NO3_2.CEL

description: SAMPLE 2


title: chip-Fnr_Fnr8myc_glucose_NH4CL_NO3_1

description: Sample 10


title: affyexp_delta-fnr_glucose_NH4Cl_NO3_2.CEL

description: SAMPLE 5


title: control, biological rep 5

source_name: PBS

value: control


title: control, biological rep 3


title: rHDL, biological rep 1


title: Lipid-free apolipoprotein A-I, biological rep 4

value: Lipid-free apolipoprotein A-I


title: control, biological rep 4


title: Neuroretina 8-week diabetic, Biological replica_3

city: Barcelona

first: Cristina

last: Hernández

address: Passeig Vall d'Hebron, 119-129

department: Diabetes and Metabolism

institute: Vall d'Hebron - Research Institute

hyb_protocol: Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0). RMA algorithm was used to normalize the arrays and summarized the probes.

source_name: Neuroretina 8-week old db/db mouse: BKS.Cg- + Leprdb/+ Leprdb/OlaHsd

label_protocol: 200 ng of total RNA were used to synthesize sense ssDNA with the Ambion WT Expression Kit. Next, ssDNA was fragmented and labelled with a biotinylated compound.

growth_protocol: 8-weeks old db/db diabetic mice and their lean non-diabetic littermates were purchased from Harlan Laboratories.

extract_protocol: RNA was isolated using the Rneasy Mini Kit (Qiagen, Germany) according to manufacturer`s instructions.

treatment_protocol: Mice were first euthanized by cervical dislocation and then eyes were rapidly removed. Neuroretina was obtained and snap frozen for RNA isolation.

tag: genetic background strain

tag: tissue

value: Neuroretina

value: 8-week old

value: db/db

tag: phenotype

value: diabetic


title: control, biological rep 2


title: Neuroretina 8-week lean non-diabetic, Biological replica_3

source_name: Neuroretina 8-week old db/+ mouse: BKS.Cg- (lean)/OlaHsd

tag: age

value: db/+

value: lean non-diabetic


title: Lipid-free apolipoprotein A-I, biological rep 5


title: Neuroretina 8-week lean non-diabetic, Biological replica_1


title: Lipid-free apolipoprotein A-I, biological rep 3


title: Mouse round spermatids, biological rep 2, chip E

description:
Sptd_E.bar
Affymetrix Mouse Tiling 1.1R Array Set

source_name: Mouse round spermatids

tag: strain

value: Balb/c

tag: gender

value: male

value: 60 days

value: round spermatids


title: Mouse round spermatids, biological rep 3, chip E


title: Neuroretina 8-week diabetic, Biological replica_2

tag: genotype


title: Neuroretina 8-week lean non-diabetic, Biological replica_2


title: Neuroretina 8-week lean non-diabetic, Biological replica_4


title: Neuroretina 8-week diabetic, Biological replica_4


title: Lipid-free apolipoprotein A-I, biological rep 2

value: Coronary Artery Endothelial Cells


title: Mouse round spermatids, biological rep 1, chip E


title: Neuroretina 8-week diabetic, Biological replica_1


title: Lipid-free apolipoprotein A-I, biological rep 1


title: Mouse pachytene spermatocytes, biological rep 3, chip E

description:
Spcy_E.bar
Affymetrix Mouse Tiling 1.1R Array Set

source_name: Mouse pachytene spermatocytes

value: pachytene spermatocytes


title: Post, biological rep 4 (#5)

description: TaqMan microRNA Low-Density Arrays Pools A & B

data_processing: Ct values were calculated by SDS 1.2 software (Applied Biosystems) and normalized to mean array Ct values and expressed as 2-(Ct[microRNA]—Ct[mean array]).

extract_protocol:
HDL were immunoprecipitated from cell culture media using anti-apolipoprotein A-I columns. Total RNA was isolatedfrom purified HDL using Qiazol miRNAeasy kits (Qiagen) and quantified by spectrophotometry
Reverse transcription was performed using Human MegaPlex RT Primer pools. cDNA was amplified using human MegaPlex PreAmp Primer Pools and PreAmp Master mix
The amplified samples were loaded into Taqman microRNA arrays Pool A (377 miRNAs) and pool B (373 miRNAs).
Analysed using the 7900 Real Time PCR System (Applied Biosystems)

treatment_protocol: HCAEC were incubated at 37 °C for 16-24 h native HDL (final total protein concentration 1 mg/ml).

tag: material

value: Density-gradient ultracentrifugation prepared and apolipoprotein A-I immunoprecipitated human HDL

value: post-incubation with cells


title: Pre, biological rep 4 (#5)

value: pre-incubation with cells


title: Pre, biological rep 3 (#4)


title: Post, biological rep 3 (#4)


title: Pre, biological rep 2


title: Post, biological rep 2


title: Mouse pachytene spermatocytes, biological rep 2, chip E


title: control, biological rep 1

value: control


title: Mouse pachytene spermatocytes, biological rep 1, chip E


title: Mouse type A spermatogonia, biological rep 2, chip E

description:
Spga_E.bar
Affymetrix Mouse Tiling 1.1R Array Set

source_name: Mouse type A spermatogonia

value: 6 days

value: type A spermatogonia


title: Pre, biological rep 1


title: Post, biological rep 1


title: Mouse type A spermatogonia, biological rep 1, chip E


title: chip-ArcA_ArcA8myc_glucose_NH4CL_NO3_1

description: Sample 4

value: harboring ArcA-8myc

value: biotin conjugated anti-c-myc antibody

value: Santa Cruz Biotechnology

value: HRP-conjugated sheep anti-mouse IgG

value: Amersham Biosciences


title: Mouse round spermatids, biological rep 3, chip J

description:
Sptd_J.bar
Affymetrix Mouse Tiling 1.1R Array Set

value: Balb/c


title: Mouse pachytene spermatocytes, biological rep 2, chip J

description:
Spcy_J.bar
Affymetrix Mouse Tiling 1.1R Array Set

value: male


title: Mouse round spermatids, biological rep 1, chip J

value: 60 days


title: Mouse pachytene spermatocytes, biological rep 3, chip J


title: Mouse round spermatids, biological rep 3, chip B

description:
Sptd_B.bar
Affymetrix Mouse Tiling 1.1R Array Set

value: round spermatids


title: Mouse type A spermatogonia, biological rep 3, chip J

description:
Spga_J.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse round spermatids, biological rep 1, chip B


title: Mouse round spermatids, biological rep 2, chip B


title: Mouse type A spermatogonia, biological rep 3, chip E


title: Mouse round spermatids, biological rep 3, chip L

description:
Sptd_L.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 2, chip B

description:
Spcy_B.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 1, chip B


title: Mouse round spermatids, biological rep 2, chip L


title: Resting T-Cells CR-2

description: Expression of miRNAs from Resting T-Cells

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55ÂC in a hybridization oven  (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Arrays were scanned at 5mm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v3.0 (miRNA Microarray System Protocol, Agilent Technologies).Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 10 and protocol miRNA_105_Jan09

data_processing:
GeneView Signal values were normalized based on three different methods: VSN-invariant method, VSN2 and quantiles (Huber 2002, Pradervand 2009) as implemented in several Bioconductor packages. The overlapping was good. Limma package from Bioconductor was used for statistical analysis
Norm_All_data_miRNA.txt on Series record includes log2 quantile normalized signals

source_name: Resting Cells culture #2

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3' end of each RNA molecule by using T4 RNA ligase.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) and the miRNeasy mini kit (Quiagen),

treatment_protocol: When indicated, T lymphoblasts were activated with PMA (50ng ml-1) plus ionomycin (500ng ml-1). Exosomes were isolated from cell supernatants by several centrifugation and filtration steps . Briefly, cells were centrifuged (320g for 5 min) and the supernatant filtered through 0.22 um membranes. Exosomes were pelleted by ultracentrifugation at 100000g for 60 min at 4C (Beckman Coulter Optima L-100 XP).

value: Cell

value: Resting


title: Activated T-Cells CA-2

description: Expression of miRNAs from Activated T-Cells

source_name: Activated Cells culture #2

value: Activated


title: Resting T-Cells CR-1

source_name: Resting Cells culture #1


title: Mouse round spermatids, biological rep 2, chip J


title: Activated T-Cells CA-1

source_name: Activated Cells culture #1


title: Mouse type A spermatogonia, biological rep 3, chip B

description:
Spga_B.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 3, chip L

description:
Spcy_L.bar
Affymetrix Mouse Tiling 1.1R Array Set

value: pachytene spermatocytes


title: Activated T-Cell Exosomes EA-1

description: Expression of miRNAs from Exosomes from activated T-cells

source_name: Activated Exosomes culture #1

value: Exosome


title: Activated T-Cell Exosomes EA-2

source_name: Activated Exosomes culture #2


title: Mouse pachytene spermatocytes, biological rep 2, chip L


title: Resting T-Cell Exosomes ER-1

description: Expression of miRNAs from Exosomes from resting T-cells

source_name: Resting Exosomes culture #1


title: Mouse type A spermatogonia, biological rep 2, chip B


title: Resting T-Cell Exosomes ER-2

source_name: Resting Exosomes culture #2


title: Mouse type A spermatogonia, biological rep 1, chip B


title: Mouse pachytene spermatocytes, biological rep 1, chip J


title: Mouse pachytene spermatocytes, biological rep 1, chip L


title: Mouse round spermatids, biological rep 3, chip D

description:
Sptd_D.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse type A spermatogonia, biological rep 2, chip J


title: Mouse type A spermatogonia, biological rep 3, chip L

description:
Spga_L.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse round spermatids, biological rep 2, chip D


title: Mouse type A spermatogonia, biological rep 1, chip J


title: Mouse type A spermatogonia, biological rep 2, chip L


title: Mouse round spermatids, biological rep 1, chip D


title: Mouse type A spermatogonia, biological rep 1, chip L


title: Mouse pachytene spermatocytes, biological rep 3, chip D

description:
Spcy_D.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 3, chip B


title: Mouse round spermatids, biological rep 3, chip N

description:
Sptd_N.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse round spermatids, biological rep 1, chip L


title: Mouse pachytene spermatocytes, biological rep 2, chip D


title: Mouse round spermatids, biological rep 2, chip N


title: Mouse round spermatids, biological rep 1, chip N


title: Mouse type A spermatogonia, biological rep 3, chip D

description:
Spga_D.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 3, chip N

description:
Spcy_N.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 2, chip N


title: Mouse type A spermatogonia, biological rep 2, chip D


title: Mouse pachytene spermatocytes, biological rep 1, chip D


title: Mouse type A spermatogonia, biological rep 1, chip D


title: Mouse pachytene spermatocytes, biological rep 1, chip N


title: Mouse type A spermatogonia, biological rep 3, chip N

description:
Spga_N.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse round spermatids, biological rep 1, chip K

description:
Sptd_K.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse type A spermatogonia, biological rep 2, chip N


title: Mouse pachytene spermatocytes, biological rep 3, chip K

description:
Spcy_K.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse type A spermatogonia, biological rep 1, chip N


title: Mouse round spermatids, biological rep 2, chip C

description:
Sptd_C.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 1, chip K


title: Mouse pachytene spermatocytes, biological rep 2, chip K


title: Mouse round spermatids, biological rep 1, chip C


title: Mouse type A spermatogonia, biological rep 3, chip K

description:
Spga_K.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 2, chip C

description:
Spcy_C.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse type A spermatogonia, biological rep 1, chip K


title: Mouse pachytene spermatocytes, biological rep 1, chip C


title: Mouse type A spermatogonia, biological rep 3, chip C

description:
Spga_C.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse round spermatids, biological rep 3, chip M

description:
Sptd_M.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse round spermatids, biological rep 1, chip M


title: Mouse type A spermatogonia, biological rep 2, chip C


title: Mouse round spermatids, biological rep 2, chip M


title: Mouse round spermatids, biological rep 3, chip K


title: Mouse type A spermatogonia, biological rep 1, chip C


title: Mouse pachytene spermatocytes, biological rep 1, chip M

description:
Spcy_M.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 3, chip M


title: Mouse pachytene spermatocytes, biological rep 2, chip M


title: Mouse round spermatids, biological rep 2, chip K


title: Mouse type A spermatogonia, biological rep 3, chip M

description:
Spga_M.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse round spermatids, biological rep 3, chip C


title: Mouse type A spermatogonia, biological rep 2, chip M


title: Mouse round spermatids, biological rep 3, chip A

description:
Sptd_A.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse pachytene spermatocytes, biological rep 3, chip A

description:
Spcy_A.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse round spermatids, biological rep 2, chip A


title: Mouse pachytene spermatocytes, biological rep 2, chip A


title: Mouse pachytene spermatocytes, biological rep 3, chip C


title: Mouse type A spermatogonia, biological rep 2, chip K


title: Mouse pachytene spermatocytes, biological rep 1, chip A


title: Mouse type A spermatogonia, biological rep 3, chip A

description:
Spga_A.bar
Affymetrix Mouse Tiling 1.1R Array Set


title: Mouse type A spermatogonia, biological rep 2, chip A


title: Mouse type A spermatogonia, biological rep 1, chip M


title: Mouse round spermatids, biological rep 1, chip A


title: Mouse type A spermatogonia, biological rep 1, chip A


title: Astrocytes differentiated from NCRM-5 NSCs

city: Bethesda

first: Nasir

last: Malik

state: MD

address: 50 South Drive/Room 1146

department: NIAMS

institute: NIH

description: NSC derived astrocytes

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with the Gene Expression package of Illumina's Genome Studio software

source_name: Day 42 differentiated astrocytes

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

extract_protocol: 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: NSC differentiated astrocytes


title: Neurons differentiated from NCRM-1 NSCs

description: NSC derived neurons

source_name: Day 14 differentiatied neurons

value: NSC differentiated neurons

tag: passage

value: Neurons differentiated from NSCs for 14 days


title: NCRM-5 NSCs passage 6

description: NSC line 2

source_name: cultured neural stem cell line

value: neural stem cell

value: passage 6


title: EV_1

city: Zurich

first: Ram Mohan

last: Ram Kumar

address: Forchstrasse 340

department: Orthopaedics

country: Switzerland

institute: University Hospital Balgrist, University of Zurich, Zurich, Switzerland

description: Gene expression in SaOS- 2 cells transfected with empty vector and  ΔNp63α

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 25 x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851B) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-107-Sept 09 and Grid: 028004_D_F_20110708) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SaOS-2 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the low input quick amplification 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.

growth_protocol: SaOS- 2-ΔNp63α and SaOS-2-EV cells were cultured under standard conditions and trypsinised at 75% confulence.

extract_protocol: Total RNA was isolated using Rneasy MiniKit from Qiagen ( Valencia, CA, USA) following manufacturers instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: SaOS-2-ΔNp63α and SaOS-2-EV cells were cultured in in Dulbecco’s Modified Eagle Medium (DMEM containing 4.5 g/l glucose)/Ham F12 (Invitrogen, Carlsbad, CA, USA) (1:1) supplemented with 10% fetal calf serum (FCS), 1 unit/ml penicillin G, and 1 μg/ml streptomycin. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2

value: osteoblastic

value: retroviral transfection (empty vector)


title: Np63_2

value: retroviral transfection (ΔNp63α carrying  vector)


title: Np63_3


title: EV_2


title: Np63_1


title: T47D_PRB_synch_R5020_6h_rep2

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
PRB.synch.R5020.2
Replicate 2 of 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were quantile normalized using Genedata Analyst software using default settings, but are not log2 transformed.

source_name: T47D cells stably expressing PR-B vector, synchronized at G2/M with nocodazole, treated with R5020 vehicle for 6 hours

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: parental cell line

tag: tissue derivation

value: breast cancer

tag: stable vector integration

tag: cell synchronization

value: nocodazole

tag: time point

value: 6 hr


title: T47D_PRB_synch_R5020_6h_rep1

description:
PRB.synch.R5020.1
Replicate 1 of 3.


title: NCRM-1 NSC passage 5

description: NSC line 1

value: passage 5


title: EV_3


title: Jejunum tissue: healthy uninfected macaque biological rep 3 [JEJ UI 34249]

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from healthy macaque jejunum tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rhesus macaque 3' IVT arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.6

organism: Macaca mulatta

source_name: Healthy uninfected macaque jejunum tissue

label_protocol: Biotinylated cRNA were prepared according to the standard protocols described in the Affymetrix Gene Expression Analysis Technical Manual

extract_protocol: RNA was extracted with the Qiagen Rneasy kit according to the manufacturer's instructions.

value: jejunal mucosa

value: 4-6 years


title: Jejunum tissue: SIV infected, untreated macaque biological rep 3 [JEJ NT 34030]

description: Gene expression data from SIV infected, untreated macaque jejunum tissue


title: T47D_PRB_synch_R5020_6h_rep3

description:
PRB.synch.R5020.3
Replicate 3 of 3.


title: KD1.3 4954590048_K #CJ105-6

city: New Haven

first: Qin

last: Yan

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

description:
Sample name: KD1.3
RBP2-si1: siRNA against RBP2 #1

data_processing: The unnormalized data were normalized using lumi package in R

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed by electrophoresis in agarose gel.

tag: cell line

value: breast cancer cell line MDA-MB231

tag: genotype/variation


title: Jejunum tissue: SIV infected, untreated macaque biological rep 1 [JEJ NT 30085]

source_name: SIV infected, untreated macaque jejunum tissue


title: Jejunum tissue: healthy uninfected macaque biological rep 1 [JEJ UI 33675]


title: Jejunum tissue: SIV infected, untreated macaque biological rep 2 [JEJ NT 31353]


title: T47D_PRB_synch_vehicle_6h_rep2

description:
PRB.synch.EtOH.2
Replicate 2 of 3.

source_name: T47D cells stably expressing PR-B vector, synchronized at G2/M with nocodazole, treated with ethanol vehicle for 6 hours

value: vehicle

tag: treatment

value: ethanol vehicle


title: LCC2 shLRH-1 rep2

city: Sherbrooke

first: Nicolas

last: Gévry

state: Québec

address: 2500 boulevard de l'université

institute: Université de Sherbrooke

data_processing: Log2 transformation and quantile normalization of the data were performed with FlexArray 1.6.3 software

source_name: LCC2, shRNA LRH-1

label_protocol: Biotinylated cRNA were prepared according to standard Illumina protocol at McGill University & Genome Quebec Innovation Centre

growth_protocol: LCC2 are maintained in DMEM without phenol red containing 5% charcoal-dextran treated FBS, glutamine and antibiotics.

extract_protocol: Total RNA was isolated using the GenElute mammalian total RNA miniprep kit (Sigma).

treatment_protocol: Cells were transduced with shLRH-1 or shCTL lentiviruses for 4 days before mRNA extraction.

tag: endocrine sensitivity

value: endocrine resistant (Tamoxifen)


title: T47D_PRB_synch_vehicle_6h_rep3

description:
PRB.synch.EtOH.3
Replicate 3 of 3.


title: LCC9 shCTL rep2

source_name: LCC9, shRNA Control

growth_protocol: LCC9 are maintained in DMEM without phenol red containing 5% charcoal-dextran treated FBS, glutamine and antibiotics.

tag: tissue

value: endocrine resistant (Tamoxifen and Fulvestrant)


title: LCC9 shLRH-1 rep1

source_name: LCC9, shRNA LRH-1


title: LCC9 shLRH-1 rep2


title: LCC9 shCTL rep1


title: T47D_PRB_synch_vehicle_6h_rep1

description:
PRB.synch.EtOH.1
Replicate 1 of 3.


title: LCC2 shLRH-1 rep1


title: T47D_PRB_unsynch_R5020_6h_rep3

description:
PRB.unsynch.R5020.3
Replicate 3 of 3.

source_name: T47D cells stably expressing PR-B vector, unsynchronized, treated with R5020 for 6 hours


title: KD1.2 4954590048_I #CJ105-5

description:
Sample name: KD1.2
RBP2-si1: siRNA against RBP2 #1


title: KD2.3 4954590048_F #CJ105-9

description:
Sample name: KD2.3
RBP2-si2: siRNA against RBP2 #2


title: T47D_PRB_unsynch_R5020_6h_rep1

description:
PRB.unsynch.R5020.1
Replicate 1 of 3.


title: LCC2 shCTL rep2

source_name: LCC2, shRNA Control


title: KD1.1 4954590048_G #CJ105-4

description:
Sample name: KD1.1
RBP2-si1: siRNA against RBP2 #1


title: T47D_PRB_unsynch_vehicle_6h_rep3

description:
PRB.unsynch.EtOH.3
Replicate 3 of 3.

source_name: T47D cells stably expressing PR-B vector, unsynchronized, treated with ethanol vehicle for 6 hours


title: T47D_PRB_unsynch_R5020_6h_rep2

description:
PRB.unsynch.R5020.2
Replicate 2 of 3.


title: Luc.3 4954590048_E #CJ105-3

description:
Sample name: Luc.3
Luc: control siRNA against luciferase

value: control


title: T47D_PRB_unsynch_vehicle_6h_rep1

description:
PRB.unsynch.EtOH.1
Replicate 1 of 3.


title: Luc.1 4954590048_A #CJ105-1

description:
Sample name: Luc.1
Luc: control siRNA against luciferase


title: KD2.2 4954590048_D #CJ105-8

description:
Sample name: KD2.2
RBP2-si2: siRNA against RBP2 #2


title: Luc.2 4954590048_C #CJ105-2

description:
Sample name: Luc.2
Luc: control siRNA against luciferase


title: LCC2 shCTL rep1


title: MCF7 shLRH-1 rep2

source_name: MCF7, shRNA LRH-1

growth_protocol: MCF7 are growth in DMEM containing 10% fetal bovine serum (FBS), glutamine and antibiotics.

value: endocrine sensitive


title: KD2.1 4954590048_B #CJ105-7

description:
Sample name: KD2.1
RBP2-si2: siRNA against RBP2 #2


title: MCF7 shCTL rep2

source_name: MCF7, shRNA Control


title: MCF7 shCTL rep1


title: WT KR-72 0 vs 30 min_exp1

status: Public on Feb 26 2014

city: Seoul

first: Hyojeong

last: Kwon

address: Yonsei street

country: South Korea

institute: Yonsei university

description: WT1 0 vs KR-72 30min

hyb_protocol: After checking labeling efficiency, cyanine 3-labeled and cyanine 5-labeled cRNA target were combined and fragmented by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60°C for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Cryptococcus neoformans 3X20K microarray (MYcroarray.com, USA). The arrays hybridized at 57°C for 17 h using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were visualized with Axon GenePix 4000B Scanner (Axon Instrument, CA)

data_processing: The data quantification was performed using GenePix Pro 6.0 (Axon Instrument, CA).

organism: Cryptococcus neoformans H99

source_name: WT1 0time

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent’s Low Input Quick Amp WT Labeling kit, two color (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 0.2 µg total RNA was mixed with WT primer mix and incubated at 65°C for 10min. cDNA master mix (5X First strand buffer, 0.1M DTT, 10mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to the reaction mixer. The samples were incubated at 40°C for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 70°C for 15min.   The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was performed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40°C for 2 hours.

growth_protocol: The wild-type H99 strain was grown in 50 ml YPD medium at 30°C for 16 h. Then 7.5 ml of the overnight culture was inoculated into 150 ml of fresh YPD medium and further incubated for 4 h at 30°C  to an optical density at 600 nm (OD600 =1.0)

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 14 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor). 400 µl of the supernatant was transferred to a new round-bottom tube, add 400 µl of 100% EtOH and mix thoroughly by pipetting. Then transfer all contents from the tube into RNeasy spin column (QIAGEN) and centifuge at 12,000 rpm for 30 sec, descated flow through. Then add 350 µl RW1, centrifuge at 12,000 rpm for 30 sec and discard flow through. Add 10 µl DNaseI (IAGEN) stock to 70 µl RDD and mix by inverting. Then 80 µl of  DNaseI mix directly into spin column by incubaion at 37°C for 15 min. Add 350 µl RW1, centrifuge at 12,000 rpm for 30 sec and discard flow through. Add 500 µl of RPE, centrifuge at 12,000 rpm for 30 sec and discard flow through. Then Add 500 µl of RPE, centrifuge at 12,000 rpm for 2 min and discard flow through. Place RNeasy spin column onto fresh 2 ml collection tube, centrifuge at 12,000 rpm for additional 1 min and discard flow through and collection tube. Then Place RNeasy spin column in a new 1.5 ml collection tube, add 100 µl RNase free water (preheated at 65°C) into the column, allow to stand for 1 min and centrifuge at 12,000 rpm for 1 min. Store the elute at -70°C.

treatment_protocol: KR-72 was added to the exponentially grown culture at a final concentration of 1 µg/ml, which is a MIC for C. neoformans, and further incubated at 30°C for 60 min. At each time point (0, 30, and 60 min), a portion of the cells (50 ml culture) was sampled, precipitated by centrifugation, frozen in liquid nitrogen, and lyophilized overnight.

tag: kr-72 treatment

value: non-treated

tag: time

value: 30 min

source_name: WT1 30min

value: treated


title: WT KR-72 0 vs 60 min_exp2

description: WT2 0 vs KR-72 60min

source_name: WT2 0time

value: 60 min

source_name: WT2 60min


title: WT KR-72 0 vs 30 min_exp2

description: WT2 0 vs KR-72 30min

source_name: WT2 30min


title: WT KR-72 0 vs 60 min_exp3

description: WT3 0 vs KR-72 60min

source_name: WT3 0time

source_name: WT3 60min


title: Jejunum tissue: healthy uninfected macaque biological rep 2 [JEJ UI 33842]

source_name: Healthy uninfected macaque jejunum tissue

tag: age


title: T47D_PRB_unsynch_vehicle_6h_rep2

description:
PRB.unsynch.EtOH.2
Replicate 2 of 3.

value: breast cancer


title: MCF7 shLRH-1 rep1


title: WT KR-72 0 vs 30 min_exp3

description: WT3 0 vs KR-72 30min

source_name: WT3 30min


title: WT KR-72 0 vs 60 min_exp1

description: WT1 0 vs KR-72 60min

source_name: WT1 60min


title: Ischiatic_nerve_SJ600-5

city: Tartu

first: Kaie

last: Lokk

address: Riia 23

country: Estonia

institute: University of Tartu

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing:
The raw data were subject to quality control and normalization using the standard protocols suggested for the bioconductor R package minfi. All probes containing single nucleotide polymorphisms and CpG sites from the X and Y chromosomes were removed from the analysis.
matrix processed value definition: Average Beta
matrix signal intensities value definition: Matrix signal intensities (non-normalized) contains unmethylated (signal A) and methylated (Signal B) signal intensities

label: Cy5 and Cy3

source_name: Autopsy

label_protocol: According to Illumina protocol

extract_protocol: DNA was extracted from 25 mg samples of the tissue specimens using the NucleoSpin® Tissue kit (Macherey-Nagel GmbH, Düren, Germany)

tag: gender

value: male


title: Medulla_oblongata_SJ600-5


title: Aorta_thoracic_SJ600-5


title: Gallbladder_SJ600-5

value: Gallbladder


title: Bladder_SJ600-5

value: Bladder


title: Gastric_mucosa_SJ600-5


title: Tonsils_SJ600-5_1

value: Tonsils


title: Bone_SJ600-5

value: Bone


title: Aorta_thoracic_KT538


title: Splenic_artery_SJ600-5


title: Lymph_node_SJ600-5


title: Bone marrow_yellow_SJ600-5

value: Bone marrow_yellow


title: Tonsils_SJ600-5_2


title: Gallbladder_KT538


title: Adipose_subcutaenous_SJ600-5


title: Aorta_abdominal_SJ600-5


title: Bone marrow_red_SJ600-5

value: Bone marrow_red


title: Medulla_oblongata_KT538


title: Adipose_abdominal_SJ600-5


title: Ischiatic_nerve_KT538


title: Bone marrow_yellow_KT538


title: Tonsils_KT538


title: Aorta_abdominal_KT538


title: Bone marrow_red_KT538


title: Joint_cartilage_SJ600-5


title: Coronary_artery_KT538


title: Bladder_KT538


title: Lymph_node_KT538


title: Bone_KT538


title: Gastric_mucosa_KT538


title: Joint_cartilage_KT538


title: Coronary_artery_SJ600-5


title: Splenic_artery_KT538


title: Adipose_subcutaenous_KT538


title: Adipose_abdominal_KT538


title: Ischiatic_nerve_KA522


title: Aorta_abdominal_KA522


title: Gallbladder_KA522


title: Medulla_oblongata_KA522


title: Bladder_KA522


title: Aorta_thoracic_KA522


title: Tonsils_KA522_2


title: Gastric_mucosa_KA522


title: Bone marrow_red_KA522


title: Lymph_node_KA522_1


title: Lymph_node_KA522_2


title: Coronary_artery_KA522


title: Bone_KA522


title: Adipose_abdominal_KA522


title: Coronary_artery_BM419/4

value: female


title: Tonsils_KA522_1


title: Splenic_artery_KA522


title: Aorta_thoracic_BM419/4


title: Lymph_node_BM419/4


title: leukocyte J695JJ

city: Oklahoma City

first: Bart

last: Frank

state: OK

institute: OMRF

hyb_protocol: cRNA was hybridized to Illumina WG-6 v3 or Illumina HT-12 v4 human whole genome microarrays, and stained  according to the manufacturer’s directions.

scan_protocol: Scanning was performed using Illumina's iScan scanner

data_processing: Because of microarray product changes in the course of the study, raw data were reduced to contain 39426 common probes between the microarrays. Data in Matrix (raw) table contain values from Illumina's Genome Studio software and detection p-values above background. Sample tables contain variance stabilized and robust spline values from the lumi package. Batch effects were removed using the ComBat algorithm in the sva package.

source_name: whole blood leukocytes

label_protocol: cRNA was produced from reverse transcribed cDNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin).

extract_protocol: RNA was purified from whole blood PAXgene specimens using a PAXgene Blood RNA kit (Qiagen,Valencia, CA) as recommended by the manufacturer, including a DNAse (Qiagen) step to remove genomic DNA. Globin transcripts were reduced using GLOBINclear-Human (Ambion , Austin, TX ).

treatment_protocol: 2.5 ml of blood was collected in a PAXgene tube (PreAnalytiX GmbH, Hilden, Germany). Samples were stored at -80 C prior to RNA extraction.

tag: Sex

value: F

tag: group

value: juvenile idiopathic arthritis patient

tag: month of visit

tag: patient id


title: Bone marrow_yellow_KA522


title: leukocyte J530JJ


title: Tonsils_BM419/4_2


title: Gallbladder_BM419/4


title: Medulla_oblongata_BM419/4


title: leukocyte J679JJ


title: leukocyte J669JJ


title: leukocyte J704JJ

value: M


title: leukocyte J686JJ


title: Joint_cartilage_KA522


title: Ischiatic_nerve_BM419/4


title: leukocyte J654JJ


title: leukocyte J672JJ


title: leukocyte J701JJ


title: leukocyte J690JJ


title: leukocyte J698JJ


title: leukocyte J675JJ


title: Adipose_subcutaenous_KA522


title: Tonsils_BM419/4_1


title: Bladder_BM419/4


title: leukocyte J683JJ


title: Aorta_abdominal_BM419/4


title: Bone_BM419/4


title: Adipose_subcutaenous_BM419/4


title: Bone marrow_red_BM419/4


title: Gastric_mucosa_BM419/4


title: C3H gamma 6h 3-1

city: Chiba

first: Kaori

last: Imadome

state: Chiba

address: Anagawa 4-9-1

department: Research Center of Charged Particle Therapy

country: Japan

institute: National institute of radiological sciences

description: 6 hours after gamma irradiation at 10 Gy

hyb_protocol: according to standard Agilent protocol

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Signals were calculated by the Agilent Feature Extraction software and automatically underwent Lowess normalization.

source_name: Lung

label_protocol: Agilent Quick Amp Labeling Kit

extract_protocol: ISOGEN (NIPPON GENE) + RNeasy Mini Kit (QIAGEN)

tag: mouse strain

value: lung


title: leukocyte J708JJ


title: C3H gamma 6h 3-2


title: C3H gamma 6h 1-2


title: C3H gamma 6h 1-3


title: C3H gamma 6h 1-1


title: C3H gamma 6h 2-3


title: C3H gamma control 3-1

description: no irradiation


title: C3H gamma 6h 3-3


title: C3H gamma control 2-3

description: no irradiation


title: leukocyte J660JJ


title: Splenic_artery_BM419/4


title: C3H gamma control 2-2

description: no irradiation


title: C3H gamma control 3-2

description: no irradiation


title: leukocyte J573JJ


title: C3H gamma control 3-3

description: no irradiation


title: C3H gamma control 1-1

description: no irradiation


title: C3H gamma control 1-3

description: no irradiation


title: leukocyte J596JJ


title: C3H carbon 6h 3-2

description: 6 hours after carbon-ion irradiation at 10 Gy


title: leukocyte J615JJ


title: C3H gamma 6h 2-1


title: Adipose_abdominal_BM419/4


title: leukocyte J602JJ


title: C3H carbon 6h 3-3


title: leukocyte I674JJ


title: C3H carbon 6h 3-1


title: leukocyte J547JJ


title: C3H carbon 6h 1-3


title: leukocyte I699JJ


title: leukocyte J533JJ


title: C3H carbon 6h 2-2


title: leukocyte J569JJ


title: C3H carbon 6h 2-3


title: leukocyte I697JJ


title: C3H carbon 6h 2-1


title: C3H carbon control 3-2

description: no irradiation


title: C3H carbon 6h 1-2


title: leukocyte J620JJ


title: leukocyte J658JJ


title: leukocyte I694JJ


title: leukocyte J604JJ


title: C3H gamma 6h 2-2


title: leukocyte J560JJ


title: leukocyte I691JJ


title: C3H carbon control 3-3

description: no irradiation


title: C3H carbon 6h 1-1


title: leukocyte I683JJ


title: C3H carbon control 2-2

description: no irradiation


title: leukocyte J617JJ


title: leukocyte I685JJ


title: C3H carbon control 3-1

description: no irradiation


title: C3H carbon control 2-1

description: no irradiation


title: C3H carbon control 2-3

description: no irradiation


title: C3H carbon control 1-3

description: no irradiation


title: B6J gamma 6h 3-3


title: C3H carbon control 1-1

description: no irradiation


title: leukocyte I680JJ


title: leukocyte I675JJ


title: B6J gamma 6h 3-1


title: leukocyte J564JJ


title: leukocyte J607JJ


title: leukocyte J665JJ


title: B6J gamma 6h 2-1


title: B6J gamma 6h 2-2


title: B6J gamma 6h 3-2


title: leukocyte I676JJ


title: leukocyte J635JJ


title: B6J gamma 6h 2-3


title: B6J gamma 6h 1-3


title: leukocyte J632JJ


title: C3H carbon control 1-2

description: no irradiation


title: C3H gamma control 2-1

description: no irradiation


title: leukocyte J622JJ


title: leukocyte I714JJ


title: leukocyte I711JJ


title: leukocyte I712JJ


title: B6J gamma 6h 1-1


title: leukocyte J599JJ


title: leukocyte J628JJ


title: B6J gamma 6h 1-2


title: B6J gamma control 3-2

description: no irradiation


title: leukocyte J553JJ


title: C3H gamma control 1-2

description: no irradiation


title: leukocyte J588JJ


title: leukocyte I709JJ


title: leukocyte J625JJ


title: leukocyte I706JJ


title: leukocyte I705JJ


title: B6J gamma control 1-3

description: no irradiation


title: B6J gamma control 2-3

description: no irradiation


title: B6J gamma control 2-2

description: no irradiation


title: B6J gamma control 2-1

description: no irradiation


title: leukocyte I710JJ


title: B6J gamma control 3-3

description: no irradiation


title: B6J carbon 6h 3-2


title: leukocyte I708JJ


title: B6J carbon 6h 3-1


title: B6J gamma control 1-1

description: no irradiation


title: B6J gamma control 1-2

description: no irradiation


title: leukocyte J594JJ


title: leukocyte J571JJ


title: leukocyte J550JJ


title: B6J gamma control 3-1

description: no irradiation


title: leukocyte I703JJ


title: B6J carbon 6h 2-3


title: leukocyte J541JJ


title: B6J carbon 6h 3-3


title: B6J carbon 6h 2-2


title: leukocyte I698JJ


title: B6J carbon 6h 2-1


title: B6J carbon 6h 1-2


title: B6J carbon 6h 1-1


title: leukocyte I695JJ


title: leukocyte I704JJ


title: leukocyte J536JJ


title: leukocyte I696JJ


title: B6J carbon 6h 1-3


title: leukocyte J544JJ


title: leukocyte J581JJ


title: leukocyte I988JJ


title: leukocyte J612JJ


title: leukocyte J591JJ


title: B6J carbon control 3-2

description: no irradiation


title: leukocyte I682JJ


title: B6J carbon control 3-3

description: no irradiation


title: B6J carbon control 3-1

description: no irradiation


title: leukocyte J554JJ


title: leukocyte J585JJ


title: B6J carbon control 1-3

description: no irradiation


title: leukocyte I681JJ


title: B6J carbon control 2-3

description: no irradiation


title: B6J carbon control 2-1

description: no irradiation


title: leukocyte I671JJ

value: healthy control


title: B6J carbon control 2-2

description: no irradiation


title: leukocyte J692JJ


title: A/J gamma 6h 2-2

value: A/JSlc


title: leukocyte J678JJ


title: B6J carbon control 1-2

description: no irradiation


title: leukocyte I670JJ


title: A/J gamma 6h 3-2


title: B6J carbon control 1-1

description: no irradiation


title: A/J gamma 6h 3-3


title: A/J gamma 6h 3-1


title: leukocyte J700JJ


title: A/J gamma 6h 2-3


title: leukocyte J657JJ


title: leukocyte I672JJ


title: A/J gamma 6h 1-3


title: leukocyte J664JJ


title: leukocyte I669JJ


title: A/J gamma 6h 2-1


title: leukocyte I668JJ


title: leukocyte J682JJ


title: leukocyte I667JJ


title: A/J gamma control 3-3

description: no irradiation


title: A/J gamma 6h 1-2


title: A/J gamma control 3-2

description: no irradiation


title: leukocyte J694JJ


title: A/J gamma control 2-2

description: no irradiation


title: leukocyte I666JJ


title: A/J gamma control 3-1

description: no irradiation


title: A/J gamma control 1-2

description: no irradiation


title: A/J gamma control 1-3

description: no irradiation


title: A/J gamma 6h 1-1


title: leukocyte I665JJ


title: leukocyte I662JJ


title: leukocyte J668JJ


title: A/J carbon 6h 3-2


title: A/J gamma control 1-1

description: no irradiation


title: leukocyte I663JJ


title: leukocyte I664JJ


title: A/J gamma control 2-3

description: no irradiation


title: A/J gamma control 2-1

description: no irradiation


title: leukocyte J716JJ


title: A/J carbon 6h 3-3


title: leukocyte J714JJ


title: leukocyte J532JJ


title: leukocyte J713JJ


title: leukocyte I661JJ


title: leukocyte J715JJ


title: A/J carbon 6h 2-3


title: A/J carbon 6h 3-1


title: A/J carbon 6h 2-2


title: leukocyte I659JJ


title: A/J carbon 6h 2-1


title: A/J carbon 6h 1-3


title: leukocyte J535JJ


title: leukocyte I660JJ


title: leukocyte I658JJ


title: leukocyte J717JJ


title: A/J carbon 6h 1-2


title: leukocyte J712JJ


title: A/J carbon control 3-2

description: no irradiation


title: leukocyte J711JJ


title: A/J carbon control 3-3

description: no irradiation


title: leukocyte I654JJ


title: pollen coat adhesion replicate 1

city: Ikoma

first: Megumi

last: Iwano

state: Nara

address: 8916-5 Takayama

department: Biological Sciences

institute: NAIST

description:
biological replicate 1 of 3
Raw spot intensity data were lost, and therefore unavailable

hyb_protocol: For each array, 1 µg Cy3- and Cy5-labeled cRNA was hybridized on a 1x44K Arabidopsis 3 Gene Expression Microarray (Agilent Technologies).

scan_protocol: Slides were scanned with an FLA-8000 scanner (Fujifilm), and signal intensity was quantified with Array Vision RLS 8.0 software (Genicon Sciences and Imaging Research).

data_processing:
GeneSpring version 6.0 (Agilent Technologies) was used for LOWESS normalization.
The expression ratios between either (i) 0 min (raw data) and 15 min (control data) after pollination with WT pollen, or (ii) before (raw data) and at 15 min (control data) after adhesion with pollen coat were calculated from the signal intensities of Cy3 (raw data) and Cy5 (control data).

organism: Arabidopsis thaliana

source_name: before pollen coat adhesion

label_protocol: For each sample, 500 ng total RNA was used, and cRNA was labeled with Cy3-CTP for samples at 0 min after pollination and non-treatment pollen coat samples, or with Cy5-CTP for samples at 15 min after pollination or pollen coat adhesion.

growth_protocol: Freshly opened A. thaliana Col-0 flowers at stage 13 were collected from 4-5-week-old plants.

extract_protocol: Total RNA was extracted with an RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer’s protocol.

treatment_protocol: Stigmas were collected either (i) immediately or at 15 min after pollination, or (ii) before or at 15 min after treatment with pollen coat.

tag: ecotype

value: stigmas

source_name: 15 min after pollen coat adhesion


title: leukocyte J538JJ


title: leukocyte I656JJ


title: pollination replicate 3

description:
biological replicate 3 of 3
Raw spot intensity data were lost, and therefore unavailable

source_name: 0 min after pollination

source_name: 15 min after pollination


title: pollen coat adhesion replicate 3


title: A/J carbon control 3-1

description: no irradiation


title: A/J carbon 6h 1-1


title: pollination replicate 1


title: pollen coat adhesion replicate 2

description:
biological replicate 2 of 3
Raw spot intensity data were lost, and therefore unavailable


title: leukocyte I657JJ


title: A/J carbon control 2-2

description: no irradiation


title: A/J carbon control 2-3

description: no irradiation


title: Brain_Treated_Rep2

city: Munich

first: Sven

middle: Peter

last: Wichert

state: Bavaria

address: Nussbaumstr. 7

department: Psychiatry and Psychotherapy

institute: Ludwig-Maximilians-University Munich

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array  . Arrays were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Partek Genomic Suite and normalized with gc-rma Method. The data is in log2 scale.

source_name: PMD_treated_brain lysate

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Male mice, homozygous for an autosomal murine Plp1 transgene and maintained on the C57Bl/6 background, were used as bona fide models for human PMD (“PMD mice”). Plp1 overexpression was 1.8 fold and motor symptoms in PMD mice were already measurable at study start at 3 weeks of age.

extract_protocol: RNA from total brain was isolated at study end from 13 weeks old mice according to the manufacturer’s instructions (RNeasy lipid tissue minikit; Qiagen) using TRIzol reagent (Invitrogen).

treatment_protocol: Lonaprisan or vehicle was administered by daily subcutaneous injections. Lonaprisan was dosed at 125mg/kg body weight and suspended in a mixture of 90% sesame oil and 10% benzylbenzoate. In one control group, wildtype mice received vehicle without Lonaprisan. Treatment started at 3 weeks of age (time of weaning) and was performed for 10 weeks.

tag: strain background

value: homozygous for an autosomal murine Plp1 transgene; PMD model

value: 3 weeks

tag: treated with

value: Lonaprisan (125mg/kg body wt) for 10 weeks

value: brain


title: Grid2 deleted mouse 3

city: Ibaraki

first: Hiroshi

last: Takemori

state: Osaka

address: 7-6-8, Saito-Asagi

institute: National Institute of Biomedical Innovation

description: Grid2 deleted mouse

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: GeneSpring 12.6

source_name: cerebellar total RNA

label_protocol: Affymetrix protocol

growth_protocol: 12 weeks old female mouse

extract_protocol: EZ1 RNA extraction kit

treatment_protocol: EZ1 RNA extraction kit

tag: strain

value: 12 weeks


title: Grid2 deleted mouse 2

description: Grid2 deleted mouse


title: Brain_Treated_Rep3

tag: genotype/variation

value: male


title: leukocyte I653JJ


title: A/J carbon control 2-1

description: no irradiation


title: Brain_Plac_Rep3

source_name: PMD_placebo_brain lysate

value: Placebo (vehicle)


title: Brain_Plac_Rep1


title: Brain_Plac_Rep2


title: Control mouse 3

description: Control mouse


title: Control mouse 2

description: Control mouse


title: Brain_Treated_Rep1


title: A/J carbon control 1-3

description: no irradiation


title: Grid2 deleted mouse 1

description: Grid2 deleted mouse


title: A/J carbon control 1-1

description: no irradiation


title: A/J carbon control 1-2

description: no irradiation


title: pollination replicate 2


title: lung_adenocarcinoma_DNA (85050222): aCGH

status: Public on Feb 25 2014

city: Vancouver

first: Ian

middle: Michael

last: Wilson

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics

institute: British Columbia Cancer Research Centre

description: no additional information

hyb_protocol: Hybridization was performed as described previously (Nat Genet. 2004 Mar;36(3):299-303) for 40 hours.

scan_protocol: Slides were scanned at 10uM resolution on a Perkin Elmer ScanArray Express.

data_processing:
Data were extracted from images using SoftWorx Tracker software.  Systematic biases were removed from Log2 ratios (Cy3/Cy5) using CGHNorm (BMC Bioinformatics. 2005 Nov 18;6:274).  Only clones with SD<=0.075 and SNR>3 (for both channels) were used for further work.
VALUEs represent CGHnorm normalized log2 ratios, where bad array spots (not found etc) are blank.  This data has not been filtered for SNR or SD.

source_name: lung, adenocarcinoma

label_protocol: Labeling was performed as described previously (Nat Genet. 2004 Mar;36(3):299-303).  Briefly, tumors were labeled with cy3 dUTP using random primers and Klenow fragment.  Diploid reference was labeled with cy5 dUTP.

growth_protocol: Tissues were excised during surgical ressection for tumor removal.

extract_protocol: Tumour and normal samples were obtained during surgical resection.  After pathology review, tumors were microdissected to ensure tumor cells comprised 80% of cells extracted.  DNA was extracted using proteinase K digestion, followed by phenol:chloroform extraction and ethanol precipitation.

tag: disease state

value: adenocarcinoma

tag: sample number

source_name: diploid male reference

tag: reference

value: diploid male gDNA


title: lung_adenocarcinoma_DNA (85050241): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85060251): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070021): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85050167): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85060256): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85060311): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070053): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85060201): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070069): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85050147): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85060068): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85060144): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070081): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070159): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85060354): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85060358): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070093): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85050208): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070061): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070049): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85070109): aCGH

description: no additional information


title: TET 133 mg/kg BW 11 day, sample 005

city: Bilthoven

first: Alexa

last: Vitins

address: P.O. Box 1

country: Netherlands

institute: RIVM

hyb_protocol: According to the Affymetrix Hybridization, Wash and Stain Kit (#901530)

scan_protocol: According to Affymetrix protocols

data_processing: Cell Intensity Files generated for each GeneChip using the Affymetrix GeneChip Command Console (v3.0) software were normalized using the Robust Multichip Average (RMA) algorithm from http://arrayanalysis.org (BiGCaT Maastricht University).  RMA normalized data were transformed to Log2 by arrayanalysis.org for further analysis.  Additionally, the quality of microarray images was inspected visually (http://arrayanalysis.org, BiGCaT Maastricht University).

source_name: Mouse liver after 11 day TET treatment

label_protocol: According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit (#901229)

extract_protocol: Upon sacrifice, liver was immediately dissected. Central half of the left lateral lobe was collected in RNA later and kept for a maximum of one week at 4 oC and frozen at -80 oC until use for RNA isolation. RNA was isolated using the RNeasy Mini Kit.

treatment_protocol: Mice treated for 1, 4, 11 days with vehicle or compound by oral gavage

tag: treatment

value: TET 133 mg/kg BW 11 day

value: 10 weeks

tag: weight

tag: tissue

value: liver


title: lung_adenocarcinoma_DNA (85050140): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85050031): aCGH

description: no additional information


title: lung_adenocarcinoma_DNA (85040031): aCGH

description: no additional information


title: KH_vs_TH

city: Hohhot

first: Wei

last: Wang

address: Inner Mongolia Hohhot City Saihan District Zhao Wuda road 306

country: China

institute: College of Life Sciences Chinese Inner Mongolia Agricultural University

description: CNV analysis of KH vs Thoroughbred

hyb_protocol: Hybridization was processing 60h at 42°C in Roche-NimbleGen hybridization system12.

scan_protocol: Arrays were scanned on an Roche-NimbleGen MS200 scanner.

data_processing: Arrays were processed using NimbleScan,which transformed image signal to digital signal, following using segMNT algorithm to analyse the normalized signal ratio.

organism: Equus caballus

source_name: KH DNA

label_protocol: The sample labelling was using NimbleGen Dual-Color DNA Labeling Kit (05223547001).

extract_protocol: The genomic DNA was extracted using Promega Genomic DNA Purification Kit (A1620).

treatment_protocol: Blood was directly collected from horse

tag: genotype

value: Wild type

tag: breed

value: Kazakh horse

value: blood

source_name: TH DNA

value: wild type

value: Thoroughbred


title: VPA 500 mg/kg BW 11 day, sample 006

source_name: Mouse liver after 11 day VPA treatment

value: VPA 500 mg/kg BW 11 day

tag: gender

tag: age


title: lung_adenocarcinoma_DNA (85070085): aCGH

description: no additional information


title: Control mouse 1

description: Control mouse

value: female


title: AH_vs_TH

description: CNV analysis of AH vs Thoroughbred

source_name: AH DNA

value: Abaga horse


title: lung_adenocarcinoma_DNA (85050011): aCGH

description: no additional information


title: lung_non-malignant_DNA (85070160): MP

description: For each normal/tumor pair, the sample numbers are paired but offset by one with the tumor being the lower of the two numbers.  For example, 85040001 is the adenocarcinoma tumor profile that pairs with 85040002.

hyb_protocol: Hybridization was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.

scan_protocol: Scanning was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.

data_processing:
Data processing was performed according to Illumina directions by the Illumina Cspro service center at Oxford University.  Data were normalized using the average setting.  Software was BSGX version 3.2.3.
Beta values (Intensity Ratio Values) represent methylation level of the CpG locus. ß-values were calculated using the ratio of intensities between methylated and unmethylated alleles, i.e., (Intensity of methylated bead type)/(Intensity of methylated bead type + Intensity of unmethylated bead type).

label: Cy3 and Cy5

source_name: lung, non-malignant

label_protocol:
Bisulfite conversion and labelling was carried out according to Illumina directions by the Illumina Cspro service center at Oxford University.
Bisulfite conversion leads to the deamination of non-methylated cytosines to uracils, while methylated cytosines are refractory to the effects of bisulfite and remain cytosine.
Methylated alleles labeled with Cy3, unmethylated labeled with Cy5

extract_protocol: Tumour and normal samples were obtained during surgical ressection.  After pathology review, tumors were microdissected to ensure tumor cells comprised 80% of cells extracted.  DNA was extracted using proteinase K digestion, followed by phenol:chloroform extraction and ethanol precipitation.

value: control


title: lung_adenocarcinoma_DNA (85040040): aCGH

description: no additional information


title: lung_non-malignant_DNA (85070094): MP


title: lung_adenocarcinoma_DNA (85070081): MP