title: P149_CD8

city: Solna

first: David

last: Gomez-Cabrero

state: Stockholm

address: Karolinska University Hospital Solna

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol. (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 software and the charm bioconductor package v1.0.1 using a) quantile and b) subset-quantile normalization. Percent methylation calculated.

source_name: input fraction of DNA from PBMC

label_protocol: 1 µg DNA per sample was sheared, McrBC digested and gel fractionated before labeling and hybridization onto arrays covering 2.1M CpG sites according protocol (Ladd-Acosta et al. 2010).

growth_protocol: No growth protocol

extract_protocol: CD4+ and CD8+ T-cells, CD56+ NK-cells and neutrophils were isolated from peripheral blood, from  healthy male donors (mean age ~38 years) as described in Reinius et al. (Reinius et al. 2012). DNA was extracted using the Puregene extraction kit (Gentra systems, Minneapolis, USA). After extraction the DNA was subsequently stored with bar-code at -20°C. Quality control was done by 1% agarose gel to detect degradation. Sera was aliquoted and stored with bar code in liquid nitrogen (-180° Celsius) at the KI Biobank.

treatment_protocol: No treatment

tag: individual

value: peripheral blood

value: CD8+ T cells

tag: dna fraction

value: input

source_name: Methyl-depleted fraction of DNA from PBMC

value: methyl-depleted


title: P043_CD56

status: Public on Nov 24 2016

type: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell type

value: CD56 NK cells


title: R3 26.06.14

type: RNA

city: London

first: Pierre

last: Guermonprez

address: 1st floor NHH, Guy's Campus,

department: CIBCI

country: United Kingdom

institute: King's College London

hyb_protocol: Hybridization cocktails were prepared as recommended by NuGEN and hybridised to Affymetrix Mouse Gene 1.0 ST arrays overnight.

scan_protocol: Arrays were washed and stained using Affymetrix Fluidics Station FS450 and GeneChip Hybridisation Wash Stain kit and scanned in GCS3000 7G scanner with Autoloader.

data_processing: Data was analyzed using Gene Pattern software (Broad Institute)

label: Biotin

molecule: total RNA

organism: Mus musculus

label_protocol: The Encore Biotin Module (NuGEN) kit was used according to manufacturer's instructions to label the cDNA

growth_protocol: Mice grown under spcific pathogen free conditons until 8 weeks of age were culled and bone marrow extracted under sterile conditions to be sorted by flow cytometry

extract_protocol: Cell pellets were lysed in RLT buffer (Rneasy kit- Qiagen). The NuGen Ovation Pico WTA v2 kit was used to process 1ng RNA per sample into SPIA amolifid cDNA

tag: strain

value: Steady state bone marrow

value: Ly6Chi CD115+ cells

tag: cell type (sorted)


title: P218_CD56


title: P149_CD4

value: CD4+ T cells


title: P105_Neu

value: neutrophils


title: P149_Neu


title: P043_Neu


title: P218_CD4


title: RAstudy_PAIR7_ACPA-_Healthy

extract_protocol: DNA was extracted using the Puregene extraction kit (Gentra systems, Minneapolis, USA). After extraction the DNA was subsequently stored with bar-code at -20°C. Quality control was done by 1% agarose gel to detect degradation. Sera was aliquoted and stored with bar code in liquid nitrogen (-180° Celsius) at the KI Biobank.

tag: acpa status

value: ACPA -

tag: disease status

value: Healthy

value: peripherial blood

value: PBMC


title: RAstudy_PAIR1_ACPA+_RheumatoidArthritis

description: Sample19_RAstudyPAIR1_ACPA+_RheumatoidArthritis

value: ACPA +

value: Rheumatoid Arthritis


title: P160_CD56


title: P160_Neu


title: P043_CD4


title: RAstudy_PAIR2_ACPA+_RheumatoidArthritis

description: Sample21_RAstudyPAIR2_ACPA+_RheumatoidArthritis


title: RAstudy_PAIR1_ACPA-_Healthy


title: P160_CD4


title: RAstudy_PAIR3_ACPA+_RheumatoidArthritis

description: Sample23_RAstudyPAIR3_ACPA+_RheumatoidArthritis


title: P105_CD56


title: P218_Neu


title: R1 26.06.14


title: R2 26.06.14


title: RAstudy_PAIR6_ACPA-_Healthy


title: P149_CD56


title: P105_CD4


title: S8_U2OS_Dox-CM354

city: New York

first: Zichen

last: Wang

state: NY

address: 1468 Madison Ave

department: Pharmacological Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent W hole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.

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

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: U2OS, Dox 300ng/ml, CM354, 1.5uM

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Total RNA was isolated from U2OS cells using TRIzol (Invitrogen) and DNase treated with the TURBO DNA-free kit (Ambion). RNA samples were further purified using the RNeasy MinElute Cleanup kit (Qiagen). The RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

tag: cell line

tag: treatment


title: RAstudy_PAIR2_ACPA-_Healthy


title: S6_U2OS_CM354


title: RAstudy_PAIR3_ACPA-_Healthy


title: S7_U2OS_Dox

source_name: U2OS, Dox 300ng/ml

value: Doxorubicin


title: S5_U2OS_untreated

source_name: U2OS, untreated

value: untreated


title: FRT cells_2D pool vs. 3D pool

city: Madrid

first: Petrina

last: Koumarianou

state: Madrid

address: 4th Arturo Duperier st.

department: Departamento de Fisiopatología Endocrina y del Sistema Nervioso

country: Spain

institute: Instituto de Investigaciones Biomédicas "Alberto Sols"

description: Pool of FRT 2D confluent monolayers made of 4 biological replicates vs. a pool of 3D FRT follicles made of 4 biological replicates

hyb_protocol: Microarray: Rat Gene Expression G3 60K (Agilent microarray design ID 028279, P/N G4853A). Microarray sequences and annotations are listed in sheet '028279_rn4_20121204'. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 10.7), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

data_processing: Data from hybridised microarray images were quantitated, corrected by additive detrending and submitted to dye bias normalisation after bias detection by linear and Lowess curve fitting methods (Agilent FeatureExtraction (FE) Software). Lowess normalisation reduces spurious bias by merging two-color data, and applying a smoothing adjustment that corrects non-linear dye-specific variation. Raw data signals are thresholded to 1, and replicated probe signals for the individual channels (Cy5 and Cy3) are summarized by computing their geometric mean. Normalised signal values are obtained by Cy5/Cy3 ratio computing and Log base2 transformation. Thresholding is a simple substitution step that removes very small expression values or negative values, so that there would not be large negative values or missing values in the log transformed data. Normalisation involves Log2 data transformation, which generates a roughly normal distribution and allows to use statistical parametric tests (student’s t-test, limma, etc).

organism: Rattus norvegicus

source_name: Pooled FRT monolayers

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases.Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores.

extract_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 8.1 to 9.6 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

value: Fischer

tag: condition

value: pool 2D

source_name: Pooled FRT follicles

value: pool 3D


title: S4_U2OS_Dox-CM354


title: FRT cells_3D replicate 3 vs. 2D pool

description: 3D FRT follicles biological replicate 3 of 4 vs. a pool of FRT 2D confluent monolayers made of 4 biological replicates

source_name: FRT follicles


title: FRT cells_3D replicate 4 vs. 2D pool

description: 3D FRT follicles biological replicate 4 of 4 vs. a pool of FRT 2D confluent monolayers made of 4 biological replicates


title: S2_U2OS_CM354


title: RAstudy_PAIR7_ACPA+_RheumatoidArthritis

description: Sample17_RAstudyPAIR7_ACPA+_RheumatoidArthritis

value: input

value: methyl-depleted


title: RAstudy_PAIR6_ACPA+_RheumatoidArthritis

description: Sample15_RAstudyPAIR6_ACPA+_RheumatoidArthritis


title: Low blue + low R:FR light, rep2

status: Public on Nov 23 2016

city: Utrecht

first: Ronald

last: Pierik

address: Padualaan 8

department: Plant Ecophysiology

country: Netherlands

institute: Utrecht University

description:
23LowBlueRFR
Controls are 'Control' plants.

hyb_protocol: The (#900720) GeneChip Hybridization, Wash and Stain Kit was used for hybridization, washing, staining and scanning of the chips.

scan_protocol: The software program Affymetrix 'GeneChip Command Console (v3.1)' was used to operate the staining, washing and scanning of the GeneChips and visual inspection of the array images. Chips were scanned using the Affymetrix 3000G scanner.

data_processing: Data were processed using the Bioconductor packages in R and using the RMA normalization algorithm.

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis petioles, low R:FR + low blue light

label_protocol: The Affymetrix 3'IVT-Express Labeling Kit was used to synthesize biotin-labeled cRNA. From each RNA sample, 100 ng was used as input for the labelling reactions.

growth_protocol: Arabidopsis thaliana plants were sown, stratified (4˚C) for 3 days and then transferred to a growth chamber (9 h. light (180 µmol / m2 / s, 20°C, 70% RH), 15 h dark) where they were transferred to individual pots after 10 d and grown until 28 days after sowing.

extract_protocol: Total RNA was isolated from homogenized material using the RNeasy Plant Mini Kit (Qiagen) with on-column DNA digestion following the company's instructions.

treatment_protocol: Plants were grown single in pots that were either kept separate (single plants; control) or placed in a 2066 plants / m2 dense canopy directly after transfer to these pots. For competition, 2 young petioles per plant (37 d old) were harvested in liquid N2 and petioles from 4 plants were pooled per biological replicate. For light treatments, petioles of 29-day-old plants were harvested 24 h after start of the light treatments.

tag: ecotype

value: petiole

tag: age

value: 29 days

tag: growth condition

value: single

value: low R:FR light + low blue light

tag: treatment duration

value: 24 hr


title: S1_U2OS_untreated


title: Low blue light, rep3

description:
21LowBlue
Controls are 'Control' plants.

source_name: Arabidopsis petioles, low blue light

value: low blue light


title: Low R:FR light, rep3

description:
18LowRFR
Controls are 'Control' plants.

source_name: Arabidopsis petioles, low R:FR light

value: low R:FR light


title: Low blue light, rep1

description:
19LowBlue
Controls are 'Control' plants.


title: Low blue light, rep2

description:
20LowBlue
Controls are 'Control' plants.


title: Low blue + low R:FR light, rep3

description:
24LowBlueRFR
Controls are 'Control' plants.


title: Low blue + low R:FR light, rep1

description:
22LowBlueRFR
Controls are 'Control' plants.


title: FRT cells_3D replicate 2 vs. 2D pool

description: 3D FRT follicles biological replicate 2 of 4 vs. a pool of FRT 2D confluent monolayers made of 4 biological replicates


title: Low R:FR light, rep2

description:
17LowRFR
Controls are 'Control' plants.


title: RAstudy_PAIR5_ACPA-_Healthy

value: ACPA -

value: Healthy

value: peripherial blood

value: PBMC


title: S3_U2OS_Dox

value: Doxorubicin


title: P043_CD8

value: peripheral blood

value: CD8+ T cells


title: Low R:FR light, rep1

description:
16LowRFR
Controls are 'Control' plants.


title: Control light, rep2

description:
14Control
Control for 'lowRFR', 'LowBlue', and 'LowBlueRFR' plants.

source_name: Arabidopsis petioles, control light

value: control light


title: High density plants, rep3

description:
12LateCan
Controls are 'LateSing' plants.

source_name: Arabidopsis petioles, dense canopy

value: 37 days

value: high density canopy


title: Control light, rep1

description:
13Control
Control for 'lowRFR', 'LowBlue', and 'LowBlueRFR' plants.

value: petiole


title: Ssmv1_mock

city: changchun

first: he

middle: hong

last: li

state: jilin

address: remin street 5268

country: China

institute: northeast normal university

description: Gene expression data from Ssmv1 mock inoculated

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Soybean Genome Array.

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

data_processing: The raw gene expression data were acquired by processing GeneChip hybridization images with GeneChip Operating Software (GCOS), and normalized with GeneSpring GX 10 software by using Robust Multichip Average (RMA) method.  The only available RMA values are for the probe sets identified with differential expression. These RMA values are available in a data matrix on the series record called "RMA_differential_expression.txt ". The CHP files contain the MAS5.0 signal.

organism: Glycine max

source_name: soybean cultivar Ssmv1

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: Soybean cultivars Rsmv1 and Ssmv1 Soybean plants were grown in a greenhouse at 26ºC with a 16 h/8 h light/dark cycle.

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

treatment_protocol: Twelve-day-old seedling were used for SMV inoculation according to the procedures by Zhou et al. (2014) with some modification. Briefly, inoculums were prepared by grinding equal amount of SMV1 and SMV3 infected soybean leaf tissues in liquid nitrogen, and then resuspended in 0.01 mol/L phosphate buffer (pH 7.0) at a ratio of 1g/10mL. The first trifoliolate leaves of the inoculation and mock groups were wounded by gently rubbed with 600 mesh sandpaper pre-dipped with the SMV inoculums or PBS buffer, respectively. The experiments were repeated twice, and for each experiment, 5 plants of each cultivars were used for SMV inoculation, and another 5 for mock treatment.After 10 days of inoculation, when mild mosaic symptoms were observed in the inoculatedSsmv1 plants, the third trifoliolates of SMV inoculated Rsmv1 and Ssmv1 plants, as well as the corresponding leaves from mock plants were collected and frozen in liquid nitrogen.

value: leaves (V3)

tag: cultivar


title: Single control plants, rep2

description:
08LateSing
Control for 'LateCan' plants.

source_name: Arabidopsis petioles, single

value: single


title: Rsmv1_inoculated

description: Gene expression data from Rsmv1 SMV inoculated

source_name: soybean cultivar Rsmv1


title: Single control plants, rep1

description:
07LateSing
Control for 'LateCan' plants.


title: Rsmv1_mock

description: Gene expression data from Rsmv1 mock inoculated


title: Single control plants, rep3

description:
09LateSing
Control for 'LateCan' plants.


title: FRT cells_3D replicate 1 vs. 2D pool

description: 3D FRT follicles biological replicate 1 of 4 vs. a pool of FRT 2D confluent monolayers made of 4 biological replicates

value: Fischer

value: pool 2D


title: High density plants, rep1

description:
10LateCan
Controls are 'LateSing' plants.


title: RAstudy_PAIR4_ACPA-_Healthy

value: input

value: methyl-depleted


title: P105_CD8


title: Ssmv1_inoculated

description: Gene expression data from Ssmv1 SMV inoculated


title: PAIR4_ACPA+_Healthy

value: ACPA +


title: PAIR4_ACPA-_Healthy

value: ACPA -

value: Healthy


title: RAstudy_PAIR5_ACPA+_RheumatoidArthritis

description: Sample13_RAstudyPAIR5_ACPA+_RheumatoidArthritis

value: Rheumatoid Arthritis

value: peripherial blood

value: PBMC


title: PAIR3_ACPA-_Healthy


title: PAIR5_ACPA-_Healthy


title: PAIR5_ACPA+_Healthy


title: PAIR2_ACPA+_Healthy


title: RAstudy_PAIR4_ACPA+_RheumatoidArthritis

description: Sample11_RAstudyPAIR4_ACPA+_RheumatoidArthritis


title: Control light, rep3

description:
15Control
Control for 'lowRFR', 'LowBlue', and 'LowBlueRFR' plants.

value: 29 days

value: 24 hr


title: High density plants, rep2

description:
11LateCan
Controls are 'LateSing' plants.

value: 37 days

value: control light


title: PAIR2_ACPA-_Healthy


title: IFM_462

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Newly diagnosed multiple myeloma patient

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Affymetrix Genotyping Console 4.0 for processing SNPs, default parameters. birdseed-v2 / GenomeWideSNP_6.na32.annot.db / genome-version-ucsc=hg19 / genome-version-ncbi=GRCh37.1

source_name: Peripheral-blood

label_protocol: According to manufacturer protocol

extract_protocol: DNA was extracted using the DNA AllPrep DNA/RNA MiniKit (Qiagen, Valencia, CA). DNA quality and quantity were assessed using the Nanodrop Spectrophotometer (NanoDrop Technologies, Inc. Wilmington, DE).

value: Peripheral-blood

tag: cells

value: purified CD138+ plasma

tag: disease state

value: multiple myeloma


title: IFM_465


title: IFM_460


title: PAIR1_ACPA-_Healthy

source_name: input fraction of DNA from PBMC

tag: dna fraction


title: IFM_463

tag: tissue


title: IFM_459


title: IFM_458


title: IFM_464


title: IFM_455


title: IFM_467


title: IFM_466


title: IFM_457


title: IFM_461


title: IFM_453


title: PAIR3_ACPA+_Healthy

tag: cell type

source_name: Methyl-depleted fraction of DNA from PBMC


title: IFM_452


title: PAIR1_ACPA+_Healthy


title: IFM_456


title: IFM_469


title: IFM_445


title: IFM_454


title: IFM_446


title: IFM_450


title: IFM_447


title: IFM_444


title: IFM_448


title: IFM_443


title: IFM_451


title: IFM_440


title: IFM_442


title: IFM_438


title: IFM_435


title: IFM_432


title: IFM_428


title: IFM_437


title: IFM_426


title: IFM_433


title: IFM_424


title: IFM_427


title: IFM_425


title: IFM_436


title: IFM_439


title: IFM_430


title: IFM_420


title: IFM_422


title: IFM_421


title: IFM_416


title: IFM_418


title: IFM_415


title: IFM_413


title: IFM_412


title: IFM_414


title: IFM_411


title: IFM_434


title: IFM_406


title: IFM_410


title: IFM_408


title: IFM_405


title: IFM_404


title: IFM_401


title: IFM_407


title: IFM_403


title: IFM_441


title: IFM_431


title: IFM_468


title: IFM_400


title: IFM_399


title: IFM_402


title: IFM_397


title: IFM_449


title: IFM_429


title: IFM_398


title: IFM_423


title: IFM_417


title: IFM_396


title: IFM_409


title: IFM_394


title: IFM_395


title: IFM_392


title: IFM_390


title: IFM_393


title: IFM_386


title: IFM_388


title: IFM_381


title: IFM_389


title: IFM_391


title: IFM_385


title: IFM_387


title: IFM_383


title: IFM_378


title: IFM_419


title: IFM_382


title: IFM_380


title: IFM_384


title: IFM_370


title: IFM_379


title: IFM_375


title: IFM_376


title: IFM_371


title: IFM_373


title: IFM_372


title: IFM_369


title: IFM_367


title: IFM_366


title: IFM_368


title: IFM_374


title: IFM_363


title: IFM_377


title: IFM_365


title: IFM_362


title: IFM_364


title: IFM_359


title: IFM_360


title: IFM_357


title: IFM_354


title: IFM_361


title: IFM_356


title: IFM_358


title: IFM_351


title: IFM_355


title: IFM_341


title: IFM_346


title: IFM_349


title: IFM_353


title: IFM_348


title: IFM_343


title: IFM_342


title: IFM_350


title: IFM_347


title: IFM_344


title: IFM_352


title: IFM_338


title: IFM_345


title: IFM_334


title: IFM_337


title: IFM_335


title: IFM_340


title: IFM_333


title: IFM_339


title: IFM_327


title: IFM_328


title: IFM_322


title: IFM_329


title: IFM_324


title: IFM_325


title: IFM_314


title: IFM_323


title: IFM_332


title: IFM_318


title: IFM_317


title: IFM_336


title: IFM_319


title: IFM_312


title: IFM_309


title: IFM_307


title: IFM_321


title: IFM_330


title: IFM_320


title: IFM_311


title: IFM_315


title: IFM_306


title: IFM_305


title: IFM_326


title: IFM_331


title: IFM_301


title: IFM_297


title: IFM_304


title: IFM_308


title: IFM_300


title: IFM_295


title: IFM_296


title: IFM_313


title: IFM_293


title: IFM_294


title: IFM_292


title: IFM_290


title: IFM_298


title: IFM_291


title: IFM_289


title: IFM_282


title: IFM_284


title: IFM_299


title: IFM_288


title: IFM_287


title: IFM_281


title: IFM_286


title: IFM_279


title: IFM_283


title: IFM_280


title: IFM_285


title: IFM_302


title: IFM_272


title: IFM_310


title: IFM_316


title: IFM_278


title: IFM_277


title: IFM_275


title: IFM_303


title: IFM_274


title: IFM_276


title: IFM_273


title: IFM_270


title: IFM_269


title: IFM_265


title: IFM_268


title: IFM_266


title: IFM_259


title: IFM_257


title: IFM_271


title: IFM_262


title: IFM_267


title: IFM_261


title: IFM_258


title: IFM_263


title: IFM_254


title: IFM_260


title: IFM_255


title: IFM_253


title: IFM_251


title: IFM_264


title: IFM_256


title: IFM_239


title: IFM_250


title: IFM_237


title: IFM_249


title: IFM_248


title: IFM_236


title: IFM_231


title: IFM_235


title: IFM_233


title: IFM_246


title: IFM_243


title: IFM_229


title: IFM_234


title: IFM_242


title: IFM_232


title: IFM_244


title: IFM_226


title: IFM_228


title: IFM_224


title: IFM_241


title: IFM_247


title: IFM_240


title: IFM_227


title: IFM_225


title: IFM_223


title: IFM_245


title: IFM_252


title: IFM_222


title: IFM_230


title: IFM_238


title: IFM_219


title: IFM_220


title: IFM_218


title: IFM_214


title: IFM_217


title: IFM_221


title: IFM_215


title: IFM_203


title: IFM_206


title: IFM_200


title: IFM_208


title: IFM_198


title: IFM_204


title: IFM_199


title: IFM_205


title: IFM_197


title: IFM_209


title: IFM_194


title: IFM_210


title: IFM_207


title: IFM_216


title: IFM_211


title: IFM_213


title: IFM_196


title: IFM_193


title: IFM_192


title: IFM_202


title: IFM_191


title: IFM_189


title: IFM_188


title: IFM_195


title: IFM_212


title: IFM_187


title: IFM_186


title: IFM_201


title: IFM_190


title: IFM_183


title: IFM_178


title: IFM_179


title: IFM_184


title: IFM_182


title: IFM_185


title: IFM_169


title: IFM_172


title: IFM_168


title: IFM_167


title: IFM_171


title: IFM_177


title: IFM_176


title: IFM_180


title: IFM_159


title: IFM_173


title: IFM_164


title: IFM_170


title: IFM_174


title: IFM_162


title: IFM_161


title: IFM_165


title: IFM_163


title: IFM_157


title: IFM_166


title: IFM_160


title: IFM_156


title: IFM_181


title: IFM_158


title: IFM_175


title: IFM_154


title: IFM_152


title: IFM_155


title: IFM_150


title: IFM_153


title: IFM_146


title: IFM_149


title: IFM_151


title: IFM_144


title: IFM_136


title: IFM_137


title: IFM_133


title: IFM_147


title: IFM_148


title: IFM_143


title: IFM_141


title: IFM_135


title: IFM_139


title: IFM_142


title: IFM_145


title: IFM_132


title: IFM_140


title: IFM_131


title: IFM_138


title: IFM_128


title: IFM_130


title: IFM_134


title: IFM_129


title: IFM_122


title: IFM_126


title: IFM_127


title: IFM_125


title: IFM_124


title: IFM_123


title: IFM_121


title: IFM_115


title: IFM_108


title: IFM_105


title: IFM_120


title: IFM_104


title: IFM_100


title: IFM_103


title: IFM_119


title: IFM_113


title: IFM_114


title: IFM_102


title: IFM_101


title: IFM_118


title: IFM_117


title: IFM_112


title: IFM_106


title: IFM_116


title: IFM_109


title: IFM_111


title: IFM_097


title: IFM_099


title: IFM_095


title: IFM_094


title: IFM_098


title: IFM_096


title: IFM_093


title: IFM_110


title: IFM_092


title: IFM_107


title: IFM_091


title: IFM_090


title: IFM_087


title: IFM_088


title: IFM_083


title: IFM_086


title: IFM_074


title: IFM_078


title: IFM_085


title: IFM_089


title: IFM_081


title: IFM_073


title: IFM_077


title: IFM_082


title: IFM_076


title: IFM_075


title: IFM_072


title: IFM_064


title: IFM_071


title: IFM_080


title: IFM_063


title: IFM_066


title: IFM_070


title: IFM_067


title: IFM_068


title: IFM_065


title: IFM_060


title: IFM_079


title: IFM_057


title: COPD 7B

city: Birmingham

first: Stanley

middle: Ikenna

last: Ejiofor

state: West Midlands

address: Mendelsohn Way

department: Clinical and Experimental Medicine

institute: University of Birmingham

description:
biological replicate 7 of 7
human vastus replicate subject 7

hyb_protocol: Agilent Gene Expression kit used.  Hybridization master mix (GE blocking agent/Hybridization buffer) were added to labelled cDNA, placed onto microarray slides and hybridized at 65oC for 17hours.

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

source_name: Baseline muscle sample

label_protocol: Agilent suretag labelling kit was used. 300ng of total RNA were primed with 2.5ul at 95oC for 10minutes then 9.5ul of master mix was added and incubated at 37C for 2hours

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. 100ng of extracted RNA was amplified using the Transplex Whole Transcriptome Amplification kit (Sigma WTA-2)

value: subject7 vastuls lateralis sample

tag: diagnosis

value: Chronic Obstructive Pulmonary Disease (COPD)

source_name: muscle sample following Treatment B (oxygen)


title: COPD 3A

description:
biological replicate 6 of 7
human vastus replicate subject 3

scan_protocol: Agilent Feature Extraction Software (v 10.7.3.1)

value: subject3 vastuls lateralis sample

source_name: muscle sample following Treatment A (air)


title: COPD 7A


title: IFM_050


title: IFM_054


title: IFM_058


title: COPD 24A

description:
biological replicate 5 of 7
human vastus replicate subject 24

value: subject24 vastuls lateralis sample


title: IFM_059


title: IFM_055


title: COPD 20A

description:
biological replicate 4 of 7
human vastus replicate subject 20

value: subject20 vastuls lateralis sample

value: subject 20 vastus lateralis


title: IFM_052


title: COPD 18B

description:
biological replicate 3 of 7
human vastus replicate subject 18

value: subject18 vastuls lateralis sample

value: subject 18 vastus lateralis


title: IFM_049


title: COPD 18A


title: COPD 20B


title: IFM_069


title: IFM_046


title: COPD 3B


title: COPD 13A

description:
biological replicate 2 of 7
human vastus replicate subject 13

value: subject13 vastuls lateralis sample

value: subject 13 vastus lateralis


title: IFM_084


title: IFM_048


title: COPD 13B


title: IFM_047


title: IFM_053


title: COPD 10A

description:
biological replicate 1 of 7
human vastus replicate subject 10

value: subject10 vastuls lateralis sample

value: subject 10 vastus lateralis


title: IFM_045


title: COPD 10B


title: COPD 24B


title: IFM_044


title: IFM_043


title: IFM_042


title: IFM_061


title: IFM_062


title: IFM_037


title: IFM_040


title: IFM_035


title: IFM_036


title: IFM_041


title: IFM_056


title: IFM_034


title: IFM_031


title: IFM_039


title: IFM_038


title: IFM_032


title: IFM_024


title: IFM_029


title: IFM_026


title: IFM_030


title: IFM_021


title: IFM_027


title: IFM_028


title: IFM_025


title: IFM_022


title: IFM_023


title: IFM_015


title: Csac_7-2-Csac_Ptri

city: Raleigh

first: Robert

middle: M

last: Kelly

state: MI

address: Campus Box 7905

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

description: Loop #3

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42 degree C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95oC in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42oC to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42 degree C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42 degree C with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT with 0.5X SSC w/ 0.2% SDS. 3 wash cycles at RT with 0.5X SSC           I

scan_protocol: Images were aquired with a GenePix 4000B scanner (Molecular Devices) using 532 nm and 635 nm lasers simultaneously. An automatic photomultiplier (PMT) gain adjustment was used to balance the 532 nm and 635 nm channels prior to scanning the whole slide. A pixel size of 10 microns was selected for the image resolution. Separate images were saved for the 532 and 635 nm scans, and analyzed together using  GenePix Pro (v6.0) software.

data_processing: Signals for each channel were obtained using GenePix Pro (v6.0) using circular features and were background substrated using the median local intensity around the spot. Once all the slides were quantitated, data from the dye-flip was analyzed with JMP Genomics 5.0 (SAS, NC), normalized using ANOVA (Loop #3), Quantiles (Loop #1) or Lowess (Loop #2) then ANOVA to estimate the global fixed effects of dye & treatment and the random effects array and block followed by using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001).

organism: Caldicellulosiruptor saccharolyticus

source_name: Cell Pellet

label_protocol: 10 ug RNA was mixed with 6 ug random primers, and primed at 70˚C for 10 min. Reverse transcription used Superscript III (Invitrogen) and a dNTP mixture: dATP, dCTP, dGTP, dTTP, aa-dUTP (1:1:1:0.33:0.67). Samples were incubate at 46 ˚C overnight. cy-dyes (GE Healthcare) were resuspend in DMSO and added to cDNA resuspended in 4.5 uL of 0.1M sodium carbonate buffer, pH 9.0. Labeling was allowed to proceed for 2 hr in th dark. cy-dye labeled cDNA was then cleaned using a Qiagen PCR clean up column.

growth_protocol: C. saccharolyticus (DSM 8903) was obtained as a freeze-dried culture from the German Collection of Microorganisms and Cell Cultures (DSMZ [http://www.dsmz.de]). After reanimation, C. saccharolyticus was maintained on DSMZ640 medium at 70˚C with the following changes: Trypticase, FeCl3 x 6H2O, resazurin and Cysteine-HCl x H2O were omitted and 0.5% (w/v) Na2S x 9H2O was added as a reducing agent. Polysaccharides and biomass used include: crystalline cellulose (Avicel PH-101, FMC); glucomannan (konjac); pectin (practical grade); birchwood xylan (Sigma); dilute acid pretreated switchgrass (Panicum virgatum, –20/+80 mesh fraction; pretreatment was in a Sunds reactor at the National Renewable Energy Laboratory [NREL]), dilute acid pretreated poplar (P. trichocarpa x deltoides, provided by NREL), P. trichocarpa and genetically modified as4CL, 7-1 and 7-2 P. trichocarpa (ground to 80 mesh). For the biomass microarray experiment, all polysaccharides and biomass were added at a concentration of 1 g/L, noting that acid-treated poplar and switchgrass were added at a wet weight.  All cultures were sub-cultured four times on the applicable substrate in 50mL batch cultures under N2 headspace in 125 ml serum bottles prior to inoculation for cell harvesting. Cell densities (cells/ml) were monitored using epifluorescence microscopy.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen) and columns from a RNeasy kit (Qiagen). Biological repeats were used for all conditions, and total RNA was pooled prior to the reverse transcriptase reaction.

treatment_protocol: Cultures (500 mL) in 1L 45-mm-diameter screw top bottles were inoculated with cells in exponential phase to a density of 1 x 10^6 cells/ml. Cells were harvested when the culture reached mid-log phase, typically around 3-4 x 10^7 cells/ml.  In the case of biomass cultures, harvested culture was first filtered through a coffee filter into chilled centrifuge bottles, then rapidly cooled in an ethanol-dry ice bath, after which the cells were centrifuged at 5,000 rpm for 15 minutes and the cell pellet was stored at -80°C.

tag: growth substrate

value: P. trichocarpa '7-2'

tag: growth phase

value: mid-exponental

value: P. trichocarpa (Loop3)

value: mid-exponential


title: Csac_Ptri-Csac_7-1

description: Loop #3

value: P. trichocarpa '7-1'


title: Csac_7-1-Csac_7-2

description: Loop #3


title: IFM_018

value: Peripheral-blood

value: purified CD138+ plasma

value: multiple myeloma


title: Csac_aSWG-Csac_aPTD

description: Loop #2

value: Dilute Acid Pretreated switchgrass

value: Dilute Acid Pretreated P. trichocarpa x deltoides


title: IFM_020


title: IFM_016


title: Csac_as4CL-Csac_aSWG

description: Loop #2

value: P. trichocarpa 'as4cL1-12'


title: Csac_aPTD-Csac_Ptri

description: Loop #2

value: P. trichocarpa (Loop2)


title: Csac_Pectin versus Csac_Glman

description: Loop #1

value: Pectin

value: Konjac Glucomannan


title: IFM_019


title: IFM_012


title: IFM_013


title: IFM_017


title: IFM_009


title: IFM_033


title: Csac_Xylan versus Csac_Pectin

description: Loop #1

value: Birchwood Xylan


title: Csac_Glman versus Csac_Avicel

description: Loop #1

value: Konjac glucomannan

value: Avicel F-101


title: Csac_Avicel versus Csac_Xylan

description: Loop #1


title: IFM_051


title: IFM_010


title: IFM_006


title: IFM_003


title: Csac_Ptri-Csac_as4CL

description: Loop #2


title: IFM_004


title: IFM_011


title: SAMPLE 150

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description: Methylation data from brain tumor sample.

hyb_protocol: Illumina iScan System according to the manufacturer's protocol

scan_protocol: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'

data_processing:
Unmethylated and methylated signal intensities in Matrixsignal.txt file.
Average Beta

label: biotin/DNP

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: brain tumor

value: OTHER

tag: mgmt

value: meth

tag: egfr

value: noamp

tag: pdgfra

tag: pten

value: loss

value: balanced


title: IFM_002

value: Peripheral-blood

value: purified CD138+ plasma


title: IFM_001

value: multiple myeloma


title: SAMPLE 149

value: amp


title: SAMPLE 138


title: SAMPLE 142

value: unmeth


title: SAMPLE 143


title: SAMPLE 135


title: SAMPLE 136


title: SAMPLE 141


title: IFM_008


title: SAMPLE 134


title: IFM_014


title: SAMPLE 152


title: IFM_005


title: SAMPLE 146


title: SAMPLE 131


title: SAMPLE 144


title: SAMPLE 130


title: SAMPLE 148


title: SAMPLE 139


title: SAMPLE 129


title: SAMPLE 145


title: SAMPLE 127


title: SAMPLE 151


title: SAMPLE 133


title: SAMPLE 128


title: SAMPLE 125


title: SAMPLE 140


title: SAMPLE 121


title: SAMPLE 123


title: SAMPLE 126


title: SAMPLE 117


title: SAMPLE 118


title: SAMPLE 124


title: SAMPLE 116


title: SAMPLE 122


title: SAMPLE 110


title: SAMPLE 147


title: SAMPLE 114


title: SAMPLE 111


title: SAMPLE 113


title: SAMPLE 119


title: SAMPLE 112


title: SAMPLE 120


title: IFM_007


title: SAMPLE 105


title: SAMPLE 104


title: SAMPLE 107


title: SAMPLE 132


title: SAMPLE 101


title: SAMPLE 102


title: SAMPLE 106


title: SAMPLE 100


title: SAMPLE 115


title: SAMPLE 99


title: SAMPLE 96


title: SAMPLE 95


title: SAMPLE 97


title: SAMPLE 94


title: SAMPLE 137


title: SAMPLE 89


title: SAMPLE 88


title: SAMPLE 85


title: Liver_CJ Wt ZT18 30wk_mouse1

city: Houston

first: Loning

last: Fu

state: Texas

address: One Baylor Plaza

department: Medicine

institute: Baylor College of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarray Kit (G4852A) 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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray C Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61 × 21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100 and Grid: 028005_D_F_20110614) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Liver_CJ Wt ZT18 30wk_mouse1

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

extract_protocol: RNA was extracted using Trizol regeant then purified by using Life Technologies PureLink RNA Mini (Carlsbad,CA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57BL/6 Wildtype (Wt) mice were single-housed in either steady 12hr light/12hr dark cycles (NS) or subjected to chronic jet-lag (CJ) were mice are transferred between two mouse rooms different only at the time of light onset: Room 1 6:00am to 6:00pm light/6:00pm to 6:00am dark and Room 2 10:00am to 10:00pm dark/10:00pm to 10:00am light. Livers from entrained (NS) and chronic jet-lagged (CJ) wildtype mice at 12 weeks and 30 weeks were collected at ZT2, 10 & 18 and snap-frozen.

tag: strain

value: liver

tag: gender

value: male

value: 30 weeks


title: SAMPLE 103


title: Liver_NS Wt ZT18 30wk_mouse2

source_name: Liver_NS Wt ZT18 30wk_mouse2

tag: age


title: SAMPLE 86


title: Liver_CJ Wt ZT18 30wk_mouse3

source_name: Liver_CJ Wt ZT18 30wk_mouse3


title: Liver_NS Wt ZT18 30wk_mouse3

source_name: Liver_NS Wt ZT18 30wk_mouse3


title: SAMPLE 87


title: SAMPLE 90


title: SAMPLE 84


title: Liver_CJ Wt ZT18 30wk_mouse2

source_name: Liver_CJ Wt ZT18 30wk_mouse2


title: Liver_NS Wt ZT18 30wk_mouse1

source_name: Liver_NS Wt ZT18 30wk_mouse1


title: SAMPLE 77


title: SAMPLE 82


title: SAMPLE 80


title: SAMPLE 76


title: SAMPLE 79


title: Liver_NS Wt ZT18 12wk_mouse2

source_name: Liver_NS Wt ZT18 12wk_mouse2

value: 12 weeks


title: Liver_NS Wt ZT18 12wk_mouse1

source_name: Liver_NS Wt ZT18 12wk_mouse1


title: Liver_NS Wt ZT18 12wk_mouse3

source_name: Liver_NS Wt ZT18 12wk_mouse3


title: SAMPLE 75


title: SAMPLE 98


title: SAMPLE 78


title: Liver_CJ Wt ZT10 30wk_mouse2

source_name: Liver_CJ Wt ZT10 30wk_mouse2


title: Liver_CJ Wt ZT10 30wk_mouse3

source_name: Liver_CJ Wt ZT10 30wk_mouse3


title: Liver_CJ Wt ZT10 30wk_mouse1

source_name: Liver_CJ Wt ZT10 30wk_mouse1


title: Liver_NS Wt ZT10 30wk_mouse2

source_name: Liver_NS Wt ZT10 30wk_mouse2


title: Liver_CJ Wt ZT18 12wk_mouse3

source_name: Liver_CJ Wt ZT18 12wk_mouse3


title: Liver_NS Wt ZT10 30wk_mouse3

source_name: Liver_NS Wt ZT10 30wk_mouse3


title: Liver_NS Wt ZT10 30wk_mouse1

source_name: Liver_NS Wt ZT10 30wk_mouse1


title: SAMPLE 81

source_name: brain tumor


title: Liver_CJ Wt ZT10 12wk_mouse3

source_name: Liver_CJ Wt ZT10 12wk_mouse3


title: SAMPLE 74


title: SAMPLE 83


title: SAMPLE 73


title: Liver_CJ Wt ZT10 12wk_mouse2

source_name: Liver_CJ Wt ZT10 12wk_mouse2


title: SAMPLE 91


title: Liver_NS Wt ZT10 12wk_mouse3

source_name: Liver_NS Wt ZT10 12wk_mouse3


title: Liver_CJ Wt ZT2 30wk_mouse2

source_name: Liver_CJ Wt ZT2 30wk_mouse2


title: Liver_CJ Wt ZT18 12wk_mouse1

source_name: Liver_CJ Wt ZT18 12wk_mouse1


title: Liver_NS Wt ZT10 12wk_mouse1

source_name: Liver_NS Wt ZT10 12wk_mouse1


title: Liver_CJ Wt ZT10 12wk_mouse1

source_name: Liver_CJ Wt ZT10 12wk_mouse1


title: Liver_CJ Wt ZT2 30wk_mouse1

source_name: Liver_CJ Wt ZT2 30wk_mouse1


title: Liver_NS Wt ZT2 30wk_mouse2

source_name: Liver_NS Wt ZT2 30wk_mouse2


title: Liver_NS Wt ZT2 30wk_mouse1

source_name: Liver_NS Wt ZT2 30wk_mouse1


title: Liver_CJ Wt ZT2 12wk_mouse2

source_name: Liver_CJ Wt ZT2 12wk_mouse2


title: Liver_CJ Wt ZT2 12wk_mouse1

source_name: Liver_CJ Wt ZT2 12wk_mouse1


title: SAMPLE 72


title: SAMPLE 69


title: SAMPLE 93


title: Liver_CJ Wt ZT18 12wk_mouse2

source_name: Liver_CJ Wt ZT18 12wk_mouse2


title: Liver_NS Wt ZT2 12wk_mouse2

source_name: Liver_NS Wt ZT2 12wk_mouse2


title: SAMPLE 67


title: Liver_NS Wt ZT2 12wk_mouse1

source_name: Liver_NS Wt ZT2 12wk_mouse1


title: SAMPLE 68


title: SAMPLE 108


title: mesenchymal stromalcells, maternal side of placenta patient no. 30

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

hyb_protocol: Standard Affymetrix procedures

data_processing: The CEL file data were normalized with the Robust Multichip Average (RMA) method.

label_protocol: Standard Affymetrix procedures

growth_protocol: MSCs were isolated from human bone marrow or term placenta, seeded in TCPS flasks and expanded in DMEM medium enriched with serum and antibiotics to their second passage

extract_protocol: RNA was extracted using the RNeasy Kit by Qiagen

treatment_protocol: MSCs were rinsed with PBS, detached with trypsin, washed and resuspended in PBS to count yield and viability

value: adult cells, fulfill ISCT inclusion criteria


title: SAMPLE 66


title: SAMPLE 109


title: mesenchymal stromalcells, maternal side of placenta patient no. 47


title: mesenchymal stromal cells, fetal side of placenta patient no. 47


title: mesenchymal stromal cells, fetal side of placenta patient no. 31


title: mesenchymal stromalcells, maternal side of placenta patient no. 46 rep2


title: SAMPLE 92


title: SAMPLE 65


title: mesenchymal stromal cells, fetal side of placenta patient no. 46 rep2


title: Liver_NS Wt ZT10 12wk_mouse2

source_name: Liver_NS Wt ZT10 12wk_mouse2


title: mesenchymal stromal cells, fetal side of placenta patient no. 46 rep1


title: mesenchymal stromalcells, maternal side of placenta patient no. 46 rep1


title: mesenchymal stromal cells, fetal side of placenta patient no. 45


title: mesenchymal stromalcells, maternal side of placenta patient no. 45


title: SAMPLE 64

source_name: brain tumor


title: mesenchymal stromal cells, fetal side of placenta patient no. 30


title: mesenchymal stromalcells, maternal side of placenta patient no. 33


title: mesenchymal stromal cells, fetal side of placenta patient no. 33


title: SAMPLE 71


title: SAMPLE 61


title: SAMPLE 62


title: SAMPLE 51


title: SAMPLE 60


title: SAMPLE 70


title: mesenchymal stromal cell, bone marrow, patient KKG


title: SAMPLE 55


title: SAMPLE 58


title: SAMPLE 59


title: SAMPLE 54


title: mesenchymal stromal cell, bone marrow, patient SRF


title: mesenchymal stromal cell, bone marrow, patient ANB


title: SAMPLE 56


title: mesenchymal stromal cells, fetal side of placenta patient no. 35


title: SAMPLE 49


title: mesenchymal stromal cell, bone marrow, patient BEH


title: SAMPLE 53


title: mesenchymal stromal cell, bone marrow, patient SDK


title: SAMPLE 57


title: mesenchymal stromal cell, bone marrow, patient HNC


title: SAMPLE 46


title: SAMPLE 52


title: mesenchymal stromal cell, bone marrow, patient BRM


title: mesenchymal stromal cell, bone marrow, patient GSK


title: mesenchymal stromal cell, bone marrow, patient WHR


title: mesenchymal stromal cell, bone marrow, patient LQ


title: SAMPLE 50


title: mesenchymal stromal cell, bone marrow, patient BRD


title: SAMPLE 63


title: SAMPLE 48


title: SAMPLE 45


title: tumor_negative control_rep3

city: Urbana

first: William

middle: G

last: Helferich

state: Illinois

address: 905 S Goodwin Avenue

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Champaign

hyb_protocol: It was performed as described in the GeneChip Expresion Analysis Technical Manual (Affymetrix, Santa Clara, CA; Rev. 4).

data_processing: The data were analyzed withGCRMA using using the Bioconductor package for Affymetrix arrays with the R software. A linear model was fit to the log2-intensity transformed intensity data for each probe ID using Limma package of bioconductor [18] in preparation for differential expression analysis of  the data. Empirical Bayes method was subsequently used to borrow information across genes making the analyses stable even. Present/Marginal/Absent (P/M/A) calls are good criteria to filter out the unexpressed probes . The probes which are “Present” on at least 1 array or “Marginal” on at least 2 arrays were reserved for further analysis.

source_name: tumor

label_protocol: Target labeling was performed using total RNA for cDNA synthesis and preparing the biotinylated antisense cRNA using SuperScript II (Invitrogen Life Techologies, Rockville, MD) and EnzoBioArray High Yield RNA Transcript Labeling Kit (Enzo diagnostics, farmingdale, NY).

growth_protocol: MCF-7 tumor cells from each treatment group were collected at week twelve upon mice scarification surgery and were immediately frozen by submersion into liquid nitrogen for RNA isolation

tag: cell line

tag: diet group

value: NC


title: SAMPLE 44

value: brain tumor


title: SAMPLE 42

value: OTHER


title: tumor_soy flour_rep2

scan_protocol: It was performed as described in the GeneChip Expresion Analysis Technical Manual (Affymetrix, Santa Clara, CA; Rev. 4).

value: MS


title: SAMPLE 40

value: noamp


title: tumor_mixed isoflavones_rep3

extract_protocol: It was performed as described in the GeneChip Expresion Analysis Technical Manual (Affymetrix, Santa Clara, CA; Rev. 4).

value: MI


title: SAMPLE 43

value: meth

value: balanced


title: tumor_mixed isoflavones_rep1

treatment_protocol: It was performed as described in the GeneChip Expresion Analysis Technical Manual (Affymetrix, Santa Clara, CA; Rev. 4).


title: tumor_mixed isoflavones_rep2


title: tumor_negative control_rep2


title: tumor_negative control_rep1


title: SAMPLE 41

value: loss


title: SAMPLE 35


title: SAMPLE 37


title: tumor_soy flour_rep3


title: SAMPLE 34


title: SAMPLE 32


title: SAMPLE 36


title: tumor_positive control_rep2

value: PC


title: tumor_positive control_rep1


title: SAMPLE 33

value: amp


title: SAMPLE 31

value: unmeth


title: tumor_soy flour_rep1


title: SAMPLE 29


title: 731_8_VPA

city: Okinawa

first: Gakuya

last: Takamatsu

address: 207 Uehara

department: Department of Molecular & Cellular Physiology

country: Japan

institute: Graduate School of Medicine, University of the Ryukyu

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: All hybridized microarray slides were scanned by an Agilent scanner. Relative hybridization intensities and background hybridization values were calculated using Agilent Feature Extraction Software (9.5.1.1).

data_processing: Raw signal intensities and Flags for each probe were calculated from hybridization intensities (gProcessedSignal), and spot information (gIsSaturated, etc.), according to the procedures recommended by Agilent. Flag criteria on GeneSpring Software. Absent (A): “Feature is not positive and significant” and “Feature is not above background”. Marginal (M): “Feature is not Uniform”, “Feature is Saturated”, and “Feature is a population outlier”. Present (P): others. And the raw signal intensities of all samples were normalized by quantile algorithm with ‘preprocessCore’ library package on Bioconductor software.

source_name: 1 mM VPA with 0.1 % DMSO

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies)

growth_protocol: Cultures were prepared from embryonic day 18 C57BL6/J mice. Cerebrum was dissected and minced. The pieces were dissociated by 0.125 % trypsin for 10 min at 37 ℃. The cells were resuspended in DNase I for 10 min at 37 ℃ and triturated gently through a flame-polished Pasteur pipette. The cells was resuspended in neurobasal medium supplemented with 2 % B27 supplement, 0.5 mM L-glutamine and 1 % penicillin/streptomycin. Cells were seeded onto dishes coated by 5 μg/ml poly-L-lysine and 10 μg/ml laminin at density of 500 cells / mm2. Cultures were kept at 37°C in a 5% CO2 incubator. Culture medium was partly changed every three days.

extract_protocol: The total RNA was isolated from the cells using TRIzol Reagent (Invitrogen). RNA samples were quantified by an ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality was confirmed with a Experion System (Bio-Rad Laboratories, Hercules, CA).

treatment_protocol: Cells were treated at DIV 10 for 24 h with 1 mM valproate acid, 0.1 % DMSO, or 100 µM lamotrigine.

value: primary cerebral cells

tag: treatment time


title: SAMPLE 30


title: 731_7_LTG

description: Treatment of lamotrigine was performed for the reseach of antiepileptic drugs, but this microarray data was not used in the present study about HDAC inhibitor.

source_name: 100 µM LTG (lamotrigine) with 0.1 % DMSO


title: SAMPLE 47


title: SAMPLE 38


title: SAMPLE 27


title: SAMPLE 22


title: SAMPLE 25


title: K9 BM-MSC bio rep 3

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: gene expression data from canine BM-MSC at low passage

hyb_protocol: Hybridization was performed according to Affymetrix Cartridge Array Hybridization on the GeneChip® Instrument protocol with wash protocol FS450_0002

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner

data_processing: Image files were converted to log2 expression values with RMA (Robust Multiarray Average) background correction and quantile normalization, as implemented by a statistical/visualization package (Partek Genomics Suite v6.6; St Louis, MO

label: WT Plus

organism: Canis lupus familiaris

source_name: canine bone marrow derived MSC

label_protocol: cDNA was prepared according to Affymetrix Genechip WT Plus Reagent Kit  protocol

growth_protocol: Adipose and bone marrow were collected following protocols approved by the IACUC. Collected tissue was minced and digested using collagenase, and plated in T75 culture flask with MSC media.

extract_protocol: RNA extracted using Qiagen RNeasy mini kit

treatment_protocol: MSC were collected at passage 3 using trypsin

value: BM-MSC


title: SAMPLE 28


title: K9 BM-MSC bio rep 2


title: 731_9_CT

source_name: 0.1% DMSO


title: SAMPLE 24


title: SAMPLE 26


title: SAMPLE 21


title: SAMPLE 17


title: SAMPLE 14


title: SAMPLE 20


title: RCH_input_all

type: SRA

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital

department: Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine

library_source: genomic

data_processing:
Nascent RNA-seq reads were aligned to the hg18 genome using STAR
Read counts were determined using featureCounts (Subread package)
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam. Duplicates were removed prior to subsequent analysis
CaptureC reads were mapped and analysed using the CaptureC 'CCanalyser3' pipeline (https://github.com/telenius/captureC/releases) using bowtie2 for paired-end reads with genome build hg18
Genome_build: hg18
Supplementary_files_format_and_content: Rpkm table was generated using edgeR
Supplementary_files_format_and_content: CaptureC_combinedReads.txt is a text file containing the reads from the WIG file of the Capture-C track, around the region that is investigated.

source_name: Leukemia cell line (RCH-ACV)

growth_protocol: Cells were continuously grown in IMDM (SEM) or RPMI1640 (RCH-ACV) with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5

extract_protocol:
108 fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's protocol accompanying the NEBNext DNA (Part# E6040) or Ultra RNA (Part# E7530) Library Prep Master Mix Set.

value: Paediatric pre B-cell line derived from cALL with t(1;19)(q23;p13) translocation


title: SAMPLE 18


title: RCH_PBX_ChIPseq

tag: chip antibody


title: SAMPLE 16


title: K9 Ad-MSC bio rep2

description: gene expression data from canine Ad-MSC at low passage

source_name: canine adipose derived MSC

value: Ad-MSC


title: K9 Ad-MSC bio rep1


title: RCH_E2A_ChIPseq

value: E2A (Cell Signaling, 12258/1)


title: SAMPLE 11


title: K9 BM-MSC bio rep 1


title: SAMPLE 15


title: SEM_P300_input

source_name: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: SEM_P300_ChIPseq


title: SAMPLE 10

value: brain tumor


title: SEM_E2A_input


title: SAMPLE 19

value: OTHER


title: SEM_E2A_ChIPseq


title: SAMPLE 13


title: tumor_positive control_rep3


title: SAMPLE 8


title: SAMPLE 23


title: Double Knockdown #1

city: DALLAS

first: KANGSAN

last: KIM

state: TX

address: 5323 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

description: 36hour after siRNA knockdown

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: HUVEC

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: EGM2 media

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

treatment_protocol: 20nM siRNA with Lipofectamine RNAiMax

value: Endothelial cell

value: HUVEC

tag: genotype/variation

value: Sox7/Sox17 knockdown


title: Double Knockdown #2

description: 36hour after siRNA knockdown


title: Sox7 Knockdown #2

description: 36hour after siRNA knockdown

value: Sox7 knockdown


title: SEM_CaptureC

description: DNA-capture

data_processing:
Library strategy: 3C-Seq
Nascent RNA-seq reads were aligned to the hg18 genome using STAR
Read counts were determined using featureCounts (Subread package)
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam. Duplicates were removed prior to subsequent analysis
CaptureC reads were mapped and analysed using the CaptureC 'CCanalyser3' pipeline (https://github.com/telenius/captureC/releases) using bowtie2 for paired-end reads with genome build hg18
Genome_build: hg18
Supplementary_files_format_and_content: Rpkm table was generated using edgeR
Supplementary_files_format_and_content: CaptureC_combinedReads.txt is a text file containing the reads from the WIG file of the Capture-C track, around the region that is investigated.

extract_protocol:
2x107 fixed cells were lysed in 0.2% NP40 lysis buffer and Dounce homogenized. 3C-library DNA was sonicated and regions of interested were captured using 120bp oligonucleotides.
Libraries were prepared according to Illumina's protocol accompanying the NEBNext DNA (Part# E6040) or Ultra RNA (Part# E7530) Library Prep Master Mix Set.


title: Sox17 Knockdown #2

description: 36hour after siRNA knockdown

value: Sox17 knockdown


title: SAMPLE 9

tag: tissue

value: noamp

value: balanced

value: loss


title: Control #1

description: 36hour after siRNA knockdown

tag: cell type

value: control


title: SEM_siMLLAF4_Rep3

description: nascent RNA

library_source: transcriptomic

extract_protocol:
108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
Libraries were prepared according to Illumina's protocol accompanying the NEBNext DNA (Part# E6040) or Ultra RNA (Part# E7530) Library Prep Master Mix Set.

treatment_protocol: cells were treated with 300pmol siMA6 (MLL-AF4)


title: Sox17 Knockdown #1

description: 36hour after siRNA knockdown


title: SAMPLE 39

value: unmeth

value: amp


title: MSC_9829118144_R03C02

city: Hangzhou

first: Donger

last: Zhou

address: Jiefang Road 88#

institute: Zhejiang University

description:
fibroblasts
SAMPLE 1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina’s iScan scanner using standard recommended Illumina scanner setting

data_processing: GenomeStudio v1.0 Software

label: Cy5 and Cy3

source_name: cultured cells

label_protocol: Standard Illumina Protocol

growth_protocol: 09.05CAFs were maintained in RPMI 1640 (Life Technology, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS) under standard conditions. Human mesenchymal stem cells (MSCs) were cultured in Alpha Modified Eagle Medium (αMEM) media containing 10% premium selected FBS (Atlanta Biologicals, Flowery Branch, GA, USA).

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Mesenchymal stem cells and 09.05CAFs which was primary cultured fibroblasts either cultured alone or co-cultured with pancreatic tumor cells then purified by anti-FAP antibody coupled Dynabeads.

tag: culture methods

value: cultured alone


title: SAMPLE 12


title: SEM_siControl_Rep1

description: nascent RNA

treatment_protocol: cells were treated with 300pmol siMM (control)


title: MSC+10.05T_9829118144_R05C02

description:
fibroblasts purified from coculture
SAMPLE 3

value: cocultured and then purified


title: SEM_siControl_Rep3

description: nascent RNA


title: 09.05F_9829118144_R04C02

description:
fibroblasts
SAMPLE 2


title: Sox7 Knockdown #1

description: 36hour after siRNA knockdown


title: K9 Ad-MSC bio rep3

value: Ad-MSC


title: SEM_siControl_Rep2

description: nascent RNA

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: SAMPLE 7

value: brain tumor


title: SAMPLE 3

value: OTHER


title: SAMPLE 4


title: SAMPLE 5

value: meth


title: SAMPLE 2


title: Control #2

description: 36hour after siRNA knockdown

value: Endothelial cell

value: HUVEC


title: GSC-222_si-JAG1_rep1

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

institute: Nagoya City University Graduate School of Medical Sciences

description: Gene expression in si-JAG1 treated Giloma stem cell 222

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 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8×60K array slides (G4851B, Agilent Technologies) at 65 °C with rotation at 10 rpm for 17 hours in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA, Agilent Technologies) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Giloma stem cell, 222, si-JAG1, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: GSCs were cultured in Neurobasal Medium (Life Technologies) containing N2 and B27 supplements (Life Technologies), along with human recombinant basic fibroblast growth factor and epidermal growth factor (20 ng/ml each; R&D Systems) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000.

treatment_protocol: GSCs were transfected with 20 nM si-Notch1, si-JAG1 or control non-targeting siRNA (AM4611, Applied Biosystems) using Lipofectamine 2000 (Life Technologies). 72 h after the transfection of siRNA, total RNA was extracted from GSCs and the effects were validated.  For blocking of Notch signaling in GSCs, the γ-secretase inhibitor DAPT (N-[N-(3,5-difluorophenacetyl)-l-alanyl]-S-phenylglycine t-butyl ester, Sigma-Aldrich) and RO4929097 (Selleck Chemicals) were added, and the medium was changed every other day.

value: Human glioblastoma

value: male


title: GSC-222_si-Notch1_rep1

description: Gene expression in si-Notch1 treated Giloma stem cell 222

source_name: Giloma stem cell, 222,si-Notch1, replicate 1


title: GSC-222_si-NC_rep1

description: Gene expression in si-NC treated Giloma stem cell 222

source_name: Giloma stem cell, 222, si-NC, replicate 1


title: GSC-222_si-TUG1_rep2

description: miRNA expression in si-TUG1 treated Giloma stem cell 222

hyb_protocol: Labeled samples were hybridized to SurePrint G3 Human miRNA 8x60K Microarray (G4872A, Agilent Technologies) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 5 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol miRNA_107_SEP09 and Grid: 070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Giloma stem cell, 222, si-TUG1, replicate 2

label_protocol: 100 ng of total RNA was labeled with pCp-Cy3 (Agilent Technologies) and 15 units of T4 RNA ligase (GE Healthcare) at 16°C for 2 hours. Labeled samples were purified with MicroBio-Spin 6 columns (Bio-Rad, Richmond, CA).

treatment_protocol: GSCs were transfected with 20 nM siRNA targeting TUG1 or control non-targeting siRNA (AM4611, Applied Biosystems) using Lipofectamine 2000 (Life Technologies). 72 h after the transfection of siRNA, total RNA was extracted from GSCs and the effects were validated.


title: GSC-222_si-TUG1_rep1

source_name: Giloma stem cell, 222, si-TUG1, replicate 1


title: GSC-222_DAPT_rep1

description: Gene expression in DAPT treated Giloma stem cell 222

source_name: Giloma stem cell, 222, DMSO, replicate 1


title: GSC-222_DAPT_RO4929097_rep1

description: Gene expression in RO4929097 treated Giloma stem cell 222

source_name: Giloma stem cell, 222, RO4929097, replicate 1


title: GSC-222_DMSO_rep1

description: Gene expression in DMSO treated Giloma stem cell 222

source_name: Giloma stem cell, 222, DAPT, replicate 1


title: GSC-1228_DAPT_RO4929097_rep1

description: Gene expression in RO4929097 treated Giloma stem cell 1228

source_name: Giloma stem cell, 1228, RO4929097, replicate 1


title: 09.05F+10.05T_9479614032_L

description:
fibroblasts purified from coculture
SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label_protocol: Biotinylated cRNA were prepared in standard Illumina protocol.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit following the standard protocal.


title: GSC-1228_DAPT_rep1

description: Gene expression in DAPT treated Giloma stem cell 1228

source_name: Giloma stem cell, 1228, DMSO, replicate 1


title: MSC+10.05T_9479614032_J


title: GSC-222_si-NC_rep2

description: miRNA expression in si-NC treated Giloma stem cell 222

source_name: Giloma stem cell, 222, si-NC, replicate 2


title: GSC-1228_si-Notch1_rep1

description: Gene expression in si-Notch1 treated Giloma stem cell 1228

source_name: Giloma stem cell, 1228,si-Notch1, replicate 1


title: GSC-1228_DMSO_rep1

description: Gene expression in DMSO treated Giloma stem cell 1228

source_name: Giloma stem cell, 1228, DAPT, replicate 1


title: SAMPLE 6

description: Methylation data from brain tumor sample.

source_name: brain tumor

value: noamp


title: GSC-1228_si-NC_rep1

description: Gene expression in si-NC treated Giloma stem cell 1228

source_name: Giloma stem cell, 1228, si-NC, replicate 1


title: GSC-1228_si-JAG1_rep1

description: Gene expression in si-JAG1 treated Giloma stem cell 1228

source_name: Giloma stem cell, 1228, si-JAG1, replicate 1


title: 09.05F+10.05T_9829118144_R06C02

source_name: cultured cells


title: MSC_9479614032_F

description:
fibroblasts
SAMPLE 1


title: GSC-222_si-NC_rep1


title: GSC-1228_si-TUG1_rep2

description: miRNA expression in si-TUG1 treated Giloma stem cell 1228

source_name: Giloma stem cell, 1228, si-TUG1, replicate 2


title: GSC-222_rep1

description: Gene expression in Giloma sten cell 222

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: glioma stem cells (GSCs)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.

growth_protocol: GSCs were cultured in Neurobasal Medium (Life Technologies) containing N2 and B27 supplements (Life Technologies), along with human recombinant basic fibroblast growth factor and epidermal growth factor (20 ng/ml each; R&D Systems) at 37℃ in a humidified incubator with 5% CO2.

value: glioma stem cells (GSCs)


title: GSC-1228_si-TUG1_rep1

source_name: Giloma stem cell, 1228, si-TUG1, replicate 1


title: 09.05F_9479614032_H

description:
fibroblasts
SAMPLE 2


title: GSC-1228_si-NC_rep2

description: miRNA expression in si-NC treated Giloma stem cell 1228

source_name: Giloma stem cell, 1228, si-NC, replicate 2


title: GSC-1228_si-NC_rep1


title: HMB-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep4

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 4 of 4. GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep1

hyb_protocol: On each two-colour microarray 825 ng of cRNA from GO exposed cells (Cy5) and 825 ng of cRNA from control cells (Cy3) were hybridized using Gene Expression Hybridization Kit (Agilent Technologies, USA) according to the manufacturers protocol. RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using the Agilent DNA microarray scanner and Agilent Feature Extraction software 10.7.3.1. according to the standard manufacturer’s procedures and LOWESS normalization.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

organism: Equus caballus

source_name: HMB-treated equine satellite cells_Cy5

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).

growth_protocol: Equine satellite cells were cultured in Primaria culture flask (BD, USA). The growth medium (10%FBS/10%HS/DMEM/AB) was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate. After obtaining 80% of confluence proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB). FBS - fetal bovine serum, HS - horse serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9,2 were included into the analysis.

treatment_protocol: After the 2nd day of differentiation 50µg β-hydroxy-β-methylbutyrate (HMB) was added and cells were incubated for 24h. Control cells were incubated in differentiation medium.

value: 3rd day of differentiation

tag: satellite cell origin

value: m. semitendinosus

value: satellite cell


title: HMB-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep3

description: Biological replicate 3 of 4. GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep1


title: MRC-5_SWCNT, rep2

city: Bukit Jalil

first: Chee-Onn

last: Leong

country: Malaysia

institute: International Medical University

description: Gene expression of MRC-5 cells treated with 100 ug/mL regular-length pristine SWCNTs for 72h

hyb_protocol: The ssDNA was then biotin labeled, fragmented and hybridized to Affymetrix Human Gene 1.0 ST arrays for 16 hours at 45C with rotation at 60 rpm.

scan_protocol: Arrays were then washed and stained using the FS450_0007 fluidics protocol and scanned using an Affymetrix 3000 7G scanner.

data_processing: The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.1 software for array QC. RMA normalization was performed on the samples to generate the quality control (QC) metrics that we routinely use to determine data quality. These include, perfect match mean (PM_Mean), Background mean (Bgd_Mean), positive and negative probes (POS vs NEG AUC), bacterials spike controls, and polyA controls.

label_protocol: The RNA samples were processed according to the Affymetrix recommended protocol and Origen Labs’ SOP for whole transcript analysis. Briefly, 300ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create cRNA which was then converted to single stranded DNA (ssDNA).

growth_protocol: MRC-5 cells were maintained in RPMI 1640 medium containing 10% fetal bovine serum (FBS), 100 IU/ml penicillin, and 100 μg/ml streptomycin at 37°C, 5% CO2.

extract_protocol: Total RNA from cells was extracted using Qiagen RNA isolation kit (Qiagen, Valencia, CA, USA) according to the manufacturers’ protocol. RNA purity was examined by spectrophotometric determination at 260/280 nm.

treatment_protocol: Cells were treated with vehicle control (PBS) or 100 ug/mL regular-length pristine SWCNTs for 72h

value: embryonic lung fibroblast cell line MRC-5

tag: treatment

value: SWCNT


title: MRC-5_Control, rep 2

description: Gene expression of MRC-5 cells treated with vehicle control for 72h

value: Control


title: SAMPLE 1

tag: mgmt

value: balanced

value: loss


title: g7_83

status: Public on Nov 22 2016

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

institute: Washington University School of Medicine

description: Gene expression in HPCs

hyb_protocol: The balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (6ul).  The hybridization solutions were applied to Agilent Mouse v2 4x44K microarrays (G4846A-026655).  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy5 fluorescence, according to manufacturer's specifications.

data_processing: Gridding and analysis of images was performed using Feature Extraction (v11.5.1.1, Agilent Technologies).

source_name: Bone marrow

label_protocol: RNA samples were amplified using SIGMA WTA2 RNA amplification system. Amplified cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy5/DY-ULS (2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled cDNA was purified with Qiagen PCR purification columns according to manufacturer’s protocol.  cDNAs were quantitated on a Nanodrop spectrophotometer. Detailed protocol can be found at http://www.kreatech.com/fileadmin/user_upload/Documenten/PDF/12_man_EA-021-022-023__D0.6.pdf

growth_protocol: HSCs and HPCs harvested directly from mouse by flow cytometry

extract_protocol: RNA was prepared using the Qiagen RNAeasy micro plus columns

treatment_protocol: No treatments.  Cells were harvested directly from mice by flow cytometry

tag: developmental stage

tag: genotype

value: Runx f/+, VC

value: HPC


title: g8_37

description: Gene expression in HPCs

value: ITD; Runx f/+, VC


title: HMB-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep2

description: Biological replicate 2 of 4. GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep1


title: g8_35

description: Gene expression in HPCs


title: g7_32

description: Gene expression in HPCs


title: MRC-5_Control, rep 1

source_name: MRC-5 cells treated with vehicle control for 72h


title: GSC-222 BrU-TUG1

hyb_protocol: A total of 4 µg of labelled DNA was then hybridized to human promoter ChIP-chip microarray (G4874A, Agilent) for 48 h at 65°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 2x400k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol ChIP_107_Sep09 and Grid: 027954_D_F_20101112) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: GSC-222 BrU-TUG1

label_protocol: Amplified products were labeled with Cy5 for immunoprecipitated DNA samples and Cy3 for input DNA using BioPrime Array CGH Genomic Labeling System (Life Technologies).

extract_protocol: 10 nM BrU-labeled TUG1 RNA (2108 to 2885 nucleotides) was transfected into GSCs using Lipofectamin 2000 (Life Technologies). After 72h of transfection, GSCs were crosslinked with 0.5 % of formaldehyde and their chromatin fractions were extracted and homogenized. Chromatin and BrU-labeled TUG1 RNA mixtures were immunoprecipitated using anti-BrU antibodies (MI-11-3, MBL) and Dynabeads Protein G (Life Technologies). Equivalent amounts of DNA, which was extracted from immunoprecipitated by BrU-labeled TUG1 RNA, and total input DNA were amplified in parallel using a random primer method with the GenomePlex Complete Whole Genome Amplification Kit (15 cycles), according to the manufacturer's instructions (Sigma-Aldrich).

source_name: Input DNA from 222-GSC


title: g6_30

description: Gene expression in HPCs

value: ITD


title: g6_82

description: Gene expression in HPCs


title: SEM_siMLLAF4_Rep2

description: nascent RNA

source_name: Leukemia cell line (SEM)

value: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation


title: g8_38

description: Gene expression in HPCs


title: g7_34

description: Gene expression in HPCs


title: g7_33

description: Gene expression in HPCs


title: g8_36

description: Gene expression in HPCs


title: MRC-5_SWCNT, rep1

source_name: MRC-5 cells treated with 100 ug/mL regular-length pristine SWCNTs for 72h


title: g5_26

description: Gene expression in HPCs

value: wt


title: g6_80

description: Gene expression in HPCs


title: HMB-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep1

description: Biological replicate 1 of 4. GO-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep1


title: g5_25

description: Gene expression in HPCs


title: g6_27

description: Gene expression in HPCs


title: g5_24

description: Gene expression in HPCs


title: g5_23

description: Gene expression in HPCs


title: g4_16

description: Gene expression in HPCs

source_name: Liver


title: g4_21

description: Gene expression in HPCs


title: g3_13

description: Gene expression in HPCs


title: GSC-1228 BrU-TUG1

source_name: GSC-1228 BrU-TUG1

growth_protocol: GSCs were cultured in Neurobasal Medium (Life Technologies, Carlsbad, CA) containing N2 and B27 supplements (Life Technologies), along with human recombinant basic fibroblast growth factor and epidermal growth factor (20 ng/ml each; R&D Systems, Minneapolis, MN).  at 37 ºC in a humidified incubator with 5% CO2.

value: Human glioblastoma

source_name: Input DNA from 1228-GSC


title: g3_11

description: Gene expression in HPCs


title: IPFF_117

description: Gene expression in HPCs

value: Adult

value: ITD/+; Stat5 f/f, Mx


title: g1_77

description: Gene expression in HPCs


title: g2_06

description: Gene expression in HPCs


title: g4_20

description: Gene expression in HPCs


title: g4_17

description: Gene expression in HPCs


title: g2_78

description: Gene expression in HPCs


title: g1_01

description: Gene expression in HPCs


title: g2_08

description: Gene expression in HPCs


title: II_124

description: Gene expression in HPCs

value: ITD/ITD


title: g1_03

description: Gene expression in HPCs


title: g4_15

description: Gene expression in HPCs


title: g1_02

description: Gene expression in HPCs


title: IPFF_113

description: Gene expression in HPCs

value: ITD/+; Stat5 f/+, Mx


title: g2_07

description: Gene expression in HPCs


title: II_121

description: Gene expression in HPCs


title: g1_04

description: Gene expression in HPCs


title: IPFP_112

description: Gene expression in HPCs


title: II_123

description: Gene expression in HPCs


title: IPFP_120

description: Gene expression in HPCs


title: IP_105

description: Gene expression in HPCs

value: ITD/+


title: II_122

description: Gene expression in HPCs


title: IPFF_118

description: Gene expression in HPCs


title: IPFF_119

description: Gene expression in HPCs


title: IP_JM63

description: Gene expression in HPCs


title: IP_108

description: Gene expression in HPCs


title: IP_106

description: Gene expression in HPCs


title: IPFP_114

description: Gene expression in HPCs


title: IP_JM61

description: Gene expression in HPCs


title: WT_JM48

description: Gene expression in HPCs

value: wildtype


title: IP_JM62

description: Gene expression in HPCs


title: WT_103

description: Gene expression in HPCs


title: WT_101

description: Gene expression in HPCs


title: WT_104

description: Gene expression in HPCs


title: RP_ITD_Adult_16502

description: Gene expression in HPCs

value: FLT3 ITD/+


title: IP_107

description: Gene expression in HPCs


title: RP_ITD_P14_16499

description: Gene expression in HPCs


title: WT_JM45

description: Gene expression in HPCs


title: RP_WT_Adult_16487

description: Gene expression in HPCs


title: RP_WT_Adult_16485

description: Gene expression in HPCs


title: WT_102

description: Gene expression in HPCs


title: RP_WT_Adult_16486

description: Gene expression in HPCs


title: RP_WT_Adult_16488

description: Gene expression in HPCs


title: RP_ITD_P0_16496

description: Gene expression in HPCs


title: RP_ITD_P0_16493

description: Gene expression in HPCs


title: RP_ITD_Adult_16898

description: Gene expression in HPCs


title: RP_WT_P0_16479

description: Gene expression in HPCs


title: RP_ITD_P14_16500

description: Gene expression in HPCs


title: RP_ITD_Adult_16501

description: Gene expression in HPCs


title: RP_WT_P14_16483

description: Gene expression in HPCs


title: RP_ITD_P0_16908

description: Gene expression in HPCs


title: RP_ITD_P14_16498

description: Gene expression in HPCs


title: RP_WT_P0_16480

description: Gene expression in HPCs


title: RP_ITD_Adult_16503

description: Gene expression in HPCs


title: RP_WT_P14_16484

description: Gene expression in HPCs


title: RP_WT_P0_16478

description: Gene expression in HPCs


title: RP_WT_P14_16481

description: Gene expression in HPCs


title: RP_ITD_P0_16495

description: Gene expression in HPCs


title: RP_WT_P0_16477

description: Gene expression in HPCs


title: RP_ITD_E14.5_16489

description: Gene expression in HPCs


title: RP_ITD_E14.5_16491

description: Gene expression in HPCs


title: RP_WT_E14.5_16475

description: Gene expression in HPCs


title: RP_ITD_E14.5_16490

description: Gene expression in HPCs


title: RP_WT_E14.5_16473

description: Gene expression in HPCs


title: HSC_ITD_Adult_16892

description: Gene expression in HSCs

value: HSC


title: HSC_WT_Adult_16456

description: Gene expression in HSCs


title: HSC_ITD_Adult_16471

description: Gene expression in HSCs


title: RP_ITD_E14.5_16492

description: Gene expression in HPCs


title: HSC_WT_Adult_16455

description: Gene expression in HSCs


title: RP_WT_E14.5_16476

description: Gene expression in HPCs


title: RP_WT_E14.5_16474

description: Gene expression in HPCs


title: RP_ITD_P14_16497

description: Gene expression in HPCs


title: HSC_ITD_P14_16468

description: Gene expression in HSCs


title: HSC_ITD_Adult_16472

description: Gene expression in HSCs


title: HSC_WT_P14_16451

description: Gene expression in HSCs


title: HSC_WT_P0_16446

description: Gene expression in HSCs


title: HSC_WT_P14_16449

description: Gene expression in HSCs


title: HSC_WT_P14_16450

description: Gene expression in HSCs


title: HSC_ITD_P0_16461

description: Gene expression in HSCs


title: HSC_ITD_Adult_16470

description: Gene expression in HSCs


title: HSC_ITD_P0_16464

description: Gene expression in HSCs


title: HSC_ITD_P14_16467

description: Gene expression in HSCs


title: HSC_ITD_E14.5_16457

description: Gene expression in HSCs


title: HSC_ITD_P14_16466

description: Gene expression in HSCs


title: HSC_ITD_P0_16462

description: Gene expression in HSCs


title: HSC_WT_P0_16447

description: Gene expression in HSCs


title: HSC_WT_P0_16448

description: Gene expression in HSCs


title: HSC_ITD_P14_16465

description: Gene expression in HSCs


title: HSC_WT_P0_16887

description: Gene expression in HSCs


title: HSC_ITD_E14.5_16460

description: Gene expression in HSCs


title: HSC_WT_P14_16452

description: Gene expression in HSCs


title: HSC_WT_E14.5_16886

description: Gene expression in HSCs


title: Mist1-KrasG12D;Ets2db/fl pancreatic fibroblasts, biological replicate 3

city: Columbus

first: Jason

middle: R

last: Pitarresi

state: Ohio

address: 460 W. 12th Ave

institute: Ohio State University Medical Center

description: Gene expression data from Mist1-KrasG12D;Ets2db/fl pancreatic fibroblasts

hyb_protocol: Following fragmentation, 15ug of cRNA was hybridized for 16 hours at 45°C on Affymetrix Mouse 430.2 Array GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetric GeneChip Scanner 3000

data_processing: Data were processed using Affymetrix Expression Console software. Robust Multichip Average (RMA) method was used to do background correction, quantile normalization, and expression level summarization.

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix)

growth_protocol: Fibroblasts were cultured using a modified protocol for gravity separation.

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

treatment_protocol: Fibroblasts  were grown in 10% FBS DMEM in a 37° incubator with 7% CO2

value: 23 weeks

value: Pancreas


title: T3, biological rep2

city: SuZhou

first: Tao

last: Chen

state: JiangSu

address: 199 Ren-Ai-rd

institute: Soochow University

description: miRNA expression data from TCE treated liver

hyb_protocol: The labeled RNAs were hybridized onto Affymetrix miRNA 3.0 array.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing: Affymetrix GeneChip Conmand Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then offered RMA normalization. Next, Genesrping software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. Probes that at least 100% of the values in any 1 out of 2 conditions have flags in P were chosen for further data analysis. Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test.

source_name: liver from mice exposed to TCE at 1001mg/kg b.w.

label_protocol: Total RNA were tailed with Poly A and then labeled with Biotin.

growth_protocol: B6C3F1 male mice were housed with a 12h light and 12h dark cycle at 22+/-2 °C temperature.

extract_protocol: Total RNA were purified using AllPrep DNA/RNA Mini Kit (Tiangen, Beijing, China). Turbo DNA-freeTM kit (Life Technologies, Shanghai, China) was used to remove genomic DNA contamination in purified RNA samples.

treatment_protocol: Adult B6C3F1 male mice were oral administrated with either corn oil or TCE for five days. Form each mouse, liver was excised rapidly, frozen in liquid nitrogen, and stored at -80oC.

value: B6C3F1 mouse

value: liver

value: 7 week


title: HSC_ITD_E14.5_16458

description: Gene expression in HSCs


title: T4, biological rep3

source_name: liver from mice exposed to TCE at 1002mg/kg b.w.


title: Mist1-KrasG12D;FspCre;Smofl/-pancreatic fibroblasts, biological replicate 3

description: Gene expression data from Mist1-KrasG12D;FspCre;Smofl/- pancreatic fibroblasts


title: Mist1-KrasG12D;FspCre;Smofl/-pancreatic fibroblasts, biological replicate 1


title: Mist1-KrasG12D pancreatic fibroblasts, biological replicate 3

description: Gene expression data from Mist1-KrasG12D pancreatic fibroblasts


title: C2, biological rep1

description: miRNA expression data from control liver

source_name: liver from mice exposed to vehicle control


title: Mist1-KrasG12D;FspCre;Ets2db/fl pancreatic fibroblasts, biological replicate 3

description: Gene expression data from Mist1-KrasG12D;FspCre;Ets2db/fl pancreatic fibroblasts


title: C4, biological rep3


title: Mist1-KrasG12D pancreatic fibroblasts, biological replicate 2


title: HSC_WT_E14.5_16444

description: Gene expression in HSCs


title: Mist1-KrasG12D;FspCre;Smofl/-pancreatic fibroblasts, biological replicate 2


title: Mist1-KrasG12D pancreatic fibroblasts, biological replicate 1


title: HSC_WT_E14.5_16443

description: Gene expression in HSCs


title: HSC_ITD_E14.5_16459

description: Gene expression in HSCs


title: Mist1-KrasG12D;FspCre;Ets2db/fl pancreatic fibroblasts, biological replicate 1


title: T2, biological rep1

source_name: liver from mice exposed to TCE at 1000mg/kg b.w.


title: HSC_WT_E14.5_16442

description: Gene expression in HSCs


title: Wild type pancreatic fibroblasts, biological replicate 2

description: Gene expression data from wild type pancreatic fibroblasts

source_name: Wild type

value: WT


title: Wild type pancreatic fibroblasts, biological replicate 3


title: Mist1-KrasG12D;FspCre;Ets2db/fl pancreatic fibroblasts, biological replicate 2


title: Wild type pancreatic fibroblasts, biological replicate 1


title: Mist1-KrasG12D;Ets2db/fl pancreatic fibroblasts, biological replicate 1


title: SK-3C LC134 Tregs B

city: London

first: Shahram

last: Kordasti

state: London

address: Rayne Institute, 123 Coldharbour Lane

institute: King's College London

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Biotinylated cDNA was applied and hybridised to Human Gene 2.0 ST arrays (Affymetrix) following NuGEN's guidelines.

scan_protocol: Arrays were processed using the Hybridisation Wash Stain kit and scanned following manufacturer's guidelines (Affymetrix).

data_processing: CEL files were processed in Expression Console to generate normalised, summarised and background-corrected data (CHP files), and further analysed for differential gene expression using gene set enrichment analysis (GSEA) as described before.

source_name: Healthy donor 134

label_protocol: Total RNA (8ng) was amplified and biotin labelled using the Ovation Pico WTA V2 and Encore Biotin Module kits (NuGEN).

growth_protocol: PBMCs from healthy donors were isolated by gradient media and further sorted based on CD4,CD25,CD127,CCR4,CD45RO and CD95 expression

extract_protocol: RNA was purified from Trizol lysates following manufacturer's protocols (Invitrogen), followed by RNeasy MinElute cleanup (Qiagen).

value: healthy donor peripheral blood

tag: sub-population

value: Tregs B


title: Mist1-KrasG12D;Ets2db/fl pancreatic fibroblasts, biological replicate 2


title: SK-3B LC134 Tregs A

value: Tregs A


title: SK-3A LC134 Tcon

value: T conventional


title: SK-2B LC133 Tregs A

source_name: Healthy donor 133


title: siAF control of Knockdown 2

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: siAF control of Knockdown 2

label_protocol: Standard Illumina labelling protocol

growth_protocol: Cells were cultured in DMEM low glucose medium (PAA) supplemented with 2mM L-glutamine, 100U/ml penicillin/streptomycin, 5,000U/ml heparin and 10% human platelet lysate (HPL) in a humidified atmosphere at 5% CO2. Cells were seeded at a densitiy of 5000/cm2 and passaged at 80% confluency.

extract_protocol: Total RNA was extracted using NucleoSpin miRNA kit (Macherey-Nagel, Düren, Germany) acording to manufacturers instruction

treatment_protocol: For siRNA mediated knockdown MSCs were seeded at a density of 5000/cm². At 80% confluence medium was changed and transfection of 10µM siRNA was performed with 3% HiPerfect transfection reagent (Qiagen, Hilden, Germany) dissolved in serum free DMEM. After 48h total RNA was isolated or medium change occurred in the case of differentiation assays. ANRIL siRNA (si04378563; Qiagen) and HOTAIR siRNA (5'-GAACGGGAGUACAGAGAGA-3'; MWG, Huntsville, USA) were used for knockdown. For control we used the AllStars Neg. siRNA (AF 488, Qiagen, Hilden, Germany), which has no human target sequence and carries an AlexaFluor488 molecule. Overexpression experiments were performed according to permission of the district council Düsseldorf, Germany (Az. 53.02.01-K-1.118/12). The plasmids lzrs-HOTAIR and lzrs-GFP were purchased from Addgene (Cambridge, USA; #26110 and #21961, respectively). Plasmids were transduced into E.coli plasmid-DNA isolation was realized with the NucleoBond Xtra Maxi Prep (Macherey-Nagel, Düren, Germany) according to manufacturer´s instructions. Next amphotrophic Phoenix cells were treated with a suspension of 50% HOTAIR-plasmid, 10% gagPol-plasmid and 40% env-plasmid bubble-resuspended in 2xHBS and Calciumchloride. Efficiency of transfection was surveyed after 24h in the GFP transfected cell subset (Figure S1) and medium was changed. 72h hours after transfection supernatants with viruses were harvested and transferred onto non-confluent MSCs at passage 4.

value: ANRIL siRNA (si04378563; Qiagen) transfection

value: Mesenchymal stromal cell


title: SK-2C LC133 Tregs B


title: HOTAIR overexpression 1

source_name: HOTAIR overexpression 1

value: lzrs-HOTAIR plasmid transduced


title: HOTAIR knockdown 3

source_name: HOTAIR knockdown 3

value: HOTAIR siRNA (5'-GAACGGGAGUACAGAGAGA-3' transfection


title: untreated control of Overexpression 3

source_name: untreated control of Overexpression 3

value: lzrs-GFP plasmid transduced


title: HOTAIR overexpression 2

source_name: HOTAIR overexpression 2


title: SK-1B LC128 Tregs A

source_name: Healthy donor 128


title: HOTAIR knockdown 1

source_name: HOTAIR knockdown 1