title: Ji_Batch6_41

description:
STANSUB_SLVP021-041-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Female


title: zebrafish embryo 310

status: Public on Jan 01 2017

type: RNA

city: Amsterdam

first: Han

last: Rauwerda

state: Nederland

address: Sciencepark 904

department: SILS

country: Netherlands

institute: University of Amsterdam

hyb_protocol: The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide). ). Hybridization took place for 17 hours at 65°C. In order to avoid confounding with spawn, samples have been randomized with respect to labeling batch and hybridization chamber.

scan_protocol: The microarrays were scanned in an ozone-free room with a DNA microarray scanner G2565CA (Agilent Technologies). Data was retrieved with Feature Extraction Software version 9.5.3 (Agilent Technologies).

data_processing: The quality of the microarray data was assessed via multiple quality-control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Handling, analysis and visualization of all data was performed in R (http://cran.r-project.org/) using the Bioconductor packages affy, limma and maanova (Gentleman et al. 2004). Log2 transformed Cy3 data was subjected to a procedure, similar to the one described in (Pagano et al. 2016, doi:10.1016/j.dib.2016.04.045), in which probes were identified as expressed or non-expressed probes. Here a log variance cut-off value of -2 was used to separate low and high variant probes and the per microarray cut-off for the likelihood of a probe to be expressed was set to 20%, thus avoiding too many false negatives. Hence, in this step for each array, individual probes were called ‘present’ or ‘not-present’. Next, we defined that a probe to be truthfully expressed must be called ‘present’ in at least 6 samples in one moving window of 30 with the samples ordered in epiboly stage to avoid false positives. Next all ‘present’ probes were quantile normalized and collapsed into transcripts using the R Bioconductor affy package. In the procedure no background removal was applied.

molecule: total RNA

organism: Danio rerio

source_name: whole embryo

label_protocol: Amplification and labeling of RNA was done in an identical fashion as described in (de Jong et al. 2010, doi: 10.1186/1756-0500-3-73) in a one-round mRNA amplification per zebrafish embryo using the Amino-allyl MessageAmp II kit (Applied Biosystems). Test samples were labeled with Cy3 and a reference sample was labeled with Cy5. The reference sample was made by pooling equimolar amounts of RNA from test samples and is mentioned here for completeness only, since in the analysis a one dye approach has been applied. The yield and CyDye incorporation were again measured with the NanoDrop ND-1000

growth_protocol: Zebrafish were handled and maintained according to standard protocols (http://ZFIN.org). The local animal welfare committee (DEC) of the University of Leiden, the Netherlands specifically approved this study. All protocols adhered to the international guidelines specified by the EU Animal Protection Directive 86/609/EEC.

extract_protocol: RNA was extracted from single embryos using the procedure described in (de Jong et al. 2010, doi: 10.1186/1756-0500-3-73). The amount of RNA per μl was measured on the Nano- Drop ND-1000 (Thermo Scientific; Supplemental File S3). RNA integrity was assessed with the BioAnalyzer (Agilent Technologies) using the RNA pico 6000 kit (Agilent Technologies).

treatment_protocol: Embryos were obtained by placing a female and a male, both of genotype ABTL, overnight in a tank separated by transparent, but watertight division. Approximately 1 hour after the start of the light period the division was removed after which spawning and fertilization took place, generally in one or more pushes. Embryos were retrieved by transferring both animals to a different tank and sieving the remaining water. In total from 9 pairs, embryos were obtained ('Spawn'). Embryos were maintained at 28.5 °C in egg water (60 μg/ml Instant Ocean sea salts).

tag: developmental stage

value: epiboly ~ 59

tag: spawn

tag: genotype

value: wild type ABTL

source_name: pool of whole embryos

value: late blastula, early gastrula

value: all


title: Ji_Batch6_40

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

country: USA

institute: stanford

description:
STANSUB_SLVP021-028-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

data_processing: Genespring GX 12.6., RMA normalization: median of all samples

label: biotin

organism: Homo sapiens

tag: tissue

value: whole blood

tag: time point

value: day 0 (before vaccination)

tag: Sex

value: Male

tag: age

tag: race

value: Caucasian or White,Asian


title: High-sugar rep4

city: Seoul

first: Jooyoung

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using background subtraction and quantile normalization with Illumina GenomeStudio Software v.2011.1.

organism: Mus musculus

source_name: Mouse liver

label_protocol: Biotinylated cRNA were prepared with the using Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: Total RNA was isolated from liver tissues with Ambion RNAqueous-4PCR Kits (Ambion, Austin, TX, USA) according to the manufacturer’s protocol. RNA concentrations were quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA). The integrities of mRNA were confirmed by 1% agarose gel electrophoresis.

tag: strain

value: 16 weeks

tag: diet

value: High-sugar

value: liver

tag: gender


title: BHK21 cell_Cirp−/−_48h_rep1

city: Chengdu

first: Cheng

last: TANG

state: Sichuan

address: No 16  Yihuan Lu South Sect.4,

country: China

institute: Southwest University for Nationalities

description: Cirp−/− BHK21 cell

hyb_protocol: Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5.26) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.

source_name: BHK21 cell,Cirp−/−,48h

label_protocol: Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

growth_protocol: Cirp−/−, or control BHK21 cells at a density of 2.0×105 cells/mL were inoculated into six-well plates containing 2.5 mL of Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and then cultured at 37 °C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA from Cirp−/− and control BHK21 cells at 24, 48, and 72 h was extracted using TRIzol reagent (Applied Biosystems Inc., Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: Before RNA extract, the cells were washed three times by the phosphate buffer solution (PBS).

tag: cell line

tag: treatment

value: Cirp−/− knockdown

tag: time


title: BHK21 cell_Cirp−/−_24h_rep2

description: Cirp−/− BHK21 cell

source_name: BHK21 cell,Cirp−/−,24h


title: BHK21 cell_Cirp−/−_48h_rep2

description: Cirp−/− BHK21 cell


title: BHK21 cell_Cirp−/−_24h_rep1

description: Cirp−/− BHK21 cell


title: BHK21 cell_control_72h_rep3

description: normal BHK21 cell

source_name: BHK21 cell,control,42h

value: control


title: High-fat rep6

description: replicate 6

value: High-fat


title: Ji_Batch6_35

description:
STANSUB_SLVP021-025-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Asian


title: High-sugar rep2

description: replicate 2


title: zebrafish embryo 449

value: epiboly ~ 50


title: BHK21 cell_control_72h_rep2

description: normal BHK21 cell


title: Ji_Batch6_32

description:
STANSUB_SLVP021-022-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Female


title: Ji_Batch6_47

description:
STANSUB_SLVP021-024-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Caucasian or White


title: BHK21 cell_control_48h_rep2

description: normal BHK21 cell


title: High-fat rep2

description: replicate 2


title: zebrafish embryo 511-2

value: epiboly ~ 55

value: wild type ABTL


title: [2%, 2%2]

city: Kualalumpour

first: sanaz

last: koosha

address: Department of pharmacology, faculty of medicine, UM

department: pharmacology

country: Malaysia

institute: university of Malaya

description: Non-Alcoholic Fatty Liver Disease (NAFLD)

hyb_protocol: Hybridization mix was prepared. The target was denatured and the mixture was incubated. The Agilent SureHyb Gasket was placed into an Agilent Chamber base. Immediately, hybridisation mix was pipetted onto the gasket slide. Array was placed onto the Gasket slide. The hybridisation chamber was placed in the hybridisation oven and hybridised. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Data were extracted using Feature Extraction Software (version 10.7.3.1) and uploaded into the CytoSure™ Interpret software (version 4.2.5), normalized and converted into .cgh files. The data were segmented using a modified Circular Binary Segmentation (CBS) algorithm.

source_name: treated with 2% green tea extract

label_protocol: Reaction tubes were prepared as a mixture of 18 μL of c DNA sample (or reference), 10 μL of random primer and 10 μL of reaction buffer. The reactions were mixed and centrifuged for 15 s, followed by denaturation in a PCR block with a heated lid at 99°C for 20 min. Immediately after, the tubes were placed on ice for 5 min. On ice, the followings were added to the tubes: 10 μL of dCTP labelling mix, 1 μL of Cy3-dCTP (for sample) / 1 μL of Cy3-dCTP (for reference), and 1 μL of Klenow. The mixture was centrifuged for 15 s and incubated at 37°C for 2 h. Following that, the mixture was incubated at 65°C for 10 min, then placed on ice for 5 min. The mixture was centrifuged for 15 s.

growth_protocol: Male healthy wild type mice (C57BL/6) will be obtained from Animal House Unit, Faculty of Medicine, University of Malaya, Malaysia. They will be singly housed in wire bottomed cages at 25 ± 3 oC temperature, 50-60 % humidity, and a 12 h light–dark cycle. They will be maintained at standard housing conditions and free access to standard diet and water ad libitum during the experiment.

extract_protocol: total RNA extrated by QIAamp RNA Mini Kit

treatment_protocol: Group 4 (2%1,2%2,2%5,2%7): High fat diet + 200mg/kg Green tea extract group (high dose treatment group) will be orally administrated.

tag: group

value: high fat

value: 7-8 weeks

value: male


title: BHK21 cell_control_72h_rep1

description: normal BHK21 cell


title: BHK21 cell_control_48h_rep3

description: normal BHK21 cell


title: High-fat rep5

description: replicate 5

value: Male


title: Ji_Batch6_46

description:
STANSUB_SLVP021-009-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: whole blood

value: day 0 (before vaccination)


title: High-fat rep3

description: replicate 3

value: 16 weeks


title: zebrafish embryo 367-2

value: epiboly ~ 59

value: late blastula, early gastrula

value: all


title: Ji_Batch6_43

description:
STANSUB_SLVP021-005-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record


title: High-fat rep4

description: replicate 4

value: High-fat

value: liver


title: zebrafish embryo 335-2

value: epiboly ~ 42


title: zebrafish embryo 488-2

value: epiboly ~ 54


title: zebrafish embryo 334-2

value: epiboly ~ 47


title: Ji_Batch6_49

description:
STANSUB_SLVP021-002-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: Female

value: Asian


title: BHK21 cell_control_48h_rep1

description: normal BHK21 cell

value: control


title: Control rep5

description: replicate 5

value: Control


title: BHK21 cell_control_24h_rep3

description: normal BHK21 cell

source_name: BHK21 cell,control,24h


title: Control rep6

description: replicate 6


title: High-fat rep1

description: replicate 1


title: zebrafish embryo 143

value: epiboly ~ 51

value: wild type ABTL


title: zebrafish embryo 156-2

value: epiboly ~ 56


title: Control rep4

description: replicate 4

value: Male


title: BHK21 cell_control_24h_rep1

description: normal BHK21 cell


title: BHK21 cell_control_24h_rep2

description: normal BHK21 cell


title: Ji_Batch6_45

description:
STANSUB_SLVP021-001-2012
Baseline (day 0)
whole blood  transcripts
protocol manuals are available on the series record

value: whole blood

value: day 0 (before vaccination)


title: Control rep3

description: replicate 3

value: 16 weeks


title: zebrafish embryo 412-2

value: epiboly ~ 71

value: late blastula, early gastrula

value: all


title: zebrafish embryo 397-2

value: epiboly ~ 49


title: zebrafish embryo 399-2

value: epiboly ~ 65


title: zebrafish embryo 325-2


title: SH_BDNF_rep1.1

city: Porto Alegre

first: Marco

middle: Antonio

last: De Bastiani

state: Rio Grande do Sul

address: Ramiro Barcelos 2600

department: Biochemistry

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: replicate 1 (batch2)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45ºC on GeneChip Human PrimeView (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Raw CEL files were analysed using the R/Bioconductor pipeline. The data was normalized by Robust Multi-array Average (RMA) in the AFFY package, log (base 2) transformed,  and batch-corrected with ComBat in the SVA package.

source_name: SH-SY5Y cell line differentiated for 7d after serum decrease to 1% and RA 10 uM treatment with BDNF 50 ng/ml addition at day 4 (1% FBS medium and RA maintenance at day 4)

label_protocol: Samples were prepared according to standard Affymetrix protocol, from 100 ng of total RNA.

growth_protocol: SH-SY5Y human neuroblastoma cells were cultured in DMEM/F12 medium (DMEM – cat. #1210-046/Life Technologies; F12 – cat. #21700-075/Life Technolgies)  supplemented with 10% FBS (cat. #FB0010S/Cripion Biotecnolgia LTDA) and antibiotics. AR-only differentiation protocols were carried by decreasing FBS to 1% and adding retinoic acid (RA) 10 uM, with medium and RA maintenance at day 4. In BDNF differentiation protocol, in addition to FBS decrease and RA, BDNF 50 ng/ml was added at day 4, with medium and RA maintenance

extract_protocol: RNAs were isolated from cells using the extraction protocol with TRIzol Reagent (Life Technologies) with posterior purification and treatment with DNAse (Qiagen RNeasy Mini Kit and Qiagen RNase-Free DNase Set, respectively) according to manufacter's instructions.

treatment_protocol: All-trans retinoic acid (cat. #BML-GR100/Enzo Life Science) was used in all the differentiation protocols. Purified protein BDNF (cat. #cyt-207/ProSpec-Tany TechnoGene Ltd.) was used in BDNF differentiation protocol.

value: 7 days cell culture in 1% FBS medium and RA 10 uM with BDNF 50 ng/ml addition at day 4


title: SH_differentiated_7d_rep1.2

description: technical replicate of SH_differentiated_7d_rep1.1 (batch2)

source_name: SH-SY5Y cell line differentiated for 7d after serum decrease to 1% and RA 10 uM treatment (1% FBS medium and RA maintenance at day 4)

value: 7 days cell culture in 1% FBS medium and RA 10 uM


title: Control rep1

description: replicate 1

value: liver


title: SH_differentiated_7d_rep2.2

description: technical replicate of SH_differentiated_7d_rep2.1 (batch2)


title: zebrafish embryo 211

value: epiboly ~ 50


title: zebrafish embryo 492


title: 800R_rep1

city: pamplona

first: Ivan

last: Jáuregui Mosquera

state: Navarra

address: Campus de Arrosadia, s/n,  Dpto. Ciencias del Medio Natural

country: Spain

institute: Universidad Pública de Navarra

description: Gene expression after 5 weeks CO2 tratment. Sample collected 4h from the beginning of the light period

hyb_protocol: 1.65 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 the microarrays. They were incubated in SureHyb microarray hybridization chambers with gasket slides (Agilent Technologies) at 65ºC for 17 h in an rotary oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 s with acetonitrile and 30 s in Agilent's stabilization and drying solution, then air dried.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: Normalization and differential expression analysis of the data was done using limma R package (Smyth 2004). Normalization was carried out using quantile method and Bayes statistics were applied to determine the differential expression between the comparisons. Statistical significance was corrected for multiple testing using the Benjamini-Hochberg procedure. For this study, the significant difference in gene expression was Q value < 0.05 and log2 fold change > 0.5.

organism: Arabidopsis thaliana

source_name: Root of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by    NucleoSpin® Gel and PCR Clean-up column purification (Macherey-Nagel, Düren, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Arabidopsis thaliana, Columbia 0 ecotype (col 0) plants grown under hydroponic conditions.

extract_protocol: Total RNA was isolated according to Liao et al.(2004).

tag: ecotype

value: Columbia 0

value: root


title: zebrafish embryo 506-2

value: epiboly ~ 52

value: wild type ABTL


title: SH_differentiated_7d_rep2.1

description: replicate 2 (batch2)


title: SH_differentiated_4d_rep4

description: replicate 4 (batch2)

source_name: SH-SY5Y cell line differentiated for 4d after serum decrease to 1% and RA 10 uM treatment

value: 4 days cell culture in 1% FBS medium and RA 10 uM


title: SH_differentiated_4d_rep2

description: replicate 2 (batch2)


title: zebrafish embryo 472

value: epiboly ~ 51


title: 800R_rep3

source_name: Root of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 3


title: SH_BDNF_rep1.2

description: technical replicate of SH_BDNF_rep1.1 (batch2)


title: SH_differentiated_7d_rep1.1

description: replicate 1 (batch2)


title: SH_differentiated_4d_rep3

description: replicate 3 (batch2)


title: zebrafish embryo 216

value: epiboly ~ 61


title: 800R_rep2

source_name: Root of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 2


title: 400R_rep2

source_name: Root of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 2


title: SH_differentiated_4d_rep1

description: replicate 1 (batch2)


title: 400R_rep3

source_name: Root of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 3


title: SH_proliferative_rep6

description: replicate 6 (batch2)

source_name: SH-SY5Y cell line undifferentiated

value: 7 days cell culture in 10% FBS medium


title: zebrafish embryo 401

source_name: whole embryo


title: zebrafish embryo 526

value: epiboly ~ 47

source_name: pool of whole embryos


title: zebrafish embryo 228

value: epiboly ~ 56

value: late blastula, early gastrula


title: zebrafish embryo 206

value: epiboly ~ 67

value: all


title: 400R_rep1

source_name: Root of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 1


title: zebrafish embryo 254

value: epiboly ~ 45


title: SH_proliferative_rep3

description: replicate 3 (batch1)


title: SH_proliferative_rep4

description: replicate 4 (batch1)


title: 800L_rep2

source_name: Leaf of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 2

value: leaf


title: 800L_rep1

source_name: Leaf of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 1


title: 400L_rep2

source_name: Leaf of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 2


title: SH_proliferative_rep5

description: replicate 5 (batch2)


title: 800L_rep3

source_name: Leaf of Arabidopsis thaliana plant exposed to 800 ppm [CO2]. Rep 3


title: SH_proliferative_rep1

description: replicate 1 (batch1)


title: SH_proliferative_rep2

description: replicate 2 (batch1)


title: 400L_rep3

source_name: Leaf of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 3


title: zebrafish embryo 439

value: epiboly ~ 55


title: zebrafish embryo 244

value: epiboly ~ 69


title: zebrafish embryo 450


title: zebrafish embryo 209

value: epiboly ~ 54


title: 400L_rep1

source_name: Leaf of Arabidopsis thaliana plant exposed to 400 ppm [CO2]. Rep 1

value: Columbia 0


title: Dex vs Mock

city: Bunkyo-ku

first: Mitsutomo

last: Abe

state: Tokyo

address: 7-3-1 Hongo

department: Department of Biology

country: Japan

institute: The University of Tokyo

hyb_protocol: 0.825ug of Cy3-labelled cRNA and 0.825ug of cRNA Cyanine-5 (Cy5) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Arabidopsis (V4) Gene Expression Microarry 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 (G2565CA) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT and Red PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA and Cyanine-5 (Cy5) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown on MS medium supplemented with 1% sucrose at 22ºC under the LD conditions.

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

treatment_protocol: Dex treatments were performed as described in Yamaguchi et al., (2005). Seedlings were submerged for 2h in 1 μM Dex.

value: whole seedling

tag: genotype/variation

value: day 7 (ZT14)

value: Dex treatment

value: Mock treatment


title: WT vs fe-1 -2

description: Biological replicate 2 of 2

value: day 7 (ZT15)

value: nontreatment

source_name: WT (L.er)

value: WT


title: zebrafish embryo 289

tag: developmental stage

value: epiboly ~ 52

value: wild type ABTL


title: Control rep2

description: replicate 2

source_name: Mouse liver

value: 16 weeks

value: Control

value: liver

value: Male


title: zebrafish embryo 348

value: epiboly ~ 55

tag: spawn

value: late blastula, early gastrula

value: all


title: zebrafish embryo 463

value: epiboly ~ 74

tag: genotype


title: zebrafish embryo 389

value: epiboly ~ 53


title: SScReg_1697_base_LA

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description: SSc patient

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Axon scanner

data_processing: Images were quantified using GenePixPro

source_name: Sample: Human Tissue Biopsy

label_protocol: 200ng of total RNA was reversed transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini following manufacturers protocol

treatment_protocol: Storage of human tissue in RNAlater

tag: tissue

value: skin biopsy

tag: subject

tag: disease state

value: SSc patient

source_name: Universal Human Reference

tag: reference

value: Universal Human Reference


title: SScReg_1702_LA

description: SSc patient


title: SScReg_1717_base_RA

description: SSc patient


title: WT vs fe-1 -1

description: Biological replicate 1 of 2

value: whole seedling

tag: age

value: day 7 (ZT15)


title: zebrafish embryo 202

value: epiboly ~ 49


title: zebrafish embryo 499

value: epiboly ~ 63


title: SScReg_1702_LF

description: SSc patient


title: zebrafish embryo 311

value: epiboly ~ 57

value: wild type ABTL


title: SScReg_1610_base_LA_p50-8

description: SSc patient

value: MMF, MTX


title: SScReg_1696_base_LA

description: SSc patient

value: NR


title: zebrafish embryo 199

value: epiboly ~ 58


title: SScReg_1606_base_LA_p50-2

description: SSc patient

value: MMF


title: SScReg_1669_base_LA_p50-5

description: SSc patient


title: zebrafish embryo 519

value: epiboly ~ 45

value: late blastula, early gastrula


title: SScReg_1582_base_LA

description: SSc patient


title: SScReg_1606_06mo_LA_p50-2

description: SSc patient


title: SScReg_1547_base_LF

description: SSc patient


title: rLEC HNF4α transduction + AZA treatment, biological rep3 miRNA

city: Jette

first: jennifer

last: bolleyn

address: Laarbeeklaan 103

country: Belgium

institute: Vrije universiteit Brussel

description: miRNA expression data from HNF4a transduced rLEC exposed to a non-cytotoxic concentration of 20 µM 5' azacytidine for 7 days

hyb_protocol: 21.5 μL biotin labeled RNA was hybridized to a Genechip® miRNA 4.0 array and then placed in a Genechip Hybridization Oven-645 (Affymetrix) rotating at 60 rpm at 48 ºC for 16-18 h. After incubation, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix) and stained with the Affymetrix HWS kit as indicated by the manufacturer’s protocols.

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G

data_processing: Robust Multiarray Analysis and detection above background for data summarization, normalisation and quality control were done with Affymetrix expression console software

organism: Rattus norvegicus

source_name: rLEC transduced with a lentiviral vector containing HNF4a and exposed to 20 µM of azacytidine  for 7 days

label_protocol: Total RNA (130 ng) was labelled using the FlashTag™ Biotin HSR RNA Labeling kit following the manufacturer’s instructions (Affymetrix).

growth_protocol: rLEC were isolated from 8-day old male Sprague-Dawley rats, subcultivated and cryoperserved as previously described. Cryoperserved rLEC, previously collected at passage 12 were subcultivated at 75% confluency and rLEC growth medium was changed every two days.

extract_protocol: Total RNA enriched with small RNA (≤ 200nt) was isolated using the mirVana™miRNA isolation kit (Ambion, Inc., USA) according to the manufacturer’s instructions.

treatment_protocol: rLECs were transduced at 50% confluency with a viral titer of 2.09 x 109 TU/ml. After transduction, the cells were subcultivated at 75% confluency. rLECs containing the lentiviral vectors encoding HNF4α were puromycin selected (twice). 10 µg/ml puromycin was added to the growth medium and the cells were incubated at 37°C for 24 hours. After the puromycin selection, cells were washed and growth medium was changed. This was done every 2 days until 75% confluency was reached. AZA treatment consisted of the exposure to the non-cytotoxic concentration of 20 µM 5' azacytidine for 7 days.

value: male

value: liver


title: rLEC HNF4α transduction + AZA treatment, biological rep2 miRNA


title: rLEC AZA treatment, biological rep3 miRNA

description: miRNA expression data from rLEC exposed to a non-cytotoxic concentration of 20 µM 5' azacytidine for 7 days

source_name: rLEC exposed to 20 µM of azacytidine for 7 days


title: rLEC HNF4α transduction + AZA treatment, biological rep1 miRNA


title: SScReg_1402_LA

description: SSc patient

value: skin biopsy


title: zebrafish embryo 273

value: epiboly ~ 50

value: all


title: zebrafish embryo 318

value: epiboly ~ 56


title: rLEC AZA treatment, biological rep1 miRNA


title: zebrafish embryo 426

value: epiboly ~ 71


title: SScReg_1547_base_LA

description: SSc patient

value: SSc patient

value: Universal Human Reference


title: SScReg_1402_LF

description: SSc patient


title: zebrafish embryo 544

value: epiboly ~ 52


title: zebrafish embryo 343-1

value: epiboly ~ 51

value: wild type ABTL


title: SScReg_1402_12mo_LF

description: SSc patient


title: rLEC AZA treatment, biological rep2 miRNA


title: rLEC HNF4α transduction, biological rep3 miRNA

description: miRNA expression data from HNF4a transduced rLEC

source_name: rLEC transduced with a lentiviral vector containing HNF4a


title: SScReg_1303_base_RF

description: SSc patient


title: zebrafish embryo 469

value: epiboly ~ 49


title: SScReg_1402_12mo_LA

description: SSc patient


title: zebrafish embryo 437

value: epiboly ~ 47


title: zebrafish embryo 176

value: epiboly ~ 64


title: rLEC HNF4α transduction, biological rep1 miRNA


title: SScReg_1271_base_LA

description: SSc patient

value: MMF


title: rLEC HNF4α transduction, biological rep2 miRNA


title: SScReg_1303_base_RA

description: SSc patient


title: rLEC control condition, biological rep1 miRNA

description: miRNA expression data from untreated rLEC

source_name: untreated rLEC


title: rLEC control condition, biological rep2 miRNA


title: zebrafish embryo 319

source_name: whole embryo

value: epiboly ~ 48

value: late blastula, early gastrula


title: zebrafish embryo 356

source_name: pool of whole embryos


title: SScReg_1075_base_LF

description: SSc patient


title: zebrafish embryo 320

value: epiboly ~ 44


title: zebrafish embryo 183


title: SScReg_1073_base_LF

description: SSc patient

value: skin biopsy

value: Cytoxan


title: zebrafish embryo 373

value: epiboly ~ 59

value: all


title: zebrafish embryo 448

value: epiboly ~ 56


title: SScReg_1011_base_LF

description: SSc patient

value: SSc patient


title: zebrafish embryo 502

value: epiboly ~ 53


title: SScReg_1073_base_LA

description: SSc patient

value: Universal Human Reference


title: rLEC control condition, biological rep3 miRNA

value: male

value: liver


title: SScReg_1011_base_LA

description: SSc patient


title: SScMH_55_base_LF_p50-9

description: SSc patient


title: zebrafish embryo 363

value: epiboly ~ 58

value: wild type ABTL


title: zebrafish embryo 239


title: SScMH_52_base_LF_p50-7

description: SSc patient


title: zebrafish embryo 155

value: epiboly ~ 54


title: Untreated non-tumor rep1

type: genomic

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

description: DNA methylation status of non-tumor tissue

hyb_protocol: Samples were hybridized onto a Nimblegen 2.1M Deluxe mouse promoter array following NimbleGen’s protocol.

scan_protocol: The microarray slides were scanned using the Agilent G2565BA DNA Microarray Scanner.  Images were processed using the NimbleScan software.

data_processing: The log2(Cy5) values were normalized using loess curve fitting conditioning on GC content as described in BMC Bioinformatics 2009, 10:173.  The multple signal values from same probe within array were averaged.  Furthermore, the resulting signal values for MIRA were quantile normalized independently to adjust for between sample variations

molecule: genomic DNA

source_name: Methylated DNA from Untreated non-tumor rep1

label_protocol: Input and ChIP DNA were amplified (WGA2; Sigma-Aldrich), labeled with Cy3 and Cy5 (TriLink Biotechnologies), respectively, according to NimbleGen’s protocol.

growth_protocol: Housed individually

extract_protocol: Genomic DNA purified from  liver were sonicated using a Bioruptor (Diagenode) to generate 200–500-bp fragments. Methylated DNA fragments were enriched using the MethylCollector Ultra kit (Active Motif) according to the manufacturer’s protocol.

treatment_protocol: Frozen liver tissue/tumors were collected for DNA extraction at necropsy of control and high dose mice at 18 months

tag: strain

value: Male

tag: tumor status

value: non-tumor

source_name: Input DNA from Untreated non-tumor rep1


title: zebrafish embryo 384

value: epiboly ~ 45

value: late blastula, early gastrula


title: zebrafish embryo 539

value: epiboly ~ 49


title: SScMH_50_base_RA_p50-6

description: SSc patient

value: skin biopsy


title: SScMH_47_12mo_LF_p50-3

description: SSc patient

value: MMF


title: Untreated non-tumor rep2

source_name: Methylated DNA from Untreated non-tumor rep2

tag: gender

source_name: Input DNA from Untreated non-tumor rep2


title: zebrafish embryo 266

value: epiboly ~ 46

value: all


title: DE-71 treated non-tumor rep1

source_name: Methylated DNA from DE-71 treated non-tumor rep1

source_name: Input DNA from DE-71 treated non-tumor rep1


title: zebrafish embryo 479

value: epiboly ~ 51


title: zebrafish embryo 174

value: epiboly ~ 70


title: zebrafish embryo 436

value: epiboly ~ 50


title: zebrafish embryo 345


title: DE-71 treated non-tumor rep2

source_name: Methylated DNA from DE-71 treated non-tumor rep2

source_name: Input DNA from DE-71 treated non-tumor rep2


title: SScMH_50_base_RF_p50-6

description: SSc patient

value: SSc patient

value: Universal Human Reference


title: Untreated tumor rep2

description: DNA methylation status of hepatocellular carcinoma

source_name: Methylated DNA from Untreated tumor rep2

value: liver

value: tumor

source_name: Input DNA from Untreated tumor rep2


title: zebrafish embryo 173

value: epiboly ~ 71

value: wild type ABTL


title: SScMH_47_06mo_LA

description: SSc patient

source_name: Sample: Human Tissue Biopsy

source_name: Universal Human Reference


title: zebrafish embryo 417

value: epiboly ~ 63


title: SScMH_47_06mo_LF

description: SSc patient


title: zebrafish embryo 477


title: SScMH_47_12mo_LA_p50-3

description: SSc patient


title: SScMH_47_base_LF

description: SSc patient


title: SScMH_55_base_LA_p50-9

description: SSc patient


title: zebrafish embryo 432

value: epiboly ~ 48


title: SScMH_45_base_LF

description: SSc patient


title: Untreated tumor rep1

source_name: Methylated DNA from Untreated tumor rep1

value: Male

source_name: Input DNA from Untreated tumor rep1


title: DE-71 treated tumor rep2

source_name: Methylated DNA from DE-71 treated tumor rep2

source_name: Input DNA from DE-71 treated tumor rep2


title: zebrafish embryo 388

source_name: whole embryo

source_name: pool of whole embryos

value: late blastula, early gastrula


title: zebrafish embryo 517

value: epiboly ~ 47


title: DE-71 treated tumor rep1

source_name: Methylated DNA from DE-71 treated tumor rep1

source_name: Input DNA from DE-71 treated tumor rep1


title: SScMH_45_12mo_LF

description: SSc patient

value: skin biopsy

value: MMF


title: SScMH_45_06mo_LF

description: SSc patient

value: MMF, Plaquenil


title: zebrafish embryo 158

value: epiboly ~ 57

value: all


title: zebrafish embryo 376

value: epiboly ~ 51


title: zebrafish embryo 213

value: epiboly ~ 54


title: SScMH_44_base_LA

description: SSc patient

value: SSc patient

value: Universal Human Reference


title: SScMH_45_06mo_LA

description: SSc patient


title: zebrafish embryo 542

value: epiboly ~ 44


title: zebrafish embryo 234

value: epiboly ~ 61


title: SScMH_45_base_LA

description: SSc patient


title: SScMH_44_base_LF

description: SSc patient


title: zebrafish embryo 164

value: epiboly ~ 68

value: wild type ABTL


title: SScMH_44_12mo_LA

description: SSc patient


title: SScMH_44_06mo_LF

description: SSc patient


title: zebrafish embryo 508

value: epiboly ~ 55


title: zebrafish embryo 215

value: epiboly ~ 63


title: zebrafish embryo 298

value: epiboly ~ 58

value: late blastula, early gastrula


title: SScMH_44_06mo_LA

description: SSc patient

value: skin biopsy


title: SScReg_1075_base_LA

description: SSc patient


title: SScMH_43_base_LF

description: SSc patient


title: zebrafish embryo 369

value: epiboly ~ 60


title: SScMH_45_12mo_LA

description: SSc patient

value: MMF


title: SScMH_44_12mo_LF

description: SSc patient


title: zebrafish embryo 336

value: epiboly ~ 45


title: SScMH_43_base_LA

description: SSc patient


title: zebrafish embryo 268

value: epiboly ~ 50

value: all


title: SScMH_42_base_LF

description: SSc patient

value: MTX


title: zebrafish embryo 265

value: epiboly ~ 49


title: zebrafish embryo 214


title: SScMH_42_12mo_LA

description: SSc patient

value: SSc patient

value: Universal Human Reference


title: zebrafish embryo 219

value: epiboly ~ 56


title: zebrafish embryo 277

value: epiboly ~ 46


title: SScMH_42_base_LA

description: SSc patient


title: zebrafish embryo 516

value: epiboly ~ 52

value: wild type ABTL


title: zebrafish embryo 379

value: epiboly ~ 53


title: zebrafish embryo 435

value: epiboly ~ 51


title: YPDGdelta2_vs_YP20delta2

city: Burjassot (Valencia)

first: Marcel·lí

last: del Olmo

address: Dr Moliner, 50

department: Bioquímica i Biologia Molecular

institute: Universitat de València

description: Biological replicate 1/2

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

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

organism: Saccharomyces cerevisiae

source_name: YPD yeast cells

label_protocol: 10 µg of total RNA reversed transcribed with SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: yeast cultures were kept in the exponential growth phase for 16h. OD600=0,8 cells were exposed to the osmotic stress conditions considered 20% (w/v) glucose (YP20), 1M sorbitol (YPS) or YPD (no stress conditions) during 30 min

extract_protocol: total RNA isolation using the protocol described in Carrasco et al., 2003

treatment_protocol: Stress caused by 20% (w/v) glucose or 1M Sorbitol during 30 minutes

source_name: YP20 yeast cells

value: 20% (w/v) glucose


title: SScMH_42_06mo_LF

description: SSc patient

value: skin biopsy


title: SScMH_42_12mo_LF

description: SSc patient


title: SScMH_42_06mo_LA

description: SSc patient


title: SScMH_41_06mo_LF

description: SSc patient


title: zebrafish embryo 165

value: epiboly ~ 54

value: late blastula, early gastrula


title: zebrafish embryo 514

value: epiboly ~ 74


title: SScMH_41_base_LF

description: SSc patient


title: SScMH_40_base_LF

description: SSc patient

value: MTX, Plaquenil


title: YP20delta3_vs_YPDGdelta3

description: Biological replicate 2/2


title: zebrafish embryo 157

value: epiboly ~ 62

value: all


title: zebrafish embryo 423

value: epiboly ~ 57


title: SScMH_47_base_LA

description: SSc patient

value: SSc patient


title: YPD5delta2_vs_SORBdelta2

description: Biological replicate 1/2

source_name: YPS yeast cells

value: 1M Sorbitol during 30 minutes


title: SORBdelta3_vs_YPD5delta3

description: Biological replicate 2/2


title: SScMH_52_base_LA_p50-7

description: SSc patient

value: Universal Human Reference


title: SScMH_41_06mo_LA

description: SSc patient

value: MMF


title: SScMH_41_base_LA

description: SSc patient


title: Tumor crypts isolated from 12 adenomas, biological rep2

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: gene expression data from tumor crypts

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: AOM/DSS-induced colon adenomas

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: mice have access to an adequate supply of  drinking water and food.

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

treatment_protocol: Acute colitis was induced by providing 1% DSS  in drinking water ad libitum for 2 days. For tumor induction, 6-8-week-old male Lgr5-lacZ mice were injected intraperitoneally with AOM (Sigma) at a dose of 12.5mg/kg body weight. After 5 days, mice were fed 2% DSS in the drinking water for 5 days, followed by 14 days of regular water. This cycle was repeated twice with 1.5% DSS and 1.0% DSS, respectively

value: colon tumor

value: Lgr5-lacZ het

value: 90 days after AOM treatment


title: SScMH_40_base_LA

description: SSc patient


title: zebrafish embryo 486

value: epiboly ~ 50

value: wild type ABTL


title: zebrafish embryo 166

value: epiboly ~ 60


title: zebrafish embryo 351

value: epiboly ~ 52


title: Tumor crypts isolated from 12 adenomas, biological rep1

description: gene expression data from tumor crypts


title: SScMH_39_base_LF

description: SSc patient

value: skin biopsy


title: Colonic crypts isolated from 2 control mice, biological rep1

description: gene expression data from normal colon crypts

source_name: 6-8 weeks old male Lgr5-lacZ mice were fed drinking water

value: normal colon

value: 6-8 weeks


title: Colonic crypts isolated from 2 control mice, biological rep2


title: SScMH_39_base_LA

description: SSc patient


title: SScMH_38_base_LF

description: SSc patient


title: zebrafish embryo 520

value: epiboly ~ 51

value: late blastula, early gastrula


title: zebrafish embryo 394

value: epiboly ~ 45

value: all


title: SScMH_37_base_LF

description: SSc patient

value: SSc patient


title: SScMH_40_12mo_LA

description: SSc patient

value: NR

value: Universal Human Reference


title: SScMH_40_12mo_LF

description: SSc patient


title: BRAFV600E NIH3T3 Cel lvs Control wild NIH3T3 Cell

city: Xi’an

first: Yiping

last: Qu

address: The First Affiliated Hospital of Xi’an Jiaotong University

department: Department of Endocrinology

scan_protocol: Agilent Microarray Scanner (Cat#G2565BA, Agilent) Feature Extraction software 10.7 (Agilent, Santa Clara, US)

data_processing: Agilent Feature Extraction Software 11.0 was used for background subtraction and LOWESS normalization.

source_name: pEFm6-BRAF NIH3T3 cells

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: NIH3T3 cells were cultured in DMED with bovine calf serum to a final concentration of 10% at 37°C. Atmosphere: air, 95%; carbon dioxide (CO2), 5%

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

tag: strain background

value: NIH/Swiss

tag: cell line

value: day 2

tag: transfected with

source_name: pEFm6-BRAFV600E NIH3T3 cells


title: Colonic crypts isolated from 2 mice treated with DSS, biological rep2

description: gene expression data from DSS-treated crypts

source_name: 6-8 weeks old male Lgr5-lacZ mice were fed 1% DSS in normal drinking water

value: Lgr5-lacZ het


title: zebrafish embryo 425

value: epiboly ~ 55


title: SScMH_38_base_LA

description: SSc patient

source_name: Sample: Human Tissue Biopsy

tag: treatment

source_name: Universal Human Reference


title: zebrafish embryo 269

value: epiboly ~ 47

value: wild type ABTL


title: zebrafish embryo 473

value: epiboly ~ 48


title: zebrafish embryo 342

value: epiboly ~ 50


title: Colonic crypts isolated from 2 mice treated with DSS, biological rep1

value: normal colon


title: SScMH_37_base_LA

description: SSc patient

value: skin biopsy


title: SScMH_37_24mo_LF

description: SSc patient

value: MMF


title: Mx-PHx 36 hour

city: Shanghai

first: Lijian

last: Hui

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy for Sciences

description: Gene expression 36 hours after PHx and 1 week after poly(IC) treatment

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

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20090416) 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

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

extract_protocol: Total RNA was isolated from tissues by Trizol (Invitrogen) and further purified by RNeasy mini Kit and RNase-Free DNase Set following manufacturer's introductions,

treatment_protocol: 2 months after BMT, mice were treated with poly(IC). Then PHx was performed and liver was analyzed 1 week later.

value: Mxcre-

value: male or femal

value: 36 hours after PHx, 1 week after poly(IC) treatment, 2 months after irradiation and bone marrow transplantation


title: Mx-PHx 48 hour

description: Gene expression 48 hours after PHx and 1 week after poly(IC) treatment

value: 48 hours after PHx, 1 week after poly(IC) treatment, 2 months after irradiation and bone marrow transplantation


title: Mx+PHx 48 hour

value: Mxcre+


title: Mx+PHx 36 hour


title: zebrafish embryo 442

value: epiboly ~ 54

value: late blastula, early gastrula

value: all


title: Mx+PHx 24 hour

description: Gene expression 24 hours after PHx and 1 week after poly(IC) treatment

value: 24 hours after PHx, 1 week after poly(IC) treatment, 2 months after irradiation and bone marrow transplantation


title: SScMH_37_24mo_LA

description: SSc patient

value: SSc patient

value: Universal Human Reference


title: Mx+PHx 0 hour

description: Gene expression 1 week after poly(IC) treatment

value: 1 week after poly(IC) treatment, 2 months after irradiation and bone marrow transplantation


title: Mx-PHx 24 hour


title: zebrafish embryo 245

value: epiboly ~ 69

value: wild type ABTL


title: zebrafish embryo 316

value: epiboly ~ 55


title: zebrafish embryo 281

value: epiboly ~ 49


title: zebrafish embryo 186

value: epiboly ~ 61


title: zebrafish embryo 438

value: epiboly ~ 52


title: SScMH_36_base_LF

description: SSc patient

value: skin biopsy


title: zebrafish embryo 236

value: epiboly ~ 58


title: zebrafish embryo 461

value: epiboly ~ 65


title: PAH-Keap1KD rep2

city: Sendai

first: Masahiro

last: Nezu

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University School of Medicine

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model US82800151.

data_processing: The data were analyzed and normalized with GeneSpring software. After normalization, the data was baseline transformed to the median of all samples.

source_name: PAH-Keap1KD mouse placenta

label_protocol: 300 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: For placental labyrinth zone, placentae from the pregnant mice at 16.5 gestational days were harvested  and kindly separate labyrinth zone from maternal decidua

treatment_protocol: For NP mice female hAGT mice were mated with male hAGT mice. For PAH mice female hAGT mice were mated with male hREN mice with the same Nrf2 activity

value: Placental labyrinth zone

value: female

value: 16 weeks


title: SScMH_36_base_LA

description: SSc patient


title: SScMH_35_base_LF

description: SSc patient

value: MTX


title: PAH-Nrf2KO rep2

source_name: PAH-Nrf2KO mouse placenta


title: SScMH_36_06mo_LF

description: SSc patient

value: MMF


title: zebrafish embryo 257

source_name: whole embryo

value: epiboly ~ 45

value: late blastula, early gastrula

value: all


title: SScMH_35_06mo_LF

description: SSc patient

value: SSc patient

value: MMF, MTX

value: Universal Human Reference


title: SScMH_35_24mo_LA

description: SSc patient


title: PAH-Keap1KD rep1


title: SScMH_36_06mo_LA

description: SSc patient


title: Mx-PHx 0 hour

value: Mxcre-

value: male or femal

value: 1 week after poly(IC) treatment, 2 months after irradiation and bone marrow transplantation


title: PAH rep1

source_name: PAH mouse placenta

value: PAH


title: zebrafish embryo 181

value: epiboly ~ 48

value: wild type ABTL

source_name: pool of whole embryos


title: PAH rep2

value: Placental labyrinth zone


title: SScMH_35_24mo_LF

description: SSc patient

value: skin biopsy


title: PAH-Nrf2KO rep1

value: female

value: 16 weeks


title: NP rep2

source_name: NP mouse placenta

value: normal pregnancy


title: CD3 lymphocytes from MD74

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

country: Germany

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

description: Sample name: MD74T

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Feature Extraction Software (version 10.7.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: Protocol Version 6.2.1, Feb 2010, Agilent. Same gender reference/control DNA was purchased from Kreatech as pool.

extract_protocol: Genomic DNA was extracted from whole bone marrow, whole peripheral blood or CD3 lymphocytes isolated from peripheral blood at diagnosis. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: M

tag: who

tag: iPSs

value: peripheral blood

tag: cell type

value: CD3 lymphocytes

source_name: control DNA

tag: sample type

value: gender-matched, pooled reference/control DNA (Kreatech)


title: SScMH_35_06mo_LA

description: SSc patient

value: SSc patient

value: MMF, MTX


title: SScMH_34_base_LF

description: SSc patient

value: Plaquenil

value: Universal Human Reference


title: zebrafish embryo 367-1

city: Amsterdam

first: Han

last: Rauwerda

address: Sciencepark 904

data_processing: The quality of the microarray data was assessed via multiple quality-control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Handling, analysis and visualization of all data was performed in R (http://cran.r-project.org/) using the Bioconductor packages affy, limma and maanova (Gentleman et al. 2004). Log2 transformed Cy3 data was subjected to a procedure, similar to the one described in (Pagano et al. 2016, doi:10.1016/j.dib.2016.04.045), in which probes were identified as expressed or non-expressed probes. Here a log variance cut-off value of -2 was used to separate low and high variant probes and the per microarray cut-off for the likelihood of a probe to be expressed was set to 20%, thus avoiding too many false negatives. Hence, in this step for each array, individual probes were called ‘present’ or ‘not-present’. Next, we defined that a probe to be truthfully expressed must be called ‘present’ in at least 6 samples in one moving window of 30 with the samples ordered in epiboly stage to avoid false positives. Next all ‘present’ probes were quantile normalized and collapsed into transcripts using the R Bioconductor affy package. In the procedure no background removal was applied.

tag: developmental stage

value: epiboly ~ 59

tag: spawn

tag: genotype

value: late blastula, early gastrula

value: all


title: zebrafish embryo 335-1

value: epiboly ~ 42

value: wild type ABTL


title: zebrafish embryo 511-1

value: epiboly ~ 55


title: SScMH_34_24mo_LF

description: SSc patient

tag: tissue

value: skin biopsy

tag: subject

tag: disease state


title: CD3 lymphocytes from MD44

description: Sample name: MD44T

hyb_protocol: Protocol Version 6.2.1, Feb 2010, Agilent.

source_name: CD3 lymphocytes isolated from peripheral blood

value: F

value: RCMD

value: low


title: SScMH_33_base_LA

description: SSc patient

tag: reference


title: SScMH_34_base_LA

description: SSc patient


title: CD3 lymphocytes from MD116

description: Sample name: MD116T

value: M

value: peripheral blood


title: zebrafish embryo 488-1

value: epiboly ~ 54


title: CD3 lymphocytes from MD51

description: Sample name: MD51T

value: CD3 lymphocytes

value: gender-matched, pooled reference/control DNA (Kreatech)


title: zebrafish embryo 413-2

value: epiboly ~ 57


title: NP rep1

value: Placental labyrinth zone

value: female

tag: age

value: 16 weeks

value: normal pregnancy


title: SScMH_34_24mo_LA

description: SSc patient

value: SSc patient

value: Plaquenil

value: Universal Human Reference


title: SScMH_33_base_LF

description: SSc patient

value: skin biopsy


title: bone marrow from PD91

description: Sample name: PD91

source_name: bone marrow

tag: gender

value: F

value: bone marrow

value: MDS tumor cells


title: zebrafish embryo 334-1

value: epiboly ~ 47

value: wild type ABTL

value: late blastula, early gastrula

value: all


title: CD3 lymphocytes from MD140

description: Sample name: MD140T

value: peripheral blood

value: CD3 lymphocytes

value: gender-matched, pooled reference/control DNA (Kreatech)


title: zebrafish embryo 156-1

value: epiboly ~ 56


title: bone marrow from PD89

description: Sample name: PD89

value: RCMD


title: zebrafish embryo 383


title: bone marrow from PD160

description: Sample name: PD160


title: SScMH_33_24mo_LA

description: SSc patient


title: muscle_insulin_sub20

city: Stockholm

first: Juleen

last: Zierath

address: Von Eulersväg 4a

department: Molecular medicine and surgery

country: Sweden

institute: Karolinsk Institutet

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned using the Illumina iScan system using standard recommended settings

data_processing:
Illumina BeadStudio software v2010.3 was used without normalization, followed by m-value calculation, color adjustment and quantile normalization using Bioconductor package Lumi
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: skeletal muscle biopsy, insulin stimulated, subject 20

label_protocol: Standard Illumina Protocol

growth_protocol: no sample growth

extract_protocol: Genomic DNA and mRNA was extracted from intact human muscle and cultured myotubes using AllPrep DNA/RNA kit or DNAeasy and RNAeasy kits (Qiagen, Hilden, Germany). DNA and RNA concentration was measured with Nanodrop 1000 (Thermo Fisher Scientific). Genomic DNA was bisulfite treated using EpiTect Fast Bisulfite Conversion Kit (Qiagen).

treatment_protocol: A skeletal muscle biopsy (~2 g of muscle) was excised and placed in oxygenated Krebs-Henseleit buffer (KHB) containing 5 mM HEPES and 0.1% bovine serum albumin (BSA; RIA Grade; Sigma, St. Louis, MO). Smaller muscle strips were dissected from the biopsy specimen and mounted on Plexiglas clamps, placed in oxygenated KHB containing 5 mM HEPES 0.1% BSA, 15 mM mannitol and 5 mM glucose and transported to the laboratory. Thereafter, muscle strips were incubated in the absence (basal) or presence of insulin (120 nM) for 60 min in individual glass vials containing oxygenated KHB plus the addition of 5 mM HEPES 0.1% BSA, 15 mM mannitol and 5 mM glucose. Muscle strips were frozen in liquid nitrogen for subsequent methylation analysis.

value: Male

tag: stimulation

value: insulin stimulated


title: SScMH_33_24mo_LF

description: SSc patient

value: SSc patient


title: zebrafish embryo 325-1

institute: University of Amsterdam

label_protocol: Amplification and labeling of RNA was done in an identical fashion as described in (de Jong et al. 2010, doi: 10.1186/1756-0500-3-73) in a one-round mRNA amplification per zebrafish embryo using the Amino-allyl MessageAmp II kit (Applied Biosystems). Test samples were labeled with Cy3 and a reference sample was labeled with Cy5. The reference sample was made by pooling equimolar amounts of RNA from test samples and is mentioned here for completeness only, since in the analysis a one dye approach has been applied. The yield and CyDye incorporation were again measured with the NanoDrop ND-1000

extract_protocol: RNA was extracted from single embryos using the procedure described in (de Jong et al. 2010, doi: 10.1186/1756-0500-3-73). The amount of RNA per μl was measured on the Nano- Drop ND-1000 (Thermo Scientific; Supplemental File S3). RNA integrity was assessed with the BioAnalyzer (Agilent Technologies) using the RNA pico 6000 kit (Agilent Technologies).

value: epiboly ~ 49


title: zebrafish embryo 399-1

value: epiboly ~ 65


title: SScMH_33_12mo_LF

description: SSc patient

value: skin biopsy

value: MMF

value: Universal Human Reference


title: SScMH_33_12mo_LA

description: SSc patient


title: SScMH_33_06mo_LF

description: SSc patient


title: zebrafish embryo 397-1


title: zebrafish embryo 506-1

value: epiboly ~ 52


title: bone marrow from PD123

description: Sample name: PD123

value: M

value: RCMD-RS

value: low

value: bone marrow

value: MDS tumor cells


title: muscle_basal_sub19

source_name: skeletal muscle biopsy, basal, subject 19

value: basal


title: SScMH_33_06mo_LA

description: SSc patient


title: zebrafish embryo 412-1

value: epiboly ~ 71

value: wild type ABTL

value: late blastula, early gastrula

value: all


title: SScMH_35_base_LA

description: SSc patient

value: SSc patient

value: MTX


title: bone marrow from PD122

description: Sample name: PD122

value: F

value: gender-matched, pooled reference/control DNA (Kreatech)


title: muscle_insulin_sub4

source_name: skeletal muscle biopsy, insulin stimulated, subject 4

value: Male

value: insulin stimulated


title: muscle_insulin_sub19

source_name: skeletal muscle biopsy, insulin stimulated, subject 19


title: muscle_basal_sub20

source_name: skeletal muscle biopsy, basal, subject 20


title: muscle_basal_sub4

source_name: skeletal muscle biopsy, basal, subject 4


title: bone marrow from PD103

description: Sample name: PD103


title: bone marrow from NM21696

description: Sample name: NM21696


title: bone marrow from NM21947

description: Sample name: NM21947

value: RCMD


title: zebrafish embryo 371

value: epiboly ~ 61


title: zebrafish embryo 179

value: epiboly ~ 70


title: SScMH_32_24mo_RA

description: SSc patient

source_name: Sample: Human Tissue Biopsy

value: skin biopsy

value: MMF

source_name: Universal Human Reference

value: Universal Human Reference


title: bone marrow from NM21384

description: Sample name: NM21384

value: M

value: RARS

value: bone marrow

value: MDS tumor cells


title: zebrafish embryo 390

value: epiboly ~ 49

value: wild type ABTL

value: late blastula, early gastrula

value: all


title: HCT116 TET1-knockdown #2 [DNA methylation]

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description:
raw data file: 9426021173_R03C01_Grn.idat, 9426021173_R03C01_Red.idat
HCT116 stable TET1-knockdown clone 2
HCT116_TET1KD2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

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

data_processing:
BeadStudio software V2011.1
The non_normalized.txt contains unmethylated and methylated signal intensities

source_name: HCT116 TET1-knockdown

growth_protocol: HCT116 cells were cultured in McCoy's 5A medium supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Genomic DNA was extracted using the standard phenol-chloroform method.

treatment_protocol: Cells were transfected with each TET1 knockdown vector or a pcDNA6.2-GW/EmGFP-miR-neg control plasmid (Thermo Fisher Scientific), after which they were selected with 0.6 mg/ml G418.

tag: cell line

value: colorectal cancer (CRC) cells

value: TET1 knockdown vector


title: zebrafish embryo 402

hyb_protocol: The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide). ). Hybridization took place for 17 hours at 65°C. In order to avoid confounding with spawn, samples have been randomized with respect to labeling batch and hybridization chamber.

scan_protocol: The microarrays were scanned in an ozone-free room with a DNA microarray scanner G2565CA (Agilent Technologies). Data was retrieved with Feature Extraction Software version 9.5.3 (Agilent Technologies).

value: epiboly ~ 51


title: Colo320DM TET1-knockdown #3 [DNA methylation]

description:
raw data file: 9376525053_R06C01_Grn.idat, 9376525053_R06C01_Red.idat
Colo320DM stable TET1-knockdown clone 3
Colo320_TET1KD3

source_name: Colo320DM TET1-knockdown

growth_protocol: Colo320DM cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

treatment_protocol: Cells were transfected with each TET1 knockdown vector or a pcDNA6.2-GW/EmGFP-miR-neg control plasmid (Thermo Fisher Scientific), after which they were selected with 1.0 mg/ml G418.

tag: transfected with


title: SScMH_32_24mo_RF

description: SSc patient

value: SSc patient

tag: treatment


title: zebrafish embryo 501

source_name: whole embryo

value: epiboly ~ 68


title: SScMH_32_12mo_RF

description: SSc patient


title: HCT116 TET1-knockdown #1 [DNA methylation]

description:
raw data file: 9426021173_R03C01_Grn.idat, 9426021173_R03C01_Red.idat
HCT116 stable TET1-knockdown clone 1
HCT116_TET1KD1


title: SScMH_32_12mo_RA

description: SSc patient


title: bone marrow from NM21692

description: Sample name: NM21692

tag: who

value: RCMD

value: low

value: gender-matched, pooled reference/control DNA (Kreatech)


title: SScMH_31_base_LF

description: SSc patient

value: skin biopsy

value: Universal Human Reference


title: SScMH_31_base_LA

description: SSc patient


title: Colo320DM TET1-knockdown #2 [DNA methylation]

description:
raw data file: 9376525053_R06C01_Grn.idat, 9376525053_R06C01_Red.idat
Colo320DM stable TET1-knockdown clone 2
Colo320_TET1KD2


title: HCT116 control #1 [DNA methylation]

description:
raw data file: 9426020105_R06C02_Grn.idat, 9426020105_R06C02_Red.idat
HCT116 negative control clone 1
HCT116_CONT1

source_name: HCT116 control


title: bone marrow from NM20370

description: Sample name: NM20370

value: M

tag: iPSs


title: zebrafish embryo 407

value: epiboly ~ 52

source_name: pool of whole embryos


title: zebrafish embryo 500


title: bone marrow from MD74

description: Sample name: MD74B

value: bone marrow

tag: cell type

value: MDS tumor cells


title: bone marrow from MD69

description: Sample name: MD69

value: F

tag: sample type


title: bone marrow from MD72

description: Sample name: MD72

value: RARS


title: HCT116 control #2 [DNA methylation]

description:
raw data file: 9426020105_R06C02_Grn.idat, 9426020105_R06C02_Red.idat
HCT116 negative control clone 2
HCT116_CONT2


title: bone marrow from MD93H

description: Sample name: MD93H


title: zebrafish embryo 227

tag: developmental stage

value: epiboly ~ 56

value: wild type ABTL

value: late blastula, early gastrula

value: all


title: Colo320DM TET1-knockdown #1 [DNA methylation]

description:
raw data file: 9376525053_R06C01_Grn.idat, 9376525053_R06C01_Red.idat
Colo320DM stable TET1-knockdown clone 1
Colo320_TET1KD1

value: colorectal cancer (CRC) cells

value: TET1 knockdown vector


title: SScMH_30_24mo_LF

description: SSc patient

value: SSc patient

value: MMF


title: Colo320DM control #2 [DNA methylation]

description:
raw data file: 9376525053_R06C01_Grn.idat, 9376525053_R06C01_Red.idat
Colo320DM negative control clone 2
Colo320_CONT2

source_name: Colo320DM control


title: zebrafish embryo 418

value: epiboly ~ 57

tag: spawn


title: SScMH_30_12mo_LF

description: SSc patient

value: skin biopsy


title: zebrafish embryo 340

value: epiboly ~ 47

tag: genotype


title: zebrafish embryo 341

value: epiboly ~ 43


title: SScMH_30_12mo_LA

description: SSc patient

tag: tissue

value: Universal Human Reference


title: SScMH_29_Base_LF

description: SSc patient

tag: subject

value: MTX


title: bone marrow from MD51

description: Sample name: MD51B

value: RCMD

value: low

value: bone marrow

value: MDS tumor cells

source_name: control DNA

value: gender-matched, pooled reference/control DNA (Kreatech)


title: bone marrow from MD144

description: Sample name: MD144

value: F


title: SScMH_29_base_LA

description: SSc patient

tag: disease state


title: SScMH_30_24mo_LA

description: SSc patient

tag: reference


title: SScMH_28_36mo_LF

description: SSc patient


title: Colo320DM control #3 [DNA methylation]

description:
Colo320DM negative control clone 3
Colo320_CONT3


title: zebrafish embryo 248

value: epiboly ~ 68

value: wild type ABTL

value: late blastula, early gastrula

value: all


title: bone marrow from MD140

description: Sample name: MD140B


title: bone marrow from MD121

description: Sample name: MD121

value: RARS


title: zebrafish embryo 352

value: epiboly ~ 54


title: SScMH_28_36mo_LA

description: SSc patient

value: skin biopsy

value: SSc patient

value: MMF


title: bone marrow from MD44

description: Sample name: MD44B


title: zebrafish embryo 218

value: epiboly ~ 59


title: GpatHF-HF240

first: Thais

last: de Castro Barbosa

state: Stockholm

address: von Eulers väg 4a

department: Physiology and Pharmacology

institute: Karolinska Institutet

hyb_protocol: Affymetrix GeneTitan instruments were used for hybridization, wash, stain and scanning of Rat Gene 1.1 ST Array Plates

scan_protocol: Arrays were scanned in a Affymetrix GeneTitan Scanner

data_processing: Generated CEL files were preprocessed using Affymetrix Expression Console using the Probe Logarithmic Intensity Error (PLIER) method for summarization, PM-GCBG for background correction and Global Median for normalization.

label: Biotin

source_name: Rat gonadal white adipose tissue - Grandpaternal HFD on HFD diet

label_protocol: 200 ng of total RNA was used as input to generate sense-strand cDNA with  Ambion® WT Expression kit (Life Technologies: PN 4425209). The generated sense-strand cDNA was fragmented and biotin labelled using Affymetrix® GeneChip WT Terminal Labeling Kit (Affymetrix: PN 900671).

growth_protocol: Sprague-Dawley female rats were maintaned under a temperature-controlled environment and 12:12-h light:dark cycle. Adult females were fed either a control chow diet or a high-fat diet (42/45% energy from fat) for 12 weeks. Gonadal white adipose tissue was dissect and store at -80C until use.

extract_protocol: Total RNA was extracted using the RNeasy Lipid Tissue kit from Qiagen according to manufacturer’s instructions.  RNA quality was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies), and RNA concentration was measured on a NanoDrop (Thermo Scientific).

tag: strain

value: Sprague-Dawley

value: female

tag: age

value: adult

tag: fed on

value: hig-fat diet for 12 wks

tag: grandpaternal diet

value: hig-fat diet

value: Gonadal white adipose tissue


title: Colo320DM control #1 [DNA methylation]

description:
raw data file: 9376525053_R06C01_Grn.idat, 9376525053_R06C01_Red.idat
Colo320DM negative control clone 1
Colo320_CONT1

tag: cell line

value: colorectal cancer (CRC) cells

tag: transfected with


title: zebrafish embryo 468

value: epiboly ~ 49


title: GpatHF-HF211

tag: gender


title: SScMH_28_24mo_LF

description: SSc patient

tag: treatment

value: Universal Human Reference


title: zebrafish embryo 193

value: epiboly ~ 51

value: wild type ABTL

value: late blastula, early gastrula


title: GpatHF-HF204


title: bone marrow from MD116

description: Sample name: MD116B

source_name: bone marrow

value: M

tag: who

value: RCMD

tag: iPSs

value: low

value: bone marrow

tag: cell type

value: MDS tumor cells

value: gender-matched, pooled reference/control DNA (Kreatech)


title: GpatHF-HF195

value: Sprague-Dawley

value: female


title: zebrafish embryo 328

tag: developmental stage

value: epiboly ~ 47

tag: spawn

value: all


title: bone marrow from MD117

description: Sample name: MD117

tag: tissue

tag: sample type


title: GpatHF-CD238

source_name: Rat gonadal white adipose tissue - Grandpaternal HFD on Chow diet

value: adult

value: normal (chow) diet for 12 wks

value: hig-fat diet

value: Gonadal white adipose tissue


title: GpatHF-HF172

value: hig-fat diet for 12 wks


title: SScMH_28_12mo_LA

description: SSc patient

value: skin biopsy

tag: subject

tag: disease state

value: SSc patient

value: MMF

value: Universal Human Reference


title: GpatHF-HF171

tag: strain


title: zebrafish embryo 324

value: epiboly ~ 46

tag: genotype

value: wild type ABTL

value: late blastula, early gastrula


title: SScMH_28_12mo_LF

description: SSc patient

tag: reference


title: zebrafish embryo 396

value: epiboly ~ 54


title: SScMH_27_12mo_LF

description: SSc patient

value: Cytoxan


title: SScMH_27_24mo_LA

description: SSc patient


title: zebrafish embryo 303

value: epiboly ~ 52


title: GpatHF-CD201

value: Sprague-Dawley

value: female

tag: age

tag: fed on

tag: grandpaternal diet


title: SScMH_28_24mo_LA

description: SSc patient


title: zebrafish embryo 313

value: epiboly ~ 62

value: all


title: GpatHF-CD193

tag: gender

value: adult

value: normal (chow) diet for 12 wks

value: hig-fat diet


title: SScMH_27_24mo_LF

description: SSc patient

value: skin biopsy

tag: treatment


title: zebrafish embryo 177

value: epiboly ~ 56


title: Bone marrow PD123

city: Badalona

first: Mar

last: Mallo

address: Ctra de Can Ruti, s/n, camí de les escoles. Edifici IMPPC

institute: Josep Carreras Leukaemia Research Institute

description: Hybridized to 6.0 Array

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 then washed using Affymetrix fluidics stations, and scanned according to the manufacturer's instructions.

data_processing:
CEL files, generated by AGCC Viewer. CNCHP and LOHCHP, generated by Genotyping Console (all provided by Affymetrix)
CNCHP (from 6.0 arrays) provide data for copy number and LOH analysis. LOCHP provides data for LOH analysis in case of 250K_Nsp arrays

source_name: Bone marrow

label_protocol: As per manufacturer (Affymetrix)

tag: tissue/cell type

value: Bone marrow


title: SScMH_27_12mo_LA

description: SSc patient

value: SSc patient

value: Universal Human Reference


title: zebrafish embryo 470

value: epiboly ~ 48

value: wild type ABTL


title: SScMH_26_36mo_LA

description: SSc patient

value: MTX


title: GpatHF-CD177

value: Gonadal white adipose tissue


title: GpatHF-CD170


title: zebrafish embryo 374

value: epiboly ~ 61

value: late blastula, early gastrula


title: GpatHF-CD169

value: Sprague-Dawley

value: female


title: SScMH_26_24mo_LF

description: SSc patient


title: Bone marrow PD160

description: Hybridized to 6.0 Array


title: zebrafish embryo 451

value: all


title: GpatHF-CD210

value: adult


title: SScMH_26_24mo_LA

description: SSc patient


title: Bone marrow PD89

description: Hybridized to 6.0 Array


title: SScMH_26_36mo_LF

description: SSc patient


title: Bone marrow PD122

description: Hybridized to 6.0 Array


title: zebrafish embryo 413-1

value: epiboly ~ 57


title: CD3 lymphocytes from NM21692B

description: Hybridized to 6.0 Array

source_name: CD3 lymphocytes isolated from peripheral blood


title: SScMH_26_12mo_LA

description: SSc patient


title: Bone marrow PD103

description: Hybridized to 6.0 Array


title: zebrafish embryo 338

value: epiboly ~ 43


title: GpatCD-HF232

source_name: Rat gonadal white adipose tissue - Grandpaternal Chow on HFD diet

value: hig-fat diet for 12 wks

value: normal (chow) diet


title: GpatCD-HF231


title: zebrafish embryo 393

value: epiboly ~ 53


title: Bone marrow NM21692B

description: Hybridized to 6.0 Array

value: Bone marrow


title: zebrafish embryo 491

value: epiboly ~ 51


title: SScMH_25_36mo_LA

description: SSc patient

value: skin biopsy

value: SSc patient

value: MMF

value: Universal Human Reference


title: Bone marrow NM21696

description: Hybridized to 6.0 Array


title: Bone marrow PD91

description: Hybridized to 6.0 Array


title: GpatCD-HF226

value: Gonadal white adipose tissue


title: GpatCD-HF219


title: SScMH_25_36mo_LF

description: SSc patient


title: SScMH_25_24mo_LF

description: SSc patient


title: zebrafish embryo 194

value: epiboly ~ 47

value: wild type ABTL

value: late blastula, early gastrula


title: Bone marrow NM21384

description: Hybridized to 6.0 Array


title: Bone marrow NM21947

description: Hybridized to 6.0 Array


title: SScMH_25_24mo_LA

description: SSc patient


title: GpatCD-HF188

value: Sprague-Dawley

value: female


title: Bone marrow MD140B

description: Hybridized to 6.0 Array


title: Bone marrow NM20370B

description: Hybridized to 6.0 Array


title: SScMH_23_24mo_LF

description: SSc patient


title: zebrafish embryo 175

value: epiboly ~ 74

value: all


title: GpatCD-HF187

value: adult

value: hig-fat diet for 12 wks


title: zebrafish embryo 315

value: epiboly ~ 63


title: GpatCD-HF164

value: normal (chow) diet


title: CD3 lymphocytes from NM20370B

description: Hybridized to 6.0 Array

value: CD3 lymphocytes isolated from peripheral blood


title: zebrafish embryo 471

value: epiboly ~ 49


title: GpatCD-CD230

source_name: Rat gonadal white adipose tissue - Grandpaternal Chow on Chow diet

value: normal (chow) diet for 12 wks


title: SScMH_23_24mo_LA

description: SSc patient

value: skin biopsy

value: SSc patient

value: MMF


title: SScMH_21_36mo_LF

description: SSc patient

value: Universal Human Reference


title: REC_APB5_P8_A_rep3

city: Kobe

first: Sentaro

last: Kusuhara

state: Hyogo

address: 7-5-2 Kusunoki-cho, Chuo-ku

department: Department of Surgery

institute: Kobe University Graduate School of Medicine

description: Gene expression data from GFP-positive cells from P8 retina in APB5-treated homozygous Tie2-GFP transgenic mice

hyb_protocol: Biotin-labeled cRNA was fragmented in a 40-μl reaction mixture containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30mM magnesium acetate, and incubated at 94°C for 35 min, and then hybridized onto the MGU74v2 series of arrays.

scan_protocol: GeneChips were scanned with a GeneArray Scanner (Hewlett-Packard, Santa Clara, CA), controlled by MicroSuite 5.1 software (Affymetrix).

data_processing: The dChip software (version 1.3) was used to normalize the CEL files at probe level and compute model-based expression values using the PM only model.

label_protocol: Biotin-labeled cRNA was synthesized from the obtained RNA sample using the BioArray RNA Transcript labeling Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was isolated using RNeasy Micro-Kit (QIAGEN) and was amplified using MessageAmpII aRNA Kit (Ambion, Austin, TX) to obtain aRNA (>60μg).

treatment_protocol: Eyes from APB5-treated homozygous Tie2-GFP transgenic mice were enucleated, rinsed with PBS, and kept in staining solution (PBS containing 2mM EDTA, 0.01%, NaN3, 5% fetal calf serum, 50U/ml penicillin, and 0.05mg/ml streptomycin). The retinas were dissected under stereomicroscope, pooled in staining solution, and minced into small pieces. Collected retinal pieces were rinsed twice in PBS and digested in 10 ml of papain/DNase solution (papain (33U/ml; Sigma-Aldrich, St. Louis, MI) in Dulbecco’s PBS (Invitrogen) containing L-cysteine (0.4mg/ml; Nacalai tesque, Kyoto, Japan), EDTA (0.50mM; Sigma), and DNase I (125U/ml; Sigma)) for 60 min at 37°C with gentle agitation. Following digestion, cells were pelleted and treated two times with DNase/ovomucoid solution (a solution containing ovomucoid (2mg/ml; Sigma), DNase I (125 U/ml; Sigma), and BSA (1mg/ml; Wako, Osaka, Japan)) in Dulbecco’s PBS for 60 min at 37°C with gentle agitation. Digested retinal cells were filtered through nylon mesh, centrifuged at 300x g for 5 min to pellet cells, resuspended again with 10ml of DNase/ovomucoid solution incubated at 37°C for 60 min. Cells were rinsed twice in staining solution, pelleted, resuspended with staining solution containing 5µg/ml of propidium iodide, and filtered through nylon mesh. These cells were analyzed and sorted by FACS Aria (Becton Dickinson, San Jose, CA).

value: postnatal day 8

value: retiina

value: endothelial


title: REC_APB5_P8_A_rep2

source_name: GFP-positive cells from P8 retina in APB5-treated homozygous Tie2-GFP transgenic mice


title: GpatCD-CD229

value: Sprague-Dawley

value: female

value: Gonadal white adipose tissue


title: Bone marrow MD121

description: Hybridized to 6.0 Array

value: Bone marrow


title: Bone marrow MD144

description: Hybridized to 6.0 Array


title: zebrafish embryo 308

value: epiboly ~ 50

value: wild type ABTL

value: late blastula, early gastrula

value: all


title: SScMH_21_36mo_LA

description: SSc patient

source_name: Sample: Human Tissue Biopsy


title: zebrafish embryo 159

value: epiboly ~ 55


title: GpatCD-CD216

value: adult

value: normal (chow) diet for 12 wks

value: normal (chow) diet


title: GpatCD-CD225


title: SScMH_21_24mo_LA

description: SSc patient

value: skin biopsy

value: SSc patient

value: MMF

source_name: Universal Human Reference


title: REC_APB5_P8_A_rep1

value: postnatal day 8

value: retiina


title: GpatCD-CD186

value: Sprague-Dawley


title: SScMH_19_36mo_LF

description: morphea patient

value: morphea patient

value: Universal Human Reference


title: Bone marrow MD140T

description: Hybridized to 6.0 Array

value: CD3 lymphocytes isolated from peripheral blood


title: CD3 lymphocytes from MD116B

description: Hybridized to 6.0 Array


title: GpatCD-CD185

value: female

value: Gonadal white adipose tissue


title: zebrafish embryo 323

value: epiboly ~ 45

value: wild type ABTL

value: late blastula, early gastrula


title: Bone marrow MD93H

description: Hybridized to 6.0 Array

value: Bone marrow


title: zebrafish embryo 361

value: epiboly ~ 63

value: all


title: SScMH_19_36mo_LA

description: morphea patient

value: skin biopsy


title: Roots of ysl1ysl3 double mutant plants with normal iron nutrition, biological rep1

city: Amherst

first: Elsbeth

middle: Lewis

last: Walker

state: Massachusetts

address: 611 North Pleasant St

department: Biology Department

institute: University of Massachusetts

description: Gene expression data from roots of ysl1ysl3 double mutant plants with normal iron nutrition

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

source_name: Roots of 13 day old seedlings

label_protocol: Biotinylated cRNA were prepared according to Affymetrix 3’ IVT Express Kit Manual from 500ng of total RNA.

extract_protocol: Qiagen RNeasy plant

value: Roots

value: 13 day old seedlings

value: Normal iron conditions

value: Columbia (Col0) ysl1ysl3 double mutant


title: zebrafish embryo 225

value: epiboly ~ 56


title: Roots of ysl1ysl3 double mutant plants with normal iron nutrition, biological rep3


title: SScMH_21_24mo_LF

description: SSc patient

value: SSc patient

value: MMF


title: zebrafish embryo 522

value: epiboly ~ 50


title: Bone marrow MD117

description: Hybridized to 6.0 Array


title: zebrafish embryo 378

value: epiboly ~ 52


title: zebrafish embryo 306


title: Shoots of ysl1ysl3 double mutant plants with normal iron nutrition, biological rep3

description: Gene expression data from shoots of ysl1ysl3 double mutant plants with normal iron nutrition

source_name: Shoots of 13 day old seedlings

value: Shoots


title: Roots of ysl1ysl3 double mutant plants with normal iron nutrition, biological rep2


title: Bone marrow MD116B

description: Hybridized to 6.0 Array


title: GpatCD-CD162

value: Sprague-Dawley

value: female

value: adult

value: normal (chow) diet for 12 wks

value: normal (chow) diet

value: Gonadal white adipose tissue


title: Shoots of ysl1ysl3 double mutant plants with normal iron nutrition, biological rep1


title: SScMH_19_24mo_LA

description: morphea patient

value: skin biopsy

value: morphea patient

value: MMF, Plaquenil

value: Universal Human Reference


title: SScMH_19_24mo_LF

description: morphea patient


title: zebrafish embryo 540

source_name: whole embryo

value: epiboly ~ 55

value: wild type ABTL

value: late blastula, early gastrula

value: all


title: Bone marrow MD69

description: Hybridized to 6.0 Array

value: Bone marrow


title: Bone marrow MD74B

description: Hybridized to 6.0 Array


title: Shoots of ysl1ysl3 double mutant plants with normal iron nutrition, biological rep2

value: 13 day old seedlings

value: Normal iron conditions

value: Columbia (Col0) ysl1ysl3 double mutant


title: Roots of WT plants after iron withdrawal for 3 days, biological rep3

description: Gene expression data from roots of WT plants after iron withdrawal for 3 days

value: Roots

value: Medium prepared without iron

value: Columbia (Col0) wild type


title: zebrafish embryo 284

value: epiboly ~ 47


title: IFN-gamma-treated HeLa cells

city: Nagasaki

first: Yoshinao

last: Kubo

address: 1-12-4 Sakamoto

institute: Nagasaki University

hyb_protocol: The cRNA was added to a hybridization buffer, and hybridizaed to the whole human genome oligo microarray Ver.2 for 17 hr.

scan_protocol: After the washing, the images were observed by the Agilent microarray scanner.

data_processing: Fluorescent intensities of the spots were measured by the Feature Extraction Software (v.10.7.3.1).

source_name: IFN-gamma-treated HeLa cells

label_protocol: 100 ng of total RNA were reverse-transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase.  The cRNA was synthesized by in vitro transcription in the presence of Cy3-conjugated CTP.

growth_protocol: HeLa cells were cultured by the standard protocol.

extract_protocol: Total RNA extracted using the Quagen RNA isolation kit following manufacturer's instructions

treatment_protocol: HeLa cells were treated with 0.2µg/ml for 3 days.

tag: cell line

value: HeLa cells

tag: treated with

value: 0.2µg/ml IFN-gamma for 3 days


title: zebrafish embryo 170

treatment_protocol: Embryos were obtained by placing a female and a male, both of genotype ABTL, overnight in a tank separated by transparent, but watertight division. Approximately 1 hour after the start of the light period the division was removed after which spawning and fertilization took place, generally in one or more pushes. Embryos were retrieved by transferring both animals to a different tank and sieving the remaining water. In total from 9 pairs, embryos were obtained ('Spawn'). Embryos were maintained at 28.5 °C in egg water (60 μg/ml Instant Ocean sea salts).

tag: developmental stage

value: epiboly ~ 58

source_name: pool of whole embryos


title: zebrafish embryo 240

value: epiboly ~ 70

tag: spawn


title: SScMH_18_base_LA

first: Tammara

last: Wood

address: WTRB 674

description: SSc patient

data_processing: Images were quantified using GenePixPro

tag: tissue

value: skin biopsy

value: SSc patient

value: Universal Human Reference


title: SScMH_18_base_LF

description: SSc patient


title: Roots of WT plants after iron withdrawal for 3 days, biological rep1


title: Roots of WT plants after iron withdrawal for 3 days, biological rep2


title: zebrafish embryo 302

value: epiboly ~ 49

value: wild type ABTL

value: late blastula, early gastrula


title: SScMH_18_36mo_LA

description: SSc patient


title: SScMH_18_36mo_LF

description: SSc patient


title: SScMH_17_36mo_LA

description: SSc patient

value: MMF


title: Bone marrow MD72

description: Hybridized to 6.0 Array

value: Bone marrow


title: control untreated HeLa cells

source_name: HeLa cells

value: none (untreated control)


title: HT18

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: The analysis of raw data was performed with nSlover Analysis Software provided by NanoString Technologies. Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalizeed to the geometric mean of the 90 most highly expressed miRNAs.

source_name: tonsils

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility

extract_protocol: Ambion RecoverAll from Formalin Fixed Paraffin Embedded material

value: tonsils

value: healthy tonsils

tag: hpv status


title: HT19


title: zebrafish embryo 146

value: epiboly ~ 50

value: all


title: CD3 lymphocytes from MD51T

description: Hybridized to 6.0 Array

value: CD3 lymphocytes isolated from peripheral blood


title: Shoots of WT plants after iron withdrawal for 3 days, biological rep3

description: Gene expression data from shoots of WT plants after iron withdrawal for 3 days

value: Shoots

value: 13 day old seedlings

value: Medium prepared without iron

value: Columbia (Col0) wild type


title: Bone marrow MD51B

description: Hybridized to 6.0 Array


title: HT16


title: zebrafish embryo 196

value: epiboly ~ 53


title: SScMH_16_36mo_LF

city: Lebanon

institute: Dartmouth Medical School

description: SSc patient

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Axon scanner

label_protocol: 200ng of total RNA was reversed transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini following manufacturers protocol

value: skin biopsy

tag: subject

value: SSc patient

value: Universal Human Reference


title: Shoots of WT plants after iron withdrawal for 3 days, biological rep1


title: SScMH_17_24mo_LA

description: SSc patient

tag: disease state


title: SScMH_16_24mo_LF

description: SSc patient


title: SScMH_16_36mo_LA

description: SSc patient


title: SScMH_16_24mo_LA

description: SSc patient


title: Shoots of WT plants after iron withdrawal for 3 days, biological rep2


title: Roots of WT plants with normal iron nutrition, biological rep3

description: Gene expression data from roots of WT plants with normal iron nutrition

value: Roots

value: Normal iron conditions


title: Rspo1 1

city: Lyon

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

country: France

institute: Institut Neuromyogene

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

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: the data were RMA normalized  and  analysed with Partek Genomic Suit

source_name: Rpos1 null_primary myoblasts

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: Cells were grown in Ham F10 media with 20%FBS and 2ng/ml bFGF for 5 passage. Differentiation was induced by serum removal and culture in DMEM with 2% HS.

treatment_protocol: Differentiating myocytes harvested fater 24 hrs in differentiating conditions.

tag: strain background

tag: genotype/variation

value: limb muscles

tag: cell type

value: Primary myoblasts


title: Roots of WT plants with normal iron nutrition, biological rep1

tag: genotype


title: SScMH_14_36mo_LF

description: SSc patient

value: MMF, Cytoxan, Plaquenil

tag: reference


title: Roots of WT plants with normal iron nutrition, biological rep2


title: Wild Type 2

source_name: WT_primary myoblasts

value: wild-type


title: CD3 lymphocytes from MD74T

description: Hybridized to 6.0 Array


title: HT15

value: tonsils

value: healthy tonsils


title: Rspo1 2


title: Wild Type 1


title: CD3 lymphocytes from MD44T

description: Hybridized to 6.0 Array

value: CD3 lymphocytes isolated from peripheral blood


title: Shoots of WT plants with normal iron nutrition, biological rep3

description: Gene expression data from shoots of WT plants with normal iron nutrition

value: Shoots


title: HT14


title: Bone marrow MD44B

description: Hybridized to 6.0 Array

value: Bone marrow


title: SScMH_14_36mo_LA

description: SSc patient


title: HT13


title: Shoots of WT plants with normal iron nutrition, biological rep1

value: 13 day old seedlings


title: HT12


title: SScMH_14_24mo_LF

description: SSc patient

value: Cytoxan, Plaquenil


title: Shoots of WT plants with normal iron nutrition, biological rep2

value: Columbia (Col0) wild type


title: HT11


title: HT10


title: REC_APB5_P8_B_rep1

tag: age

value: postnatal day 8

value: retiina

value: endothelial


title: HT9


title: REC_APB5_P8_B_rep2


title: REC_APB5_P8_B_rep3


title: HT8


title: SScMH_14_24mo_LA

description: SSc patient

value: skin biopsy

value: SSc patient

value: Universal Human Reference


title: SScMH_13_Base_LF

description: SSc patient


title: HT7


title: HT5


title: REC_APB5_P8_C_rep3


title: HT3


title: REC_APB5_P8_C_rep1


title: SScMH_13_base_LA

description: SSc patient


title: REC_APB5_P8_C_rep2


title: HT2


title: TR70

value: oropharyngeal squamous cell carcinoma

value: HPV+


title: HT1


title: TR69


title: TR45

value: HPV-


title: HT4

value: tonsils


title: TR35


title: SScMH_12_36mo_LA

description: SSc patient

value: MMF


title: TR44


title: SScMH_10_36mo_LF

description: SSc patient


title: SScMH_12_36mo_RF

description: SSc patient


title: TR34


title: SScMH_12_24mo_LA

description: SSc patient


title: SScMH_07_36mo_LF

description: SSc patient

value: MA


title: SScMH_12_24mo_RF

description: SSc patient


title: SScMH_06_36mo_RA

description: SSc patient


title: SScMH_08_36mo_LF

description: SSc patient


title: SScMH_03_36mo_LF

description: SSc patient

value: NR


title: SScMH_06_36mo_RF

description: SSc patient


title: SScMH_08_36mo_LA

description: SSc patient


title: SScMH_10_36mo_LA

description: SSc patient


title: SScMH_07_36mo_LA

description: SSc patient


title: TR76


title: UpsM t90_2

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description: biological sample of cells grown in presence of singlet oxygen for 90 minutes 4-6

hyb_protocol: The ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech) was used for RNA labeling and fragmentation

scan_protocol: Total RNA of three independent experiments of two different growth phases were pooled and hybridized to one array. Two arrays were hybridized with independent experimental runs. Gene chip hybridization and scanning were performed according to the specifications from Agilent.

data_processing: Scanned on an Agilent High Resolution Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides pBBRUpsMx2 total cells replicate 2

label_protocol: Total RNA was isolated by using the hot phenol method (Janzon et al., 1986). After DNase I treatment the RNA was purified by using mixtures of phenol-chloroform-isoamylalcohol and chloroform-isoamylacohol. The RNA was further purified by RNeasy®MinElute™ spin columns (Qiagen) following the manufacturer’s instructions.

growth_protocol: R. sphaeroides strains grown under high oxygen tension or singlet oxygen stress

extract_protocol: Cells were harvested either under high aeration or under sinlget oxygen stress for 90 minutes.

value: R. sphaeroides pBBRUpsMx2

tag: protocol

value: singlet oxygen for 90 minutes

source_name: R. sphaeroides 2.4.1 pBBR total cells

value: R. sphaeroides pBBR


title: SScMH_03_36mo_LA

description: SSc patient

tag: treatment


title: TR86


title: UpsM t0_2

description: biological sample of cultures grown in aerobic conditions 4-6

value: aerobic condition


title: UpsM t0_1

description: biological sample of cultures grown in aerobic conditions 1-3

source_name: R. sphaeroides pBBRUpsMx2 total cells replicate 1


title: TR58


title: SScMH_01_base_LF

description: SSc patient

value: ASCT, MMF


title: UpsM t90_1

description: biological sample of cells grown in presence of singlet oxygen for 90 minutes 1-3


title: SScMH_01_base_LA

description: SSc patient


title: SScMH_01_36mo_LF

description: SSc patient


title: TR31


title: TR40


title: ctrl_rep6

city: Guangzhou

first: Liang

last: Zhang

state: Guangdong

address: Xingnan Road 521

department: Translational Medicine Research Center

institute: Guangdong Women and Children Hospital

hyb_protocol: Labeled cDNAs were combined and hybridized to a custom microarray

scan_protocol: washing and scanning, image data were extracted using Agilent Feature Extraction software.

data_processing: Signals were normalized by using loess normalization.

source_name: pooled ctrl

label_protocol: The dual-color approach was adopted in our study, samples were labeled with Cy3 and common reference made up of several heathy controls were labeled with Cy5 by using klenow enzyme, respectively.

extract_protocol: Briefly, total RNA was extracted from nucleated cells using the Whole-Blood RNA Isolation Kit following the manufacturer’s instructions and formaldehyde agarose gel electrophoresis was used to check the quality of it. Purified RNA was reversely transcribed to cDNA and amplified using the Low-Input Quick AmpWT Labeling Kit (Agilent).

value: heathy controls

source_name: Whole-Blood

tag: disease

value: none, healthy control


title: HT17

value: healthy tonsils


title: TR63


title: TR64


title: TR47


title: TR41


title: ctrl_rep7