title: Type L ECs from WT mice, biological rep3

status: Public on Jun 30 2017

type: RNA

city: Changsha

first: Xianghang

last: Luo

state: Hunan

address: 87# Xiangya Road

country: China

institute: Endocrinology Research Center, The Xiangya Hospital of Central South University

description: Type L ECs from WT mice-3

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse miRNA（8*60K，Design ID:070155)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.5(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

molecule: total RNA

organism: Mus musculus

source_name: Type L ECs from WT mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Sorted CD31hiEmcnhi and CD31loEmcnlo endothelial cells from mice were cultured in dishes coated with fibronectin and cultured in endothelial cell growth medium (EBM-2, Clonetics; Lonza) supplemented with EGM-2 Single Quots (CC-4176, Clonetic; Lonza).

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Culture medium was changed every third day.

tag: strain

tag: genotype/variation

value: wild type

tag: gender

value: male

tag: age

value: 1 month

tag: tissue

value: Bone marrow

tag: cell type

value: CD31loEmcnlo endothelial cells (type L ECs)


title: Type H ECs from WT mice, biological rep2

description: Type H ECs from WT mice-2

source_name: Type H ECs from WT mice

value: CD31hiEmcnhi endothelial cells (Type H Ecs)


title: Type H ECs from WT mice, biological rep1

description: Type H ECs from WT mice-1


title: WT vs. 35S:RAP2.6L, rep2

city: York

first: Katherine

last: Denby

address: Department of Biology

country: United Kingdom

institute: University of York

hyb_protocol: The microarray experiments were carried out using the CATMA (version 4) microarray (Allemeersh et al., 2005; http://www.catma.org). Labelled samples were hybridized to slides overnight at 42°C. Following hybridization, slides were washed.

scan_protocol: Slides were scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5). Scanned data were quantified using ImaGene 8.0 software (BioDiscovery, Inc.).

data_processing: The data from each time point were normalized and fit to a linear model using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004). Raw data were normalized within arrays using a PrintTip lowess transformation and normalized between arrays using the quantile-normalization. A least squares method was then used to fit the data to a linear model. The file processed_data_all_probes.txt contains the log2 Cy3/Cy5 values for all probes on the array including the controls. This file is available on the series record. The sample data table includes log2 ratio representing test/reference for non-control probes.

organism: Arabidopsis thaliana

label_protocol: Cy3- and Cy5-labelled cDNA probes were prepared by reverse transcribing 5 µg of aRNA with Cy3- or Cy5-dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50 µl hybridization buffer (10 mg/mL Bovine serum albumin, 5 x SSC, 0.1% SDS).

growth_protocol: Arabidopsis Ws and RAP2.6L-overexpressing plants were grown under a 16:8 hr light:dark cycle at 20°C, 70% humidity and light intensity of 110 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1).

extract_protocol: Total RNA was isolated from three individual leaves for each genotype using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol.

tag: genotype

value: leaf

source_name: WT

value: wild-type (Ws)


title: Type H ECs from WT mice, biological rep3

description: Type H ECs from WT mice-3


title: WT vs. 35S:RAP2.6L, rep5


title: Mouse_colon_untreated_wild_type_biological_rep8

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Gene expression data from mouse colon with or without AOM+DSS induced colitis. Conducted in wildtype mice or in mice with inactivated cytoglobin gene (Cygb -/-)

hyb_protocol: The labeled samples were hybridized to the Mouse Gene 2.0 ST GeneChip array according to the manufacture's protocol (Affymetrix, Santa Clara, CA, USA)

scan_protocol: The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450, and the arrays were scanned in the Affymetrix GeneArray® 3000 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol. Cell intensity files (CEL files) were generated in the GeneChip® Command Console® Software (AGCC) (Affymetrix, Santa Clara, CA, USA).

data_processing: The RMA algorithm was used for the gereration of quantile normalized expression measures

label: Biotin

source_name: Distal colon

label_protocol: RNA was amplified and labeled using the WT Plus Expression Kit (Affymetrix) according to manufactures instructions. 250 ng total RNA was used as input

extract_protocol: Total RNA was extracted using mirVana miRNA isolation kit (Ambion/Life Technologies, USA) following the manufacturer’s protocol.

treatment_protocol: Female  Cygb -/- mice and wt littermates were injected i.p. with 7.4 mg/kg AOM, followed by one cycle of 3% DSS on week 2 for 7 days. All mice were euthanized by cervical dislocation in week 5,  3 weeks after the end of the first DSS cycle.

value: Adult (18-24 weeks)

value: Wild type

tag: treatment

value: Untreated


title: WT vs. 35S:RAP2.6L, rep4


title: WT vs. 35S:RAP2.6L, rep6


title: Mouse_colon_untreated_wild_type_biological_rep7


title: Type L ECs from WT mice, biological rep1

description: Type L ECs from WT mice-1


title: WT vs. 35S:RAP2.6L, rep3


title: Type L ECs from WT mice, biological rep2

description: Type L ECs from WT mice-2


title: Mouse_colon_untreated_wild_type_biological_rep6


title: Mouse_colon_DSS_AOM_colitis_CYGB_knockout_biological rep5

value: Cygb -/-

value: AOM+DSS


title: WT vs. 35S:RAP2.6L, rep1


title: Mouse_colon_untreated_CYGB_knockout_biological_rep8


title: Mouse_colon_untreated_CYGB_knockout_biological_rep7


title: Mouse_colon_DSS_AOM_Colitis_wild_type_biological_rep7


title: Mouse_colon_DSS_AOM_colitis_CYGB_knockout_biological rep4


title: Mouse_colon_DSS_AOM_Colitis_wild_type_biological_rep6


title: Mouse_colon_untreated_wild_type_biological_rep5


title: Mouse_colon_untreated_CYGB_knockout_biological_rep6


title: Mouse_colon_DSS_AOM_Colitis_wild_type_biological_rep8


title: Mouse_colon_DSS_AOM_Colitis_wild_type_biological_rep5


title: Mouse_colon_untreated_wild_type_biological_rep4


title: Mouse_colon_DSS_AOM_Colitis_wild_type_biological_rep3


title: Mouse_colon_DSS_AOM_Colitis_wild_type_biological_rep4


title: Mouse_colon_untreated_wild_type_biological_rep3


title: Mouse_colon_DSS_AOM_colitis_CYGB_knockout_biological rep3


title: Mouse_colon_DSS_AOM_Colitis_wild_type_biological_rep2


title: siGATA3-2 H

city: Taipei

first: Min-Chuan

last: Huang

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

department: Graduate Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

description: Gene expression after 72 hours transfection

hyb_protocol: Agilent Gene Expression Hybridization Kits was used for hybridization according to the manufacturer’s instruction. Briefly, 16 ul of dye labeled cDNA in water was fragmented at 98°C for 3 mins in a reaction volume of 40 ul containing 4 ul Agilent 10x blocking agenr and 20 ul of Agilent 2xGExHybridization Buffer HI-RPM and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (G4851B) at 65°C and rotated at 10 rpm for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (US9230696) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid:072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: OEC-M1 cells siGATA3-2 H

label_protocol: cDNA prepared from 10μg of total RNA were labeled with aa-dUTP using Invitrogen SuperScriptTM Plus Indirect cDNA Labeling System according to the manufacturer's protocol, followed by aa-cDNA column purification (QIAGEN, Valencia, CA).  Alexa/CyDye was incorporated to aa-cDNA followed by column purification with Alexa/CyDye-cDNA cRNA purification (Qiagen).

growth_protocol: In 10% FBS/RPMI

extract_protocol: RNA was prepared using the Genejet RNA Purification kit (Thermo Scientific) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Hypoxia (H, 1% O2) for 18 hours

tag: oxygen level

tag: cell line

tag: transfection


title: siHIF1A-2 H

source_name: OEC-M1 cells siHIF1A-2 H


title: siHIF1A-3 H

source_name: OEC-M1 cells siHIF1A-3 H


title: siHIF1A-1 H

source_name: OEC-M1 cells siHIF1A-1 H


title: siGATA3-3 H

source_name: OEC-M1 cells siGATA3-3 H


title: siControl-3 H

source_name: OEC-M1 cells siControl-3 H

value: siControl


title: siControl-1 H

source_name: OEC-M1 cells siControl-1 H


title: siGATA3-1 H

source_name: OEC-M1 cells siGATA3-1 H


title: siControl-2 H

source_name: OEC-M1 cells siControl-2 H


title: Array-Set I_single animal / chip_FL2 line_Testis_12w_biological rep7

city: Dummerstorf

first: Alexander

last: Sobczak

state: Mecklenburg Western-Pomerania

address: Wilhelm-Stahl-Allee 2

department: Institute for Reproductive Biology

country: Germany

institute: Leibniz Institute for Farm Animal Biology Dummerstorf (FBN)

description: first transcriptome profiling: hypothesis generation for differential expression

hyb_protocol: Labeled samples were hybridized to GeneChip® Mouse Transcriptome Arrays 1.0 (GPL 20258, Affymetrix Inc.) for 16h at 45°C inside GeneChip® Hybridization Oven 645 (Affymetrix Inc.). Hybridization and following washing and staining steps were performed in GeneChip® Fluidics Station 450 according to standard protocols.

scan_protocol: Scanning of the microarray was conducted at 1.56 micron resolution with GeneChip® Scanner 3000 7G (Affymetrix Inc.). Image processing was accomplished with help of software Affymetrix GeneChip® Command Console 4.0 (AGCC 4.0).

data_processing: Data analysis was performed with Expression Console (Version V1.4.1.46, Affymetrix Inc.) using the SST-RMA algorithm for normalization. Further comparative analysis was done with Transcriptome Analysis Console (Version V3.0.0.466, Affymetrix Inc.).

source_name: FL2 line: FBN proprietary Outbred Mouse Line, 172nd generation, 12w/13w, testis

label_protocol: 100ng total RNA was converted to fragmented biotinylated cDNA using the standard WT Plus protocol (Affymetrix Inc.)

growth_protocol: The animals were maintained in a specific pathogen-free (SPF) environment with defined hygienic conditions at a temperature of 22.5°C, at least 40% humidity and a controlled light regime with a 12:12-h light-dark cycle. Mice were fed with water and pellet concentrate ad libitum. Bucks involved in 2nd or 4th replicate of two-factorial breeding experiment (both array sets) were allowed to mate at age of 10w with simultaneously caged females of 3 different lines each (FL1, FL2, Ctrl). The mating period was granted for 2 weeks, following preparation of these males at age of 12/13 w for array experiment. Advantageously, all our two-factorial breeding experiment samples could be provided simultaneously regardless any line-affiliation in contrast to routinely generated standard breeding animals that require line-specific breeding periods. Thus, a more suitable comparability could be ensured.

extract_protocol: Total RNA from mouse testis was extracted using the RNeasy Plus Mini Kit (Qiagen®) including removal of genomic DNA. Isolated RNA was checked for integrity and quantity by an  electrophoretic assay performed on a 2100 Bioanalyzer nanochip (Agilent).

treatment_protocol: 12/13 weeks old murine bucks were euthanized with carbon dioxide gas prior to removal and preparation of testis. Gained samples were preserved by submerging in RNAlater® RNA Stabilization Solution (Ambion®/Thermo Fisher Scientific) according to the manufacturers protocol.

value: FL2 line, FBN outbred long-term selection mouse line, high Fertility Line 2 (also known as DUC),  estrus synchronized with gestagen chlormadinone acetate up to 23rd generation, 172nd generation

tag: selection criteria

value: high litter size and high litter birth weight at first delivery

tag: background

value: two-factorial breeding experiment, 4th replicate

value: testis


title: Array-Set II_mouse pool / chip (n=8)_Ctrl line_Testes_12w_verifying biological pool rep

description: second transcriptome profiling: verification of differential expression with biologically independent replicates as pool - comparison single group vs. pool -  selection for validated candidates

source_name: Ctrl line: FBN proprietary Outbred Mouse Line, 170th generation, 12w/13w, testes pool of 8 animals

value: Ctrl line, FBN outbred long-term selection mouse line, unselected Control Line (also known as FzTDU), 170th generation

value: randomly selected

value: two-factorial breeding experiment, 2nd replicate

value: male


title: Array-Set I_single animal / chip_FL2 line_Testis_12w_biological rep8


title: Array-Set II_mouse pool / chip (n=8)_FL1 line_Testes_12w_verifying biological pool rep

source_name: FL1 line: FBN proprietary Outbred Mouse Line, 170th generation, 12w/13w, testes pool of 8 animals

value: FL1 line, FBN outbred long-term selection mouse line, high Fertility Line 1 (also known as DUK), 170th generation


title: Array-Set I_single animal / chip_FL2 line_Testis_12w_biological rep4


title: Array-Set I_single animal / chip_FL2 line_Testis_12w_biological rep6


title: Array-Set II_mouse pool / chip (n=8)_FL2 line_Testes_12w_verifying biological pool rep

source_name: FL2 line: FBN proprietary Outbred Mouse Line, 170th generation, 12w/13w, testes pool of 8 animals

value: FL2 line, FBN outbred long-term selection mouse line, high Fertility Line 2 (also known as DUC),  estrus synchronized with gestagen chlormadinone acetate up to 23rd generation, 170th generation


title: Array-Set I_single animal / chip_FL2 line_Testis_12w_biological rep5


title: Array-Set I_single animal / chip_FL2 line_Testis_12w_biological rep3


title: Array-Set I_single animal / chip_FL2 line_Testis_12w_biological rep2


title: Array-Set I_single animal / chip_FL1 line_Testis_12w_biological rep8

source_name: FL1 line: FBN proprietary Outbred Mouse Line, 172nd generation, 12w/13w, testis

value: FL1 line, FBN outbred long-term selection mouse line, high Fertility Line 1 (also known as DUK), 172nd generation


title: untreated HA22T/VGH cells (Input DNA)

type: genomic

city: Brescia

first: Alessandro

last: Salvi

address: viale Europa 11

country: Italy

institute: University of Brescia

description: Fraction: input DNA

hyb_protocol: Array Washing and Staining was performed with the use of the Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 7G (Affymetrix) and raw data were extracted with the GeneChip Operating System (GCOS) software from Affymetrix.

data_processing:
The raw data were imported into Partek® Genomics Suite® (PGS) software version 6.6, normalized with the RMA algorithm and converted to log2 values. Hierarchical clustering and Principal Component Analysis were performed on the raw data to assess the quality and reproducibility of the sample. For each cellular condition, the two IP CEL files were normalized through subtraction of log2 IN signal intensity at each of 4.6 million array probes of log2 IP signal. The differences between sorafenib treated and untreated cells were analyzed using ANOVA. Significantly differentially methylated regions (DMR) were obtained using the MAT algorithm (model-based analysis of tiling arrays algorithm) with the following parameters: p-value threshold<0.001, sliding window=2.000 bp, minimum number of probes in a region=10.
Methylation_data_elaborated_in_PGS
Normalyzed_methylation_data_elaborated_in_PGS
The resulting txt file is generated by the Partek Genomics Suite Software version 6.6 using ANOVA followed by Mat algorithm, using the following parameters: p-value threshold<0.001, sliding window=2.000 bp, minimum number of probes in a region=10

label: biotin

molecule: genomic DNA

source_name: untreated HA22T/VGH cells

label_protocol: A total of 200 ng of IN and IP DNA was amplified with the Affymetrix Chromatin Immunoprecipitation Assay Protocol. Hybridation on Human Promoter 1.0R array was performed using the reagents contained in GeneChip®Hybridization, Wash, and Stain Kit (Affymetrix) using GeneChip® hybridization oven 640 (Affymetrix).

growth_protocol: HA22T⁄VGH HCC cells were maintained in RPMI-1640 (Life Technologies) supplemented with 10% fetal bovine serum at 37°C in a 5% CO2 incubator.

extract_protocol: Genomic DNA was extracted from treated and untreated cells using Wizard Genomic DNA Purification Kit (Promega) according to the manufacturer’s instructions and quantified using NanoDrop (Thermo Fisher Scientific). Global DNA methylation profiles of sorafenib treated and untreated cells were obtained by methylated DNA immunoprecipitation coupled with Affymetrix Human Promoter 1.0R Tiling Arrays (MeDip-chip) using a modification of the Affymetrix chromatin immunoprecipitation assay protocol. Genomic DNA from sorafenib treated and untreated cells was fragmented using micrococcal nuclease (New England Biolabs) to obtain DNA fragments ranging from 200 to 500 nucleotides and used them as input (IN) DNA. Agilent Bioanalyzer with the RNA 6000 Nano LabChip Kit was used to check the size of fragmented DNA. Part of IN DNA (4 µg) was immunoprecipitated (IP) with 10 µl of anti-5-MethylCytosine Antibody (Eurogentec, BI-MECY-0100) using Dynabeads® Protein G immunoprecipitation kit (Life Technologies). The methylated enriched DNA was purified by standard phenol/chloroform procedure and isopropanol precipitated. The MeDip was performed in duplicate for each DNA sample starting with initial fragmentation step.

treatment_protocol: HA22T/VGH cells were cultured in 10 cm Ø plates up to almost confluence and were treated with sorafenib (5 µM) or solvent (0.1% DMSO) for 24 hours.

value: Treatment with solvent (0.1% DMSO) for 24 hours

tag: antibody


title: untreated HA22T/VGH cells replicate 2 (MeDip)

description: Fraction: MeDip DNA

source_name: untreated HA22T/VGH cells + MeDIP


title: untreated HA22T/VGH cells replicate 1 (MeDip)

description: Fraction: MeDip DNA


title: sorafenib treated HA22T/VGH cells replicate 2 (MeDip)

description: Fraction: MeDip DNA

source_name: sorafenib treated HA22T/VGH cells + MeDIP

value: Treatment with sorafenib (5 µM) for 24 hours


title: Array-Set I_single animal / chip_FL2 line_Testis_12w_biological rep1


title: Mouse_colon_DSS_AOM_colitis_CYGB_knockout_biological rep2

source_name: Distal colon

value: Adult (18-24 weeks)


title: sorafenib treated HA22T/VGH cells (Input DNA)

description:
Differentially_methylated_regions_found_with_PGS_analysis
Fraction: input DNA

source_name: sorafenib treated HA22T/VGH cells

value: Treatment with sorafenib (5 µM)  for 24 hours


title: sorafenib treated HA22T/VGH cells replicate 1 (MeDip)

description: Fraction: MeDip DNA


title: Array-Set I_single animal / chip_FL1 line_Testis_12w_biological rep7


title: Array-Set I_single animal / chip_FL1 line_Testis_12w_biological rep5


title: Array-Set I_single animal / chip_Ctrl line_Testis_12w_biological rep7

source_name: Ctrl line: FBN proprietary Outbred Mouse Line, 172nd generation, 12w/13w, testis

value: Ctrl line, FBN outbred long-term selection mouse line, unselected Control Line (also known as FzTDU), 172nd generation


title: Array-Set I_single animal / chip_FL1 line_Testis_12w_biological rep3


title: Array-Set I_single animal / chip_FL1 line_Testis_12w_biological rep1


title: Array-Set I_single animal / chip_FL1 line_Testis_12w_biological rep4


title: Array-Set I_single animal / chip_FL1 line_Testis_12w_biological rep6


title: Array-Set I_single animal / chip_FL1 line_Testis_12w_biological rep2


title: Array-Set I_single animal / chip_Ctrl line_Testis_12w_biological rep3


title: Array-Set I_single animal / chip_Ctrl line_Testis_12w_biological rep8


title: Array-Set I_single animal / chip_Ctrl line_Testis_12w_biological rep4


title: Array-Set I_single animal / chip_Ctrl line_Testis_12w_biological rep5


title: Array-Set I_single animal / chip_Ctrl line_Testis_12w_biological rep1


title: Array-Set I_single animal / chip_Ctrl line_Testis_12w_biological rep6


title: Array-Set I_single animal / chip_Ctrl line_Testis_12w_biological rep2


title: SA synovial biopsy 3

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

description:
tissue: synovial biopsy tissue (15–20 synovial samples per patient) was obtained by needle arthroscopy of the affected knee of patients with systemic lupus erythematosus (SLE n = 4), patients with rheumatoid arthritis (RA n = 7), patients with osteoarthritis (OA n = 5), patients with seronegative arthritis (SA, n = 4) and patients with microcrystalline arthritis (MIC n = 5). For each patient, 4–6 synovial samples were snap-frozen in liquid nitrogen and stored at −80° for later RNA extraction. The same amount of tissue was also kept at −80° for future immunostaining experiments on frozen sections. The remaining material was stored in formaldehyde and paraffin-embedded for conventional optical evaluation and immunostaining of selected cell markers.
patients: all patients with SLE met the American College of Rheumatology (ACR; formerly, the American Rheumatism Association) revised classification criteria for SLE (5), all were female, and the mean age was 32 years (range 19–40 years). All SLE patients had active articular disease at the time of synovial tissue sampling, and none had received immunosuppressive therapy; some of the SLE patients were receiving nonsteroidal antiinflammatory drugs. All patients with RA met the ACR classification criteria for RA (6) and all had early (<1 year's duration) active disease at the time of tissue sampling. Among the patients with RA, 2 were female and 5 were male, and the mean age was 51 years (range 37–69 years). In these patients, the mean C-reactive protein (CRP) level was 25 mg/liter (range 9–96 mg/liter), and the mean Disease Activity Score in 28 joints (including the CRP) (7) was 5.08 (range 3.76–5.82). None of the RA patients had received any treatment, except with nonsteroidal antiinflammatory drugs. Among the patients with OA, 5 were female and 1 was male, and the mean age was 63.2 years (range 51–73 years). The diagnosis of seronegative arthritis was based on the presence of psoriasis or x-ray evidence of sacro-iliacal joint involvement). The diagnosis of microcrystalline arthritis was based on the identification of urate or calcium pyrophosphate crystals in the synovial fluid.

hyb_protocol: GeneChip Human Genome U133 Plus 2.0 arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts and originating from 39,000 genes; Affymetrix UK) were hybridized overnight at 45°C in monoplicate cultures with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the GeneChip Fluidics Station (Affymetrix UK).

scan_protocol: The slides were scanned on a GeneChip Scanner 3000.

data_processing: Analysis of gene expression data was performed on GeneSpring (Agilent) after normalization by robust multi-array analysis. The systemic sclerosis tenosynovial samples were compared to synovial biopsy samples harvested previously by our group in patients with several rheumatic conditions (GSE36700). ANOVA and t tests were performed, using osteoarthritis samples as the comparator in the latter case. GOTERM pathway analyses were done (on all transcripts overexpressed in systemic sclerosis compared to osteoarthritis samples, with a fold change threshold > 2) using DAVID.

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with seronegative arthritis

label_protocol: Labeling of RNA (complementary RNA [cRNA] synthesis) was performed according to a standard Affymetrix procedure (One-Cycle Target Labeling kit; Affymetrix UK, High Wycombe, UK). Briefly, total RNA was first reverse transcribed into single-stranded complementary DNA (cDNA) using a T7-Oligo(dT) Promoter Primer kit (Affymetrix UK) and Superscript II reverse transcriptase. RNase H was then added together with Escherichia coli DNA polymerase I and E coli DNA ligase, followed by a short incubation with T4-DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7-RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated cRNA was cleaned and fragmented by a 35-minute incubation at 95°C.

extract_protocol: Total RNA was extracted from synovial biopsy tissue using the Nucleospin RNA II extraction kit (Macherey-Nagel, Düren, Germany), which included DNase treatment of the samples.

value: synovial biopsies

tag: disease state

value: Seronegative arthritis

value: m

value: NSAIDs


title: SA synovial biopsy 2

value: f


title: SA synovial biopsy 1


title: MIC synovial biopsy 2

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with microcrystalline arthritis

value: Microcrystalline arthritis

value: NSAIDs/colchicine


title: MIC synovial biopsy 5


title: SA synovial biopsy 4


title: MIC synovial biopsy 4

value: colchicine


title: Mouse_colon_untreated_CYGB_knockout_biological_rep5

value: Cygb -/-

value: Untreated


title: Mouse_colon_untreated_CYGB_knockout_biological_rep4


title: SLE synovial biopsy 2

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with lupus arthritis

value: Systemic lupus erythematosus


title: MIC synovial biopsy 3


title: SLE synovial biopsy 3


title: SLE synovial biopsy 4


title: SLE synovial biopsy 1


title: Mouse_colon_untreated_CYGB_knockout_biological_rep3


title: Mouse_colon_untreated_CYGB_knockout_biological_rep2


title: MIC synovial biopsy 1


title: RA synovial biopsy 7

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with rheumatoid arthritis

value: Rheumatoid arthritis


title: Mouse_colon_untreated_wild_type_biological_rep2

value: Wild type


title: Mouse_colon_DSS_AOM_colitis_CYGB_knockout_biological rep1

value: AOM+DSS


title: RA synovial biopsy 5


title: Mouse_colon_untreated_CYGB_knockout_biological_rep1

value: Adult (18-24 weeks)


title: RA synovial biopsy 6


title: RA synovial biopsy 4


title: mouse, biological rep3

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

country: USA

institute: NCI/NIH

description:
mouse_3
Gene expression data from iPS cell and mouse
Rag1-/- mice injected with T cells derived from mouse

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

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

data_processing: The data were analyzed with R (BioConductor) and normalized using the Robust Multiarray Averaging (RMA) normalization method

source_name: transgenic mice from embryonic day 12 to 13

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

growth_protocol: Growth was in vivo for 25 days

extract_protocol: RNeasy micro kit.  The extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Once cells were injected into the mice, no further interventions were performed until sacrifice 25 days later and immediate sorting of marked cells.

tag: protocol

value: Pmel-1 transgenic mouse naïve T cells were injected into Rag1-/- mice

value: spleen

value: live, CD45+ cells derived from Pmel-1 transgenic mouse naïve T cells

value: 6 weeks


title: Mouse_colon_DSS_AOM_Colitis_wild_type_biological_rep1


title: RA synovial biopsy 3

value: synovial biopsies


title: mouse, biological rep2

description:
mouse_2
Gene expression data from iPS cell and mouse
Rag1-/- mice injected with T cells derived from mouse


title: RA synovial biopsy 1

value: m

value: NSAIDs


title: iPS cell, biological rep1

description:
iPS_1
Gene expression data from iPS cell and mouse
Rag1-/- mice injected with T cells derived from iPS

value: iRTE were injected into Rag1-/- mice

value: live, CD45+ cells derived from iRTE


title: iPS cell, biological rep2

description:
iPS_2
Gene expression data from iPS cell and mouse
Rag1-/- mice injected with T cells derived from iPS


title: OA synovial biopsy 3

source_name: Synovial biopsies (n = 4 to 6), obtained by needle arthroscopy from the swollen knee of a patient with osteoarthritis

value: Osteoarthritis

value: f


title: iPS cell, biological rep3

description:
iPS_3
Gene expression data from iPS cell and mouse
Rag1-/- mice injected with T cells derived from iPS


title: mouse, biological rep1

description:
mouse_1
Gene expression data from iPS cell and mouse
Rag1-/- mice injected with T cells derived from mouse


title: Mouse_colon_untreated_wild_type_biological_rep1

value: Untreated


title: SSc tenosynovial biopsy 3

hyb_protocol: GeneChip Human Genome U133 Plus 2.0 arrays were hybridized overnight at 45°C with 10ug fragmented biotinylated cRNA.

scan_protocol: The slides were then washed and stained using a EukGE-WS2v5 fluidics protocol on a GeneChip Fluidics Station 450, before being scanned on a GeneChip Scanner 3000 (Affymetrix).

source_name: Patient with systemic sclerosis and tenosynovial involvement

label_protocol: Complementary RNA (cRNA) was synthetized from 1ug total RNA, and biotin-labeled according to a standard Affymetrix procedure (GeneChip® 3' IVT express kit, Affymetrix).

extract_protocol: RNA was extracted from the tenosynovial biopsy samples using a NucleoSpin RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips. All samples had a RNA integrity number _ 6.4.

treatment_protocol: Five tenosynovial biopsies were obtained from diffuse systemic sclerosis patients undergoing surgical procedures due to refractory pain and/or loss of function caused by tenosynovitis, and snap-frozen in liquid nitrogen, next kept at -80°C

value: tenosynovial biopsy

value: diffuse systemic sclerosis


title: OA synovial biopsy 5


title: SSc tenosynovial biopsy 5


title: OA synovial biopsy 1


title: RA synovial biopsy 2

value: Rheumatoid arthritis


title: OA synovial biopsy 4


title: S3

city: Taoyuan

first: Yi-Ru

last: Pan

address: 5 Fu-Hsing Street, Kwei-Shan,

institute: Chang Gung Memorial Hospital, Linkou

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit

scan_protocol: GeneChip® Scanner 3000

data_processing: the data was pre-processed using the rma method from the Affymetrix Expression Console software

source_name: primary site

label_protocol: biotin

growth_protocol: DLBCLcells were growth in 3D collagen gels for 24 hours

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

treatment_protocol: No treatment

tag: isolation site


title: SSc tenosynovial biopsy 1


title: L3

source_name: metastatic lymph node

value: lymph node


title: SSc tenosynovial biopsy 4


title: S2


title: SSc tenosynovial biopsy 2


title: CTRL_4h_rep2

city: Paris

first: Sadri

last: ZNAIDI

address: 25 rue du Docteur Roux

department: Mycology Department

country: France

institute: Institut Pasteur

hyb_protocol: Gene Expression Hybridization Kit (Cat# 5188-5242) from Agilent Technologies was used to prepare 50 µl of purified labeled samples as recommended by the manufacturer, followed by hybridization to the GPL19289 platform.

scan_protocol: Images of Cy5 and Cy3 fluorescence were generated by scanning the expression arrays using an Axon Autoloader 4200AL scanner (Molecular Devices, Downington, PA). Images were analyzed with the GenePix Pro 6.1.0.2 software (Molecular Devices, Downington, PA).

data_processing: GenePix Results (GPR) files were imported into the Arraypipe 2.0 for spot filtering, background subtraction (limma normexp BG correction) and Lowess global normalization of signal intensities

organism: Candida albicans

source_name: Untreated control, grown in YPD medium during 4h

label_protocol: First-strand cDNA synthesis and Cy5/Cy3 labeling from 20 µg total RNA was performed using the Superscript III indirect cDNA labeling system (Invitrogen).

growth_protocol: Total RNA was extracted from strains carrying the PTET-SKN7 fusion or the empty vector control (PTET only, control), pre-grown overnight in 10 ml YPD at 30ºC then diluted in fresh YPD medium supplemented or not with 3 µg.mL−1 anhydrotetracycline (ATc) to an OD600 nm of 0.3 and re-grown for 2 (samples 3-5 and 11-13) and 4 (samples 6-8 and 14-16) hours.

extract_protocol: Total RNA was extracted using the hot phenol method as decribed in Znaidi et al. (2013) PLoS Pathogens 9: e1003519.

treatment_protocol: See growth protocol

value: C. albicans strain carrying CIp-PTET (empty)

source_name: ATc-treated at a concentration of 3 µg/mL in YPD medium for 4h


title: CTRL_2h_rep1

source_name: Untreated control, grown in YPD medium during 2h

source_name: ATc-treated at a concentration of 3 µg/mL in YPD medium for 2h


title: OA synovial biopsy 2


title: CTRL_4h_rep3


title: L1


title: SI


title: CTRL_2h_rep2


title: CTRL_2h_rep3


title: L2


title: CTRL_0h_rep1

source_name: Untreated control, grown in YPD medium during 0h

source_name: ATc-treated at a concentration of 3 µg/mL in YPD medium for 0h


title: CTRL_0h_rep2


title: CTRL_4h_rep1


title: SKN7_2h_rep2

value: C. albicans strain carrying CIp-PTET-SKN7


title: SKN7_0h_rep1


title: SKN7_2h_rep1


title: SKN7_0h_rep2


title: SKN7_4h_rep1


title: SKN7_2h_rep3


title: SKN7_4h_rep2


title: DMSO rep2

city: Fujisawa

first: Yoshinori

last: Ishikawa

state: Kanagawa

address: 26-1 Muraoka-Higashi 2-chome

department: Oncology Drug Discovery Unit

country: Japan

institute: Takeda Pharmaceutical Company Ltd.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

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

extract_protocol: RNA was purified with extracted with QIAGEN RNeasy mini kit with DNase I treatment with  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Treatment with test article or DMSO for 24 hours

tag: agent

value: DMSO

value: AML cell line


title: Pevonedistat 1000 nM rep1

value: Pevonedistat 1000 nM


title: T-3775440+Pevonedistat rep2


title: SKN7_4h_rep3


title: DMSO rep1


title: T-3775440 50 nM rep1


title: T-3775440+Pevonedistat rep1


title: Pevonedistat 1000 nM rep2


title: placebo treatment, day7 after IRI, R37L

city: Vienna

first: Julia

last: Wilflingseder

address: Währinger Gürtel 18-20

department: Nephrology and Dialysis

country: Austria

institute: Medical University of Vienna

description:
kidney tissue in RNAlater, stored at -80°C
Gene expression data from zero-hour biopsy

hyb_protocol: cDNA were hybridized for 18 hr at 45C on GeneChip Human ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 7G.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

organism: Rattus norvegicus

source_name: placebo treatment, day7 after IRI, R37L

label_protocol: Total RNA (200 ng per sample) was amplified and labeled using the Applause WT-Amp ST and Encore Biotin Module kit (NuGEN, San Carlos, CA)

value: kidney


title: placebo treatment, day7 after IRI, R50L

source_name: placebo treatment, day7 after IRI, R50L


title: T-3775440 50 nM rep2


title: anti-miR-182 treatment, day7 after IRI, R61L


title: anti-miR-182 treatment, day2 after IRI, R95L


title: placebo treatment, day2 after IRI, R93L

source_name: placebo treatment, day2 after IRI, R93L


title: placebo treatment, day2 after IRI, R96L

source_name: placebo treatment, day2 after IRI, R96L


title: anti-miR-182 treatment, day7 after IRI, R99L


title: anti-miR-182 treatment, day7 after IRI, R77L


title: placebo treatment, day2 after IRI, R101L


title: anti-miR-182 treatment, day2 after IRI, R103L


title: placebo treatment, day7 after IRI, R100L


title: SKN7_ChIP_Upper array

hyb_protocol: The labeled DNA was speed-vaced and the pellets were resuspended in 104 µl of H2O. 26 µl of Agilent 10X blocking agent and 130 µl of Agilent 2X Hybridization Buffer were added for a total of 260 µl hybridization mix. Samples were heated at 95ºC for 3 minutes and incubated immediately at 37ºC during 30 min. 245 µl were dispensed onto each of the 2x400k Agilent gaskets. The hybridization chambers were assembled and rotated overnight at 65ºC as per the manufecturer's protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol

data_processing: Data were normalized using Quantile normalization

source_name: Candida albicans untagged strains, treated with 3 µg/mL of anhydrotetracycline for 2h in YPD medium at 30ºC

label_protocol: The IP DNA (40 µl out of 50 µl) fragments were blunted with T4 DNA polymerase and ligated to unidirectional linkers. The DNA was amplified by ligation-mediated PCR in the presence of aminoallyl-modified dUTP. Labeling was carried out post-PCR using monoreactive Cy dye N-hydroxysuccinimide esters (Cy5/Cy3 monoreactive dye packs; Amersham Biosciences) that react specifically with the aminoallyl-modified dUTP [5-(3-aminoallyl)-2′ deoxyuridine-5′-triphosphate; Sigma-Aldrich]. Labeled IP DNA from the tagged strain (Cy5) and the untagged control strain (Cy3) were mixed and hybridized to C. albicans tiling arrays (platform GPL13696)

growth_protocol: Cells were grown overnight in 2 ml YPD at 30°C, diluted to an OD600 nm of 0.2 in fresh medium and re-grown for 1 hour. The medium was supplemented with 3 µg/ml anhydrotetracycline and cells were allowed to grow for 2 additional hours at 30ºC.

extract_protocol: PTET-SKN7-3xHA (Tagged) and PTET-SKN7 (untagged control) were grown overnight in 2 ml YPD at 30°C, diluted to an OD600 nm of 0.2 in YPD medium supplemented with 3 µg/ml anhydrotetracycline and grown during 2 hours at 30°C.  Cultures were treated with 1% formaldehyde (cross-linking) and snap-frozen in liquid nitrogen. Total cell extracts were prepared by bead beating using a FastPrep-24 instrument (MP Biomedicals) with 10 runs during 1 min each at 6.0 m/sec and 1 minute on ice in between. Soluble chromatin fragments were prepared by sonicating the extracts 6 times during 20 sec at power 8 (knob position) for an output signal amplitude of 15 (Microns, Peak to Peak) using a probe sonicator (MSE), yielding a majority of ~200-500 bp DNA fragments. Immunoprecipitation was conducted overnight at 4ºC with 500 µl of clarified sonicated extracts and mouse monoclonal anti-HA antibody (Santa Cruz Biotech) coupled with magnetic beads (Pan-mouse immunoglobulin G Dynabeads; Dynal Biotech, Brown Deer, WI) at 4ºC.

tag: sample type

value: Immunoprecipitated DNA

source_name: Candida albicans strains expressing a 3xHA-tagged version of the SKN7 gene placed under the control of a tetracycline derivative-inducible promoter, treated with 3 µg/ml anhydrotetracycline for 2h in YPD medium at 30ºC.


title: anti-miR-182 treatment, day2 after IRI, R102L


title: PD1222 in Anaerobic continuous culture (CSTR) replicate 1

type: mixed

city: Richmond

first: Georgios

last: Giannopoulos

state: Virginia

address: 1000 W Cary st

department: Biology

institute: Virginia Commonwealth University

hyb_protocol: CyDye-labelled DNA samples were mixed with hybridisation buffer (Morpholine-4-ethanesulfonic acid (MES) hydrate (pH 6.5)  50 mM, Sodium chloride 1 M, 99% Formamide 20% (w/v), EDTA 20 mM, Triton X-100  1% (w/v)) and applied to microarray slides in a tight chamber at 55°C for 60 hours at 8 rpm

scan_protocol: Scanned on an GenePix 4000B scanner (Axon Instruments, Inc.).Images were quantified using Axon GenePix Pro7

data_processing: BABAR R-package was used in R v2.9.2 (Alston et al 2010, BMC Bioinformatics 11:73) was used for background subtraction and LOWESS normalization.

organism: Paracoccus denitrificans PD1222

label_protocol: Total RNA  (10 μg) was converted to cDNA and fluorescently labelled by random priming to incorporate Cy5-dCTP (Amersham) using reverse transcriptase (AffinityScript, Stratagene).

growth_protocol: P. denitrifican was grown in minimal medium, containing 20mM NO3-, in continuous culture reactiors (continuous culture (CSTR)) with (aerobic) and without (anaerobic) air supply for aprox 120 hours. At 120 hours, samples were take for transcriptional analysis.

extract_protocol: Total RNA extracted using Promega SV total RNA extration kit following manufacturer's instructions

treatment_protocol: The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior centrifugation.

tag: genotype/variation

value: Wild type

tag: culture condition

value: Anaerobic continuous culture (CSTR)

source_name: Wild Type in LB

value: chromosomal DNA reference


title: PD1222 in Anaerobic continuous culture (CSTR) replicate 2


title: PD1222 in Anaerobic continuous culture (CSTR) replicate 3


title: HCmel3_ctrl_rep5_re-analyzed

city: Bonn

first: Michael

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: University Hospital Bonn

description:
excised_tumor_skin
8294816100_B

data_processing: Variance stabilization and normalisation using vsn package from bioconductor in R without background correction. Vsn was performed after integration of samples from GSE40213.

label_protocol: 100ng RNA was converted to biotinylated cRNA using one round of amplification with Illumina Labelling Kit and one round of T7 polymerase

growth_protocol: Animals were kept according to the institutional and national  guidelines for the care and use of laboratory animals with approval by the local government authorities (LANUV, NRW, Germany)

extract_protocol: Total RNA was isolated using TRI Reagent and purified using Rneasy columns (Quiagen).  RNA quality was assayed using Agilent Bioanalyzer

treatment_protocol: The adoptive pmel-1 T cell transfer protocol consists of chemotherapeutic  conditioning with a single dose of cyclophosphamide, intravenous injection of CD8+ TCR-transgenic pmel-1 T cells directed against the endogenous melanocytic antigen gp100, activation of T cell in vivo with a gp100-expressing adenovirus vaccine and stimulation of the innate immune system with CpG/polyI:C.

tag: tissue

value: Non-treated (NT)

tag: strain

tag: tissue preparation


title: PD1222 in Aerobic continuous culture (CSTR) replicate 3

value: Aerobic continuous culture (CSTR)


title: HCmel3_relapse_rep5_re-analyzed

description:
excised_tumor_skin
8294816100_E

tag: treatment


title: HCmel3_relapse_rep1_re-analyzed

description:
excised_tumor_skin
8294816099_D


title: PD1222 in Aerobic continuous culture (CSTR) replicate 1


title: HCmel3_relapse_rep3_re-analyzed

description:
excised_tumor_skin
8294816099_F


title: HCmel3_ctrl_rep2_re-analyzed

description:
excised_tumor_skin
8294816099_B


title: HCmel3_melanoma_Non-treated (NT)_rep8

description:
excised_tumor_skin
3999483059_F


title: HCmel3_ctrl_rep3_re-analyzed

description:
excised_tumor_skin
8294816099_C


title: HCmel3_melanoma_Non-treated (NT)_rep6

description:
excised_tumor_skin
3999483059_D


title: HCmel3_melanoma_Non-treated (NT)_rep4

description:
excised_tumor_skin
3998897075_A


title: HCmel3_ctrl_rep4_re-analyzed

description:
excised_tumor_skin
8294816100_A


title: PD1222 in Aerobic continuous culture (CSTR) replicate 2


title: HCmel3_melanoma_Non-treated (NT)_rep7

description:
excised_tumor_skin
3999483059_E


title: HCmel3_relapse_rep2_re-analyzed

description:
excised_tumor_skin
8294816099_E


title: ctrl16

city: Kurume

first: Yuuichirou

last: Hirata

address: 67 Asahimachi

department: Department of Surgery

institute: Kurume University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: tricuspid aortic valve, control16

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

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: condition

value: tricuspid

value: wall of ascending aorta


title: ctrl17

source_name: tricuspid aortic valve, control17


title: HCmel3_melanoma_Early-during-treatment (EDT)_rep6

description:
excised_tumor_skin
3999483058_C

value: Early-during-treatment (EDT)


title: HCmel3_ctrl_rep1_re-analyzed

description:
excised_tumor_skin
8294816099_A


title: ctrl20

source_name: tricuspid aortic valve, control20


title: HCmel3_melanoma_Early-during-treatment (EDT)_rep8

description:
excised_tumor_skin
3999483059_B


title: HCmel3_relapse_rep4_re-analyzed

description:
excised_tumor_skin
8294816100_D


title: HCmel3_melanoma_Non-treated (NT)_rep5

description:
excised_tumor_skin
3998897075_B


title: HCmel3_melanoma_Early-during-treatment (EDT)_rep7

description:
excised_tumor_skin
3999483059_A


title: ctrl10

source_name: tricuspid aortic valve, control10


title: HCmel3_melanoma_Early-during-treatment (EDT)_rep5

description:
excised_tumor_skin
3999483058_B


title: ctrl2

source_name: tricuspid aortic valve, control2


title: HCmel3_melanoma_Early-during-treatment (EDT)_rep2

description:
excised_tumor_skin
3999483050_B


title: ctrl4

source_name: tricuspid aortic valve, control4


title: patient18

source_name: bicuspid aortic valve, patient18

value: bicuspid


title: HCmel3_melanoma_Early-during-treatment (EDT)_rep4

description:
excised_tumor_skin
3999483058_A


title: patient6

source_name: bicuspid aortic valve, patient6


title: HCmel3_melanoma_Early-during-treatment (EDT)_rep3

description:
excised_tumor_skin
3999483050_C


title: patient22

source_name: bicuspid aortic valve, patient22


title: patient13

source_name: bicuspid aortic valve, patient13


title: ctrl5

source_name: tricuspid aortic valve, control5


title: patient8

source_name: bicuspid aortic valve, patient8


title: HCmel3_melanoma_Early-during-treatment (EDT)_rep1

description:
excised_tumor_skin
3999483050_A


title: HCmel3_melanoma_Non-treated (NT)_rep3

description:
excised_tumor_skin
3999483055_C


title: HCmel3_melanoma_Non-treated (NT)_rep2

description:
excised_tumor_skin
3999483055_B


title: HCmel3_melanoma_Non-treated (NT)_rep1

description:
excised_tumor_skin
3999483055_A


title: patient21

source_name: bicuspid aortic valve, patient21


title: patient15

source_name: bicuspid aortic valve, patient15


title: patient3

source_name: bicuspid aortic valve, patient3


title: SN6 occipital

city: Berlin

first: Annika

last: Vogt

address: Charitéplatz 1

department: Department of Dermatology and Allergy

institute: Charité – Universitätsmedizin Berlin

description: Gene expression after hair plucking (hair root)

hyb_protocol: Hybridization of Agilent Whole Genome Oligo Microarrays - The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600ng Cy3-labeled fragmented cRNA in hybridization puffer was hybridized overnight (17 hours, 65oC) to Agilent Whole human Genome oligo Microarrays 8x60K V2 using Agilent’s recommended hybridization chamber and oven. The microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37oC) for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), reject outliers and calculates statistical confidences.

data_processing: Preprocessing included normalization and correlation analysis of all microarray datasets. After background correction, quantile normalization was conducted between arrays and the normalized intensities were log2-transformed. For each reporter, a p-value was calculated to indicate if signal is reliable (flags). An inter-experiment correlation analysis was performed to analyze inter-sample similarity or variability. ANOVA test with repeated measurements design were applied on the normalized log2 intensity data to distinguish expression differences between all sample groups. Tukey’s post-hoc test was applied to compare the indicated groups.

source_name: Subject 6, occiput hair

label_protocol: Linear T7-based amplification of RNA - For the linear T7-based amplification step, 100ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: About 30 hairs from different scalp regions (frontal, vertex and occipital) were obtained by trichogram, a semi-invasive (plucking) method. Total RNA of the  hair roots was isolated using an RNeasy micro kit (Qiagen, Hilden, Germany) according to the manufacturer`s instruction. RNA quantity was determined using UV- spectrophotometry (NanoDrop ND-1000, Wilmington, DE) and the RNA integrity was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technoligies, Santa Clara, CA).

tag: region

value: occiput

value: Scalp hair

tag: gender

value: male

tag: disease

value: Androgenetic alopecia


title: DMBT1-/- mice non- infected_Sample 3

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description: SAMPLE 80

hyb_protocol: 60°C for 30 mins followed by 16h at 45°C

scan_protocol: BeadArray Reader protocol for DASL Gene Expression  and MouseWG-6 v2 from Illumina

data_processing: MAG, IM and Dysplasia gene expression in humans were determined using MAG as reference. For mouse data WT and DMBT1-/- analyses were done in separate using non-infected tissues as reference. For both analyses background was removed using the detection P value algorithm. Normalization was done with the cubic spline algorithm. Differential expression of genes was done using MAG (human) and non-infected (mice) values as reference.

source_name: DMBT1-/- mice non- infected

label_protocol: Streptavidin labeled cDNA was obtained following protocols from Illumina for FFPE samples (Cancer Panel). Streptavidin-labeled cDNA was then ampified using Cy3 and Cy5 labeled primers

growth_protocol: FFPE tissues of individuals with different stages of gastritis were used in this study;  6 week-old wild type and CD44-/- mice were maintained at specific pathogen free conditions.

extract_protocol: Total RNA from formalin-fixed paraffin-embedded (FFPE) tissues was extracted using the RecoverAll Total Nucleic Acid Isolation from Ambion (Austin, TX), in five 10-20µm-thick tissue sections, as recommended by the vendor. The RNA was resuspended in DEPC-water and quantified by NanoDrop (ThermoFisher Scientific, Waltham, MA). Fresh frozen gastric tissues from mice infected with H. pylori was extracted with Qiagen RNeasy kits

treatment_protocol: No treatment for patients was done. Six to 8 weeks old mice were infected with H. pylori for 4 to 6 months.

tag: strain background

tag: infected with

value: gastric tissue


title: SN5 occipital

source_name: Subject 5, occiput hair


title: DMBT1-/- mice H. pylori infected_Sample 2

description: SAMPLE 82

source_name: DMBT1-/- mice H. pylori infected

value: H. pylori


title: DMBT1-/- mice non- infected_Sample 2

description: SAMPLE 79


title: DMBT1-/- mice H. pylori infected_Sample 3

description: SAMPLE 83


title: patient12

source_name: bicuspid aortic valve, patient12


title: DMBT1-/- mice H. pylori infected_Sample 1

description: SAMPLE 81


title: DMBT1-/- mice non- infected_Sample 1

description: SAMPLE 78


title: Dysplasia_sample12

description: SAMPLE 74

source_name: Dysplasia_Gastric tissue RNA

tag: ethnic group

value: Hispanic

tag: stages of gastritis

value: Dysplasia

value: Gastric tissue


title: Dysplasia_sample11

description: SAMPLE 73


title: Dysplasia_sample8

description: SAMPLE 70


title: Dysplasia_sample9

description: SAMPLE 71


title: SKN7_ChIP_Lower array

source_name: Candida albicans untagged strains, treated with 3 µg/mL of anhydrotetracycline for 2h in YPD medium at 30ºC

value: Immunoprecipitated DNA

source_name: Candida albicans strains expressing a 3xHA-tagged version of the SKN7 gene placed under the control of a tetracycline derivative-inducible promoter, treated with 3 µg/ml anhydrotetracycline for 2h in YPD medium at 30ºC.


title: Dysplasia_sample7

description: SAMPLE 69


title: SN4 occipital

source_name: Subject 4, occiput hair


title: Dysplasia_sample10

description: SAMPLE 72


title: Dysplasia_sample6

description: SAMPLE 68


title: WT mice  H. pylori infected_Sample 1

description: SAMPLE 77

source_name: WT mice  H. pylori infected

value: wild type


title: SN3 occipital

source_name: Subject 3, occiput hair


title: SN2 occipital

source_name: Subject 2, occiput hair


title: WT mice non-infected_Sample 2

description: SAMPLE 76

source_name: WT mice non-infected


title: SN1 occipital

source_name: Subject 1, occiput hair


title: SN6 vertex

source_name: Subject 6, vertex hair

value: vertex


title: WT mice non-infected_Sample 1

description: SAMPLE 75


title: Dysplasia_sample5

description: SAMPLE 67


title: Dysplasia_sample4

description: SAMPLE 66


title: Dysplasia_sample3

description: SAMPLE 65


title: Dysplasia_sample2

description: SAMPLE 64


title: SN5 vertex

source_name: Subject 5, vertex hair


title: SN2 vertex

source_name: Subject 2, vertex hair


title: SN3 vertex

source_name: Subject 3, vertex hair


title: B6 CTRL II vs. B6 RS II

first: Hans-Joachim

last: Mollenkopf

institute: Max-Planck-Institute for Infection Biology

description:
251486840612_S01_1_3
Untreated control vs. R-spondin treated.
2nd biological replicate.

hyb_protocol: Whole mouse genome 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR) using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

source_name: B6 CTRL II

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit (Agilent Technologies) according to the supplier's instructions.

growth_protocol: C56BL/6 mice (from Charles River) were maintained in autoclaved microisolator cages and provided with sterile drinking water and chow ad libitum.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method according to the manufacturer's protocol.

treatment_protocol: Antral epithelial glands were isolated after intravenous (i.v.) injection of recombinant R-Spondin 1 (100 µg/mouse) or PBS as control.

tag: strain/background

tag: cell type

value: antral epithelial cells

value: PBS control

source_name: B6 RS II

value: R-spondin


title: SN1 vertex

source_name: Subject 1, vertex hair


title: Dysplasia_sample1

description: SAMPLE 63


title: SN4 vertex

source_name: Subject 4, vertex hair


title: B6 RS II vs. B6 CTRL II

description:
251486840612_S01_1_4
R-spondin treated vs. untreated control.
2nd biological replicate.


title: B6 RS I vs. B6 CTRL I

description:
251486840612_S01_1_2
R-spondin treated vs. untreated control.
1st biological replicate.

source_name: B6 RS I

source_name: B6 CTRL I


title: SN5 frontal

source_name: Subject 5, frontal hair

value: frontal


title: B6 CTRL I vs. B6 RS I

description:
251486840612_S01_1_1
Untreated control vs. R-spondin treated.
1st biological replicate.


title: SN6 frontal

source_name: Subject 6, frontal hair


title: SN4 frontal

source_name: Subject 4, frontal hair


title: SN2 frontal

source_name: Subject 2, frontal hair


title: Intestinal Metaplasia_sample23

description: SAMPLE 60

source_name: IM_Gastric tissue RNA

value: Intestinal Metaplasia


title: Intestinal Metaplasia_sample24

description: SAMPLE 61


title: SN1 frontal

source_name: Subject 1, frontal hair


title: Intestinal Metaplasia_sample21

description: SAMPLE 58


title: Intestinal Metaplasia_sample25

description: SAMPLE 62


title: Intestinal Metaplasia_sample19

description: SAMPLE 56


title: Intestinal Metaplasia_sample20

description: SAMPLE 57


title: Intestinal Metaplasia_sample22

description: SAMPLE 59


title: Intestinal Metaplasia_sample17

description: SAMPLE 54


title: Intestinal Metaplasia_sample16

description: SAMPLE 53


title: Intestinal Metaplasia_sample15

description: SAMPLE 52


title: AN116_AMC

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

description:
Gene expression in amniotic membrane-derived mesenchymal stromal cells
116SC

hyb_protocol: Hybridization and washing steps were using Gene Expression Wash Pack (Agilent Technology) according to the manufacturer's instructions.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent C Scanner.

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software version 10.7.3.

source_name: Amniotic membrane, mesenchymal stromal cells (AN116Storoma) P1

label_protocol: RNA was labelled with Cy3 using Genomic DNA Enzymatic Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from cells using RNAeasy mini kit (Qiagen) according to the manufacturer's instructions.

value: Amniotic membrane

value: mesenchymal stromal cell

value: control


title: Intestinal Metaplasia_sample18

description: SAMPLE 55


title: SN3 frontal

source_name: Subject 3, frontal hair

value: Scalp hair

value: male

value: Androgenetic alopecia


title: AN117_AEC_IL10_48h

description:
Gene expression after 48hr in IL-10-stimulated amniotic membrane-derived epithelial cells
117EIL10

source_name: Amniotic membrane, epithelial cells (AN117EpCam(+)) P1

value: epithelial cell

value: IL-10 stimulated


title: AN117_AMC

description:
Gene expression in amniotic membrane-derived mesenchymal stromal cells
117SC

source_name: Amniotic membrane, mesenchymal stromal cells (AN117Storoma) P1


title: Control_2

city: Yoshida-gun

first: Yusei

last: Ohshima

state: Fukui

address: 23-3 Shimoaizuki, Matsuoka,

department: Pediatrics

institute: University of Fukui

description: Gene expression data from mouse skin

hyb_protocol: Labeled cDNA were hybridized for 16 h at 45℃ on GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Gene Chip were washed and strained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GCS3000-7G Scanner (Affymetrix).

data_processing: Data were analyzed with Affymetrix GCS3000 system. The data were visualized with Subio platform version 1.20 (Subio inc, Kagoshima, Japan).

source_name: Mouse skin

label_protocol: Labeled, Sense-strand cDNA were prepared from 200 ng of total RNA using a GeneChip 3'IVT plus regent kit (Affymetrix) according to the manufacture’s instruction

growth_protocol: The BALB/c mice were bred under standard pathogen-free conditions. All animal experiments were performed in accordance with institutional guidelines as approved by the Animal Care Review Board of the University of Fukui.

extract_protocol: Total RNA was isolated from skins using an RNeasy lipid tissue mini kit (Qiagen) according to the manufacture’s instruction.

treatment_protocol: Mice were epicutaneously sensitized by application of ovalbumin (OVA) and calcipotriol (MC903) to ear skin and then orally challenged with OVA. After the first challenge, the mice were treated with application of MC903 or ethanol (EtOH) and then orally challenged again.

value: BALB/c

tag: genotype

value: female

value: skin

tag: agent

value: ethanol (EtOH)


title: AN109_AMC_IL10_48h

description:
Gene expression after 48hr in IL-10-stimulated amniotic membrane-derived mesenchymal stromal cells
K41

source_name: Amniotic membrane, mesenchymal stromal cells (AN109Stroma P1PD5)


title: AN116_AEC_IL10_48h

description:
Gene expression after 48hr in IL-10-stimulated amniotic membrane-derived epithelial cells
116EIL10

source_name: Amniotic membrane, epithelial cells (AN116EpCam(+)) P1


title: AN117_AEC

description:
Gene expression in amniotic membrane-derived epithelial cells
117EC


title: MC903_1

description: Gene expression data from mouse skin

value: wild type

value: calcipotriol (MC903)


title: AN116_AEC

description:
Gene expression in amniotic membrane-derived epithelial cells
116EC


title: Y79 TFF1 Replicate 2

city: Essen

first: Maike

last: Busch

address: Hufelandstr. 55

institute: University Hospital Essen

hyb_protocol: Agilent protocol. 10 rpm (2x GE Hybridization Buffer), 65°C for 17h

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

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and LOWESS normalization. Control spots are removed, replicate oligos are averaged.

source_name: retinoblastoma cell line Y79 overexpressing TFF1

label_protocol: Labelling of total RNA was performed as described by the manufacturer (Agilent Technologies)

growth_protocol: Cells were cultivated as suspension cultures in Dulbecco’s modified Eagle’s medium with 15 % fetal calf serum , 100 U penicillin/ml and 100 μg streptomycin/ml , 4 mM L-glutamine, 50 μM β-mercaptoethanol and 10 μg insulin/ml at 37 °C, 10 % CO2 and 95 % humidity.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA II kit (Macherey and Nagel)

treatment_protocol: Y79 cells were infected with TFF1-coding lentiviral particles or control lentiviral particles in the presence of 10 µg/ml hexadimethrine bromide

tag: cell line

value: retinoblastoma cell line Y79

tag: genotype/variation

value: overexpressing TFF1

source_name: retinoblastoma cell line Y79


title: Y79 TFF1 Replicate 1


title: Control_1

description: Gene expression data from mouse skin

tag: strain

tag: tissue


title: MC903_2

description: Gene expression data from mouse skin


title: SCD_HbAA_5

city: Raipur

first: Ipsita

last: Das

state: Chhattisgarh

address: Jail Road

department: Biochemistry

country: India

institute: Pt. Jawaharlal Nehru memorial Medical College

description: Gene expression of healthy control subjects

hyb_protocol: Cy3 labeled cRNA was hybridized using Gene Expression Hybridization Kit (Agilent Technologies). The labeled cRNA samples (targets) were hybridized to the fixed probes on the Whole Human Genome (4×44K) Oligo Microarray kit (Human GE 4×44K V2 Microarray kit), using Agilent Hybridization chamber and backing slides. Microarray slides were incubated at 65°C for 17 hours in a hybridization oven. Microarray slides were washed using Gene Expression Wash Buffers 1 and 2, to discard partially hybridized and unhybridized samples. A surfactant Triton X-102(10%) was added to buffers 1 and 2 to remove background artifacts from microarray slide without affecting the stringency of wash buffers.

scan_protocol: The microarray slides were scanned using a DNA Microarray Scanner with Surescan High- Resolution Technology (Agilent Technologies) equipped with extended dynamic range (XDR) software.

data_processing: Feature Extraction Software (Version 9.5.3) was used for data extraction from raw microarray image files (.tif). It was followed by feature extraction using Feature Extraction Software (Version 9.5.3). Data visualization, pre-processing, analysis and mining were performed using GeneSpring GX (Silicon Genetics, Redwood City, CA). During normaliztion raw signals were thresholded to 1.0; normalization algorithm used was scale; percentile target was chosen as 75. Scaling was done median of percentile target of all samples. Median value was chosen as preprocessing baseline for all samples.

source_name: Peripheral venous blood

label_protocol: cDNA was synthesized from 600 ng of total RNA using Agilent one color RNA spike-In kit and Agilent  Quick Amp Kit, One-Color. cRNA synthesis and cyanine 3 (Cy3) labeling was done using the same. Labeled cRNA samples were subjected to purification using Qiagen RNeasy® Mini Kit (Qiagen). Purified labeled cRNA samples were quantified on NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1 and Agilent 2100 Bio-analyzer

extract_protocol: Total RNA was isolated from whole blood by using QIAamp® RNA Blood Mini Kit (Qiagen). The target of RNA isolation from the whole blood was leukocytes which include lymphocytes, monocytes and granulocytes. The RBCs were not targeted for the same as they do not contain nuclei, and RNA is not synthesized in them. Only the RNA species larger than 200 nucleotides were isolated and rest other small RNAs were discarded as they do not bind to the QIAamp spin column. RNA sample was quantified by electrophoresing in Agilent 2100 Bio-analyzer, version G2938C on Agilent RNA 6000 Nano Kit (Agilent Technologies). Only, the RNA samples having RIN values ≥7 were subjected to the next step of the experiment.

treatment_protocol: Peripheral venous  blood was collected from each subject through phlebotomy, in a falcon tube containing 0.05 mg of Ethylenediaminetetraacetic acid (EDTA), under aseptic conditions.

value: Whole blood

value: Female

tag: age

tag: state

value: healthy control


title: SCD_HbAA_4

value: Male


title: daidzein+PT

city: Tsukuba

first: Keishi

last: Kadooka

address: 3-3 Midorigahara

department: R&D center

institute: NH Foods Ltd.

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

source_name: 3T3-L1, daidzein + Pig testis extracts

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: cell differentiation status

value: adipocytes


title: AN116_AMC_IL10_48h

description:
Gene expression after 48hr in IL-10-stimulated amniotic membrane-derived mesenchymal stromal cells
116SIL10

value: Amniotic membrane

value: mesenchymal stromal cell

tag: treatment


title: SCD_HbAA_6

tag: gender


title: Intestinal Metaplasia_sample14

description: SAMPLE 51

value: Hispanic

value: Intestinal Metaplasia

value: Gastric tissue


title: Intestinal Metaplasia_sample13

description: SAMPLE 50


title: Intestinal Metaplasia_sample12

description: SAMPLE 49


title: Intestinal Metaplasia_sample11

description: SAMPLE 48


title: Intestinal Metaplasia_sample9

description: SAMPLE 46


title: AN105_AEC_IL10_48h

description:
Gene expression after 48hr in IL-10-stimulated amniotic membrane-derived epithelial cells
K20

source_name: Amniotic membrane, epithelial cells (AN105EpCam(+)) P1

value: epithelial cell

value: IL-10 stimulated


title: AN109_AMC

description:
Gene expression in amniotic membrane-derived mesenchymal stromal cells
K40

value: control


title: Intestinal Metaplasia_sample8

description: SAMPLE 45


title: SCD_HbAA_2


title: Ad-MSC_IL-10_48h

description:
Gene expression after 48hr in IL-10-stimulated adipose tissue-derived MSCs
K4

source_name: Adipocyte, mesenchymal stem cells

value: Adipocyte

value: mesenchymal stem cell


title: Intestinal Metaplasia_sample10

description: SAMPLE 47


title: BM-MSC_IL-10_48h

description:
Gene expression after 48hr in IL-10-stimulated bone marrow-derived MSCs
K2

source_name: Bone marrow, mesenchymal stem cells (OF3853)

value: Bone marrow


title: daidzein

source_name: 3T3-L1, daidzein


title: MADM_P150-rep2

city: Nagoya

first: Keisuke

last: Katsushima

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

department: Department of Epigenomics

institute: Nagoya City University Graduate School of Medical Sciences

description: Gene expression in glioma

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8×60K array slides (G4858A, Agilent Technologies) at 65 °C with rotation at 10 rpm for 17 hours in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

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

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

source_name: glioma,　P150, replicate 2

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

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

value: brain tumor

tag: diagnosis

value: glioma

value: post-natal day 150


title: PT

source_name: 3T3-L1, Pig testis extracts


title: SCD_HbAA_1

value: Whole blood

value: Female

value: healthy control


title: Normal Brain_rep2

description: Gene expression in normal brain

source_name: Normal Brain, P150, replicate 2

value: brain

value: normal


title: SCD_HbAA_3


title: Ad-MSC

description:
Gene expression in adipose tissue-derived MSCs
K3


title: SCD_HbSS_SS_7

description: Gene expression of patients in steady state

value: steady


title: AN105_AEC

description:
Gene expression in amniotic membrane-derived epithelial cells
K19

value: Amniotic membrane


title: MADM_P150-rep3

description: Gene expression in glioma

source_name: glioma,　P150, replicate 3


title: PBS

source_name: 3T3-L1, control

value: adipocytes


title: Intestinal Metaplasia_sample5

description: SAMPLE 42

source_name: IM_Gastric tissue RNA

value: Hispanic

value: Intestinal Metaplasia

value: Gastric tissue


title: Normal Brain_rep1

description: Gene expression in normal brain

source_name: Normal Brain, P150, replicate 1


title: SCD_HbSS_SS_6


title: SCD_HbSS_SS_5


title: Intestinal Metaplasia_sample7

description: SAMPLE 44


title: Intestinal Metaplasia_sample6

description: SAMPLE 43


title: MADM_P150-rep1

description: Gene expression in glioma

source_name: glioma,　P150, replicate 1


title: Intestinal Metaplasia_sample4

description: SAMPLE 41


title: Intestinal Metaplasia_sample3

description: SAMPLE 40


title: hippocampal neural stem cells_6hr_2.4%sevoflurane_rep1

city: Fuzhou

first: Guo-lin

last: Lu

state: Fujian

address: No18 Daoshan Road Gulou District

institute: maternity and children Hospital of Fujian Province

description: Gene expression after 6hr in 2.4% sevoflurane-exposed hippocampal neural stem cells

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.  50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: hippocampal neural stem cells,6hr,2.4%sevoflurane,replicate1

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the whole length of the transcripts without 3′ bias using a random priming process(Arraystar Flash RNA Labeling Kit,Arraystar).The labeled cRNAs were purified using RNeasy Mini Kit(Qiagen).The concentration and specific viability of the labeled cRNAs(pmol Cy3/μg cRNA) were detected by NanoDrop ND-1000.

growth_protocol: Neural stem cells were harvested from hippocampus of postnatal 3 days Sprague-Dawley rats.Cells were cultured in serum-free and bFGF media and put in incubator with 5 % CO2 at 37 ℃ .Cell cutrue was performed on the third passage.

extract_protocol: Total RNA in rat hippocampal neural stem cells was extracted with Trizol reagent(Invitrogen,USA) on the basis of  the manufacture′s protocol.RNAs quatity and quality were accessed by NanoDrop ND-100.RNA integrity was measured by standard denaturing agarose gel electrophoresis.

treatment_protocol: When neural stem cells were in state of log phase growth,cells were exposed to 2.4% sevoflurane or 0% sevoflurane for 6 hr,and then returned to a normal incubator  with 5 % CO2 for 24 h.

value: hippocampus

value: neural stem cells

value: postnatal 3d

value: Sprague-Dawley


title: Intestinal Metaplasia_sample2

description: SAMPLE 39


title: BM-MSC

description:
Gene expression in bone marrow-derived MSCs
K1

value: Bone marrow

value: mesenchymal stem cell

value: control


title: Intestinal Metaplasia_sample1

description: SAMPLE 38


title: hippocampal neural stem cells_6hr_0%sevoflurane_rep1

description: Gene expression after 6hr in 0% sevoflurane-exposed hippocampal neural stem cells

source_name: hippocampal neural stem cells,6hr,0%sevoflurane,replicate1


title: SCD_HbSS_SS_2

value: Whole blood

value: Male


title: SCD_HbSS_SS_4


title: SCD_HbSS_SS_3


title: Multi-Focal Atrophic Gastritis_sample37

description: SAMPLE 37

source_name: MAG_Gastric tissue RNA

value: Multi-Focal Atrophic Gastritis


title: Med1cKO

city: San Francisco

first: Yuko

last: Oda

state: CA

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

description: Illumina standard label

hyb_protocol: Standard Illumina hybridization protocol done by UCLA neuroscience genomics core

scan_protocol: Standard Illumina hybridication protocol done by UCLA neuroscience genomics core

data_processing: data were normalized by using quantile method in Genome studio V2011.1

source_name: FACS sorted keratinocytes from skin

label_protocol: Standard Illumina hybridization protocol cDNA labeled by Biotin and detected by Cy3-streptoavidin

growth_protocol: Coactivator MED1 is removed from keratin 14 (K14) expressing keratinocytes by using Crelox stragety

extract_protocol: Total RNA was isolated from whole skin by using combination of RNAzol and RNAeasy RNA purification kit (Qiagen)

treatment_protocol: Whole skin was exised from back skin and RNA was extracted from each mouse

value: MED1 fl/fl Cre

value: a6+CD34- population


title: Multi-Focal Atrophic Gastritis_sample36

description: SAMPLE 36


title: SCD_HbSS_CS_6

description: Gene expression of patients in crisis state

source_name: Peripheral venous blood

value: crisis


title: CON

description: Illumina standard label

value: MED1 fl/fl C57BL6


title: Multi-Focal Atrophic Gastritis_sample35

description: SAMPLE 35

value: Hispanic


title: SCD_HbSS_CS_7


title: SCD_HbSS_SS_1

value: steady


title: AN117_AMC_IL10_48h

description:
Gene expression after 48hr in IL-10-stimulated amniotic membrane-derived mesenchymal stromal cells
117SIL10

source_name: Amniotic membrane, mesenchymal stromal cells (AN117Storoma) P1

value: Amniotic membrane

value: mesenchymal stromal cell

value: IL-10 stimulated


title: Multi-Focal Atrophic Gastritis_sample34

description: SAMPLE 34

value: Gastric tissue


title: SCD_HbSS_CS_5


title: SCD_HbSS_CS_4

value: Female


title: Multi-Focal Atrophic Gastritis_sample33

description: SAMPLE 33


title: Multi-Focal Atrophic Gastritis_sample32

description: SAMPLE 32


title: SCD_HbSS_CS_3


title: SCD_HbSS_CS_1


title: SCD_HbSS_CS_2


title: Multi-Focal Atrophic Gastritis_sample31

description: SAMPLE 31


title: Multi-Focal Atrophic Gastritis_sample30

description: SAMPLE 30


title: Multi-Focal Atrophic Gastritis_sample29

description: SAMPLE 29


title: SAMPLE 95 CD326+ uterus epithelial cell

city: HangZhou

first: Bingbing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medcine

institute: Zhejiang University

description: single cell

data_processing:
raw data was collected from the Fluidigm Real-Time PCR Analysis software
single cell data could be furthor analized in R software with the Package SINGuLAR™ 3.0

label: Eva Green

source_name: uterus

label_protocol: QPCR was performed on the 96.96 IFC using the pre-amplified product on the Fluidigm Biomark platform according to the manufacture's instructions

extract_protocol: single cells were lysed and preamplified with the kit (CellsDirect™ One-Step qRT-PCR Kit, Thermo, 11753100)

treatment_protocol: Post-natal day7 mice uterus were digested into single cell syspension by type I collagenase, then cells were labeled with anti-CD326 antibody, and sorted the CD326+ single cell into each well of 96-well plate

value: CD326+ cells sorted by FACS


title: SAMPLE 91 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 92 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 94 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 93 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample28

description: SAMPLE 28


title: SAMPLE 96 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 90 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 89 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample27

description: SAMPLE 27


title: Multi-Focal Atrophic Gastritis_sample26

description: SAMPLE 26


title: SAMPLE 88 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 87 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Case-S14

city: Parkville

first: Andrew

middle: David

last: Fox

state: VIC

address: 30 Royal Parade

department: MS Division

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

description: Bisulphite converted genomic DNA

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

scan_protocol: Illumina iScan standard protocol

data_processing: Standard background and Illumina preprocessing (R 'minfi' package), followed by SWAN normalization, then convertion to beta values (proportion methylated 0.001-0.999).

label: Cy5 and Cy3

source_name: Case-WholeBlood

label_protocol: Standard Illumina Protocol

extract_protocol: QIAamp DNA Micro kit (QIAGEN) according to standard instructions

tag: sentrix id

tag: sentrix row & column

value: WholeBlood

tag: disease state

value: Case

tag: person id


title: WholeBlood-Case-S12

description: Bisulphite converted genomic DNA

tag: cell type


title: WholeBlood-Case-S13

description: Bisulphite converted genomic DNA


title: Multi-Focal Atrophic Gastritis_sample25

description: SAMPLE 25

tag: ethnic group

tag: stages of gastritis


title: SAMPLE 86 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample24

description: SAMPLE 24


title: Multi-Focal Atrophic Gastritis_sample23

description: SAMPLE 23


title: Multi-Focal Atrophic Gastritis_sample22

description: SAMPLE 22


title: WholeBlood-Case-S10

description: Bisulphite converted genomic DNA


title: SAMPLE 84 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Case-S9

description: Bisulphite converted genomic DNA


title: Multi-Focal Atrophic Gastritis_sample21

description: SAMPLE 21


title: SAMPLE 83 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Case-S11

description: Bisulphite converted genomic DNA


title: WholeBlood-Control-L12

description: Bisulphite converted genomic DNA

source_name: Control-WholeBlood

value: Control


title: Multi-Focal Atrophic Gastritis_sample20

description: SAMPLE 20


title: Multi-Focal Atrophic Gastritis_sample19

description: SAMPLE 19


title: SAMPLE 85 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Control-L14

description: Bisulphite converted genomic DNA


title: SAMPLE 82 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 80 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 79 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample17

description: SAMPLE 17


title: WholeBlood-Control-L13

description: Bisulphite converted genomic DNA


title: WholeBlood-Control-L10

description: Bisulphite converted genomic DNA


title: WholeBlood-Control-L11

description: Bisulphite converted genomic DNA


title: WholeBlood-Control-L9

description: Bisulphite converted genomic DNA


title: Multi-Focal Atrophic Gastritis_sample18

description: SAMPLE 18


title: SAMPLE 78 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Case-S8

description: Bisulphite converted genomic DNA


title: Multi-Focal Atrophic Gastritis_sample15

description: SAMPLE 15


title: SAMPLE 77 CD326+ uterus epithelial cell

description: single cell


title: NKcell-Control-L8

description: Bisulphite converted genomic DNA

source_name: Control-NKcell

value: NKcell


title: CD8T-Control-L8

description: Bisulphite converted genomic DNA


title: WholeBlood-Control-L8

description: Bisulphite converted genomic DNA


title: Monocyte-Control-L8

description: Bisulphite converted genomic DNA

source_name: Control-Monocyte

value: Monocyte


title: SAMPLE 76 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample16

description: SAMPLE 16

value: Multi-Focal Atrophic Gastritis


title: Multi-Focal Atrophic Gastritis_sample14

description: SAMPLE 14


title: Multi-Focal Atrophic Gastritis_sample13

description: SAMPLE 13


title: Multi-Focal Atrophic Gastritis_sample11

description: SAMPLE 11


title: SAMPLE 74 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 73 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 75 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample10

description: SAMPLE 10


title: WBC-Control-L8

description: Bisulphite converted genomic DNA

source_name: Control-WBC

value: WBC


title: CD4T-Control-L8

description: Bisulphite converted genomic DNA


title: WBC-Control-L7

description: Bisulphite converted genomic DNA


title: SAMPLE 72 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample9

description: SAMPLE 9


title: SAMPLE 71 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 81 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample8

description: SAMPLE 8


title: SAMPLE 70 CD326+ uterus epithelial cell

description: single cell


title: Monocyte-Control-L7

description: Bisulphite converted genomic DNA


title: Multi-Focal Atrophic Gastritis_sample7

description: SAMPLE 7


title: SAMPLE 69 CD326+ uterus epithelial cell

description: single cell


title: Neutrophil-Control-L8

description: Bisulphite converted genomic DNA

source_name: Control-Neutrophil

value: Neutrophil


title: SAMPLE 67 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample6

description: SAMPLE 6


title: SAMPLE 68 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample3

description: SAMPLE 3


title: NKcell-Control-L7

description: Bisulphite converted genomic DNA


title: CD19B-Control-L7

description: Bisulphite converted genomic DNA


title: Multi-Focal Atrophic Gastritis_sample5

description: SAMPLE 5


title: Multi-Focal Atrophic Gastritis_sample2

description: SAMPLE 2


title: SAMPLE 65 CD326+ uterus epithelial cell

description: single cell


title: Multi-Focal Atrophic Gastritis_sample4

description: SAMPLE 4


title: SAMPLE 64 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Case-S6

description: Bisulphite converted genomic DNA


title: CD8T-Control-L7

description: Bisulphite converted genomic DNA


title: Multi-Focal Atrophic Gastritis_sample12

description: SAMPLE 12


title: WBC-Control-L6

description: Bisulphite converted genomic DNA


title: Multi-Focal Atrophic Gastritis_sample1

description: SAMPLE 1


title: SAMPLE 63 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Control-L6

description: Bisulphite converted genomic DNA


title: CD19B-Control-L6

description: Bisulphite converted genomic DNA


title: Neutrophil-Control-L7

description: Bisulphite converted genomic DNA


title: SAMPLE 62 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Case-S7

description: Bisulphite converted genomic DNA


title: Monocyte-Control-L6

description: Bisulphite converted genomic DNA


title: SAMPLE 59 CD326+ uterus epithelial cell

description: single cell


title: CD4T-Control-L7

description: Bisulphite converted genomic DNA


title: CD8T-Control-L6

description: Bisulphite converted genomic DNA


title: CD19B-Control-L8

description: Bisulphite converted genomic DNA


title: SAMPLE 58 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 66 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 57 CD326+ uterus epithelial cell

description: single cell


title: Neutrophil-Control-L6

description: Bisulphite converted genomic DNA


title: NKcell-Control-L6

description: Bisulphite converted genomic DNA


title: SAMPLE 56 CD326+ uterus epithelial cell

description: single cell


title: CD4T-Control-L6

description: Bisulphite converted genomic DNA


title: dmso ko 1

city: Gothenburg

first: Roberta

last: Kiffin

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

country: Sweden

institute: University of Gothenburg

description: DMSO-treated NOX2-/- PLB-985 sample 1

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data was analyzed using the R software package limma.

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

growth_protocol: Cells were maintained Iscoves’ Modified Dulbecco's Medium supplemented with 10% fetal calf serum, 2mM L-glutamine, 100U/ml penicillin and 100 μg/ml streptomycin at 37°C in 5% CO2

extract_protocol: RNA was extracted using the Qiagen Rneasy Mini kit according to the manufacturer's protocol.

treatment_protocol: Cells were treated with 100 μ Mhistamine dihydrochloride or 0.5% dimethylsulfoxide (DMSO) for two days.

tag: disease

value: Acute myeloid leukemia


title: WholeBlood-Control-L5

description: Bisulphite converted genomic DNA


title: his ko 3

description: HDC-treated NOX2-/- PLB-985 sample 3


title: dmso ko 4

description: DMSO-treated NOX2-/- PLB-985 sample 4


title: dmso ko 2

description: DMSO-treated NOX2-/- PLB-985 sample 2


title: dmso ko 3

description: DMSO-treated NOX2-/- PLB-985 sample 3


title: his ko 2

description: HDC-treated NOX2-/- PLB-985 sample 2


title: his ko 1

description: HDC-treated NOX2-/- PLB-985 sample 1


title: SAMPLE 55 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 54 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 60 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 61 CD326+ uterus epithelial cell

description: single cell


title: Monocyte-Control-L5

description: Bisulphite converted genomic DNA


title: SAMPLE 53 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 52 CD326+ uterus epithelial cell

description: single cell


title: CD19B-Control-L5

description: Bisulphite converted genomic DNA


title: WholeBlood-Control-L7

description: Bisulphite converted genomic DNA


title: WBC-Control-L5

description: Bisulphite converted genomic DNA


title: ctrl ko 1

description: control NOX2-/- PLB-985 sample 1


title: SAMPLE 51 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 50 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 49 CD326+ uterus epithelial cell

description: single cell


title: ctrl ko 2

description: control NOX2-/- PLB-985 sample 2


title: ctrl ko 3

description: control NOX2-/- PLB-985 sample 3


title: dmso wt 4

description: DMSO-treated WT PLB-985 sample 4

source_name: WT PLB-985


title: ctrl ko 4

description: control NOX2-/- PLB-985 sample 4


title: dmso wt 3

description: DMSO-treated WT PLB-985 sample 3


title: dmso wt 2

description: DMSO-treated WT PLB-985 sample 2


title: NKcell-Control-L5

description: Bisulphite converted genomic DNA


title: SAMPLE 48 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 47 CD326+ uterus epithelial cell

description: single cell


title: CD8T-Control-L5

description: Bisulphite converted genomic DNA


title: Neutrophil-Control-L5

description: Bisulphite converted genomic DNA


title: CD4T-Control-L5

description: Bisulphite converted genomic DNA


title: SAMPLE 46 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 45 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 44 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 43 CD326+ uterus epithelial cell

description: single cell


title: dmso wt 1

description: DMSO-treated WT PLB-985 sample 1


title: his wt 4

description: HDC-treated WT PLB-985 sample 4


title: his wt 2

description: HDC-treated WT PLB-985 sample 2


title: SAMPLE 42 CD326+ uterus epithelial cell

description: single cell


title: his wt 3

description: HDC-treated WT PLB-985 sample 3


title: WholeBlood-Control-L4

description: Bisulphite converted genomic DNA


title: SAMPLE 41 CD326+ uterus epithelial cell

description: single cell


title: his wt 1

description: HDC-treated WT PLB-985 sample 1


title: WholeBlood-Case-S4

description: Bisulphite converted genomic DNA


title: WBC-Control-L4

description: Bisulphite converted genomic DNA


title: NKcell-Control-L4

description: Bisulphite converted genomic DNA


title: ctrl wt 3

description: control WT PLB-985 sample 3


title: CD19B-Control-L4

description: Bisulphite converted genomic DNA


title: SAMPLE 39 CD326+ uterus epithelial cell

description: single cell


title: CD4T-Control-L4

description: Bisulphite converted genomic DNA


title: SAMPLE 40 CD326+ uterus epithelial cell

description: single cell


title: Monocyte-Control-L4

description: Bisulphite converted genomic DNA


title: SAMPLE 38 CD326+ uterus epithelial cell

description: single cell


title: ctrl wt 4

description: control WT PLB-985 sample 4


title: Neutrophil-Control-L4

description: Bisulphite converted genomic DNA


title: ctrl wt 1

description: control WT PLB-985 sample 1


title: SAMPLE 37 CD326+ uterus epithelial cell

description: single cell


title: CD8T-Control-L4

description: Bisulphite converted genomic DNA


title: WholeBlood-Control-L3

description: Bisulphite converted genomic DNA


title: SAMPLE 36 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 35 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 33 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 34 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 32 CD326+ uterus epithelial cell

description: single cell


title: WholeBlood-Case-S3

description: Bisulphite converted genomic DNA


title: NKcell-Control-L3

description: Bisulphite converted genomic DNA


title: WBC-Control-L3

description: Bisulphite converted genomic DNA


title: SAMPLE 31 CD326+ uterus epithelial cell

description: single cell


title: ctrl wt 2

description: control WT PLB-985 sample 2


title: CD19B-Control-L3

description: Bisulphite converted genomic DNA


title: SAMPLE 28 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 30 CD326+ uterus epithelial cell

description: single cell


title: CD8T-Control-L3

description: Bisulphite converted genomic DNA


title: SAMPLE 27 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 26 CD326+ uterus epithelial cell

description: single cell


title: SAMPLE 25 CD326+ uterus epithelial cell

description: single cell