title: Primary Ewing sarcoma 4 WCE

type: SRA

city: Charlestown

first: Martin

last: Aryee

address: 149 13th Street

department: Pathology

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
ChIP DNA and input controls were sequenced with the Hi-Seq Illumina Genome Analyzer.
ChIP-seq reads were aligned to the reference genome (hg19) using BWA or MAQ (http://maq.sourceforge.net/). Reads arising from plasmid DNA contamination were filtered for two libraries (SKNMC shFLI148.FLI1 and shFLI196.FLI1).
We extended aligned reads to 200 bp to approximate fragment sizes and derived 25-bp resolution density maps by counting the number of fragments overlapping each position with IGVtools. All density maps were normalized to 10M reads.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated in 25-bp step based on UCSC definition and converted into bigWig files using UCSC utilities.

source_name: primary Ewing sarcoma 4

growth_protocol: A673 and SKMNC Ewing sarcoma cell lines were grown in RPMI 1640 containing 10% FCS at 37°C with 5% CO2. Cells were maintained at a density between 5 x 10^5 cells/ml and 2 x 10^6 cells/ml and split every 3 – 4 days. Primary pediatric mesenchymal stem cells were cultured in IMDM containing 10% FCS and 10ng/ml PDGF-BB (Peprotec).

extract_protocol:
Chromatin from formaldehyde-fixed cells (3-10 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with the Mini-Elute PCR purification kit (Qiagen) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

treatment_protocol: shRNAs from the RNAi Consortium were used for knockdown (pLKO.1 backbone): FLI1 (TRCN0000005322), GFP (GCAAGCTGACCCTGAAGTTCAT). EWS-FLI1 was expressed using a lentiviral vector (pLIV). Lentiviruses were produced using standard protocols. Briefly, lentiviral shRNA or expression plasmids were co-transfected with GAG/POL and VSV plasmids into 293T packaging cells using FugeneHD (Roche) to produce the virus. Viral supernatant was collected 72 hours after transfection and concentrated by ultracentrifugation.

value: Ewing sarcoma

tag: chip antibody

value: WCE


title: Primary Ewing sarcoma 3 WCE

status: Public on Oct 30 2014

state: MA

country: USA

molecule: genomic DNA

organism: Homo sapiens

source_name: primary Ewing sarcoma 3

tag: cell type


title: Primary Ewing sarcoma 2 WCE

source_name: primary Ewing sarcoma 2


title: H3K27me3 in primary Ewing sarcoma 4

value: H3K27me3 (Millipore, 07-449)


title: larynx-tumor-FX11T

type: RNA

city: Beijing

first: Jugao

last: Fang

address: No. 1 Dongjiao Min Xiang, Dongcheng District

country: China

institute: Capital University of Medical Sciences attaches to Beijing Tongr

description: primary laryngeal squamous cell carcinoma

hyb_protocol: Following fragmentation, 21.5 μLof Biotin-labeled sample were hybridized for 16 hr at 48℃ on miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: Affymetrix GeneChip Command Console software (version4.0, Affymetrix) was used to analyze array images to get raw data and then offered RMA normalization. Next, Genespring software (version 12.5; Agilent Technologies) was used to proceed the following data analysis.

label: biotin

molecule: total RNA

source_name: larynx, cancer, T4N3M0

label_protocol: Biotinylated cRNA were prepared using FlashTag Biotin HSR RNA Labeling Kit.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions of mirVanaTM RNA Isolation Kit.

tag: gender

value: male

tag: tissue type

value: laryngeal cancer

tag: age

value: 55 year-old


title: H3K27me3 in primary Ewing sarcoma 2


title: H3K27me3 in primary Ewing sarcoma 1

source_name: primary Ewing sarcoma 1


title: larynx-tumor-FX3T

source_name: larynx, cancer, T2N0M0

value: 53 year-old


title: larynx-tumor-HN3T

source_name: larynx, cancer, T4N0M0

value: 56 year-old


title: H3K4me3 in primary Ewing sarcoma 2

value: H3K4me3 (Millipore, 07-473)


title: H3K4me3 in primary Ewing sarcoma 3


title: larynx-normal tissues-FX21Z

description: corresponding adjacent non-neoplastic tissues of sample FX21T

source_name: larynx,  corresponding adjacent non-neoplastic tissues

value: laryngeal normal tissues

value: 71 year-old


title: larynx-normal tissues-HN3DZ

description: corresponding adjacent non-neoplastic tissues of sample HN3DT

value: 74 year-old


title: larynx-tumor-HN3DT

source_name: larynx, cancer, T3N0M0


title: larynx-tumor-FX21T

source_name: larynx, cancer, T4N2aM0


title: H3K4me1 in primary Ewing sarcoma 3

value: H3K4me1 (Abcam, ab8895)


title: larynx-normal tissues-HN3Z

description: corresponding adjacent non-neoplastic tissues of sample HN3T


title: mc2155+pMind  vs mc2155+pMind+6189 replicate 3

status: Public on Oct 31 2014

city: Dunedin

first: Htin Lin

last: Aung

state: Otago

address: 720 Cumberland Street

department: Microbiology and Immunology

country: New Zealand

institute: University of Otago

description: Biological replicate 3 of 4.

hyb_protocol: Hybrization performed according to SOP M008 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

scan_protocol: Scanned Genepix 4000A scanner .  Images were quantified using Spotfinder (TIGR).

data_processing: Total normalization and LOWESS normalization with MIDAS software (TIGR). Raw data file: IA corresponds to Cy3 and IB corresponds to Cy5.

organism: Mycolicibacterium smegmatis

source_name: Batch culture HdB 10 mM glycerol

label_protocol: 10 µg of total RNA were reverse transcribed and labelled in a two step protocol according to SOP M007 from TIGR (Hegde, P., Qi, R., Abernathy, K. & other authors (2000). A concise guide to cDNA microarray analysis. BioTechniques 29, 548-550, 552-544, 556 passim.)

growth_protocol: strains were grown in 400 ml of Hartmans de Bont (HdB) minimal medium supplemented with 10 mM glycerol in 2 l flasks at 37°C with agitation (200 rpm). Wild-type and Dcrp1 strains were grown to an optical density (600nm) of 0.4. Cells were then harvestedfor RNA extraction. For overexpression, strains were grown in 400 ml of Hartmans de Bont (HdB) minimal medium supplemented with 10 mM glycerol and hygromycin B (50 μg/ml) in 2 l flasks at 37°C with agitation (200 rpm). Strains HLA102(pMind+Crp2) and wild-type strain (pMind) were grown to an optical density (600nm) of ~0.3. Protein expression was then induced with tetracycline (20 ng/ml). Cells were then harvested after 3 h post-induction for RNA extraction.

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

tag: genotype/variation

value: wild-type + pMind

value: wild-type + pMind +6189


title: H3K4me1 in primary Ewing sarcoma 2


title: H3K4me3 in primary Ewing sarcoma 1


title: H3K27ac in primary Ewing sarcoma 4

value: H3K27ac (Abcam, ab4729)


title: H3K27ac in primary Ewing sarcoma 3


title: H3K27ac in primary Ewing sarcoma 2


title: WDR5 ChIP-seq in MSC with EWSFLI1

source_name: MSC expressing EWSFL1

value: Mesenchymal stem cells

tag: treatment

value: WDR5 (Bethyl, A302-429A)


title: WDR5 ChIP-seq in MSC with empty vector

source_name: MSC with empty vector

value: empty vector


title: Metaplastic Carcinoma META32

type: genomic

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: Metaplastic Carcinoma META32

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Raw data were analyzed using the CRMAv2 algorithm in the aroma.affymetrix package.

label: Biotin

source_name: Metaplastic Carcinoma META32

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted using the Qiagen DNA Blood and Tissue kit

tag: phenotype

value: triple-negative

tag: diagnosis

value: Carcinoma with heterologous elements


title: H3K4me1 ChIP-seq in MSC with empty vector


title: H3K27ac ChIP-seq in MSC with empty vector


title: larynx-normal tissues-FX11Z

description: corresponding adjacent non-neoplastic tissues of sample FX11T

value: male


title: H3K4me1 ChIP-seq in MSC

source_name: MSC


title: H3K27ac ChIP-seq in MSC


title: H3K4me1 ChIP-seq in MSC with EWSFLI1


title: Metaplastic Carcinoma META33

description: Metaplastic Carcinoma META33

source_name: Metaplastic Carcinoma META33


title: H3K27ac ChIP-seq in MSC with EWSFLI1


title: larynx-normal tissues-FX3Z

description: corresponding adjacent non-neoplastic tissues of sample FX3T


title: Metaplastic Carcinoma META30

description: Metaplastic Carcinoma META30

source_name: Metaplastic Carcinoma META30

value: Carcinoma with heterologous elements - Matrix producing


title: H3K4me1 in primary Ewing sarcoma 1

value: Ewing sarcoma


title: Healthy subject [303]

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

institute: University of Bari

description: Genomic DNA extracted from whole blood was genotyped using HumanCytoSNP-12 BeadChips (Illumina).

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a HiScanSQ Reader (Illumina).

data_processing: GenomeStudio V2011.1

label: C-Bio and A-DNP

source_name: whole blood

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix  and primer/neutralization mix. After incubation the amplified DNA was fragmented with fragmentation mix, precipitated with isopropanol and precipitation mix and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was purified from peripheral blood samples by Qiagen Qiamp DNA Blood Midi kit

tag: group

value: Healthy subject

tag: family number


title: Healthy subject [420]


title: Healthy subject [418]


title: Healthy subject [251]


title: Healthy subject [247]


title: Healthy subject [449]


title: Healthy subject [244]


title: IgAN patient [246]

value: IgAN patient


title: IgAN patient [250]


title: IgAN patient [253]


title: Healthy subject [211]


title: Healthy subject [301]


title: Healthy subject [205]


title: Healthy subject [241]


title: Healthy subject [249]


title: Healthy subject [209]


title: Healthy subject [447]


title: Healthy subject [201]


title: Healthy subject [215]


title: Healthy subject [207]


title: Healthy subject [197]


title: Healthy subject [202]


title: Healthy subject [242]


title: IgAN patient [450]


title: Healthy subject [198]


title: Healthy subject [254]


title: Healthy subject [306]


title: Healthy subject [203]


title: Healthy subject [191]


title: Healthy subject [245]


title: Zebrafish embryos, Cre-activated NHA9 vs. unactivated lGl, replicate 1 of 2.

city: Moncton

first: Daniel

last: Leger

state: New Brunswick

address: 35 Providence Street

department: IARC

country: Canada

institute: Atlantic Cancer Research Institute

description:
Biological replicate 1 of 2.
NHA9a_IGIa

hyb_protocol: Equal amounts of labeled cDNA hybridized to Agilent 43,803 oligos as stated in Methods. Triplicate dye-swap experiments performed to minimize labeling inefficiencies and/or dye variation.

scan_protocol: Scanned at 5 um resolution using a GenePix 4200AL scanner.

data_processing:
SpotReader software (v 1.3.0.3) was used for feature extraction. Acuity 4 was used for LOWESS normalization and data analysis.
The data presented was filtered, essentially at the gridding process in SpotReader where malformed and low intensity spots are flagged. The criteria for spot intensity is that both channels must have at least 5x signal to background ratio (Other than that, there are no specific criteria). We visually inspect the spots and make a judgement call on each one. Only good spots are then imported into Acuity 4 for normalization and analysis, hence the reduced list of genes (20,406 data rows).
Normalized log2 ratio (Cy5/Cy3) representing the two conditions. Transcripts with expression changes ≥2-fold were considered significant.

organism: Danio rerio

source_name: NHA9 embryos

label_protocol: RNA samples were reverse-transcribed using SuperScript Plus Direct cDNA Labeling System (Invitrogen; Carlsbad, CA, USA). cDNA labeled either with Alexa Fluor® 555 (orange fluorescent dye, false-coloured green for analysis) or Alexa Fluor® 647 (far-red fluorescent dye) (Invitrogen). Any samples with low concentrations of RNA were subjected to whole genome amplification (WGA) using Amino Allyl MessageAmp II aRNA Amplification Kit (AB/Ambion).

growth_protocol: Zebrafish were maintained, bred, and developmentally staged according to Westerfield. Dalhousie University Animal Care Committee approved use of zebrafish (protocol no. 13-129). Generation of transgenic fish described in Forrester et al, Br J Haematol, 2011, 155:167-81.

extract_protocol: RNA was extracted using Trizol + RNeasy Mini Kit (QIAGEN) using manufacturer's instructions. Two samples of RNA were extracted for each experimental condition.

treatment_protocol: NUP98-HOXA9 (NHA9) expression is achieved by outcross of Tg(spi1::lox-eGFP-lox::NHA9) zebrafish line to Tg(heat shock protein 70[hsp70]::Cre) zebrafish line, followed by incubation of embryos at 37°C for one hour (‘heat-shock’). These embryos are referred to as 'Cre-activated' and labeled 'NHA9', to signify molecular recombination and removal of the lox-eGFP-lox (lGl) inducible cassette, thus permitting expression of the NHA9 oncogene. For the control condition, the Tg(spi1::lox-eGFP-lox::NHA9) zebrafish line was outcrossed to wildtype (AB) zebrafish line, and these embryos were also heat-shocked. These control embryos are referred to as 'unactivated' and labeled 'lGl' to signify that the inducible cassette remains intact, thus preventing expression of the NHA9 oncogene. Embryos were kept at 28°C until fixation. To assess the impact of NHA9 on global gene expression, embryos were heat-shocked at 24 hours post-fertilization (hpf) and RNA was extracted at 28 hpf.

value: 'Cre-activated' Tg(spi1::NHA9)

tag: developmental stage

value: 28 hours post fertilization

tag: heat-shock

value: 4 hours post heat-shock

source_name: lGl embryos


title: Zebrafish embryos, Cre-activated NHA9 vs. unactivated lGl, replicate 2 of 2.

description:
Biological replicate 2 of 2.
NHA9b_IGIb


title: Zebrafish embryos, unactivated lGl vs. Cre-activated NHA9, replicate 1 of 2, dye swap.

description:
Biological replicate 1 of 2, dye swap.
IGIa_NHA9a


title: Healthy subject [188]


title: Healthy subject [187]


title: Healthy subject [189]


title: Zebrafish embryos, unactivated lGl vs. Cre-activated NHA9, replicate 2 of 2, dye swap.

description:
Biological replicate 2 of 2, dye swap.
IGIb_NHA9b


title: Healthy subject [185]


title: IgAN patient [156]


title: Healthy subject [2432]


title: IgAN patient [22]


title: IgAN patient [2520]


title: IgAN patient [2541]


title: IgAN patient [2535]


title: Healthy subject [2400]


title: Healthy subject [2399]


title: Healthy subject [2542]


title: Healthy subject [184]


title: IgAN patient [2429]


title: Healthy subject [2518]


title: Healthy subject [2557]


title: IgAN patient [2517]


title: Healthy subject [2519]


title: Healthy subject [2398]


title: IgAN patient [2373]


title: Healthy subject [2321]


title: IgAN patient [2339]


title: Healthy subject [2252]


title: IgAN patient [2431]


title: Healthy subject [2397]


title: Healthy subject [2396]


title: Healthy subject [2320]


title: Healthy subject [2558]


title: Healthy subject [2251]


title: Healthy subject [2223]


title: Healthy subject [2249]


title: Healthy subject [2247]


title: IgAN patient [2318]


title: Healthy subject [2224]


title: Healthy subject [2430]


title: Healthy subject [2246]


title: Healthy subject [2207]


title: IgAN patient [2220]


title: Healthy subject [2250]


title: IgAN patient [2213]


title: IgAN patient [2208]


title: Healthy subject [2164]


title: Healthy subject [2161]


title: Healthy subject [2166]


title: Healthy subject [2168]


title: Healthy subject [2162]


title: Healthy subject [2151]


title: Healthy subject [2221]


title: Healthy subject [2167]


title: Healthy subject [2159]


title: Healthy subject [2160]


title: Healthy subject [2073]


title: IgAN patient [2209]


title: Healthy subject [2165]


title: Healthy subject [2039]


title: Healthy subject [2206]


title: IgAN patient [2173]


title: Healthy subject [2210]


title: IgAN patient [2172]


title: Healthy subject [2150]


title: Healthy subject [2248]


title: Healthy subject [2036]


title: Healthy subject [2144]


title: Healthy subject [2034]


title: IgAN patient [2038]


title: Healthy subject [2035]


title: Tumor-associated-macrophages_wild type_3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 5, from SAS. Gene expression profiling was performed using arrays of  Mouse430_2-type from Affymetrix. A Custom CDF Version 12 with entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying RMA.

organism: Mus musculus

source_name: WT_TS/A tumor_21 day_TAM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: TAM were isolated from tumors using CD11b MACS beads, adhered in DMEM medium supplemented with 10% FBS for 30 min and lysed for RNA isolation

extract_protocol: RNA was isolated using the RNeasy midi kit (Qiagen, Hilden, Germany) according to manufacturer's instructions

treatment_protocol: TAM were lysed 30 min after isolation without additional treatments

tag: strain background

value: Balb/c

value: wild type

value: 8-12 weeks

value: female

tag: inoculated with

value: 5x10e6 TS/A cells

tag: tissue harvested

value: TS/A tumors 21 days after tumor challenge

tag: cell type analyzed

value: tumor-associated macrophages (TAM)


title: Healthy subject [2032]


title: Tumor-associated-macrophages_wild type_2


title: Healthy subject [2030]


title: Healthy subject [2031]


title: Tumor-associated-macrophages_wild type_1


title: IgAN patient [2024]


title: Healthy subject [2015]


title: Healthy subject [2013]


title: Tumor-associated-macrophages_stabilin-1 knock out_3

source_name: stabilin-1 KO_TS/A tumor_21 day_TAM

value: stabilin-1 knock out


title: Healthy subject [2033]


title: Healthy subject [2029]


title: Healthy subject [2011]


title: Healthy subject [2001]


title: Healthy subject [1999]


title: Healthy subject [1998]


title: Human term placenta, intervention - male, biological replicate 5

city: Freising-Weihenstephan

first: Bernhard

middle: L

last: Bader

address: Gregor-Mendel Straße 2

department: Clinical Nutritional Unit - ZIEL-Research Center for Nutrition and Food Sciences

institute: Technische Universität München

description: Placenta INT male 5

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Custom Array -  NuGO_Hs1a520180 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: MADMAX (Management and analysis Database for Multi-platform microArray eXperiments) was applied for quality control, normalization (gc Robust Multichip Average (slow)) and statistical analysis. Custom CDF file 13.0.0 were used.

source_name: Human term placenta from women of the n-3 LCPUFA intervention group with male offspring

label_protocol: Per placenta, 5ug total RNA was reverse transcribed to cDNA by Gene Chip Expression 3'-Aplification one cycle cDNA Synthesis Kit. cDNA was in-vitro transcribed to biotinylated cRNAs by Chip Expression 3'-Amplification IVT labelling Kit according to the Affymetrix's GeneChip Expression Analysis Technical manual.

extract_protocol: For each placenta, placental villous fraction samples from the four quadrants were homogenised in TRIzol® Reagent (Invitrogen, Darmstadt, Germany) and pooled in equal parts for total RNA extraction by midi RNeasy Kit (Qiagen, Hilden, Germany), each according to the manusfacturer's instructions

treatment_protocol: After birth placentas were maintained and processed at 4-0°C. Placental samples were dissected from each of the four quadrants with the same distance from to the placenta center according to a standardized sampling protocol. To obtain the chorionic villous fraction of the placenta, maternal basal plate and fetal chorionic plate of each placenta sample were removed, avoiding large vessels, calcifications or other obvious abnormalities. The samples were snap-frozen and stored at -80°C until RNA extraction.

tag: tissue

value: term placenta - villous fraction

value: n-3 LCPUFA intervention

tag: offspring sex


title: Healthy subject [2012]


title: IgAN patient [2006]


title: Healthy subject [2000]


title: Human term placenta, intervention - male, biological replicate 4

description: Placenta INT male 4

value: male


title: Healthy subject [2222]


title: Tumor-associated-macrophages_stabilin-1 knock out_1

tag: gender


title: Healthy subject [1997]


title: Human term placenta, intervention - male, biological replicate 3

description: Placenta INT male 3


title: Healthy subject [2010]


title: Tumor-associated-macrophages_stabilin-1 knock out_2


title: IgAN patient [2009]


title: IgAN patient [2025]


title: Human term placenta, intervention - male, biological replicate 2

description: Placenta INT male 2


title: Human term placenta, intervention - male, biological replicate 1

description: Placenta INT male 1


title: Healthy subject [1995]


title: Human term placenta, intervention - female, biological replicate 4

description: Placenta INT female 4

source_name: Human term placenta from women of the n-3 LCPUFA intervention group with female offspring


title: Human term placenta, intervention - female, biological replicate 3

description: Placenta INT female 3


title: Human term placenta, intervention - female, biological replicate 2

description: Placenta INT female 2


title: Human term placenta, control - male, biological replicate 3

description: Placenta CON male 3

source_name: Human term placenta from women of the control group with male offspring

value: control


title: Human term placenta, control - male, biological replicate 1

description: Placenta CON male 1


title: IgAN patient [1994]


title: Human term placenta, intervention - female, biological replicate 1

description: Placenta INT female 1


title: Human term placenta, control - female, biological replicate 4

description: Placenta CON female 4

source_name: Human term placenta from women of the control group with female offspring


title: Human term placenta, control - female, biological replicate 3

description: Placenta CON female 3


title: Human term placenta, control - female, biological replicate 2

description: Placenta CON female 2


title: Human term placenta, control - female, biological replicate 1

description: Placenta CON female 1


title: IgAN patient [1992]


title: Human term placenta, control - male, biological replicate 2

description: Placenta CON male 2


title: Healthy subject [1993]

value: Healthy subject


title: Healthy subject [2008]


title: Healthy subject [1966]


title: Healthy subject [1955]


title: Male,0 mg/kg furan, individual 6

city: ottawa

first: hongyan

last: dong

address: 50 colombine Dr.

institute: health canada

hyb_protocol: Cy5-sample cRNA and Cy3-reference cRNA were hybridized to Agilent G4853A SurePrint G3 Rat GE 8 X 60K microarrays (Agilent Technologies Inc.) at 65°C overnight with Agilent hybridization solution.

scan_protocol: Slides were washed and scanned on an Agilent G2505B microarray scanner at 5 μM resolution and the data were acquired with Agilent Feature Extraction software version 10.7.3.1.

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

organism: Rattus norvegicus

source_name: rats, liver, treated with different concentration of furan

label_protocol: A total of 50 RNA samples (5 female and 5 male rats per dose group, 5 dose groups total) were labelled with Cyanine 5-CTP using Low Input Quick Amp Labelling kits (Agilent Technologies Inc.) following the manufacturer’s instruction. Universal rat reference total RNA (Agilent Technologies Inc.) was labelled with Cyanine 3-CTP.

extract_protocol: Total RNA was extracted from frozen liver tissue of 5 male and 5 female rats from each dose group with mirVana miRNA isolation kits (Ambion, Inc., Foster city, CA, USA) according to the manufacturer’s instructions. RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Mississauga, ON, Canada) and only high quality RNAs (RNA Integrity Number ≥ 8.0) were used for microarray analysis of gene expression

treatment_protocol: Seven to eight week old male or female F344 rats were exposed daily, five days per week, to furan in Mazola corn oil at doses of 0, 0.03, 0.12, 0.5 or 2 mg/kg/day by oral gavage for 90 days.

tag: strain

value: liver

tag: Sex

value: Male

value: 7-8 weeks-old

source_name: Universal rat reference total RNA

tag: tissues

value: mixed


title: Healthy subject [1928]


title: Male,0.12 mg/kg furan, individual 41

tag: age


title: Healthy subject [1965]


title: Male,0.03 mg/kg furan, individual 26


title: Healthy subject [1918]


title: Male,2 mg/kg furan, individual 87


title: Healthy subject [1996]


title: Healthy subject [1927]


title: IgAN patient [2007]

value: IgAN patient


title: IgAN patient [1915]


title: Healthy subject [1860]


title: Healthy subject [1916]


title: IgAN patient [1914]


title: Female,2 mg/kg furan, individual 82

value: Female


title: IgAN patient [1859]


title: Healthy subject [1917]


title: Healthy subject [1858]


title: Female,0.5 mg/kg furan, individual 68


title: Healthy subject [1897]


title: Healthy subject [1876]


title: Male,2 mg/kg furan, individual 83


title: Female,0.03 mg/kg furan,individual 21


title: Healthy subject [1857]


title: Female,2 mg/kg furan, individual 92


title: Male,0.5 mg/kg furan, individual 68


title: Male,0.03 mg/kg furan, individual 27


title: Healthy subject [1934]


title: Healthy subject [1829]


title: Healthy subject [1896]


title: Female,2 mg/kg furan, individual 83


title: Female,0.12 mg/kg furan, 51


title: Female,0.5 mg/kg furan, individual 62


title: Healthy subject [1854]


title: ATAC-Seq MSC pLIV empty

description: MSC.empty.ATACseq

data_processing:
Library strategy: ATAC-seq
Paired end reads were aligned to the reference genome using BWA 0.6.2
Read start sites were adjusted to represent the center of the transposon binding event (+4 bp in the plus strand and -5 bp in the minus strand). Cut site density was calculated over 150bp-wide sliding windows at 20bp steps using Bedtools. Each experiment was normalized to 10M reads.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files of ATAC-Seq cut site density

growth_protocol: The human Ewing sarcoma cell lines A673 and SKMNC were grown in RPMI 1640 containing 10% FCS at 37°C with 5% CO2. Cells were maintained between a density of 5 x 10^5 cells/ml and 2 x 10^6 cells/ml and split every 3 – 4 days. Primary pediatric mesenchymal stem cells were cultured in IMDM containing 10% FCS and 10ng/ml PDGF-BB (Peprotec).

extract_protocol:
1x10^5 cells for each condition were resuspended in lysis buffer for 10 minutes, washed, and incubated in Transposase reaction mix for 30 minutes at 37 °C (Nextera DNA sample Prep Kit, Illumina).
DNA was purified and adaptor sequences were added to the fragmented DNA by PCR to construct Illumina sequencing libraries.

treatment_protocol: EWS-FLI1 was expressed using a lentiviral vector (pLIV). Lentiviruses were produced using standard protocols. Briefly, lentiviral shRNA or expression plasmids were co-transfected with GAG/POL and VSV plasmids into 293T packaging cells using FugeneHD (Roche) to produce the virus. Viral supernatant was collected 72 hours after transfection and concentrated by ultracentrifugation using an SW41Ti rotor (Beckman Coulter) at 28,000 rpm for 120 min.

tag: cell type

value: Mesenchymal Stem Cells

tag: treatment

value: empty vector


title: Healthy subject [1827]

tag: group


title: ATAC-seq MCS pLIV EWS-FLI1

description: MSC.EF.ATACseq


title: Female,0 mg/kg furan, individual 4


title: Male,0.03 mg/kg furan, individual 25


title: Healthy subject [1856]

tag: family number


title: Male,0.5 mg/kg furan, individual 62


title: Female,0.5 mg/kg furan, individual 64


title: Female,0.12 mg/kg furan,individual 45


title: Male,0.12 mg/kg furan, individual 52


title: Healthy subject [1895]


title: Male,2 mg/kg furan, individual 81


title: AU17

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed and normalised using quantile normalization with BeadStudio software

source_name: myxoid liposarcoma

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

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

value: myxoid liposarcoma

value: F

tag: primary site

value: thigh

tag: subtype

value: ML

tag: % rc component

tag: chop rearrangement  by fish / fusion type by rt-pcr

value: CHOP rearrangement

tag: sequencing tp53

value: wt

tag: sequencing pik3ca

tag: sequencing pten

value: ND


title: IgAN patient [1785]


title: AU30

tag: tissue

value: M

value: leg

value: RC


title: IgAN patient [1741]


title: Healthy subject [1826]

value: Healthy subject


title: Healthy subject [1855]


title: Female,2 mg/kg furan, individual 85

value: liver

value: 7-8 weeks-old


title: Male,0.5 mg/kg furan, individual 63

value: Male

value: mixed


title: Female,0.03 mg/kg furan,individual 24

value: Female


title: AU29

tag: gender


title: Female,0.03 mg/kg furan,individual 32

tag: strain


title: Healthy subject [1731]


title: Male,2 mg/kg furan, individual 84

tag: Sex


title: Healthy subject [1828]


title: Male,0.12 mg/kg furan, individual 48

tag: tissues


title: Male,0 mg/kg furan, individual 5

tag: age


title: AU28

value: shoulders

value: no functional Y163C


title: AU27

value: myxoid liposarcoma

value: F

value: bottock

value: functional A129T


title: AU25

value: thigh

value: ML

value: CHOP rearrangement

value: wt


title: Male,0.03 mg/kg furan, individual 22


title: Female,0 mg/kg furan, individual 2


title: Healthy subject [2014]


title: Female,0.12 mg/kg furan,individual 44


title: AU26

value: RC


title: Healthy subject [1730]

value: Healthy subject


title: Healthy subject [1813]


title: Healthy subject [1727]


title: IgAN patient [1728]

value: IgAN patient


title: Female,0.03 mg/kg furan,individual 30

value: liver

value: 7-8 weeks-old


title: AU24


title: Healthy subject [1724]


title: Healthy subject [1726]


title: AU23

value: FUS-CHOP type I


title: IgAN patient [1725]


title: Healthy subject [1723]


title: Healthy subject [1722]


title: Male,0 mg/kg furan, individual 3

value: Male

value: mixed


title: Female,0 mg/kg furan, individual 9

value: Female


title: Cells whole embryo, biological rep 2

city: Tübingen

last: Slane

state: Baden-Württemberg

address: Spemannstrasse 35

department: Cell Biology

institute: Max Planck Institute for Developmental Biology

description:
cEMB #2
Gene expression data from cells.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000.

data_processing: The data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using "affy" package (v1.32.1).

organism: Arabidopsis thaliana

source_name: Arabidopsis embryos 8-32 cell stage, whole embryo, cells

label_protocol: Biotinylated cRNA was prepared according to the ENZO BioArray™ Single-round RNA amplification and biotin labeling system.

growth_protocol: Long day 16 hours light/8 hours dark.

extract_protocol: RNA was extracted with the Arcturus PicoPure RNA Isolation Kit.

treatment_protocol: Ovules including embryos from 8-32 cell stage were dissected from siliques and embryos were squeezed out and washed.

tag: ecotype

value: whole embryo

tag: developmental stage

value: embryo (8-32 cell stage)


title: treatment Male_86

hyb_protocol: Labelled RNA was hybridized on 8 X 15K Agilent rat miRNA microarray slides. 55C 20 rpm overnight.

scan_protocol: Arrays were scanned using an Agilent G2505B scanner (5 μM resolution).

data_processing: Feature extraction (version 10.7.3.1, Agilent Tech. Inc.) was used to acquire the fluorescence intensity of each probe

source_name: rats, liver, treated with furan

label_protocol: samples were labelled with Cy3 using miRNA Complete Labelling and Hybridization kit (Agilent Technologies Inc.)

extract_protocol: Total RNA was extracted from frozen liver tissue of 5 male and 5 female rats from each dose group with mirVana miRNA isolation kits (Ambion, Inc., Foster city, CA, USA) according to the manufacturer’s instructions. RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Mississauga, ON, Canada) and only high quality RNAs (RNA Integrity Number ≥ 8.0) were used for microarray analysis of miRNA expression

treatment_protocol: Seven to eight week old male or female F344 rats were exposed daily, five days per week, to furan in Mazola corn oil at doses of 0 or 2 mg/kg/day by oral gavage for 90 days.

value: male


title: AU21

value: myxoid liposarcoma

value: M

value: FUS-CHOP type II


title: Cells whole embryo, biological rep 1

description:
cEMB #1
Gene expression data from cells.


title: Cells whole embryo, biological rep 3

description:
cEMB #3
Gene expression data from cells.


title: AU22

value: thigh

value: CHOP rearrangement


title: Healthy subject [1721]

tag: group


title: Healthy subject [1729]

tag: family number


title: Male,0.5 mg/kg furan, individual 70


title: Male,2 mg/kg furan, individual 86


title: Male,0 mg/kg furan, individual 2


title: Male,0.12 mg/kg furan, individual 44


title: treatment Male_84


title: treatment Male_83


title: AU19

tag: primary site

value: RC

value: wt


title: treatment Male_81


title: treatment female_90

value: female


title: treatment female_83

value: liver


title: Female,2 mg/kg furan, individual 90

value: 7-8 weeks-old


title: Female,0.5 mg/kg furan, individual 72


title: treatment female_82


title: Healthy subject [1720]

value: Healthy subject


title: Female,0 mg/kg furan, individual 11


title: Female,0.12 mg/kg furan, individual 49


title: Healthy subject [1654]


title: control Male_5

source_name: rats, liver, control


title: Male, 0.12mg/kg furan, individual 42

value: Male


title: Male, 0.5 mg/kg furan, individual 65

value: mixed


title: control Male_4


title: control Male_3


title: Female, 0.5mg/kg furan, individual 70

value: Female


title: Male, 0 mg/kg furan, individual 4


title: control Male_2


title: Female, 0 mg/kg furan, individual 7


title: Female, 0.12 mg/kg furan, individual 42


title: Healthy subject [1653]


title: Healthy subject [1682]


title: treatment female_85


title: Female, 0.03 mg/kg furan, individual 23


title: control female_9


title: IgAN patient [1652]

value: IgAN patient


title: heat30_5

city: Eugene

first: Patrick

middle: C.

last: Phillips

state: OR

address: 5289 University of Oregon

department: Institute of Ecology and Evolution

institute: University of Oregon

library_source: transcriptomic

data_processing:
Base-calls were performed using Illumina software
Initial processing was performed using the process_shortreads component of Stacks. In short, reads were demultiplexed, and the barcodes were removed. Reads with ambiguous barcodes were rescued if there were fewer than 2 mismatches, and discarded otherwise. Reads failing the Illumina chastity filter were also removed.
Filtered reads were aligned to the C. remanei genome using GSNAP version 2013-03-31 with parameters -N 1 -s -w 10000 --pairmax-RNA 10000
Reads aligning to genes were counted using htseq-count with parameters -m union -s no
Genome_build: C. remanei (strain 356) v1_4 (Fierst et al, in preparation; NCBI BioProject ID PRJNA248909)
Supplementary_files_format_and_content: tab-delimited text files with read counts per gene (note: a fasta file including all transcript sequences for this dataset is linked as a Series supplementary file).

molecule: polyA RNA

organism: Caenorhabditis remanei

source_name: pooled L1 tissue

growth_protocol: Worms were maintained on NGM-lite seeded with E. coli strain OP50 at 20°C

extract_protocol:
Approximately 100,000 individuals per replicate were flash frozen in Trizol. Total RNA was extracted using a standard Trizol extraction protocol. Poly-A mRNA was isolated from total RNA using the Dynabeads mRNA purification kit (Ambion).
mRNA was sheared to 200-600nt fragments using a buffered zinc solution (RNA fragmentation kit; Ambion). cDNA was synthesized from fragments using Superscript III, and barcoded sequencing adaptors were added to enable multiplexing of samples.

treatment_protocol: Populations were age-synchronized during the embryonic stage via a standard bleaching procedure. Embryos were incubated at either 20°C or 30°C in liquid buffer without food for 20 hours. Pooled L1 larvae were passed through a 20 micron filter immediately prior to tissue collection.

value: Heat-selected, derived from PX443

tag: parental temperature

tag: larval rearing temperature

tag: batch

value: F


title: IgAN patient [1664]


title: heat30_6


title: Healthy subject [1464]


title: heat30_4


title: IgAN patient [1683]


title: normal

city: nanjing

first: jie

last: wu

address: Nanjing Agricultural University Weigang 1, Nanjing, Jiangsu Province

institute: Nanjing Agricultural University

hyb_protocol: The labeled cRNAs were hybridized onto the microarray according to the manufacturer’s standard protocols.

scan_protocol: After washing, arrays were scanned using GenePix 4000B scanner (Molecular Devices) according to the manufacturer’s protocol.

data_processing: Feature Extraction software (GenePix® Pro 7, Axon Instruments, Inc. ) was used to analyze array  images  to get  raw data. To  begin  with,  the  raw  data  was  normalized  with  the quantile algorithm. The probes that at least 1 out of all samples have flags in Detected were  chosen  for  further  data  analysis.  Differentially  expressed  genes  were  then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

organism: Bos taurus

source_name: mammary gland

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed  to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA from each sample was extracted using miRNeasy Kit（QIAGEN, Cat. 217004, Total RNA Purification Kit）according to the manufacturer’s instructions. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: breed

value: Chinese Holstein

value: mammary gland

tag: Stage

value: healthy


title: control female_7


title: heat30_3


title: control female_4


title: heat30_2

value: E


title: control female_2


title: heat30_1


title: mastitis

value: mastitis


title: AU16

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

value: myxoid liposarcoma

value: M

value: arm

tag: subtype

value: ML

tag: % rc component

tag: chop rearrangement  by fish / fusion type by rt-pcr

value: CHOP rearrangement

tag: sequencing tp53

value: no functional R280K

tag: sequencing pik3ca

tag: sequencing pten


title: Healthy subject [1466]

source_name: whole blood

value: Healthy subject


title: Healthy subject [1462]


title: Healthy subject [1463]


title: Healthy subject [1459]


title: heat20_5

tag: strain


title: AU13

tag: tissue

tag: age

tag: gender

value: thigh

value: RC

value: FUS-CHOP type II

value: wt


title: Healthy subject [1461]

tag: group

tag: family number


title: AU15

tag: primary site

value: leg


title: AU12

value: bottock

value: polymorphism 213


title: Healthy subject [1460]


title: heat20_3

value: Heat-selected, derived from PX443

tag: developmental stage

tag: parental temperature

tag: larval rearing temperature

value: F


title: AU11

value: FUS-CHOP type I


title: heat20_2

tag: batch

value: E


title: Healthy subject [1457]


title: Healthy subject [1455]


title: heat20_1


title: control30_6

value: Control-selected, derived from PX443

value: D


title: Healthy subject [1458]


title: AU08

value: myxoid liposarcoma

value: M

tag: subtype

value: polymorphism 264


title: AU09

tag: % rc component


title: AU10

tag: chop rearrangement  by fish / fusion type by rt-pcr

value: CHOP rearrangement


title: heat20_4


title: control30_5


title: AU07

value: thigh

value: ML

tag: sequencing tp53


title: Healthy subject [1454]

value: Healthy subject


title: heat20_6


title: control30_4


title: Healthy subject [1453]


title: AU14

value: wt

tag: sequencing pik3ca


title: control30_3


title: control30_2

value: C


title: IgAN patient [1651]

value: IgAN patient


title: Healthy subject [1452]


title: AU06

value: pelvis

value: FUS-CHOP type II

tag: sequencing pten


title: control30_1

tag: strain


title: Healthy subject [1465]


title: control20_6


title: Healthy subject [1450]


title: IgAN patient [1449]


title: Healthy subject [1451]


title: control20_5


title: control20_4


title: IgAN patient [1215]


title: Healthy subject [1380]


title: control20_3


title: Monocyte-RCC-untreated-1

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: According to the BeadChip array manufacturer's protocol.

data_processing: Array data were extracted at the probe level with no background correction using Illumina's BeadStudio software. These raw data were quantile normalized. Statistical analysis and differential gene expression were carried out using the limma package in R 2.12.2/Bioconductor. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate.

source_name: RCC patient

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: Monocytes were plated in 6-well tissue culture plates (Nunclon, Denmark) at 1-2 x10^6 cells per well and incubated in complete IMDM medium containing 5% (v/v) human serum and 1% (v/v) penicillin/streptomycin, in a humidified incubator at 37 °C and 5% CO2.

extract_protocol: Total RNA was extracted from monocytes using an RNeasy Mini Kit (Qiagen) as per the manufacturer's specifications. Extracted RNA was run and quantified on a Bioanalyser (Agilent) for quality control and used subsequently in the microarray assay.

treatment_protocol: None.

tag: cell type

value: monocytes

tag: disease state

value: renal cell carcinoma (RCC)


title: Monocyte-RCC-untreated-2

scan_protocol: According to the BeadChip array manufacturer's protocol.


title: Monocyte-RCC-untreated-4


title: Healthy subject [1216]


title: Monocyte-RCC-untreated-5


title: Healthy subject [1202]


title: control20_2


title: IgAN patient [788]


title: IgAN patient [789]


title: control20_1


title: ancestor30_5

value: A


title: ancestor30_6


title: ancestor30_2


title: AU05

tag: tissue

tag: age

tag: gender

value: growin


title: Mononcyte-healthy-untreated-3

source_name: healthy donor

growth_protocol: Monocytes were plated in 6-well tissue culture plates (Nunclon, Denmark) at 1-2 x10^6 cells per well and incubated in complete IMDM medium containing 10% (v/v) human serum and 1% (v/v) penicillin/streptomycin, in a humidified incubator at 37 °C and 5% CO2.

value: healthy


title: IgAN patient [782]

tag: group

tag: family number


title: Mononcyte-healthy-untreated-2


title: ancestor30_1

tag: developmental stage

tag: parental temperature


title: ancestor30_3

tag: larval rearing temperature

tag: batch

value: B


title: Mononcyte-healthy-untreated-1


title: ancestor20_4


title: ancestor20_5


title: ancestor20_3


title: ancestor20_2


title: FemaleFatbody_DamOnly_R3

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: Three biological replicates were collected for treatment (UAS-DamDsxF) and control (UAS-Dam). One Dye Flip was performed.

hyb_protocol: Hybridization was performed by NimbleGen.  DamDsxF and DamOnly samples for each replicate were hybridized to the same array. For example, the samples FemaleFatbody_DamDsxF_R1 and FemaleFatbody_DamOnly_R1 were hybridized to the same array.

scan_protocol: Scanning was performed by NimbleGen.

data_processing:
The Series supplementary file "FemaleFatbody_DsxF_DamIDarray_Normalized_Data.txt" contains the normalized probe intensities, DamDsxF and DamOnly means, log2 Fold Change (DamDsxF/DamOnly), pvalues from a ttest and Benjamini-Hochberg adjusted p-values for the ttest. This file also contains the genomic coordinates used for the probes.  For this analysis, we forced all probe lengths to be identical.  To do this, we used the actual probe start position and added 50 bp (the median probe length on the array) to the start position to make the end position.  The actual probe coordinates can be obtained from the .GFF files available on the series entry. Probe intensities were quantile normalized using the R package PreProcessCore (Ben Bolstad) available through BioConductor.  A cut-off for the signal detection limit was determined by calculating the mean of all the random probes on the array.  The 95th percentile of the mean random probe signal was used as the signal cutoff. For these arrays, the 95th percentile of the mean random probes was 364. Any probe where both DamDsxF and DamOnly mean intensities were 364 or below were considered below detection level and removed from the dataset. All calculations were performed in R. The data present in"FemaleFatbody_DsxF_DamIDarray_Normalized_Data.txt" are the data that were used to define DSXF occupied regions (peaks).  Peaks were identified by selecting probes that had an adjusted p-value at or below 0.01 and a positive log2 Fold Change.  Significant probes were considered members of a single peak when they occurred within 1 kb of each other. BEDTools v.2.16.2 was used to combine significant probes present within a 1 kb window into peaks.
The Scaled Log2Ratio Data files (.GFF) were provided by NimbleGen. We did not use these files for analyzing the data in our study but are providing them so they will be available to others. This file contains the ratio of the input signals for the experimental and test samples that were co-hybridized to the array. The log2 ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the biweight mean for the log2-ratio values for all features on the array from each log2-ratio value. View log2-ratio data files (.GFF) using SignalMap software.  They can also be opened in a text editor.

organism: Drosophila melanogaster

label_protocol: Labeling was performed by NimbleGen.

extract_protocol: Genomic DNA was extracted using components of Qiagen's DNEasy Blood and Tissue kit (Qiagen, Valencia, CA, USA).  Samples processed for DamID-seq were homogenized in 175 µl PBS and incubated with 200 mg of RNAse A for 2 minutes at room temperature.  Tissue was lysed with 20 µl of proteinase K and 200 µl of buffer AL for ten minutes at 70 °C. 200 µl of ethanol were added to each sample and they were transferred to the spin columns after which genomic DNA extraction continued following manufacturer's instructions with the exception of a 30 minute incubation prior to first elution and a second elution step after a 10 minute incubation. Genomic DNA extracted for DamID-chip was extracted following manufacturer's protocol except for the following modifications: a 1.5 hr incubation with lysis buffer prior to the addition of proteinase K, addition of 400 µl of Buffer AL and 300 µl of 100% ethanol, two rounds of both AW1 and AW2 and an incubation with the elution buffer for 30 minutes prior to two rounds of elution. 2.5 - 3 µg of fatbody genomic DNA and 0.3 µg of ovary genomic DNA was used for selective PCR amplification of methylated DNA. DNA was incubated with 10-30 units of DpnI in 50-100 µl of Buffer 4 (New England Biolabs , Ipswich, MA, USA). DpnI was inactivated at 80 °C for 20 minutes and digested DNA was purified through a Qiagen PCR Purification Qiaquick column following manufacturer's protocol and eluted in 30 µl ddH20. One-half of the DpnI reaction products were ligated to 40 pmol of the doublestranded DamID adaptors (top strand :  5'-CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA-3'; bottom strand: 5'-TCCTCGGCCG-3') for 2 hours at 16 °C with 400 units of T4 ligase (New England Biolabs, Ipswich, MA, USA) or 5 units of T4 ligase (Roche, Indianapolis, IN, USA) in a 20 µl reaction volume.  All 20 µl of the adapter-ligated DNA were then subjected to DpnII digestion with 10 units of DpnII in a 80 µl reaction volume for at least one hour. PCR amplification was performed with 20 µl of the DpnII digested DNA in an 80 µl volume with 100 pmol PCR primer (5'-TCCTCGGCCG-3'), 16 nmol of each dNTP and 1.6 µl PCR Advantage enzyme mix in 1X PCR Advantage Reaction Buffer (Clontech, Mountain View, CA, USA) or 62.5 pmol PCR primer (5'-TCCTCGGCCG-3'), 16 nmol of each dNTP, 80 nmol MgCl2 in 1X buffer with 8 units of taq polymerase (Fermentas, Pittsburgh, PA, USA). DNA was amplified with the following program: 10 minutes at 68 °C, 1 minute at 94 °C, 5 minutes at 65 °C and 15 minutes at 68 °C, followed by 3 cycles of 1 minute at 94 °C, 1 minute at 65 °C and 10 minutes at 68 °C and then 17 cycles of 1 minute at 94 °C, 1 minute at 65 °C and 2 minutes at 68 °C.  DNA was purified through a Qiaquick column (Qiagen, Valencia, CA, USA).

tag: Sex

value: Female

value: Fatbody

value: 5 day-old adult


title: ancestor20_1


title: Healthy subject [553]


title: IgAN patient [761]


title: FemaleFatbody_DamOnly_R2


title: ancestor30_4


title: Inv-Dsg2 transgenic #2

city: Philadelphia

first: My

last: Mahoney

state: PA

address: 233 South 10th Street, Suite 428  BLSB

department: Dermatology & Cutaneous Biology

institute: Thomas Jefferson University

description: The microarrays utilize nucleic acid hybridization of a biotin-labeled complementary RNA (cRNA) target with DNA oligonuleotide probes attached to a gel matrix.

hyb_protocol: The microarrays were hybridized in 6X SSPE with 50% formamide at 37oC for 20 hours, washed in 0.75X TrisNaClTween (TNT) buffer at 46oC for 1 hour, followed by blocking in TrisNaCl Blocking buffer (TNB) at RT for 30 min and then processed using Streptavidin-Alexa 647 conjugate in TNB buffer (1:250) at RT for 30 min. Stained chips were then washed for 15 min at RT in 1X TNT buffer for 60 min.

scan_protocol: Washed slides were scanned using a PerkinElmer ScanArray® XL5000 Scanner, acquire fluorescent signals for each spot.

data_processing:
Fluorescent intensities for each spot on the array were analyzed by image processing as 16-bit images using PerkinElmer Quant Array 3.0 software .
Signal intensities for each spot were calculated by subtracting background (based on the median intensity of the area surrounding each spot) from total intensities. Raw data were normalized and analyzed using GeneSpring software (Version 7.2).

source_name: 6 week old backskin

label_protocol: First strand cDNA were synthesized from 5 µg total RNA by reverse transcription  which in turn was used to generate biotin-labeled cRNA.

growth_protocol: Details of generation of transgenic mice can be found in Brennen, D., et al 2007, JCS p758. All mice were back-crossed to C57BI/6J five times.

extract_protocol: Mouse skin tissues, stored in RNAlater, were pulverized with a mortal and pestle and homogenized in a Dounce homogenizer. Total RNA was isolated using TRIzol. cDNA was synthesized from 2 µg  using hexa-random primers and M-MLV reverse transcriptase.

treatment_protocol: The Involucrin-Dsg2 transgenic were not subjected to any treatment.

tag: genotype/variation

value: Inv-Dsg2 transgenic


title: ancestor20_6


title: Healthy subject [599]


title: FemaleFatbody_DamDsxF_R3


title: IgAN patient [779]


title: TG3

city: Dallas

first: Joshua

last: Mendell

state: Texas

address: 6000 Harry Hines Blvd NA 6.200

department: Molecular Biology

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumnia hybridization protocol

scan_protocol: Standard Illumnia scanning protocol

data_processing: The data were normalized using quantile normalization with Illumnia BeadStudio software

source_name: mouse intestinal epithelium

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

growth_protocol: Adult mice were given 2mg/ml doxycycline and 10mg/ml sucrose for 10 days prior to purification of intestinal epithelial cells

extract_protocol: Total RNA extracted using QIAGEN miRNeasy kit with Dnase digestion

tag: genotype

value: M2rtTA; eGFP.miR-26a


title: Healthy subject [581]

value: Healthy subject


title: IgAN patient [601]


title: IgAN patient [597]


title: FemaleFatbody_DamDsxF_R2


title: FemaleFatbody_DamOnly_R1


title: CTRL3


title: Inv-Dsg2 transgenic #1

value: Male


title: CTRL2


title: Healthy subject [557]


title: IgAN patient [552]


title: Mononcyte-healthy-untreated-4


title: Wild-type control #2

value: wild type


title: Wild-type control #1


title: FemaleFatbody_DamDsxF_R1


title: IgAN patient [551]

value: IgAN patient


title: TG1


title: TG2


title: Healthy subject [497]


title: Healthy subject [506]


title: 038_PsA_202_CD14-_wk10

status: Public on Oct 29 2014

city: Rochester

first: Christopher

last: Ritchlin

state: NY

address: 601 Elmwood Ave, BOX695

department: School of Medicine and Dentistry

institute: University of Rochester Medical Center

hyb_protocol: All samples were hybridized in parallel to different arrays on the same HT array plate using the manufacturer's protocol. Arrays were washed and stained on an Affymetrix GeneTitan instrument

scan_protocol: Arrays were scanned using an Affymetrix GeneTitan MC scanner

data_processing: Affymetrix .cel files were RMA normalized in ArrayStudio from Omicsoft Inc (version 4.1). Differential gene expression was analyzed using paired t-tests and genes were selected based on p-value (affymetrix probe sets with no associated gene annotation were not included)

label_protocol: Target was prepared from 50ng total RNA using NuGEN Ovation V2 kits, followed by NuGEN Encore biotin labeling module using the manufacturer's protocol

extract_protocol: Total RNA was isolated from CD14- cells using the RNeasy Mini Kit with DNase digestion on the column (Qiagen, Inc. Valencia, CA, USA) as per the manufacturer’s instructions.

value: M

value: primary cell

tag: cell subtype

tag: disease status

value: diseased

tag: disease

value: Psoriatic Arthritis

tag: time point


title: CTRL1


title: 224_PsA_211_CD14-_wk10

tag: cell type


title: Healthy subject [600]

extract_protocol: Genomic DNA was purified from peripheral blood samples by Qiagen Qiamp DNA Blood Midi kit


title: 040_PsA_204_CD14-_wk10

value: F


title: 146_PsA_207_CD14-_wk10


title: Healthy subject [504]


title: Healthy subject [548]


title: 108_PsA_206_CD14-_wk10


title: 032_PsA_201_CD14-_wk10


title: Healthy subject [499]


title: 086_PsA_205_CD14-_wk10


title: 228_PsA_212_CD14-_wk10


title: 134_PsA_208_CD14-_wk10


title: Healthy subject [546]


title: 096_PsA_206_CD14-_wk2


title: 220_PsA_210_CD14-_wk10


title: Healthy subject [462]


title: Healthy subject [547]


title: 004_PsA_201_CD14-_wk2


title: 120_PsA_208_CD14-_wk2


title: Healthy subject [470]


title: 136_PsA_209_CD14-_wk10


title: 020_PsA_204_CD14-_wk2


title: 072_PsA_205_CD14-_wk2


title: 226_PsA_212_CD14-_wk2


title: 012_PsA_203_CD14-_wk2


title: 198_PsA_210_CD14-_wk2


title: 132_PsA_207_CD14-_wk2


title: 206_PsA_211_CD14-_wk2


title: 090_PsA_206_CD14-_wk0


title: 008_PsA_202_CD14-_wk0


title: 010_PsA_204_CD14-_wk0


title: 212_Ps_309_CD14-_wk10

value: Psoriasis


title: 002_PsA_201_CD14-_wk0


title: 014_PsA_202_CD14-_wk2


title: 222_PsA_212_CD14-_wk0


title: 124_PsA_209_CD14-_wk2


title: 126_PsA_207_CD14-_wk0


title: 190_PsA_210_CD14-_wk0


title: 110_Ps_305_CD14-_wk10


title: 006_PsA_203_CD14-_wk0


title: 202_PsA_211_CD14-_wk0


title: 116_PsA_208_CD14-_wk0


title: 070_PsA_205_CD14-_wk0


title: 218_Ps_310_CD14-_wk10


title: 122_PsA_209_CD14-_wk0


title: 048_Ps_302_CD14-_wk10


title: 176_Ps_307_CD14-_wk10


title: 204_Ps_310_CD14-_wk2


title: 078_Ps_303_CD14-_wk10


title: 042_Ps_302_CD14-_wk2


title: 166_Ps_306_CD14-_wk10


title: 106_Ps_304_CD14-_wk10


title: 188_Ps_309_CD14-_wk2


title: 080_Ps_304_CD14-_wk0


title: 028_Ps_301_CD14-_wk2


title: 068_Ps_303_CD14-_wk2


title: 088_Ps_304_CD14-_wk2


title: 180_Ps_309_CD14-_wk0


title: 100_Ps_305_CD14-_wk2


title: 168_Ps_308_CD14-_wk0


title: 022_Ps_301_CD14-_wk0


title: 184_Ps_308_CD14-_wk2


title: 148_Ps_306_CD14-_wk2


title: 210_Ps_308_CD14-_wk10


title: 156_Ps_307_CD14-_wk0


title: 162_Ps_307_CD14-_wk2


title: 036_Ps_302_CD14-_wk0


title: 092_Ps_305_CD14-_wk0


title: 102_RA_101_CD14-_wk10

value: Rheumatoid Arthritis


title: 066_Ps_303_CD14-_wk0


title: 178_RA_104_CD14-_wk10


title: 104_RA_102_CD14-_wk10


title: 170_RA_105_CD14-_wk10


title: 194_RA_109_CD14-_wk2


title: 164_RA_107_CD14-_wk2


title: 172_RA_107_CD14-_wk10


title: 182_RA_109_CD14-_wk0


title: 082_RA_101_CD14-_wk2


title: 094_RA_103_CD14-_wk0


title: 098_RA_103_CD14-_wk2


title: 158_RA_105_CD14-_wk2


title: 192_RA_106_CD14-_wk0


title: 084_RA_102_CD14-_wk2


title: 112_RA_103_CD14-_wk10


title: 154_RA_105_CD14-_wk0


title: 196_Ps_310_CD14-_wk0


title: 186_RA_108_CD14-_wk2


title: 208_RA_108_CD14-_wk10


title: 214_RA_109_CD14-_wk10


title: 200_RA_106_CD14-_wk2


title: 152_RA_107_CD14-_wk0


title: 076_RA_102_CD14-_wk0


title: 150_RA_104_CD14-_wk0


title: 216_RA_106_CD14-_wk10


title: 160_RA_104_CD14-_wk2


title: 050_HC_510_CD14-

value: normal

value: Healthy Control


title: 144_Ps_306_CD14-_wk0


title: 174_RA_108_CD14-_wk0


title: 074_RA_101_CD14-_wk0


title: 044_Ps_301_CD14-_wk10


title: 128_HC_517_CD14-


title: 054_HC_512_CD14-


title: 230_HC_501_CD14-


title: 064_HC_516_CD14-


title: 140_HC_519_CD14-


title: 142_HC_520_CD14-


title: 052_HC_511_CD14-


title: 060_HC_515_CD14-


title: 016_HC_505_CD14-


title: 234_HC_503_CD14-


title: 030_HC_509_CD14-


title: 024_HC_507_CD14-


title: 138_HC_518_CD14-


title: 056_HC_513_CD14-


title: 232_HC_502_CD14-


title: 058_HC_514_CD14-


title: 018_HC_506_CD14-


title: 026_HC_508_CD14-


title: 151_RA_107_CD14+_wk0

extract_protocol: Total RNA was isolated from CD14+ monocytes and CD14- cells using the RNeasy Mini Kit with DNase digestion on the column (Qiagen, Inc. Valencia, CA, USA) as per the manufacturer’s instructions.

tag: response


title: 169_RA_105_CD14+_wk10

tag: age


title: 213_RA_109_CD14+_wk10


title: 075_RA_102_CD14+_wk0


title: 149_RA_104_CD14+_wk0


title: 157_RA_105_CD14+_wk2


title: 191_RA_106_CD14+_wk0


title: 215_RA_106_CD14+_wk10


title: 153_RA_105_CD14+_wk0


title: 073_RA_101_CD14+_wk0


title: 181_RA_109_CD14+_wk0


title: 171_RA_107_CD14+_wk10


title: 185_RA_108_CD14+_wk2


title: 083_RA_102_CD14+_wk2


title: 173_RA_108_CD14+_wk0


title: 193_RA_109_CD14+_wk2


title: 177_RA_104_CD14+_wk10


title: 163_RA_107_CD14+_wk2


title: 199_RA_106_CD14+_wk2


title: 159_RA_104_CD14+_wk2


title: 207_RA_108_CD14+_wk10


title: 103_RA_102_CD14+_wk10


title: 111_RA_103_CD14+_wk10


title: 093_RA_103_CD14+_wk0


title: 197_PsA_210_CD14+_wk2

value: responder


title: 019_PsA_204_CD14+_wk2


title: 225_PsA_212_CD14+_wk2


title: 101_RA_101_CD14+_wk10


title: 081_RA_101_CD14+_wk2


title: 097_RA_103_CD14+_wk2


title: 071_PsA_205_CD14+_wk2


title: 227_PsA_212_CD14+_wk10


title: 145_PsA_207_CD14+_wk10


title: 085_PsA_205_CD14+_wk10


title: 131_PsA_207_CD14+_wk2


title: 069_PsA_205_CD14+_wk0


title: 009_PsA_204_CD14+_wk0


title: 115_PsA_208_CD14+_wk0

value: nonresponder


title: 201_PsA_211_CD14+_wk0


title: 107_PsA_206_CD14+_wk10


title: 121_PsA_209_CD14+_wk0


title: 037_PsA_202_CD14+_wk10


title: 007_PsA_202_CD14+_wk0


title: 205_PsA_211_CD14+_wk2


title: 219_PsA_210_CD14+_wk10


title: 011_PsA_203_CD14+_wk2


title: 189_PsA_210_CD14+_wk0


title: 031_PsA_201_CD14+_wk10


title: 119_PsA_208_CD14+_wk2


title: 013_PsA_202_CD14+_wk2


title: 221_PsA_212_CD14+_wk0


title: 033_PsA_203_CD14+_wk10


title: 039_PsA_204_CD14+_wk10


title: 123_PsA_209_CD14+_wk2


title: Sperm LDL, +3AB, male 4

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

description: Gene expresion in larvae from sperm frozen with LDL, with zygotic inhibition of PARP with 3AB, replicate 4

hyb_protocol: Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Scanning was performed with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (channels: Green, resolution: 3µm, TIFF: 20 bit)

data_processing: Data were then obtained with the Agilent Feature Extraction software (v10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Before analysis, saturated spot, non-uniform spots and spots not significantly different from background (k=5) were flagged using the Agilent GeneSpring GX software (v.10.0.2). Probes were considered valid when corresponding spots remained present in at least 80% of the replicates of each experimental condition after the flagging procedure. Data were subsequently scale-normalized using the median value of each array.

organism: Oncorhynchus mykiss

source_name: Sperm LDL, +3AB, male

label_protocol: 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop. 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array.

extract_protocol: Total RNA was obtained using a Trizol® Reagent kit (Applied Biosystem, Foster city, CA, USA) following the manufacturer´s instructions. RNA integrity was checked with the Agilent Bioanalyzer (Agilent Technologies, Massy, France) and yield was estimated using a Nanodrop ND-1000 spectrophotometer (Labtech, Palaiseau, France).

treatment_protocol: Larvae were obtained by fertilization with fresh or frozen sperm (two protocols) and analyzed 1 day post hatch. Half of the samples were treated with 3AB 5h after fertilization to inhibit PARP activity

tag: tissue

value: whole larvae 1dph

tag: sperm source

value: LDL

tag: zygotic treatment

value: PARP inhibited


title: Sperm F, +3AB, male 3

description: Gene expresion in larvae from fresh sperm, with zygotic inhibition of PARP with 3AB, replicate 3

source_name: Sperm F, +3AB, male


title: 089_PsA_206_CD14+_wk0


title: 135_PsA_209_CD14+_wk10


title: 005_PsA_203_CD14+_wk0


title: 133_PsA_208_CD14+_wk10


title: 001_PsA_201_CD14+_wk0


title: 125_PsA_207_CD14+_wk0


title: 223_PsA_211_CD14+_wk10


title: 003_PsA_201_CD14+_wk2


title: 095_PsA_206_CD14+_wk2


title: Sperm LDL, +3AB, male 3

description: Gene expresion in larvae from sperm frozen with LDL, with zygotic inhibition of PARP with 3AB, replicate 3


title: Sperm EY, -3AB, male 4

description: Gene expresión in larvae from sperm frozen with EY, replicate 4

source_name: Sperm EY, -3AB, male

value: EY

value: PARP non-inhibited


title: Sperm LDL, -3AB, male 4

description: Gene expresión in larvae from sperm frozen with LDL, replicate 4

source_name: Sperm LDL, -3AB, male


title: 195_Ps_310_CD14+_wk0


title: 065_Ps_303_CD14+_wk0


title: 161_Ps_307_CD14+_wk2


title: 099_Ps_305_CD14+_wk2


title: Sperm F, +3AB, male 4

description: Gene expresion in larvae from fresh sperm, with zygotic inhibition of PARP with 3AB, replicate 4


title: 027_Ps_301_CD14+_wk2


title: Sperm EY, -3AB, male 3

description: Gene expresión in larvae from sperm frozen with EY, replicate 3


title: Sperm LDL, -3AB, male 3

description: Gene expresión in larvae from sperm frozen with LDL, replicate 3


title: Sperm LDL, +3AB, male 2

description: Gene expresion in larvae from sperm frozen with LDL, with zygotic inhibition of PARP with 3AB, replicate 2


title: Sperm F, -3AB, male 3

description: Gene expresion in larvae from fresh sperm, replicate 3

source_name: Sperm F, -3AB, male


title: Sperm LDL, -3AB, male 2

description: Gene expresión in larvae from sperm frozen with LDL, replicate 2


title: Sperm EY, +3AB, male 2

description: Gene expresion in larvae from sperm frozen with EY, with zygotic inhibition of PARP with 3AB, replicate 2

source_name: Sperm EY, +3AB, male


title: 105_Ps_304_CD14+_wk10


title: 047_Ps_302_CD14+_wk10


title: Sperm F, -3AB, male 2

description: Gene expresion in larvae from fresh sperm, replicate 2


title: Sperm EY, +3AB, male 1

description: Gene expresion in larvae from sperm frozen with EY, with zygotic inhibition of PARP with 3AB, replicate 1


title: Sperm F, -3AB, male 1

description: Gene expresion in larvae from fresh sperm, replicate 1


title: Sperm LDL, -3AB, male 1

description: Gene expresión in larvae from sperm frozen with LDL, replicate 1


title: 155_Ps_307_CD14+_wk0


title: 179_Ps_309_CD14+_wk0


title: 165_Ps_306_CD14+_wk10


title: 175_Ps_307_CD14+_wk10


title: 183_Ps_308_CD14+_wk2


title: 043_Ps_301_CD14+_wk10


title: 209_Ps_308_CD14+_wk10


title: Sperm F, -3AB, male 4

description: Gene expresion in larvae from fresh sperm, replicate 4


title: 211_Ps_309_CD14+_wk10


title: 217_Ps_310_CD14+_wk10


title: 087_Ps_304_CD14+_wk2


title: 187_Ps_309_CD14+_wk2


title: 077_Ps_303_CD14+_wk10


title: 091_Ps_305_CD14+_wk0


title: 167_Ps_308_CD14+_wk0


title: 041_Ps_302_CD14+_wk2


title: 203_Ps_310_CD14+_wk2


title: 057_HC_514_CD14+

value: Health Control


title: 067_Ps_303_CD14+_wk2


title: 229_HC_501_CD14+


title: 109_Ps_305_CD14+_wk10

value: M


title: 021_Ps_301_CD14+_wk0

value: primary cell


title: 147_Ps_306_CD14+_wk2

value: diseased


title: 063_HC_516_CD14+


title: 055_HC_513_CD14+


title: 035_Ps_302_CD14+_wk0


title: Sperm EY, -3AB, male 2

description: Gene expresión in larvae from sperm frozen with EY, replicate 2


title: Sperm F, +3AB, male 2

description: Gene expresion in larvae from fresh sperm, with zygotic inhibition of PARP with 3AB, replicate 2


title: Sperm LDL, +3AB, male 1

description: Gene expresion in larvae from sperm frozen with LDL, with zygotic inhibition of PARP with 3AB, replicate 1


title: Sperm F, +3AB, male 1

description: Gene expresion in larvae from fresh sperm, with zygotic inhibition of PARP with 3AB, replicate 1


title: 141_HC_520_CD14+


title: Sperm EY, -3AB, male 1

description: Gene expresión in larvae from sperm frozen with EY, replicate 1


title: 079_Ps_304_CD14+_wk0


title: 059_HC_515_CD14+


title: 049_HC_510_CD14+


title: 137_HC_518_CD14+


title: 053_HC_512_CD14+


title: 233_HC_503_CD14+


title: 127_HC_517_CD14+


title: 029_HC_509_CD14+


title: 143_Ps_306_CD14+_wk0


title: 051_HC_511_CD14+


title: 023_HC_507_CD14+


title: B31_RA_106_knee_wk10

extract_protocol: Total RNA was isolated from biopsy samples using the RNeasy Lipid Tissue Mini Kit with DNase digestion on the column (Qiagen, Inc. Valencia, CA, USA) as per the manufacturer’s instructions.  The quality and quantity of RNA was assessed using the Agilent 2100 Bioanalyzer (South Plainfield, NJ, USA) or the Caliper LabChip GX (PerkinElmer, Inc. Waltham, MA, USA).   Only those RNAs with a RNA Integrity Number (RIN, Agilent) or RNA Quality Score (RQS, PerkinElmer) of greater than 4.0 (out of 10) were submitted for microarray

tag: sample type

value: biopsy

value: knee


title: 139_HC_519_CD14+

value: F


title: B26_Ps_308_skinL_wk2

value: Lesional skin

value: Psoriasis


title: 017_HC_506_CD14+

value: normal


title: B09_Ps_303_skinL_wk2


title: 015_HC_505_CD14+


title: B20_PsA_209_knee_wk10

value: Psoriatic Arthritis


title: B34_PsA_211_knee_wk10


title: B36_PsA_212_knee_wk10


title: 025_HC_508_CD14+


title: B06_PsA_205_synfluid_wk0

value: synfluid


title: B11_PsA_205_knee_wk10


title: 231_HC_502_CD14+


title: B29_PsA_211_knee_wk0


title: B30_PsA_210_knee_wk10


title: B14_RA_103_knee_wk10

value: Rheumatoid Arthritis


title: B04_Ps_301_skinL_wk2


title: B32_Ps_309_skinL_wk2


title: B33_RA_108_knee_wk10


title: B15_RA_103_knee_wk10


title: B13_Ps_305_skinL_wk2


title: B27_PsA_210_knee_wk0


title: Chitosan_Brain_Rep3

city: Taichung

first: Chien-Yun

last: Hsiang

address: 91 Hsueh-Shih Road

country: Taiwan

institute: China Medical University

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArrayTM (Phalanx Biotech Group, Hsinchu, Taiwan).

scan_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArrayTM and scanned by an Axon 4000 scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The Cy5 fluorescent intensity of each spot was analyzed by genepix 4.1 software (Molecular Devices). The signal intensity of each spot was corrected by subtracting background signals in the surrounding. We filtered out spots that signal-to-noise ratio was less than 1 or control probes. Spots that passed these criteria were normalized by the limma package of the R program (http://www.r-project.org/).

source_name: Brain

label_protocol: Fluorescence-labeled RNA targets were prepared from 5 μg of total RNA using MessageAmpTM aRNA kit (Ambion, Austin, TX, USA) and Cy5 dye (Amersham Pharmacia, Piscataway, NJ, USA).

extract_protocol: Total RNAs were extracted according to RNeasy kit.

tag: treatment group

value: Chitosan

value: brain

tag: strain

value: FVB


title: Chitosan_Stomach_Rep1

source_name: Stomach

value: stomach


title: B37_Ps_305_skinNL_wk0

value: nonlesional skin


title: B10_PsA_205_knee_wk0

value: M


title: Chitosan_Stomach_Rep2


title: Mock_Stomach_Rep2

value: Mock


title: B28_RA_106_knee_wk0

value: diseased


title: B01_PsA_201_knee_wk0

value: biopsy


title: B07_Ps_303_skinNL_wk0


title: B22_Ps_308_skinNL_wk0


title: B25_Ps_309_skinNL_wk0


title: B03_Ps_301_skinL_wk0


title: Mock_Brain_Rep2


title: Chitosan_Brain_Rep2


title: Mock_Brain_Rep3


title: Chitosan_Stomach_Rep3


title: B02_Ps_301_skinNL_wk0


title: B24_Ps_309_skinL_wk0


title: B38_Ps_305_skinL_wk0


title: Mock_Stomach_Rep3


title: B21_RA_108_knee_wk0

value: knee


title: Mock_Brain_Rep1


title: B12_RA_103_knee_wk0

value: F


title: B23_Ps_308_skinL_wk0

value: Lesional skin


title: Mock_Stomach_Rep1


title: B08_Ps_303_skinL_wk0

value: Psoriasis


title: Chitosan_Brain_Rep1


title: Lung-Control-P21-rep2

city: Paris

first: Elodie

last: Zana-Taïeb

address: 53 avenue de l'Observatoire

institute: PremUp

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Whole lung, postnatal day 21

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Rat pups were sacrified at postnatal day 4, 10 and 21 and lung were fresh frozen. Then kept at-80°C until analysis.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen, Chatsworth, CA). Purified RNA was quantified using NanoDrop™ Spectrophotometer technology (Thermo Fischer Scientific, Wilmington, Delaware).

value: Sprague-Dawley

tag: stress

value: Control

tag: time

value: Postnatal day 21

value: whole lung


title: Lung-Control-P21-rep1


title: Silica75_3

city: Maastricht

first: Paul

middle: Michel

last: Peeters

state: Limburg

address: universiteitssingel 50

department: Respiratory Medicine

country: Netherlands

institute: Maastricht University

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 16h at 45°C on Affymetrix GeneChip Human U133A 2.0 Arrays

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

growth_protocol: Cultured cells were harvested for RNA isolation.

extract_protocol: Total RNA was extracted using the Rneasy Plus Mini Kit (Valencia, CA, USA), according to the manufacturer’s instructions.

value: Primary human bronchial epithelial cells (NHBE)

tag: exposed to

value: cristobalite silica 75x10^6 μm2/cm2


title: Silica75_2


title: Lung-IUGR-P21-Rep2

value: IUGR


title: Lung-Control-P10-rep2

source_name: Whole lung, postnatal day 10

value: Postnatal day 10


title: Silica15_3

value: cristobalite silica 15x10^6 μm2/cm2


title: Silica75_1


title: Lung-IUGR-P21-rep1


title: Control_1

value: none (unexposed control)


title: SB431542_24 h_rep1

city: Yangling

first: Juan

last: Du

state: China/Shaanxi

address: 3 Taicheng Road

institute: College of Life Sciences

description: Gene expression after 24h in SB431542 treated J1 mESCs

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). This process was performed by Shanghai Biotechnology corporation.

source_name: J1 mESC, SB431542, 24h, replicate 1

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

growth_protocol: The J1 mouse embryonic stem cell line purchased from ATCC (Manassas, VA, USA) was gelatin adapted and grown on 0.2% (w/v) gelatin coated tissue culture plates in Knockout DMEM supplemented with 15% (v/v) Knockout Serum Replacement, 1× non-essential amino acids, 100 μM β-mercaptoethanol, 2 mM glutamine, 50 units/ml Penicillin, 50 μg/ml Streptomycin, 1000 U/ml LIF (ESGRO, Millipore, USA).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: J1 mESCs maintained in medium containing 1000 U/mL LIF and treated by 3 μΜ SB431542 for 24h.

tag: cell line

tag: treatment

tag: gender

value: Inner Cell Mass

value: Embryonic Stem Cell


title: Control_2


title: Lung-Control-P10-rep1


title: Silica15_1


title: Lung-IUGR-P10-Rep2


title: DMSO_24 h_rep1

description: Gene expression after 24h in DMSO(control) treated J1 mESCs

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: J1 mESC, DMSO, 24h, replicate 1

value: DMSO


title: Lung-Control-P4-rep2

source_name: Whole lung, postnatal day 4

value: Postnatal day 4


title: Lung-IUGR-P4-Rep2


title: Control_3


title: Silica15_2


title: SB431542_24 h_rep3

source_name: J1 mESC,SB431542, 24h, replicate 3


title: Asbestos15_3

value: crocidolite asbestos 15x10^6 μm2/cm2


title: Asbestos15_2


title: DMSO_24 h_rep2

source_name: J1 mESC, DMSO, 24h, replicate 2


title: SB431542_24 h_rep2

source_name: J1 mESC, SB431542, 24h, replicate 2


title: Lung-IUGR-P4-rep1


title: Asbestos15_1


title: Lung-Control-P4-rep1


title: siRNA Control, control treatment - 2

status: Public on Oct 28 2014

city: GIF SUR YVETTE

first: Adrien

last: Georges

address: CEA/SACLAY

institute: CNRS

hyb_protocol: Labeled cRNA was then fragmented and hybridized over 1 Sureprint G3 Mm9 8x60K array (Agilent technologies), according to manufacturer’s instructions.

scan_protocol: Agilent scanner

data_processing: Raw fluorescence data was extracted using Genespring software v12 (Agilent technologies). Raw fluorescence values were then subjected to log2 transformation and 75th percentile normalization for analysis

source_name: Primary mouse ovarian follicle cells, 9 days post dissection

label_protocol: 50 ng total RNA was amplified and labeled with Cy3 using Low input Quick Amp labeling Kit (Agilent technologies) according to manufacturer’s instruction.

growth_protocol: The ovaries of 8-week old female Swiss mice (pools of 5 mice per replicate for transcriptome analysis, 20 mice per condition for ChIP experiments) were dissected and digested in DMEM/F-12 medium (Gibco) containing 1mg/mL collagenase (Sigma-Aldrich), 0,5mg/mL BSA (Sidma-Aldrich) and 2000 U/mL DNase I (Thermo-Fisher), in a ratio of 500µL per ovary, at 37°C for 30 min. Ovaries were progressively dispersed during digestion using pipette tips of decreasing size to flush the organ debris. The mix was then diluted in 10 volumes of DMEM/F-12 medium, filtered using a 500 µm membrane, spinned at 300 g. The pellet was rinsed in cold PBS and spinned again, and the pelleted debris were resuspended in a PBS/Ficoll mix of density 1.10. A PBS/Ficoll gradient was made by depositing PBS/Ficoll layers of density 1.08, 1.07, 1.06, 1.05, 1.03 and 1. The gradient was spinned at 1500 g for 20min, and 1 mL fractions were collected and diluted in 5 mL culture medium (i.e. DMEM/F-12 supplemented with 4% FBS, 1% Insulin-Transferrin-Selenium-X supplement, 1% Penicillin-Streptomycine (Gibco) and 10-7M androstenedione (Sigma-Aldrich). We then manually collected intact preantral follicles, characterized by the presence of several layers of granulosa cells around the oocyte and the absence of antrum. They mainly migrated to the 1.07/1.06 and 1.06/1.05 interfaces. Follicles were then rinsed, transferred to culture plates and grown overnight. On day 1, they were dispersed using trypsin and then cultured in monolayers. Culture medium was changed on day 3, and cells were passed on days 5 and 7. On day 7, cultue medium was replaced with hormone free medium containing Phenol Red-free DMEM/F-12 and Optimem, charcoal treated FBS (Gibco) and no androstenedione.

extract_protocol: Trizol extraction

treatment_protocol: cells were seeded 18 h before transfection in 12-well plates. For transfection, cell medium was replaced with a premade Mix containing 500 µL Optimem (Gibco), a total of 12 pmol of siRNAs (2 x 6pmol in the case of simultaneous knockdown), 200 ng pDsRed plasmid (Clontech) and 2µL Lipofectamine 2000 (Life Technologies). 6h after transfection, 1.5 mL of culture medium was added to each well, and cells were then grown for 24h before lysis in 500 µL Trizol reagent (Life Technologies). 100nM Estradiol (from 100mM stock in EtOH) or vehicle was then added to medium 10h before lysis.

value: Swiss

value: Female

value: ovary

value: cells from preantral follicles maintained 9-days in culture (mostly granulosa cells)

tag: biological material provider

value: JANVIER SAS

tag: targeted mrna

tag: biological replica #


title: siRNA Control, E2 treatment - 2

tag: cell type


title: siRNA FOXL2, E2 treatment - 2

tag: age


title: DMSO_24 h_rep3

source_name: J1 mESC, DMSO, 24h, replicate 3


title: Lung-IUGR-P10-rep1

value: Sprague-Dawley

tag: tissue

value: whole lung


title: siRNA FOXL2, E2 treatment - 1


title: siRNA FOXL2, control treatment - 2


title: siRNA Control, control treatment - 1


title: siRNA FOXL2, control treatment - 1


title: siRNA Control, E2 treatment - 1


title: NL32_control_rep2

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

country: South Korea

institute: Asan Medical Center

description: Gene expression

hyb_protocol: Cyanine 3-labled linearly amplified cRNA was mixed with 10X blocking agent, nuclease-free water, and 25X fragmentation buffer provided in the Agilent Gene Expression Hybridization Kit (Agilent Technologies), and incubated for 30 min at 60oC to fragment RNA. After adding 2X GEx hybridization buffer Hi-RPM, the amplified fragmented RNA was hybridized on a Agilent SurePrint G3 Human GE v2 8x60K Microarray Chip using a SureHyb DNA Microarray Hybridization Chamber in a DNA Microarray Hybridization Oven (Agilent Technologies) at 10 rpm, 65℃ for 17 hours.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies).

data_processing: Feature Extraction Software v9 (Agilent Technologies) was used to extract and analyze the signals. To validate the amplification process, amplified and unamplified RNAs were labeled, hybridized and compared.

source_name: NL32_control, replicate 2

label_protocol: 0.5 ug of total RNA was amplified and labeled using Agilent Quick Amp Labeling Kit. After labeling, cRNA was purified with Qiagen’s RNeasy Mini-spin columns (QIAGEN, Germantown, MD) and quantified using NanoDrop ND-1000 UV-VIS Spectrophotometer for cyanine 3 dye concentration, RNA absorbance ratio (260 nm/280 nm), and cRNA concentration.

extract_protocol: RNA was extracted using RNeasy kit from 2 normal fibroblasts obtained by treatment protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fresh normal gastric tissues were obtained from 2 gastric cancer patients and minced with scalpels in a culture dish. Samples were enzymatically dissociated in 20 ml of D/F12+serum media containing collagenase I in a 37℃ incubation for 12-15 h. After digestion, samples were centrifuged at 700 rpm for 5 min to separate epithelial cells and fibroblast cells. Fibroblast cells (named as NL14 and NL32 from two normal gastric tissues, respectively) were collected from the supernatant by centrifugation at 800 rpm for 8 min, washed twice with PBS, and cultured in D/F12 media supplemented with 10% FBS and 1% antibiotics.

value: stomach

value: normal gastric fibroblast


title: CAF32_twist1_knockdown_rep1

description: Gene expression

source_name: CAF32_twist1_knockdown, replicate 1

extract_protocol: RNA was extracted using RNeasy kit from 2 cancer-associated fibroblasts obtained by treatment protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fresh gastric cancer tissues were obtained from 2 patients and minced with scalpels in a culture dish. Samples were enzymatically dissociated in 20 ml of D/F12+serum media containing collagenase I in a 37℃ incubation for 12-15 h. After digestion, samples were centrifuged at 700 rpm for 5 min to separate epithelial cells and fibroblast cells. Cancer-associated fibroblast cells (named as CAF14 and CAF32 from two gastric cancer tissues, respevtively) were collected from the supernatant by centrifugation at 800 rpm for 8 min, washed twice with PBS, and cultured in D/F12 media supplemented with 10% FBS and 1% antibiotics.

value: gastric cancer-associated fibroblast (CAF)


title: NL14_control_rep1

description: Gene expression

source_name: NL14_control, replicate 1


title: CAF14_twist1_knockdown_rep1

description: Gene expression

source_name: CAF14_twist1_knockdown, replicate 1


title: NL14_twist1_induction_rep2

description: Gene expression

source_name: NL14_twist1_induction, replicate 2


title: NL32_twist1_induction_rep2

description: Gene expression

source_name: NL32_twist1_induction, replicate 2


title: NL32_twist1_induction_rep1

description: Gene expression

source_name: NL32_twist1_induction, replicate 1


title: NL32_control_rep1

description: Gene expression

source_name: NL32_control, replicate 1


title: NL14_control_rep2

description: Gene expression

source_name: NL14_control, replicate 2


title: CAF14_twist1_knockdown_rep2

description: Gene expression

source_name: CAF14_twist1_knockdown, replicate 2


title: NL14_twist1_induction_rep1

description: Gene expression

source_name: NL14_twist1_induction, replicate 1


title: CAF32_twist1_knockdown_rep2

description: Gene expression

source_name: CAF32_twist1_knockdown, replicate 2


title: CAF32_control_rep2

description: Gene expression

source_name: CAF32_control_, replicate 2


title: CAF14_control_rep2

description: Gene expression

source_name: CAF14_control, replicate 2


title: CAF14_control_rep1

description: Gene expression

source_name: CAF14_control, replicate 1


title: CAF32_control_rep1

description: Gene expression

source_name: CAF32_control, replicate 1


title: Erythroid Prog B Thal Day 14 3

city: Perth

first: Luke

last: Forster

state: WA

address: Hopsital Ave

department: Haematology

country: Australia

institute: PathWest

description:
Sample_Name: S24
Sample_Group: Thal3_D14
Sentrix_ID: 8795274108
Sentrix_Position: L
Group_Classification: Thal_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch3
cRNA_batch_no: cRNA_Batch4

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina Illumina iScan protocol

data_processing:
The data was normalized using loess normalization using the limma R package within Bioconductor

Normalization/filtering steps were as follows:
1) First we removed intensity gradients in the arrays using the bead array HULK function
2) We then log transformed the data
3) Following this we utilised the bead array normaliseIllumina function using ?quantile? as the method of normalisation
4) Lastly, we filtered the probes against the illuminaHumanv4.db and removed probes that had no match, Non value associated with them  or were flagged as BAD by the bead array  normaliseIllumina function.

source_name: Erythroid Progenitor

label_protocol: Ambion Illumina RNA TotalPrep RNA amplification kit

extract_protocol: Ambion miRvana miRNA isolation kit

tag: subject group

value: β-thalassaemia patient

value: male

tag: mutation

value: peripheral blood

value: haematopoietic cells

tag: time in culture

value: 14 days


title: Erythroid Prog Control Day 14 6

description:
Sample_Name: S21
Sample_Group: CtlC6_D14
Sentrix_ID: 8795274108
Sentrix_Position: I
Group_Classification: Control_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch3
cRNA_batch_no: cRNA_Batch4

value: Healthy Control

value: female


title: Erythroid Prog B Thal Day 7 2

description:
Sample_Name: S17
Sample_Group: Thal2_D7
Sentrix_ID: 8795274108
Sentrix_Position: E
Group_Classification: Thal_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch4
cRNA_batch_no: cRNA_Batch3

value: 7 days


title: Erythroid Prog Control Day 14 2

description:
Sample_Name: S8
Sample_Group: CtlC2_D14
Sentrix_ID: 8795274088
Sentrix_Position: H
Group_Classification: Control_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch2
cRNA_batch_no: cRNA_Batch2


title: LEC-Podo-high_1

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description: Total RNA was directly end-labelled and hybridized onto LNA-microRNA slides

hyb_protocol: Hybridziation at 56°C for 16 hours was performed in a Tecan HS 400 hybridization station at high agitation speed (Tecan, Austria). After hybridization, automated washing, and slide drying with low stringent (2x SSC) and high stringent (0.2x SSC) wash buffers was performed.

scan_protocol: Arrays were immediately scanned after hybridization, using the Roche Nimblegen MS200 scanner (Roche, Germany) at 10 µM resolution, 100 % laser-power and auto-gain settings

data_processing:
Feature extraction from high-resolution tiff-images was performed using GenePix software (Molecular Devices, Sunnyvale, CA). Background correction and between-array normalization were performed with LIMMA under R/Bioconductor [28] using the minimum method and quantile normalization, respectively. Log2-transformed fold changes of miRNAs in the podoplaninlow and podoplaninhigh subpopulations were calculated using lmfit. Due to the exploratory character of this study, fold changes were prioritized against p-values, and therefore miRNAs were ranked according to log2 fold change between podoplaninhigh versus podoplaninlow subpopulations and the top50 candidates’ ±1.5 fold changes were considered as potentially differentially expressed.
Values in the matrix table represent log2 transformed normalized and background corrected data. Background correction was performed in R/LIMMA using minimum and normalization was done as between-array normalization using quantile function. Only data with Average log2 expression > 9 was considered for analysis

source_name: Lymphatic endothelial cells_high podoplanin

label_protocol: miRNA microarray experiments were run as described previously [27]. In brief, epoxy-coated Nexterion glass slides were spotted using the miRBase version 16.0 locked nucleic acid (LNA) probe set consisting of 2,367 probes against human, mouse and rat miRNAs in 8 replicates (Exiqon, Denmark). For hybridization 1000 ng total RNA extracts from two biological replicates of each sorted cell population were used. End-labeling of miRNAs with Cy3 was performed using the Exiqon Power Labeling Kit (Exiqon, Denmark) together with synthetic spike-in controls according to the instructions of the manufacturer. Slides were hybridized after an initial wash step with Cy3-labeled total RNA samples for 16 h at 56°C

growth_protocol: Cells were isolated from healthy donors with authorization of a local ethics committee and informed consent by the donor. LECs were isolated from human foreskins via podoplanin selection and immortalized by stable integration of human telomerase as described elsewhere [20, 21]. For the present study, LECs were used in passages 30 to 50. HUVECs were either purchased (C2519A, Lonza, Basel, Switzerland) or isolated from fresh umbilical cords as described before [22]. In brief, freshly donated umbilical cords were stored in antibiotics-containing phosphate buffer saline (PBS) at 4°C for 3 days following 0.2 % collagenase treatment (540 U/ml) for 20 min at 37 °C and centrifugation in endothelial growth medium (EGM-2, Lonza, Basel, Switzerland). Green fluorescent protein (GFP) expressing HUVEC were purchased from Olaf pharmaceuticals (Cat. No.: GFP, Worcester, USA). Adipose-derived stem cells (ASCs) were isolated from liposuction material as described before [23]. MG63, an osteosarcoma cell line, were purchased from ATCC (CRL-1427, Manassas, USA). LECs, HUVECs and ASCs were maintained in EGM-2 with 5 % fetal calf serum (FCS; GE Healthcare, Chalfont St Giles, UK) on surfaces coated with 2 µg/ml bovine fibronectin (Sigma-Aldrich, St. Louis, USA). ASCs were cultured on non-coated surfaces. The MG63 cell line was cultured in Dulbecco’s modified Eagle’s medium (DMEM; Sigma-Aldrich, St. Louis, USA) supplemented with 10 % FCS.

extract_protocol: The cells were resuspended in Trizol (Life Technologies, Carlsbad, USA) and chloroform (Carl Roth, Karlsruhe, Germany) was added. The suspension was mixed gently, left resting for 5 min at RT and afterwards centrifuged at 12,000 x g for 15 min at 4°C. The RNA was precipitated by isopropanol for 10 min at RT. After centrifugation at 12,000 x g for 15 min at 4°C, the RNA pellet was washed with 70 % ethanol, dried at RT and resuspended in sterile water. Total RNA quality was estimated from 28S and 18S ribosomal RNA peaks on a Bioanalyzer 2100 instrument using the RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Shockwaves were applied with a defocused Dermagold® 100 device and an OP155 applicator (MTS Medical, Konstanz, Germany). The cells were either stimulated in T25 cell culture flasks, in 15 ml or in 50 ml tubes (Greiner, Kremsmünster, Austria) in PBS with 10 % EGM-2. Cells were submerged in a water bath and stimulated with a frequency of 5 Hz, 200 pulses and energy flux densities ranging from 0.03 to 0.19 mJ/mm² at a constant pressure level of 1 bar as described elsewhere [24]. For fluorescence-activated cell sorting, LECs were cultivated to a total number of around 7 x 10^6 cells. The cells were enzymatically detached, centrifuged at 100 x g for 5 min and resuspended in cold EGM-2 to a concentration of 10 x 106 cells/ 700 µl. The mixed population was sorted with a MoFlo Astrios cell sorter (BD, Franklin Lakes, USA) according to the forward scatter (FSC) values. The cell suspensions were then centrifuged again at 100 x g for 5 min and the medium supernatant was removed.

value: Lymphatic endothelial cells

tag: podoplanin expression

value: high


title: LEC-Podo-low_1

source_name: Lymphatic endothelial cells_low podoplanin

value: low


title: LEC-Podo-low_2


title: LEC-Podo-high_2


title: Erythroid Prog Control Day 14 3

description:
Sample_Name: S9
Sample_Group: CtlC3_D14
Sentrix_ID: 8795274088
Sentrix_Position: I
Group_Classification: Control_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch3
cRNA_batch_no: cRNA_Batch2


title: Erythroid Prog B Thal Day 7 3

description:
Sample_Name: S18
Sample_Group: Thal3_D7
Sentrix_ID: 8795274108
Sentrix_Position: F
Group_Classification: Thal_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch3
cRNA_batch_no: cRNA_Batch3


title: Erythroid Prog B Thal Day 7 1

description:
Sample_Name: S16
Sample_Group: Thal1_D7
Sentrix_ID: 8795274108
Sentrix_Position: D
Group_Classification: Thal_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch1
cRNA_batch_no: cRNA_Batch3


title: Erythroid Prog B Thal Day 14 4

description:
Sample_Name: S10
Sample_Group: Thal4_D14
Sentrix_ID: 8795274088
Sentrix_Position: J
Group_Classification: Thal_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch1
cRNA_batch_no: cRNA_Batch2


title: Erythroid Prog B Thal Day 14 1

description:
Sample_Name: S22
Sample_Group: Thal1_D14
Sentrix_ID: 8795274108
Sentrix_Position: J
Group_Classification: Thal_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch1
cRNA_batch_no: cRNA_Batch4


title: Erythroid Prog B Thal Day 7 4

description:
Sample_Name: S4
Sample_Group: Thal4_D7
Sentrix_ID: 8795274088
Sentrix_Position: D
Group_Classification: Thal_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch1
cRNA_batch_no: cRNA_Batch1


title: Erythroid Prog B Thal Day 7 6

description:
Sample_Name: S6
Sample_Group: Thal6_D7
Sentrix_ID: 8795274088
Sentrix_Position: F
Group_Classification: Thal_Day7
HSC_DFU_Batch_no: HSC_DFU_Batch2
cRNA_batch_no: cRNA_Batch1


title: Erythroid Prog B Thal Day 14 2

description:
Sample_Name: S23
Sample_Group: Thal2_D14
Sentrix_ID: 8795274108
Sentrix_Position: K
Group_Classification: Thal_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch4
cRNA_batch_no: cRNA_Batch4


title: Erythroid Prog Control Day 14 5

description:
Sample_Name: S20
Sample_Group: CtlC5_D14
Sentrix_ID: 8795274108
Sentrix_Position: H
Group_Classification: Control_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch2
cRNA_batch_no: cRNA_Batch4


title: Erythroid Prog Control Day 14 4

description:
Sample_Name: S19
Sample_Group: CtlC4_D14
Sentrix_ID: 8795274108
Sentrix_Position: G
Group_Classification: Control_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch1
cRNA_batch_no: cRNA_Batch4


title: Erythroid Prog B Thal Day 14 6

description:
Sample_Name: S12
Sample_Group: Thal6_D14
Sentrix_ID: 8795274088
Sentrix_Position: L
Group_Classification: Thal_Day14
HSC_DFU_Batch_no: HSC_DFU_Batch2
cRNA_batch_no: cRNA_Batch2