title: HT2 C

source_name: Stage 2, Skins from berries grown under HT regime, replicate C

value: Stage 2, 10 days after véraison


title: HT4 B

status: Public on Jun 14 2017

type: RNA

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

molecule: total RNA

organism: Vitis vinifera

source_name: Stage 4, Skins from berries grown under HT regime, replicate B

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Experiments on grapevine berries were carried out in 2012 on 6-year-old uniformly-potted plants (V. vinifera cv. Sangiovese). The vines, grafted on SO4 rootstocks, were grown in 30-liter pots containing a 1:1 mixture of sand and soil. The number of shoots was standardized to nine shoots per vine. In addition, to achieve a uniform leaf area in all the vines, the tip of each shoot was removed and 15 main leaves were maintained before the experiment started. Before full véraison at the beginning of bunch closure (BBCH 77), 10 vines were selected and cluster numbers were adjusted to 11–12 clusters per vine.

extract_protocol: Total RNA was isolated from approximately 400 mg of berry skins using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich), with modifications as described in Dal Santo et al. (2016).

treatment_protocol: The selected vines were assigned to two treatments: low temperature (LT) and high temperature (HT). Five LT vines were placed from the beginning of bunch closure to harvest in a plastic greenhouse (20 m3) where the air temperature was controlled by a cooler and a fan was used to maintain airflow. During the night, the tunnel was opened. Simultaneously, five HT vines were positioned in an identical plastic greenhouse, whose basal segment was open but all the canopies were covered to maintain similar illumination to the LT vines.

tag: cultivar

value: Sangiovese

tag: sampling timepoints

value: Stage 4, 32 days after véraison

tag: thermal treatment

value: HT, high temperature regime, 26°C as average and 41.7°C as maximum air daily temperature


title: LT2 C

source_name: Stage 2, Skins from berries grown under LT regime, replicate C

value: LT, low temperature regime, 21°C as average and 35°C as maximum air daily temperature


title: HT3 A

source_name: Stage 3, Skins from berries grown under HT regime, replicate A

value: Stage 3, 20 days after véraison


title: HT2 A

source_name: Stage 2, Skins from berries grown under HT regime, replicate A


title: leftventricle_control_2days_rep26

status: Public on Jun 15 2017

city: Jackson

first: Damian

middle: G.

last: Romero

state: MS

address: 2500 N. State St.

department: Biochemistry

country: USA

institute: University of Mississippi Medical Center

hyb_protocol: The Hy3-labeled samples and a Hy5-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA array version 11.0 (Exiqon), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 13.0 at the Sanger Institute. The hybridization was performed according to the miRCURY LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization, the microarray slides were scanned using the Agilent G2565BA Microarray Scanner System and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery).

data_processing: The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global LOWESS (LOcally WEighted Scatterplot Smoothing) regression algorithm.

organism: Rattus norvegicus

source_name: left ventricle, Control, 2 days

label_protocol: One µg total RNA from sample and reference (a pool of all tested samples) was labelled with Hy3™ and Hy5™ fluorescent labels, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon) following the procedure described by the manufacturer.

growth_protocol: Eight-week old male Sprague Dawley rats (Harlan Laboratories) were maintained on standard condition with a 12:12h light-dark cycle with ad libitum access to standard rodent chow (Teklad #8640, Harlan Laboratories) and water. Studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals, 8th Edition, 2011.

extract_protocol: Total RNA (including miRNAs) was extracted with TRI-Reagent (MRC Gene), resuspended in nuclease free water and subjected to further purification using the RNeasy Mini kit (Qiagen) following an Exiqon modified protocol to preserve miRNAs. Purified total RNA was quantified by UV absorbance using the Nanodrop spectrophotometer (Nanodrop Technolologies) and quality checked by using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Animals were uninephrectomized and the next day randomly assigned to Control or Aldosterone/Salt (ALDO/SALT) experimental groups. ALDO (0.75 µg/h, Steraloids) was administered in PEG 300 (vehicle, Fluka) by subcutaneously implanted osmotic minipumps (Alzet 2004, Durect). SALT (1.0 % NaCl) was administered in the drinking fluid instead of tap water. ALDO-treated animals were supplemented with 0.3 % KCl in the drinking fluid to avoid hypokalemia. Animals were treated for 2, 7, 14, 28 or 56 days.

tag: tissue

value: left ventricle

tag: treatment

value: Control

tag: treatment time

value: 2 days

source_name: left ventricle, pooled


title: HT2 B

source_name: Stage 2, Skins from berries grown under HT regime, replicate B


title: HT4 A

source_name: Stage 4, Skins from berries grown under HT regime, replicate A


title: LT2 A

source_name: Stage 2, Skins from berries grown under LT regime, replicate A


title: LT1 C

source_name: Stage 1, Skins from berries grown under LT regime, replicate C

value: Stage 1, at véraison


title: HT1 A

source_name: Stage 1, Skins from berries grown under HT regime, replicate A


title: LT3 C

source_name: Stage 3, Skins from berries grown under LT regime, replicate C


title: HT1 B

source_name: Stage 1, Skins from berries grown under HT regime, replicate B


title: HT1 C

source_name: Stage 1, Skins from berries grown under HT regime, replicate C


title: LT2 B

source_name: Stage 2, Skins from berries grown under LT regime, replicate B


title: LT4 A

source_name: Stage 4, Skins from berries grown under LT regime, replicate A


title: CLL66

type: genomic

city: Christchurch

first: Christine

middle: M

last: Morris

state: Canterbury

address: 2 Riccarton Ave

department: Pathology

country: New Zealand

institute: University of Otago Christchurch

description: The amine-coated 1.4 Mb BAC HumArrays (UCSF) required cross-linking of target DNA to the slide prior to hybridisation. Target DNA was cross-linked by exposing slide to 260mJ of UV using Stratalinker® 2400 UV Crosslinker (Stratagene, CA, US). After cross-linking, a GeneFrame®-65 microliter was adhered to form a well around each array.

hyb_protocol: The Cy3-dUTP labelled test and Cy5-dUTP labelled reference probes were mixed with 75 micrograms of human Cot-1 DNA (1mg/ml, Invitrogen) and precipitated. The pellet was resuspended to a final volume of 70 microliter in hybridisation buffer (50% (v/v) formamide, 2 x SSC, 4% SDS (w/v), 100mg/ml dextran sulphate), and incubated at room temperature for 1 hour. Probe mixture was then denatured at 75 degrees C for 15 minutes and incubated at 37 degrees C for 1-2 hours to allow the Cot-1 DNA to anneal to repetitive sequences within the probe DNA. Array slides were pre-warmed at 37 degrees C and 70 microliter pre-hybridisation solution (50% (v/v) formamide, 2 x SSC, 4% SDS (w/v), 100mg/ml dextran sulphate) warmed to 37 degrees C was loaded into the well formed by a GeneFrame®-65 microliter (ABgene, Epsom, UK). Slides were tilted to wet the entire surface of the array and incubated at 37 degrees C for 2 minutes. Approximately 50 microliter pre-hybridisation solution was removed by pipetting and hybridisation mixture including labelled test and reference probes was immediately applied. Slides were incubated at 37 degrees C for 48-68 hours in a hybridisation chamber humidified with 50% formamide / 2 x SSC (pH 7.0) with continuous slow rocking. Post-hybridisation, slides were rinsed briefly under a stream of PN buffer (0.1 M sodium phosphate, 0.1 % Nonidet P40, pH 8.0), once in 50% formamide / 2 x SSC (pH 7.0) at 45 degrees C for 15 minutes with occasional stirring, and once in PN buffer at room temperature for 15 minutes with gentle agitation. Slides were then submerged in PN buffer as the Geneframe was removed. Slides were rinsed in H2O and dried by centrifugation at 60 x g (Eppendorf Centrifuge 5810) for 2 minutes and stored in the dark until scanned.

scan_protocol: Slides were scanned using GenePix 4000B scanner (Axon Instruments, Burlington, California). TIFF images were acquired using the GenePix Pro 4.0 software (Axon Instruments).

data_processing: For data analysis, the TIFF image was loaded into BlueFuse software for Microarrays (version 3.4, BlueGnome, Cambridge, UK). This software automatically defined spots, performed local background correction, calculated log2 ratios, and averaged triplicate clones. Poor quality spots were excluded using a spot filter setting implemented within the software. Spot filtering was based on two criteria: 1) spots with confidence level of <0.6, and 2) clones with >2 standard deviation (SD) between triplicate spots. Array data were normalised using block Lowess normalisation method. Array CGH experiments were analysed in full awareness of large scale copy number variations in healthy populations.

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA isolated from B-cells of a CLL patient

label_protocol: Genomic DNA (600ng) was labelled with Cy3-dUTP using the BioPrime® Array CGH Genomic Labelling kit (Invitrogen, Carlsbad, CA). The protocol was according to manufacturer’s instructions with minor modifications: total reaction volume was 25 microliter, including 10 microliter of 2.5 x random primer solution, 2.5 microliter 10 x dNTP mix (4mM dATP, 4mM dCTP, 4mM dGTP, 2mM dTTP), 1 microliter of 1mM Cy3-dUTP, and 0.6 microliter exo-Klenow polymerase enzyme, which lacks both 3’-5’ and 5’-3’ exonuclease activities.

extract_protocol: Genomic DNA was isolated using a guanidium isothiocyanate DNA extraction method. 50 million cells were mixed with 45ml lysis buffer (0.32M sucrose, 5mM MgCl2, 10mM Tris Cl (pH7.5), 1% Triton X) and centrifuged for 10 minutes at 1700 x g (Eppendorf Centrifuge 5810, Eppendorf). The supernatant was removed and the cell pellet was resuspended in 5ml of guanidium solution (4M guanidium isothiocyanate (Gibco BRL), 25mM sodium acetate, 0.84% beta-mercaptoethanol) by gentle rocking for 20 minutes. DNA was precipitated with one volume of 100% isopropanol and pelleted by centrifugation for 10 minutes at 1700 x g. The DNA pellet was washed three times in 10 ml of 70% ethanol, air-dried and resuspended in 500 microliter tris-EDTA (TE, pH 8.0) (10mM Tris Cl (pH 8.0), 1mM EDTA (pH 8.0) by rocking for 24 hours at room temperature

treatment_protocol: blood sample anticoagulated in EDTA

tag: gender

value: male

tag: age at sampling

value: Magnetic beads purified B-cells

tag: leukemic b-cell proportion in the sample tissue

source_name: Genomic DNA isolated from whole blood of a healthy individual

label_protocol: Genomic DNA (600ng) was labelled with Cy5-dUTP using the BioPrime® Array CGH Genomic Labelling kit (Invitrogen). The protocol was according to manufacturer’s instructions with minor modifications: total reaction volume was 25 microliter, including 10 microliter of 2.5 x random primer solution, 2.5 microliter 10 x dNTP mix (4mM dATP, 4mM dCTP, 4mM dGTP, 2mM dTTP), 1 microliter of 1mM Cy5-dUTP, and 0.6 microliter exo-Klenow polymerase enzyme, which lacks both 3’-5’ and 5’-3’ exonuclease activities.

extract_protocol: Genomic DNA was isolated using a guanidium isothiocyanate DNA extraction method. 5ml peripheral blood was mixed with 45ml lysis buffer (0.32M sucrose, 5mM MgCl2, 10mM Tris Cl (pH7.5), 1% Triton X) and centrifuged for 10 minutes at 1700 x g (Eppendorf Centrifuge 5810, Eppendorf). The supernatant was removed and the cell pellet was resuspended in 5ml of guanidium solution (4M guanidium isothiocyanate (Gibco BRL), 25mM sodium acetate, 0.84% beta-mercaptoethanol) by gentle rocking for 20 minutes. DNA was precipitated with one volume of 100% isopropanol and pelleted by centrifugation for 10 minutes at 1700 x g. The DNA pellet was washed three times in 10 ml of 70% ethanol, air-dried and resuspended in 500 microliter tris-EDTA (TE, pH 8.0) (10mM Tris Cl (pH 8.0), 1mM EDTA (pH 8.0) by rocking for 24 hours at room temperature.

value: female

value: peripheral blood


title: CLL66 vs germline

source_name: Genomic DNA isolated from neutrophils of the patient

extract_protocol: Genomic DNA was isolated using a guanidium isothiocyanate DNA extraction method. 50 million cells were mixed with 45ml lysis buffer (0.32M sucrose, 5mM MgCl2, 10mM Tris Cl (pH7.5), 1% Triton X) and centrifuged for 10 minutes at 1700 x g (Eppendorf Centrifuge 5810, Eppendorf). The supernatant was removed and the cell pellet was resuspended in 5ml of guanidium solution (4M guanidium isothiocyanate (Gibco BRL), 25mM sodium acetate, 0.84% beta-mercaptoethanol) by gentle rocking for 20 minutes. DNA was precipitated with one volume of 100% isopropanol and pelleted by centrifugation for 10 minutes at 1700 x g. The DNA pellet was washed three times in 10 ml of 70% ethanol, air-dried and resuspended in 500 microliter tris-EDTA (TE, pH 8.0) (10mM Tris Cl (pH 8.0), 1mM EDTA (pH 8.0) by rocking for 24 hours at room temperature.

value: neutrophils


title: CLL55 vs germline


title: CLL57 vs germline


title: LT1 B

source_name: Stage 1, Skins from berries grown under LT regime, replicate B


title: CLL58 vs germline


title: CLL53


title: CLL54

source_name: Genomic DNA isolated from PBMCs of a CLL patient

value: Ficoll-Hypaque purified peripheral blood mononuclear cells (PBMC)


title: CLL55


title: CLL63


title: CLL57


title: CLL62


title: CLL52


title: CTRL C

source_name: Stage 0, Skins from control berries, Replicate C

value: Stage 0, one week before véraison

value: Control vines


title: CLL49


title: CLL45


title: CLL43


title: CLL48


title: CLL50


title: CLL46


title: CLL42


title: CLL58


title: CLL40


title: CLL41


title: CLL38


title: CLL39


title: LT1 A

source_name: Stage 1, Skins from berries grown under LT regime, replicate A

value: Sangiovese


title: CTRL B

source_name: Stage 0, Skins from control berries, Replicate B


title: CLL47


title: CTRL A

source_name: Stage 0, Skins from control berries, Replicate A


title: CLL35


title: CLL37


title: CLL30


title: CLL32


title: CLL33


title: CLL31


title: CLL36


title: CLL28


title: CLL29


title: CLL34


title: CLL26


title: CLL23


title: CLL24


title: CLL20

value: Male


title: CLL25


title: CLL16


title: CLL15


title: CLL18


title: CLL17


title: CLL13


title: CLL10

value: Magentic beads purified B-cells


title: CLL8


title: CLL7

value: magnetic beads purified peripheral blood mononuclear cells (PBMC)


title: CLL22


title: CLL4


title: CLL5


title: CLL9


title: NIPPONBARE_well_watered_rep3

city: Shanghai

first: haibin

last: wei

address: 294 Taiyuan Road

department: Institute for Nutritional Sciences

country: China

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

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: The raw data were processed with RMA function in Affy package of the BioConductor and differential gene expression was assessed using limma package on the Bioconductor.

label: biotin

organism: Oryza sativa

label_protocol: Five mg of total RNA was reverse-transcribed to cDNA, and then 2 μg cDNA was used for probe labeling according to the instructions of Affymetrix Rice Genome Array.

growth_protocol: Rice grew in cement enclosed plots.

extract_protocol: The young panicles in 2 cm length were harvested for RNA extraction.

treatment_protocol: Drought treatments were conducted at later tillering stage and allowed to dry.

tag: variety

value: NIPPONBARE

tag: developmental stage

value: reproductive development

tag: treatment group

value: well-watered (control)

value: young panicles (2 cm in length)


title: CLL2


title: NIPPONBARE_drought_stressed_rep2

value: drought-stressed


title: CLL3


title: NIPPONBARE_drought_stressed_rep3


title: NIPPONBARE_well_watered_rep2


title: NIPPONBARE_drought_stressed_rep1


title: HUHAN3_drought_stressed_rep3


title: CLL1

description: The amine-coated 1.4 Mb  BAC HumArrays (UCSF) required cross-linking of target DNA to the slide prior to hybridisation. Target DNA was cross-linked by exposing slide to 260mJ of UV using Stratalinker® 2400 UV Crosslinker (Stratagene, CA, US). After cross-linking, a GeneFrame®-65 microliter was adhered to form a well around each array.

hyb_protocol: The Cy3-dUTP labelled test and Cy5-dUTP labelled reference probes were mixed with 75 micrograms of human Cot-1 DNA (1mg/ml, Invitrogen) and precipitated. The pellet was resuspended to a final volume of 70 microliter in hybridisation buffer (50% (v/v) formamide, 2 x SSC, 4% SDS (w/v), 100mg/ml dextran sulphate), and incubated at room temperature for 1 hour. Probe mixture was then denatured at 75 degrees C for 15 minutes and incubated at 37 degrees C for 1-2 hours to allow the Cot-1 DNA to anneal to repetitive sequences within the probe DNA. Array slides were pre-warmed at 37 degrees C and 70 microliter pre-hybridisation solution (50% (v/v) formamide, 2 x SSC, 4% SDS (w/v), 100mg/ml dextran sulphate) warmed to 37 degrees C was loaded into the well formed by a GeneFrame®-65 microliter (ABgene, Epsom, UK). Slides were tilted to wet the entire surface of the array and incubated at 37 degrees C for 2 minutes. Approximately 50 microliter pre-hybridisation solution was removed by pipetting and hybridisation mixture including labelled test and reference probes was immediately applied. Slides were incubated at 37 degrees C for 48-68 hours in a hybridisation chamber humidified with 50% formamide / 2 x SSC (pH 7.0) with continuous slow rocking. Post-hybridisation, slides were rinsed briefly under a stream of PN buffer (0.1 M sodium phosphate, 0.1 % Nonidet P40, pH 8.0), once in 50% formamide / 2 x SSC (pH 7.0) at 45 degrees C for 15 minutes with occasional stirring, and once in PN buffer at room temperature for 15 minutes with gentle agitation.  Slides were then submerged in PN buffer as the Geneframe was removed. Slides were rinsed in H2O and dried by centrifugation at 60 x g (Eppendorf Centrifuge 5810) for 2 minutes and stored in the dark until scanned.


title: NIPPONBARE_well_watered_rep1


title: HUHAN3_well_watered_rep2


title: KHAUMEO_drought_stressed_rep2

value: KHAUMEO


title: KHAUMEO_well_watered_rep1


title: DOURADOAGULHA_well_watered_rep2

value: DOURADOAGULHA


title: HUHAN3_well_watered_rep1


title: DOURADOAGULHA_drought_stressed_rep3


title: EMATAYIN_drought_stressed_rep3

value: EMATAYIN


title: KHAUMEO_well_watered_rep3


title: HUHAN3_drought_stressed_rep2


title: DOURADOAGULHA_drought_stressed_rep1


title: HUHAN3_well_watered_rep3


title: EMATAYIN_drought_stressed_rep2


title: EMATAYIN_well_watered_rep3


title: MILT1444_well_watered_rep2


title: DOURADOAGULHA_well_watered_rep1


title: DOURADOAGULHA_drought_stressed_rep2


title: MILT1444_drought_stressed_rep1


title: MILT1444_well_watered_rep1


title: DOURADOAGULHA_well_watered_rep3


title: MILT1444_drought_stressed_rep3


title: MILT1444_well_watered_rep3


title: KHAUMEO_drought_stressed_rep1


title: MILT1444_drought_stressed_rep2


title: EMATAYIN_drought_stressed_rep1


title: KHAUMEO_well_watered_rep2


title: EMATAYIN_well_watered_rep1


title: KHAUMEO_drought_stressed_rep3


title: HUHAN3_drought_stressed_rep1


title: MLL&FLT3-ITD_p53-/-#1_in vitro

city: Houston

first: Zhiqiang

last: Wang

state: Texas

address: 7455 Fannin St.

department: Lymphoma and Myeloma

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value. Values below the detection threshold (determined from the P95) value for negative control probes were floored, i.e., set to the detection threshold value. Probes were then excluded for which <25% of the samples in the dataset exceeded the detection threshold value.

organism: Mus musculus

source_name: MLL&FLT3-ITD_p53-/-_in vitro

label_protocol: 200 ng of total RNA was reverse-transcribed, biotinylated, and amplified by standard Eberwine labeling with the  Illumina TotalPrep RNA Amplification Kit

growth_protocol: Syngeneic primary AML cells, generated by retroviral introduction of known AML fusion oncogenes as previously described (PMID: 19339691), were used to inoculate C57BL/6 mice. Transplanted leukemia was allowed to progress for 2-4 weeks until adequate disease burden was achieved, and then mice were sacrificed and BM was obtained by flushing mice femurs with saline. For each condition and replicate, BM was pooled from multiple mice, and BM-MSC were isolated by flow cytometric sorting for the phenotype Ter119-, CD31-, CD45-, CD105+, Sca1+, CD106+ and PDGFRα+ (CD140). In vitro co-cultures of normal mouse BM-MSC and mouse AML primary cell lines were performed as previously described (PMID: 24599548) for 48 hr, then BM-MSC (including from mono-cultures) underwent similar flow cytometric isolation.

extract_protocol: Total RNA was isolated from harvested cells with the RNAqueous Total RNA Isolation Kit (Thermo Scientific, catalog#: AM1912) with subsequent RNA quality assessment using Agilent 2100 Bioanalyzer.

tag: strain background

tag: cell type

value: bone marrow mesenchymal stromal cells (BM_MSCs)

tag: sample type

value: Harvest after in vitro culture

tag: sample group

value: AML co-cultured:MLL&FLT3-ITD_p53-/-

tag: replicate

value: one of two duplicates


title: MLL&FLT3-ITD_p53WT#2_in vitro

source_name: MLL&FLT3-ITD_p53WT_in vitro

value: AML co-cultured:MLL&FLT3-ITD_p53WT


title: EMATAYIN_well_watered_rep2


title: MLL-ENL#1_Expt2

source_name: MLL-ENL

value: Direct harvest from mice


title: Control#2_in vitro

source_name: Control_in vitro

value: Not AML-exposed (mono-culture)


title: Control#1_in vitro


title: AML-ETO#2_Expt2

source_name: AML-ETO


title: MLL&FLT3-ITD_p53WT#1_in vitro


title: MLL-ENL#2_Expt2


title: Control#2_Expt2

source_name: Control

value: Control (non-AML) mice


title: MLL&FLT3-ITD_p53-/-#2_in vitro


title: AML-ETO#1_Expt2


title: Imiquimod-treated Zfp36 KO mouse, rep5

city: Gosselies

first: Stanislas

last: Goriely

address: 8 rue A. Bolland

department: Institute for Medical Immunology

country: Belgium

institute: Université Libre de Bruxelles

hyb_protocol: Following fragmentation, 5.5 ug of sscDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Control using Affymetrix default analysis settings and global scaling as normalization method.

source_name: abdominal skin, Zfp36 KO, imiquimod-treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol WT PLUS from 200ng total RNA.

extract_protocol: Trizol extraction of skin total RNA, followed by a purification using RNeasy Mini Kit (Qiagen) was performed according to the manufacturer's instructions.

treatment_protocol: Mice were topically treated or not with imiquimod during 5 consecutive days. 4h after the last application, skins from abdomen were sampled. Skin samples were snap-frozen in liquid nitrogen immediately after collection.

tag: genotype/variation

value: zfp36 fl/fl K14 cre

value: abdominal skin

value: imiquimod


title: Imiquimod-treated Zfp36 KO mouse, rep3


title: Mock-treated Zfp36 KO mouse, rep4

source_name: abdominal skin, Zfp36 KO, mock-treated

value: mock


title: Imiquimod-treated Zfp36 KO mouse, rep2


title: Mock-treated Zfp36 KO mouse, rep5


title: MLL&FLT3-ITD_p53WT_Expt1

value: single replicate


title: Control_Expt1


title: Mock-treated Zfp36 KO mouse, rep3


title: Imiquimod-treated mouse, rep2

source_name: abdominal skin, control, imiquimod-treated

value: zfp36 fl/fl


title: Imiquimod-treated mouse, rep3


title: Imiquimod-treated mouse, rep4


title: MLL&FLT3-ITD_p53-/-_Expt1


title: Imiquimod-treated mouse, rep5


title: Mock-treated mouse, rep2

source_name: abdominal skin, control, mock-treated


title: Mock-treated mouse, rep3


title: Mock-treated mouse, rep5


title: M2-like macrophages (Peritoneal) -2

city: Saitama

first: Manabu

last: Shiraishi

address: Omiya

country: Japan

institute: Jichi Medical University

description: SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: peritoneal cavity

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

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

tag: strain

tag: age

value: 10 weeks

value: peritoneal cavity

value: M2-like macrophages


title: Mock-treated Zfp36 KO mouse, rep1

tag: tissue


title: Mock-treated mouse, rep4

tag: treatment


title: Imiquimod-treated mouse, rep1


title: M2-like macrophages (Peritoneal) -1

description: SAMPLE 5


title: Imiquimod-treated Zfp36 KO mouse, rep4


title: M2-like macrophages (Intact heart) -2

description: SAMPLE 2

source_name: heart

value: heart

tag: condition

value: intact heart


title: M2-like macrophages (MI heart) -2

description: SAMPLE 4

source_name: myocardial infarction heart

value: myocardial infarction heart


title: M2-like macrophages (MI heart) -1

description: SAMPLE 3


title: Mock-treated mouse, rep1


title: Basal lamina digested brain vessels 4

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities and then quantile normalized.

source_name: brain vessels submitted to a partial extracellular matrix digestion

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Total RNA were extracted from 2-month-old C57BL6 brain vessels submitted or not to basal lamina digestion using the Rneasy Lipid tissue kit (Qiagen).

value: 2 months

tag: gender

value: male

value: vessels extracted mechanically from the brain

tag: subjected to

value: partial basal lamina enzymatic digestion


title: Imiquimod-treated Zfp36 KO mouse, rep1


title: Mock-treated Zfp36 KO mouse, rep2


title: Basal lamina digested brain vessels 3


title: Undigested brain vessels 3

source_name: brain vessels


title: Lesional epidermis from psoriatic skin, sample 7, set 2

city: Lille

first: Denis

middle: A

last: Mogilenko

address: 1 Rue du Professeur Calmette, BP245

institute: INSERM

description:
Gene expression in human lesional psoriatic epidermis
PN7EL

hyb_protocol: 1.5 ug of Cy3-labelled cRNA was hybridized with Human Gene Expression Microarray 8x60K chip (Agilent Technologies) according to manufacturer's protocol

scan_protocol: Slides were scanned with the Agilent G2505B scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1). Data were background-corrected with 'normexp' option and quantile normalized using limma R package.

source_name: Human lesional psoriatic epidermis (laser capture microdissection), sample 7

label_protocol: 10 ng RNA were amplified with ExpressArt Kit and labeled (Cy3) with One-color microarray-based Gene Expression Analysis Low Input Quick Amp WT Labeling (Agilent Technologies) according to manufacturer's protocol

extract_protocol: RNA was isolated with Arcturus Picopure RNA isolation Kit according to manufacturer's protocol

tag: disease state

value: psoriasis

value: epidermis


title: Basal lamina digested brain vessels 1


title: Epidermis from healthy skin, sample 4, set 2

description:
Gene expression in human healthy epidermis
CN4Eh

source_name: Human healthy epidermis (laser capture microdissection), sample 4

value: control

value: female


title: Undigested brain vessels 1


title: Basal lamina digested brain vessels 2


title: Lesional epidermis from psoriatic skin, sample 14, set 2

description:
Gene expression in human lesional psoriatic epidermis
PN14EL

source_name: Human lesional psoriatic epidermis (laser capture microdissection), sample 14


title: Epidermis from healthy skin, sample 2, set 2

description:
Gene expression in human healthy epidermis
CN2Eh

source_name: Human healthy epidermis (laser capture microdissection), sample 2


title: Epidermis from healthy skin, sample 6, set 1

description:
Gene expression in human healthy epidermis
CN6Eh

source_name: Human healthy epidermis (laser capture microdissection), sample 6


title: M2-like macrophages (Intact heart) -1

description: SAMPLE 1


title: Lesional epidermis from psoriatic skin, sample 15, set 2

description:
Gene expression in human lesional psoriatic epidermis
PN15EL

source_name: Human lesional psoriatic epidermis (laser capture microdissection), sample 15


title: Lesional epidermis from psoriatic skin, sample 6, set 1

description:
Gene expression in human lesional psoriatic epidermis
PN6EL

source_name: Human lesional psoriatic epidermis (laser capture microdissection), sample 6


title: Control#1_Expt2

source_name: Control

value: bone marrow mesenchymal stromal cells (BM_MSCs)

value: Direct harvest from mice

value: Control (non-AML) mice

value: one of two duplicates


title: Undigested brain vessels 4


title: Lesional epidermis from psoriatic skin, sample 4, set 1

description:
Gene expression in human lesional psoriatic epidermis
PN4EL

source_name: Human lesional psoriatic epidermis (laser capture microdissection), sample 4


title: Epidermis from healthy skin, sample 7, set 1

description:
Gene expression in human healthy epidermis
CN7Eh

source_name: Human healthy epidermis (laser capture microdissection), sample 7


title: Lesional epidermis from psoriatic skin, sample 8, set 1

description:
Gene expression in human lesional psoriatic epidermis
PN8EL

source_name: Human lesional psoriatic epidermis (laser capture microdissection), sample 8


title: Epidermis from healthy skin, sample 1, set 2

description:
Gene expression in human healthy epidermis
CN1Eh

source_name: Human healthy epidermis (laser capture microdissection), sample 1


title: Undigested brain vessels 2


title: Ethanol-treated_day3_container

city: Nasushiobara

first: Ryo

last: Okada

state: Tochigi

address: 768 Senbonmatsu

department: Forage Crop Research Division

institute: NARO Institute of Livestock and Grassland Science

hyb_protocol: 825ng of labelled cRNA were hybridized using Gene Expression Hybridization Kit following manufacturer's instructions at NIAS RGRC Open Laboratory.

scan_protocol: Scanned with Agilent G2505C.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).
Signal after background detrend, multiplicative detrend and dye normalization by Agilent Feature Extraction Software. As previously described in Izawa, T. et al., Plant Cell. 23, 1741-1755 (2011) [PMID 21571948], data processed from the redundant 44,000 probes in the chip were summarized into expression of 27,201 genes; if multiple probes were assigned for the same gene, averaged processed data represented expression of the corresponding genes. A set of microarray data was normalized and analyzed as described in Izawa, T. et al., Plant Cell. 23, 1741-1755 (2011).

organism: Oryza sativa Japonica Group

source_name: leaf, container, Ethanol, 3 days

label_protocol: 400 ng of total RNAs were reverse-transcribed and labelled using Agilent's Quick Amp Labeling Kit following the manufacturer's instructions. Labelled cRNAs were purified with the Qiagen RNeasy Mini Kit.

growth_protocol: The rice seedlings were transplanted in a paddy field at Tsukuba (lat 140° 05’E long 36° 01’N) and then were grown until the beginning of the chemical treatments. Some plants grown in the paddy field were retransplanted in containers located in the field before chemical treatments.

extract_protocol: Total RNAs were extracted using Qiagen RNeasy Mini Kit following manufacturer's instructions.

treatment_protocol: In the paddy field, plants were treated with 1 kg/a Oryzemate granules (24% of probenazole; Meiji Seika, Tokyo, Japan) and 1 kg/a Routine granules (3% of isotianil, Bayer CropScience, Leverkusen, Germany), respectively. Plants transplanted in containers were treated with 1 kg/a Oryzemate granules (24% of probenazole; Meiji Seika, Tokyo, Japan), 1 kg/a Routine granule (3% of isotianil; Bayer CropScience, Leverkusen, Germany), 100ppm Bion (5% of ASM; Syngenta, Basel, Switzerland) as BTH, 3 kg/a V-get granules (6% of tiadinil; Nihon Nohyaku, Tokyo, Japan) and 1% ethanol, respectively. After the treatments, leaves from plants in each test section were sampled with time for total RNA preparation.

tag: cultivar

value: Nipponbare

value: leaf

tag: chemical treatment

value: Ethanol

tag: sampling time

value: 3 days after treatment

tag: location

value: Tsukuba

value: container located in field


title: Routine-treated_day1_container

source_name: leaf, container, Routine, 1 day

value: Routine

value: 1 day after treatment


title: Routine-treated_day3_container

source_name: leaf, container, Routine, 3 days


title: BTH-treated_day3_container

source_name: leaf, container, Benzothiadiazole, 3 days

value: Benzothiadiazole


title: Vget-treated_day3_container

source_name: leaf, container, V-get, 3 days

value: V-get


title: Untreated_day1_container

source_name: leaf, container, untreated, 1 day


title: Untreated_day3_container

source_name: leaf, container, untreated, 3 days


title: Oryzemate-treated_day3_container

source_name: leaf, container, Oryzemate, 3 days

value: Oryzemate


title: BTH-treated_day1_container

source_name: leaf, container, Benzothiadiazole /Bion flowable 5, 1 day

value: Benzothiadiazole /Bion flowable 5


title: Oryzemate-treated_day1_container

source_name: leaf, container, Oryzemate, 1 day


title: Untreated_day3_field_replicate1

source_name: leaf, paddy field, untreated, 3 days

value: paddy field


title: Oryzemate-treated_day3_field_replicate1

source_name: leaf, paddy field, Oryzemate, 3 days


title: Vget-tyreated_day1_container

source_name: leaf, container, V-get, 1 day


title: Routine-treated_day3_field_replicate1

source_name: leaf, paddy field, Routine, 3 days


title: Untreated_day3_field_replicate2


title: MEK inhibitor 1h_3

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

hyb_protocol: Chips were washed and stained with streptavidin-phycoerythrin using a fluidics station according to the protocols recommended by the manufacturer

scan_protocol: arrays were scanned at 1.56-µm resolution using the Affymetrix GeneChip System confocal scanner 3000

data_processing: raw CEL files were red in, normalised using robust multi-array average (rma) of the package oligo with the parameter target=”full”.

molecule: polyA RNA

source_name: hippocampus of  mouse 1h post MEK inhibitor treatment

label_protocol: The amplification and labeling of RNA samples were conducted according to the manufacturer's instructions (Affymetrix).

growth_protocol: 3 month old male C57/bl6 mice were housed with a 12 hours dark-light-schedule and experiments were performed during the dark cycle always at identical time points

extract_protocol: For RNA isolation hippocampi were dissected from fresh brains, flash frozen and stored at -80 °C. Total RNA was isolated using TRItidy-reagent (Applichem), followed by an additional purification step using RNEasy columns (Qiagen), quantified by UV-spectroscopy and its quality verified using a LabChip BioAnalyzer (AGILENT Technologies).

treatment_protocol: Kainic acid (Ascent scientific) (20 mg/kg, dissolved in PBS), SL327 (Sigma) (50mg/kg, dissolved in dimethylsulfoxide (DMSO) and mixed 1:1 with PBS) or similar amounts of DMSO/PBS were administered by intraperitoneal injection. Mice treated with kainic acid and SL327 were administered with SL327 1 hour before kainic acid injections. Animals were sacrificed at given time points after onset of seizure or at corresponding time points after SL327 or vehicle injections as described before (Hermey et al, 2013)

tag: genotype

value: wildtype

value: brain

tag: tissue compartment

value: hippocampus

value: 3 months

value: male

tag: time

tag: inhibitor


title: Routine-treated_day14_field

source_name: leaf, paddy field, Routine, 14 days

value: Nipponbare

value: leaf

value: 14 days after treatment


title: Oryzemate-treated_day30_field

source_name: leaf, paddy field, Oryzemate, 30 days

value: 30 days after treatment

value: Tsukuba


title: MEK inhibitor 1h_1


title: Routine-treated_day30_field

source_name: leaf, paddy field, Routine, 30 days

value: Routine


title: Kinate  and MEK inhibitor 1h_3

source_name: hippocampus of  mouse 1h post kinate induced seizure in the presence of MEK inhibitor

value: kinate


title: Ethanol-treated_day1_container

source_name: leaf, container, Ethanol, 1 day

value: Ethanol

value: 1 day after treatment

value: container located in field


title: Untreated_day30_field

source_name: leaf, paddy field, untreated, 30 days


title: Kinate  and MEK inhibitor 1h_2


title: Oryzemate-treated_day14_field

source_name: leaf, paddy field, Oryzemate, 14 days

value: Oryzemate


title: Routine-treated_day1_field

source_name: leaf, paddy field, Routine, 1 day

value: paddy field


title: Untreated_day14_field

source_name: leaf, paddy field, untreated, 14 days


title: Oryzemate-treated_day7_field

source_name: leaf, paddy field, Oryzemate, 7 days

value: 7 days after treatment


title: Kinate 1h_2

source_name: hippocampus of  mouse 1h post kinate induced seizure

value: wildtype

value: brain


title: Kinate 1h_3

value: hippocampus

value: 3 months


title: Routine-treated_day7_field

source_name: leaf, paddy field, Routine, 7 days

value: Nipponbare


title: Kinate  and MEK inhibitor 1h_1

value: male


title: Vehicle Control 1h_2

source_name: hippocampus of  mouse 1h post injection of PBS

value: PBS


title: Vehicle Control 1h_3


title: Routine-treated_day3_field_replicate2

value: leaf

value: 3 days after treatment


title: Untreated_day7_field

source_name: leaf, paddy field, untreated, 7 days

value: Tsukuba


title: Oryzemate-treated_day1_field

source_name: leaf, paddy field, Oryzemate, 1 day


title: Vehicle Control 1h_1


title: MEK inhibitor 1h_2


title: Untreated_day0_field

source_name: leaf, paddy field, untreated, 0 days

value: before treatment


title: Oryzemate-treated_day3_field_replicate2

source_name: leaf, paddy field, Oryzemate, 3 days


title: Untreated Control_1

source_name: hippocampus of untreated mouse


title: Untreated Control_2


title: Untreated Control_3


title: Untreated Control_4


title: MDA-MB-231 shMCT2 (10mM bHB)

status: Public on Jun 13 2017

city: Taipei

first: Chun-Kai

last: Huang

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Genomics Research Center, Academia Sinica

description: cDNA expression profiling

hyb_protocol: Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50 ℃, non-speciﬁc binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 500 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.

source_name: MDA-MB-231 shMCT2 treated w/ 10 mM β-hydroxybutyrate

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % fetal bovine serum (FBS), 2 mM L-glutamine, 1 mM non-essential amino acids (NEAA), 1 mM sodium pyruvate and antibiotics/antimycotics in a humidified 37°C incubator supplemented with 5% CO2.

extract_protocol: RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

treatment_protocol: The cells were cultured in the presence of 10 mM β-hydroxybutyrate, and PBS was used as control.

tag: cell line

tag: modification

value: 10mM bHB


title: Untreated_day1_field_replicate1

source_name: leaf, paddy field, untreated, 1 day

value: 1 day after treatment


title: MDA-MB-231 shMCT2 (PBS)

description: cDNA expression profiling

source_name: MDA-MB-231 shMCT2 cells treated w/ PBS


title: Untreated_day1_field_replicate2


title: MDA-MB-231 shLacZ (PBS)

description: cDNA expression profiling

source_name: MDA-MB-231 shLacZ treated w/ PBS

value: shLacZ


title: MCF7-shEP2, Paclitaxel (20 nM) resistant, biological rep 3

city: Zaragoza

first: Patricia

last: Sancho

state: Aragón

address: P. Isabel la Católica 1-3

department: Traslational Research Unit

country: Spain

institute: Hospital Miguel Servet IIS Aragón

hyb_protocol: Following fragmentation and labeling, 3.5 µg of ss-cDNA were hybridized for 16 hr at 45°C on GeneChip® Cartridge Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix, P/N 00-0079).

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

data_processing: The data were analyzed with Partek Genomics Suite version 6.6  using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Paclitaxel (20 nM) resistant derivative of corresponding line containing shEP300 construct

label_protocol: Biotinylated single-stranded cDNA (ss-cDNA) samples were prepared according to the standard Affymetrix protocol from 5.5 µg ss-cDNA (User Guide for GeneChip® WT PLUS Reagent Kit, Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays (P/N 703147 Rev. 3, Affymetrix).

growth_protocol: All the EP300 knocked-down and their corresponding paclitaxel resistant derivatives MCF7 cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) containing fetal calf serum (FCS) and glutamine.

extract_protocol: RNA extractions were performed using RNeasy Mini Kit from QIAGEN and according to the manufacturer's instruction. A post-extraction QC checking of the RNA sample integrity was performed by measuring RNA Integrity Number (RIN) using a bioanalyser (Agilent 2100, DE24802458, ver. 2.6).

tag: cell type

value: epithelial breast cancer cell line

tag: transfected with

value: lentiviral vector containing a shEP300 construct targeting EP300

tag: genotype/phenotype

value: containing shEP2, (a second hairpin targeting human EP300) resistant to 20 nM paclitaxel


title: MCF7-shEP2, Paclitaxel (20 nM) resistant, biological rep 2


title: MCF7-shEP2, Paclitaxel (20 nM) resistant, biological rep 1


title: MCF7-shEP1, Paclitaxel (20 nM) resistant, biological rep 3

value: containing shEP1 (a hairpin targeting human EP300) resistant to 20 nM paclitaxel


title: MCF7-shEP1, biological rep 3

source_name: MCF7 cell stably transfected with lentiviral vector containing a shEP300 construct targeting EP300

value: containing shEP1, a hairpin targeting human EP300


title: MCF7-shEP2, biological rep 1

value: containing shEP2, another hairpin targeting human EP300


title: MCF7-shEP1, Paclitaxel (20 nM) resistant, biological rep 1


title: MCF7-pGIPZ, biological rep 1

source_name: MCF7 cell stably transfected with pGIPZ lentiviral vector (control line)

value: pGIPZ lentiviral vector (control line)

value: expressing empty vector control containing pGIPZ lentiviral construct


title: MCF7-shEP1, biological rep 2


title: MCF7-shEP2, biological rep 2


title: MCF7-shEP1, biological rep 1


title: MCF7-pGIPZ, biological rep 4


title: MCF7-shEP1, Paclitaxel (20 nM) resistant, biological rep 2


title: MCF7-shEP2, biological rep 3


title: MCF7-pGIPZ, biological rep 2


title: MCF7-pGIPZ, biological rep 3


title: MDA-MB-231 shLacZ (10mM bHB)

description: cDNA expression profiling

source_name: MDA-MB-231 shLacZ treated w/ 10 mM β-hydroxybutyrate

tag: treatment


title: Kinate 1h_1

tag: strain

value: wildtype

tag: tissue

value: brain

value: hippocampus

tag: age

value: 3 months

tag: gender

value: male

value: kinate


title: DGM-12759_M0_sm (NG)

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: Sample name: DGM-12759

hyb_protocol: Labeling and hybridization were done according to Roche-NimbleGen, Inc. protocol. The array is 720K Roche NimbleGen custom array for HpII tiny fragment Enriched by Ligation-mediated PCR (HELP) assay designname 1000128_HG19_MKF_HELP_ChIP

scan_protocol: Software: NimbleScan version 2.5.26

data_processing: NimbleScan version 2.5.26 followed by quality control of arrays including assessment of MspI and HpaII intensity distributions and generation of log2 Q-centered, quantile-normalized unmethylated/methylated (HpaII/MspI) ratio.

source_name: small airway epithelium brushing, MspI

label_protocol: Labeling and hybridization were done according to Roche-NimbleGen, Inc. protocol. The array is 720K Roche NimbleGen custom array for HpII tiny fragment Enriched by Ligation-mediated PCR (HELP) assay designname 100128_HG19_MKF_HELP_ChIP

extract_protocol: Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the HELP protocol

tag: smoking status

value: waterpipe smoker

value: small airway epithelium brushing

tag: restriction enzyme

value: MspI

source_name: small airway epithelium brushing, HpaII

value: HpaII


title: DGM-12719_M0_sm (NG)

description: Sample name: DGM-12719


title: DGM-12715_M0_sm (NG)

description: Sample name: DGM-12715


title: DGM-12707_M0_sm (NG)

description: Sample name: DGM-12707


title: DGM-12750_M0_sm (NG)

description: Sample name: DGM-12750


title: DGM-12775_M0_sm (NG)

description: Sample name: DGM-12775


title: G3_H005

city: Tainan

first: Seonghoe

last: Jang

state: Tainan

address: No.59, Siraya Blvd. Xinshi Dist.

institute: Academia Sinica

description: whole parts of plant above the ground at 50-day-old were harvested.

scan_protocol: The arrays were scanned by Axon GenePix 4200AL scanner (635nm power 100 PMT 310 ) and quantify the fluoresence intensity.

data_processing:
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We ﬁltered out spots that the ﬂag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method.Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

extract_protocol: RNA extraction by Trisol solution (provided by Thermo Fisher Scientific). RNA purity was checked by optical density of NanoDrop ND-2000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧7).

value: whole parts above the ground


title: G4_H008


title: G4_H007


title: DGM-10503_M12_sm (NG)

description: Sample name: DGM-10503

value: nonsmoker


title: DGM-10475_M3_sm (NG)

description: Sample name: DGM-10475


title: DGM-10565_M12_sm (NG)

description: Sample name: DGM-10565


title: G6_H011


title: G5_H009


title: G3_H006


title: G6_H012


title: G5_H010


title: DGM-10500_M6_sm (NG)

description: Sample name: DGM-10500


title: DGM-12697_M0_sm (NG)

description: Sample name: DGM-12697


title: G2_H004


title: DGM-00342_M0_sm (NG)

description: Sample name: DGM-00342


title: G1_H002


title: DGM-10159_M12_sm (NG)

description: Sample name: DGM-10159


title: DGM-01774_M12_sm (NG)

description: Sample name: DGM-01774


title: G1_H001


title: G2_H003


title: MB_SubtypeStudy_55748_methylation

city: Toronto

first: Florence

middle: M G

last: Cavalli

state: Ontario

address: PGCRL, 686 Bay Street

department: Developmental and Stem Cell

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: Standard Illumina Protocol

scan_protocol: Samples were processed as per manufacturer’s instructions. Raw data files (.idat) generated by the Illumina iScan array scanner

data_processing: Raw data was processed in R using the minfi (v1.6.0) and IlluminaHumanMethylation450kmanifest (v0.4.0) R Bioconductor packages. We checked all samples for unexpected genotype matches by pairwise correlation of the 65 genotyping probes on the 450k arrays, allowing us to remove remaining duplicates. We ran the detectionP function from the minfi package to identify probes and samples with low quality. Samples were removed if more than 1% of their probes had a p-value above 0.01 and probes were removed if their p-value was above 0.01 in at least 5% of samples.  We removed probes on sex chromosomes as well as those located on or close to known single nucleotide polymorphisms (SNP). We retained a total of 321,174 probes for the analysis. The data was normalized using the SWAN method (Makismovic et al., Genome Biology 2012) as implemented in the minfi package.  The matrix of normalized beta values is available on the series record.

label: Cy3 and Cy5

source_name: Fresh frozen

label_protocol: Standard Illumina Protocol

extract_protocol: Snap frozen tissue was digested overnight at 55 C with Proteinase K and SDS in TE. DNA was extracted from the digest with phenol-chloroform and precipitated with ammonium acetate and ethanol. The pellet was resuspended in TE buffer. Bisulfite conversion was carried out according to the manufacturer's instructions for the Zymo EZ DNA Methylation Kit

value: medulloblastoma

tag: type

value: primary tumor

tag: subgroup

value: SHH


title: MB_SubtypeStudy_55760_methylation


title: MB_SubtypeStudy_55756_methylation


title: MB_SubtypeStudy_55752_methylation


title: MB_SubtypeStudy_55742_methylation

value: WNT


title: MB_SubtypeStudy_55739_methylation


title: MB_SubtypeStudy_55754_methylation


title: ECHM1781

city: Columbus

first: Ralf

last: Bundschuh

state: OH

address: 191 West Woodruff Avenue

department: Department of Physics

institute: The Ohio State University

description: BioSample SAMN06214556

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

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

data_processing: As described in Nucleic Acids Research, 2013, 1–11

label: Cy3, Cy5

source_name: genomic DNA from primary endometrial cancer 1781

extract_protocol: Tissue specimens were obtained at the time of surgery, snap frozen, and stored at −70°C. DNA was then isolated from tumors using proteinase K and phenol extraction or with the DNeasy Tissue Kit (Qiagen Inc, Valencia, CA).

tag: subject

value: Patient 1781

tag: tissue type

value: primary endometrial cancer

value: female

tag: race

value: White Caucasian


title: ECHM1503

description: BioSample SAMN06214537

source_name: genomic DNA from primary endometrial cancer 1503

value: Patient 1503

value: Black


title: MB_SubtypeStudy_55738_methylation


title: ECHM1648

description: BioSample SAMN06214549

source_name: genomic DNA from primary endometrial cancer 1648

value: Patient 1648


title: MB_SubtypeStudy_55734_methylation


title: MB_SubtypeStudy_55733_methylation


title: MB_SubtypeStudy_55736_methylation


title: MB_SubtypeStudy_55737_methylation


title: MB_SubtypeStudy_55731_methylation


title: MB_SubtypeStudy_55735_methylation


title: MB_SubtypeStudy_55730_methylation


title: MB_SubtypeStudy_55728_methylation


title: MB_SubtypeStudy_55759_methylation


title: MB_SubtypeStudy_55727_methylation


title: MB_SubtypeStudy_55745_methylation


title: MB_SubtypeStudy_55729_methylation


title: ECHM1768

description: BioSample SAMN06214555

source_name: genomic DNA from primary endometrial cancer 1768

value: Patient 1768


title: ECHM1359

description: BioSample SAMN06214528

source_name: genomic DNA from primary endometrial cancer 1359

value: Patient 1359


title: MB_SubtypeStudy_55723_methylation


title: MB_SubtypeStudy_55722_methylation


title: MB_SubtypeStudy_55712_methylation


title: ECHM1158

description: BioSample SAMN06214510

source_name: genomic DNA from primary endometrial cancer 1158

value: Patient 1158


title: ECHM1350

description: BioSample SAMN06214527

source_name: genomic DNA from primary endometrial cancer 1350

value: Patient 1350


title: MB_SubtypeStudy_55719_methylation


title: MB_SubtypeStudy_55721_methylation


title: MB_SubtypeStudy_55717_methylation


title: t5 no-exposure_2

city: Basel

first: Primo

last: Schär

address: Mattenstrasse 28

country: Switzerland

institute: University of Basel

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation 450 Beadchip using standard Illumina protocol.

scan_protocol: Standard Illumina Protocol

data_processing: Mean non-background corrected signal intensities for each CpG locus were extracted using Illumina GenomeStudio software. Beta values were calculated after background adjustment followed by quantile normalization of both typeI and typeII probes separately. We masked data point as “NA” for the following conditions; 1) Probes that map to regions with known germline polymorphisms, 2) those that map to multiple genomic loci, 3) those that interrogate non-CG dinucleotides. Beta values with detection P value greater than 0.05 were also replaced as NA. Furthermore, probes containing at least one “NA” across all sample set were masked as “NA”. Beta value was calculated as M/(M+U).

source_name: neutrophilic progenitor cells

growth_protocol: CD34-positive cells isolated from human cord blood of mixed donors were obtained from AllCells (Alabama, United States). Culturing of cells was routinely performed at 37°C in a humidified atmosphere with 5% CO2. CD34+ cells were propagated in Stemline II medium expansion medium (Stemcell technology) supplemented with 100 ng/mL thrombopoietin, 100 ng/mL stem cell factor, 10 ng/mL Flt3-ligand (Peprotech), 5000 U/mL Penicillin and 5 mg/mL Streptomycin (Sigma-Aldrich) for four days. For the neutrophilic differentiation, expanded CD34+ cord blood cells were seeded at a cell density of 105 cells/mL in Stemline II medium supplemented with 100 ng/mL stem cell factor, 10 ng/mL Flt3-ligand, 100 ng/mL G-CSF (Peprotech), 5000 U/mL Penicillin and 5 mg/mL Streptomycin (Sigma-Aldrich) and cultured for 5 days. Every second day, fresh cell culture medium was added (1:2 dilution).

extract_protocol: Genomic DNA was extracted from frozen cell pellets by QIAamp DNA mini kit (Qiagen) according to the manufacturer’s instructions including an RNase-treatment step

treatment_protocol: During neutrophilic differentiation, cells were exposed to a powerline-simulating ELF-MF (50 Hz, 1 mT, 5’ on/10’ off) or to the sham control (50 Hz, 7 µT, 5’ on/10’ off). Control differentiations were done in parallel, either in a µ-metal shielded compartment inside the exposure incubator or in different incubator.

value: human cord blood CD34+ cell-derived neutrophilic progenitor cells

tag: exposure conditions

value: no exposure

tag: time of differentiation [days]

tag: differentiation

value: 100 ng/ml G-CSF

tag: replicate


title: t5 no-exposure_3

tag: cell type


title: MB_SubtypeStudy_55705_methylation

value: medulloblastoma

value: primary tumor


title: MB_SubtypeStudy_55707_methylation

value: WNT


title: MB_SubtypeStudy_55702_methylation


title: CD34+_3

source_name: human cord blood CD34+ cells

value: expanded human cord blood CD34+ cells

value: no


title: MB_SubtypeStudy_55710_methylation

value: SHH


title: ECHM1138

description: BioSample SAMN06214508

source_name: genomic DNA from primary endometrial cancer 1138

value: Patient 1138

value: primary endometrial cancer

value: female

value: White Caucasian


title: ECHM1193

description: BioSample SAMN06214514

source_name: genomic DNA from primary endometrial cancer 1193

value: Patient 1193


title: t5 sham_2

value: ELF-MF (50Hz powerline, 0.007 mT, 5' on/10' off)


title: MB_SubtypeStudy_55700_methylation


title: MB_SubtypeStudy_55697_methylation


title: MB_SubtypeStudy_55698_methylation


title: CD34+_1


title: t5 ELF-MF_3

value: ELF-MF (50Hz powerline, 1 mT, 5' on/10' off)


title: MB_SubtypeStudy_55694_methylation


title: t5 ELF-MF_1


title: MB_SubtypeStudy_55695_methylation


title: t5 sham_1


title: t5 sham_3


title: MB_SubtypeStudy_55689_methylation


title: MB_SubtypeStudy_55690_methylation


title: CD34+_2


title: MB_SubtypeStudy_55686_methylation


title: Enchytraeus crypticus_UV Dose 2_rep1

city: Aveiro

first: Susana

middle: Isabel Lopes

last: Gomes

address: Campus Universitário de Santiago, Departement of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

hyb_protocol: The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)

scan_protocol: Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).

data_processing: Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.

organism: Enchytraeus crypticus

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: UV dose 1 (total UV dose - 5 days - 8100 Jm-2) , in ISO reconstituted water

label_protocol: Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).

extract_protocol: Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.

value: Whole body extracts

tag: stage of development

tag: treatment

value: UV Dose 2


title: Enchytraeus crypticus_UV Dose 2_rep2

tag: tissue

value: Adult organisms with well developed clitellum


title: t5 ELF-MF_2

value: human cord blood CD34+ cell-derived neutrophilic progenitor cells

value: 100 ng/ml G-CSF


title: Enchytraeus crypticus_UV Dose 1_rep3

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: UV dose 1 (total UV dose - 5 days - 7500 Jm-2) , in ISO reconstituted water

value: UV Dose 1


title: Enchytraeus crypticus_UV Dose 1_rep2


title: Enchytraeus crypticus_UV Dose 2_rep3


title: Enchytraeus crypticus_UV Dose 1_rep1


title: MB_SubtypeStudy_55684_methylation

value: medulloblastoma

value: primary tumor


title: Enchytraeus crypticus_Control_rep2 (UV)

source_name: Tissue: Whole body extracts (40 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: standard laboratory illumination, in ISO reconstituted water, for 5 days

value: Control


title: Enchytraeus crypticus_Control_rep3 (UV)


title: PBMCs vacci D1 (exon) biological rep1

city: Bonn

first: Chritiane

last: Neuhoff

state: NRW

address: Endenicher Allee 15

department: Institute of Animal Science

institute: University of Bonn

hyb_protocol: The hybridization of microarray probes followed by washing and staining was performed with the GeneChip® Hybridization, Wash and Stain kit (P/N 900720, Affymetrix Inc., Santa Clara, CA).

scan_protocol: Arrays were scanned by the Affymetrix GeneChip® scanner 3000 7G. The Affymetrix GeneChip® Command Console™ (AGCC) software was used to evaluate the array images and to export the reports of spot intensity data in .CEL file format.

data_processing:
Normalization and statistical analyses of microarray dataset were performed using packages of Bioconductor-platform implemented in R-project software (v3.1.2). The ‘oligo’ package was implemented for the RMA (Robust Multi-array Average) based quantile normalization of microarray data. The transcript level matrix was generated using core and the exon level matrix was generated using the probeset as target option. The differential gene expression analysis was performed using the linear analysis of microarray technique from the ‘limma’ package with empirical Bayes adjustment to the variance, followed by Benjamini and Hochberg (BH) correction for multiple testing. Genes with an FDR≤5% and a fold-change ≥1.5 were selected. In addition, To characterize the differences of transcriptional responses between pigs of vaccinated and unvaccinated group, the annotated gene expression profiles of PBMCs were subjected to an exploratory functional analysis through gene set enrichment analysis (GSEA) algorithm implemented in GSEA-P tool.
probe group file: PorGene-1_0-st‐v1
meta-probeset file: PorGene-1_0-st-v1.na34.sscr2.transcript.csv (for gene-level) and PorGene-1_0-st-v1.na34.sscr2.probeset.csv (for exon-level)

organism: Sus scrofa

source_name: PBMCs at one day after PRRSV vaccination

label_protocol: The biotin-labeled probes (sense-strand cDNA) were prepared for microarray hybridization using the GeneChip® WT PLUS Reagent kit (P/N 902281; Affymetrix Inc., Santa Clara, CA, USA)

growth_protocol: Piglets were housed at research station at Frankenforst, University of Bonn, Germany and maintained with standard feeding and husbandry protocol.

extract_protocol: The total RNA was extracted from PBMCs using the miRNeasy mini kit (P/N 217004, Qiagen, Hilden, Germany) along with on column Dnase treatment (P/N 79254, Qiagen, Hilden, Germany)

treatment_protocol: PBMCs were isolated from anticoagulated blood samples collected at right before, 1 day and 28 days post PRRSV vaccination in Pirtain pigs

tag: immunization status

value: Vaccinated

tag: breed

value: Pietrain pigs

value: Female


title: Enchytraeus crypticus_Ni-NPs EC50 7days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Ni-NPs EC50 (effect concentration on reproduction) in soil for 7 days

value: Ni-NPs EC50 7days


title: Enchytraeus crypticus_Control_rep1 (UV)


title: PBMCs vacci D0 (exon) biological rep3

source_name: PBMCs at just before PRRSV vaccination

value: pre vaccinated

tag: gender


title: PBMCs vacci D1 (exon) biological rep3


title: Enchytraeus crypticus_Ni-NPs EC20 7days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Ni-NPs EC20 (effect concentration on reproduction) in soil for 7 days

value: Ni-NPs EC20 7days


title: Enchytraeus crypticus_Ni-NPs EC50 7days_rep1


title: Enchytraeus crypticus_Ni-NPs EC50 7days_rep2


title: Enchytraeus crypticus_Ni-NPs EC20 7days_rep2


title: PBMCs vacci D28 (exon) biological rep2

source_name: PBMCs at 28 days post PRRSV vaccination


title: PBMCs vacci D28 (exon) biological rep1

source_name: PBMCs at 28 dazs post PRRSV vaccination


title: PBMCs vacci D0 (exon) biolgical rep1


title: MB_SubtypeStudy_55683_methylation

source_name: Fresh frozen

value: SHH


title: PBMCs vacci D28 (exon) biological rep3


title: PBMCs vacci D1 (exon) biological rep2


title: MB_SubtypeStudy_55681_methylation


title: MB_SubtypeStudy_55679_methylation


title: MB_SubtypeStudy_55680_methylation

value: WNT


title: MB_SubtypeStudy_55682_methylation


title: Enchytraeus crypticus_NiNO3 EC50 7days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: NiNO3 EC50 (effect concentration on reproduction) in soil for 7 days

value: Whole body extracts

value: NiNO3 EC50 7days


title: MB_SubtypeStudy_55673_methylation


title: Enchytraeus crypticus_NiNO3 EC20 7days_rep2

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: NiNO3 EC20 (effect concentration on reproduction) in soil for 7 days

value: NiNO3 EC20 7days


title: MB_SubtypeStudy_55675_methylation


title: MB_SubtypeStudy_55672_methylation


title: Enchytraeus crypticus_Ni-NPs EC20 7days_rep1

value: Adult organisms with well developed clitellum


title: MB_SubtypeStudy_55668_methylation


title: MB_SubtypeStudy_55669_methylation


title: MB_SubtypeStudy_55670_methylation


title: MB_SubtypeStudy_55667_methylation


title: Enchytraeus crypticus_NiNO3 EC50 7days_rep2


title: Enchytraeus crypticus_Ni-NPs EC50 3days_rep1

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Ni-NPs EC50 (effect concentration on reproduction) in soil for 3 days

value: Ni-NPs EC50 3days


title: Enchytraeus crypticus_Ni-NPs EC20 3days_rep1

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Ni-NPs EC20 (effect concentration on reproduction) in soil for 3 days

value: Ni-NPs EC20 3days


title: Enchytraeus crypticus_NiNO3 EC50 3days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: NiNO3 EC50 (effect concentration on reproduction) in soil for 3 days

value: NiNO3 EC50 3days


title: Enchytraeus crypticus_Control 7days_rep2 (Ni)

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: un-spiked soil for 7 days

value: Control 7days


title: Enchytraeus crypticus_NiNO3 EC50 7days_rep1


title: Enchytraeus crypticus_NiNO3 EC20 7days_rep3


title: Enchytraeus crypticus_Ni-NPs EC50 3days_rep3


title: Enchytraeus crypticus_Ni-NPs EC50 3days_rep2


title: Enchytraeus crypticus_Control 7days_rep3 (Ni)


title: Enchytraeus crypticus_Ni-NPs EC20 3days_rep2


title: Enchytraeus crypticus_NiNO3 EC20 7days_rep1


title: Enchytraeus crypticus_Ni-NPs EC20 3days_rep3


title: MB_SubtypeStudy_55676_methylation

value: medulloblastoma

value: primary tumor


title: MB_SubtypeStudy_55664_methylation


title: Enchytraeus crypticus_Control 7days_rep1 (Ni)


title: MB_SubtypeStudy_55660_methylation


title: MB_SubtypeStudy_55662_methylation


title: MB_SubtypeStudy_55654_methylation


title: MB_SubtypeStudy_55656_methylation


title: Enchytraeus crypticus_NiNO3 EC20 3days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: NiNO3 EC20 (effect concentration on reproduction) in soil for 3 days

value: NiNO3 EC20 3days


title: Enchytraeus crypticus_NiNO3 EC50 3days_rep2


title: Enchytraeus crypticus_NiNO3 EC50 3days_rep1


title: MB_SubtypeStudy_55652_methylation


title: Enchytraeus crypticus_NiNO3 EC20 3days_rep2


title: PBMCs vacci D0 (exon) biological rep2

value: Pietrain pigs

value: Female


title: MB_SubtypeStudy_55657_methylation


title: MB_SubtypeStudy_55649_methylation


title: MB_SubtypeStudy_55648_methylation


title: Enchytraeus crypticus_Cu-Field EC50 7days_rep2

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-Field EC50 (effect concentration on reproduction) in soil for 7 days

value: Cu-Field EC50 7days


title: Enchytraeus crypticus_Cu-NWires EC20 7days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-NWires EC20 (effect concentration on reproduction) in soil for 7 days

value: Cu-NWires EC20 7days


title: Enchytraeus crypticus_Cu-Field EC50 7days_rep1


title: Enchytraeus crypticus_Cu-NWires EC50 7days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-NWires EC50 (effect concentration on reproduction) in soil for 7 days

value: Cu-NWires EC50 7days


title: Enchytraeus crypticus_Cu-NWires EC20 7days_rep2


title: Enchytraeus crypticus_Control 3days_rep3 (Ni)

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: un-spiked soil for 3 days

value: Control 3days


title: Enchytraeus crypticus_NiNO3 EC20 3days_rep1

value: Whole body extracts


title: Enchytraeus crypticus_Control 3days_rep1 (Ni)


title: MB_SubtypeStudy_55642_methylation


title: Enchytraeus crypticus_Cu-Field EC20 7days_rep1

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-Field EC20 (effect concentration on reproduction) in soil for 7 days

value: Cu-Field EC20 7days


title: Enchytraeus crypticus_Cu-Field EC20 7days_rep2


title: Enchytraeus crypticus_Cu-Field EC50 7days_rep3


title: Enchytraeus crypticus_Cu-Field EC20 7days_rep3


title: MB_SubtypeStudy_55644_methylation


title: Enchytraeus crypticus_Control 3days_rep2 (Ni)


title: Enchytraeus crypticus_Cu-NWires EC50 7days_rep2


title: Enchytraeus crypticus_Cu-NPs EC20 7days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-NPs EC20 (effect concentration on reproduction) in soil for 7 days

value: Cu-NPs EC20 7days


title: Enchytraeus crypticus_Cu-NPs EC50 7days_rep2

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-NPs EC50 (effect concentration on reproduction) in soil for 7 days

value: Cu-NPs EC50 7days


title: Enchytraeus crypticus_Cu-NWires EC50 7days_rep1

value: Adult organisms with well developed clitellum


title: Enchytraeus crypticus_Cu-NWires EC20 7days_rep1


title: MB_SubtypeStudy_55640_methylation

value: SHH


title: MB_SubtypeStudy_55631_methylation


title: MB_SubtypeStudy_55647_methylation

value: WNT


title: MB_SubtypeStudy_55630_methylation


title: MB_SubtypeStudy_55632_methylation


title: MB_SubtypeStudy_55638_methylation


title: MB_SubtypeStudy_55639_methylation


title: Enchytraeus crypticus_Cu-NPs EC50 7days_rep1


title: MB_SubtypeStudy_55625_methylation


title: MB_SubtypeStudy_55628_methylation


title: Enchytraeus crypticus_Cu-NPs EC20 7days_rep2


title: Enchytraeus crypticus_CuNO3 EC50 7days_rep1

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: CuNO3 EC50 (effect concentration on reproduction) in soil for 7 days

value: CuNO3 EC50 7days


title: Enchytraeus crypticus_Cu-NPs EC20 7days_rep1


title: Enchytraeus crypticus_CuNO3 EC50 7days_rep3


title: Enchytraeus crypticus_Control 7days_rep3 (Cu)

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Hygum soil from control area for 7 days

value: Control 7days


title: Enchytraeus crypticus_CuNO3 EC50 7days_rep2


title: Enchytraeus crypticus_CuNO3 EC20 7days_rep1

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: CuNO3 EC20 (effect concentration on reproduction) in soil for 7 days

value: CuNO3 EC20 7days


title: Enchytraeus crypticus_Cu-NPs EC50 7days_rep3


title: MB_SubtypeStudy_55624_methylation

source_name: Fresh frozen

value: medulloblastoma

value: primary tumor


title: MB_SubtypeStudy_55621_methylation


title: Enchytraeus crypticus_CuNO3 EC20 7days_rep3


title: MB_SubtypeStudy_55622_methylation


title: Enchytraeus crypticus_Control 7days_rep1 (Cu)


title: Enchytraeus crypticus_Control 7days_rep2 (Cu)


title: Enchytraeus crypticus_CuNO3 EC20 7days_rep2


title: Enchytraeus crypticus_Cu-Field EC50 3days_rep1

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-Field EC50 (effect concentration on reproduction) in soil for 3 days

value: Cu-Field EC50 3days


title: Enchytraeus crypticus_Cu-NWires EC50 3days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-NWires EC50 (effect concentration on reproduction) in soil for 3 days

value: Cu-NWires EC50 3days


title: Enchytraeus crypticus_Cu-Field EC20 3days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-Field EC20 (effect concentration on reproduction) in soil for 3 days

value: Cu-Field EC20 3days


title: Enchytraeus crypticus_Cu-Field EC50 3days_rep3


title: Enchytraeus crypticus_Cu-Field EC20 3days_rep1


title: Enchytraeus crypticus_Cu-NWires EC50 3days_rep2


title: Enchytraeus crypticus_Cu-Field EC50 3days_rep2


title: MB_SubtypeStudy_55620_methylation


title: Enchytraeus crypticus_Cu-Field EC20 3days_rep2


title: MB_SubtypeStudy_55617_methylation


title: Enchytraeus crypticus_Cu-NWires EC20 3days_rep2

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-NWires EC20 (effect concentration on reproduction) in soil for 3 days

value: Cu-NWires EC20 3days


title: MB_SubtypeStudy_55616_methylation


title: MB_SubtypeStudy_55615_methylation


title: MB_SubtypeStudy_55612_methylation


title: MB_SubtypeStudy_55619_methylation


title: Enchytraeus crypticus_Cu-NWires EC20 3days_rep3


title: Enchytraeus crypticus_Cu-NWires EC20 3days_rep1


title: Enchytraeus crypticus_Cu-NWires EC50 3days_rep1


title: MB_SubtypeStudy_55608_methylation


title: MB_SubtypeStudy_55610_methylation


title: MB_SubtypeStudy_55607_methylation


title: MB_SubtypeStudy_55606_methylation


title: Enchytraeus crypticus_Cu-NPs EC50 3days_rep1

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-NPs EC50 (effect concentration on reproduction) in soil for 3 days

value: Cu-NPs EC50 3days


title: MB_SubtypeStudy_55605_methylation


title: Enchytraeus crypticus_Cu-NPs EC50 3days_rep3

value: Whole body extracts


title: Enchytraeus crypticus_Cu-NPs EC20 3days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Cu-NPs EC20 (effect concentration on reproduction) in soil for 3 days

value: Cu-NPs EC20 3days


title: Enchytraeus crypticus_Cu-NPs EC20 3days_rep2


title: Enchytraeus crypticus_Cu-NPs EC50 3days_rep2


title: Enchytraeus crypticus_CuNO3 EC50 3days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: CuNO3 EC50 (effect concentration on reproduction) in soil for 3 days

value: CuNO3 EC50 3days


title: Enchytraeus crypticus_Cu-NPs EC20 3days_rep1


title: Enchytraeus crypticus_CuNO3 EC20 3days_rep3

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: CuNO3 EC20 (effect concentration on reproduction) in soil for 3 days

value: CuNO3 EC20 3days


title: Enchytraeus crypticus_CuNO3 EC50 3days_rep1

value: Adult organisms with well developed clitellum


title: MB_SubtypeStudy_55603_methylation


title: Enchytraeus crypticus_CuNO3 EC20 3days_rep1


title: Enchytraeus crypticus_Control 3days_rep2 (Cu)

source_name: Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Hygum soil from control area for 3 days

value: Control 3days


title: MB_SubtypeStudy_55602_methylation


title: healthy control 3

city: Jinan

first: Wei

last: Li

state: Shandong

address: #44,West Wenhua Road

institute: Shandong University

description: circular RNA microarray

hyb_protocol: Five microliter 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer were used to fragment 1μg of each labeled cRNA, followed by heat at 60 °C for 30 min. Finally, 25μl 2 × Hybridization buffer was added to dilute the labeled cRNA and 50μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide, incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After incubation, the hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software (version 11.0.1.1) for raw data extraction. Quantile normalization and subsequent data processing were performed using the R software package.

source_name: bone marrow mononuclear cells from control 3

label_protocol: The enriched circRNAs were amplified and transcribed into fluorescent complementary RNA (cRNA) utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Total RNA was isolated from 10 samples using TRIzol reagent according to the manufacturer's protocol, and then treated with Rnase R to remove linear RNAs and enrich circRNAs.

value: F


title: Enchytraeus crypticus_CuNO3 EC50 3days_rep2


title: Enchytraeus crypticus_CuNO3 EC20 3days_rep2


title: MB_SubtypeStudy_55601_methylation

value: SHH


title: healthy control 4

description: circular RNA microarray

source_name: bone marrow mononuclear cells from control 4


title: healthy control 2

description: circular RNA microarray

source_name: bone marrow mononuclear cells from control 2

value: M


title: MB_SubtypeStudy_55597_methylation

value: WNT


title: MB_SubtypeStudy_55595_methylation

value: medulloblastoma


title: healthy control 1

description: circular RNA microarray

source_name: bone marrow mononuclear cells from control 1


title: MB_SubtypeStudy_55596_methylation

value: primary tumor


title: MB_SubtypeStudy_55604_methylation


title: AML4-better risk

description: circular RNA microarray

source_name: bone marrow mononuclear cells from AML 4


title: MB_SubtypeStudy_55586_methylation


title: AML2-poor risk

description: circular RNA microarray

source_name: bone marrow mononuclear cells from AML 2


title: AML5-better risk

description: circular RNA microarray

source_name: bone marrow mononuclear cells from AML 5


title: AML3-poor risk

description: circular RNA microarray

source_name: bone marrow mononuclear cells from AML 3


title: MB_SubtypeStudy_55589_methylation

source_name: Fresh frozen


title: MB_SubtypeStudy_55585_methylation


title: MB_SubtypeStudy_55582_methylation


title: MB_SubtypeStudy_55580_methylation


title: MB_SubtypeStudy_55578_methylation


title: MB_SubtypeStudy_55575_methylation


title: MB_SubtypeStudy_55565_methylation


title: Enchytraeus crypticus_Control 3days_rep1 (Cu)


title: MB_SubtypeStudy_55561_methylation


title: MB_SubtypeStudy_55563_methylation


title: Enchytraeus crypticus_Control 3days_rep3 (Cu)


title: MB_SubtypeStudy_55553_methylation


title: AML6-better risk

description: circular RNA microarray

source_name: bone marrow mononuclear cells from AML 6


title: AML1-poor risk

description: circular RNA microarray

source_name: bone marrow mononuclear cells from AML 1


title: MB_SubtypeStudy_55556_methylation


title: MB_SubtypeStudy_55549_methylation


title: MB_SubtypeStudy_55551_methylation


title: MB_SubtypeStudy_55550_methylation


title: MB_SubtypeStudy_55592_methylation


title: MB_SubtypeStudy_55546_methylation


title: MB_SubtypeStudy_55545_methylation


title: MB_SubtypeStudy_55536_methylation


title: MB_SubtypeStudy_55538_methylation


title: MB_SubtypeStudy_55535_methylation


title: MB_SubtypeStudy_55571_methylation


title: MB_SubtypeStudy_55534_methylation


title: MB_SubtypeStudy_55531_methylation


title: MB_SubtypeStudy_55530_methylation


title: MB_SubtypeStudy_55526_methylation


title: MB_SubtypeStudy_55520_methylation


title: MB_SubtypeStudy_55516_methylation


title: MB_SubtypeStudy_55525_methylation


title: MB_SubtypeStudy_55524_methylation


title: MB_SubtypeStudy_55543_methylation


title: MB_SubtypeStudy_55521_methylation


title: MB_SubtypeStudy_55512_methylation


title: MB_SubtypeStudy_55507_methylation


title: MB_SubtypeStudy_55502_methylation


title: MB_SubtypeStudy_55503_methylation


title: MB_SubtypeStudy_55505_methylation


title: MB_SubtypeStudy_55492_methylation


title: MB_SubtypeStudy_55495_methylation


title: MB_SubtypeStudy_55497_methylation


title: MB_SubtypeStudy_55490_methylation


title: MB_SubtypeStudy_55519_methylation


title: MB_SubtypeStudy_55487_methylation


title: MB_SubtypeStudy_55500_methylation


title: MB_SubtypeStudy_55504_methylation


title: MB_SubtypeStudy_55494_methylation


title: MB_SubtypeStudy_55483_methylation


title: MB_SubtypeStudy_55479_methylation


title: MB_SubtypeStudy_55493_methylation


title: MB_SubtypeStudy_55498_methylation


title: MB_SubtypeStudy_55474_methylation


title: MB_SubtypeStudy_55480_methylation


title: MB_SubtypeStudy_55485_methylation


title: MB_SubtypeStudy_55456_methylation


title: MB_SubtypeStudy_55461_methylation


title: MB_SubtypeStudy_55457_methylation


title: MB_SubtypeStudy_55523_methylation


title: MB_SubtypeStudy_55482_methylation


title: MB_SubtypeStudy_55455_methylation


title: MB_SubtypeStudy_55471_methylation


title: MB_SubtypeStudy_55477_methylation


title: MB_SubtypeStudy_55484_methylation


title: MB_SubtypeStudy_55469_methylation


title: MB_SubtypeStudy_55468_methylation


title: MB_SubtypeStudy_55481_methylation


title: MB_SubtypeStudy_55462_methylation


title: MB_SubtypeStudy_55460_methylation


title: MB_SubtypeStudy_55459_methylation


title: MB_SubtypeStudy_55433_methylation


title: MB_SubtypeStudy_55458_methylation


title: MB_SubtypeStudy_55437_methylation


title: MB_SubtypeStudy_55442_methylation


title: MB_SubtypeStudy_55443_methylation


title: MB_SubtypeStudy_55449_methylation


title: MB_SubtypeStudy_55450_methylation


title: MB_SubtypeStudy_55452_methylation


title: MB_SubtypeStudy_55445_methylation


title: MB_SubtypeStudy_55431_methylation


title: MB_SubtypeStudy_55447_methylation


title: MB_SubtypeStudy_55424_methylation


title: MB_SubtypeStudy_55444_methylation


title: MB_SubtypeStudy_55425_methylation


title: MB_SubtypeStudy_55422_methylation


title: MB_SubtypeStudy_55421_methylation


title: MB_SubtypeStudy_55440_methylation


title: MB_SubtypeStudy_55436_methylation


title: MB_SubtypeStudy_55418_methylation


title: MB_SubtypeStudy_55415_methylation


title: MB_SubtypeStudy_55411_methylation


title: MB_SubtypeStudy_55434_methylation


title: MB_SubtypeStudy_55427_methylation


title: MB_SubtypeStudy_55432_methylation


title: MB_SubtypeStudy_55410_methylation


title: MB_SubtypeStudy_55429_methylation


title: MB_SubtypeStudy_55420_methylation


title: MB_SubtypeStudy_55423_methylation


title: MB_SubtypeStudy_55404_methylation


title: MB_SubtypeStudy_55405_methylation


title: MB_SubtypeStudy_55393_methylation


title: MB_SubtypeStudy_55394_methylation


title: MB_SubtypeStudy_55397_methylation


title: MB_SubtypeStudy_55408_methylation


title: MB_SubtypeStudy_55400_methylation


title: MB_SubtypeStudy_55406_methylation


title: MB_SubtypeStudy_55401_methylation


title: MB_SubtypeStudy_55419_methylation


title: MB_SubtypeStudy_55398_methylation


title: MB_SubtypeStudy_55389_methylation


title: MB_SubtypeStudy_55390_methylation


title: MB_SubtypeStudy_55385_methylation


title: MB_SubtypeStudy_55387_methylation


title: MB_SubtypeStudy_55382_methylation


title: MB_SubtypeStudy_55381_methylation


title: MB_SubtypeStudy_55383_methylation


title: MB_SubtypeStudy_55392_methylation


title: MB_SubtypeStudy_55380_methylation


title: MB_SubtypeStudy_55377_methylation


title: MB_SubtypeStudy_55395_methylation


title: MB_SubtypeStudy_55368_methylation


title: MB_SubtypeStudy_55374_methylation


title: MB_SubtypeStudy_55386_methylation


title: MB_SubtypeStudy_55384_methylation


title: MB_SubtypeStudy_55339_methylation


title: MB_SubtypeStudy_55351_methylation


title: MB_SubtypeStudy_55348_methylation


title: MB_SubtypeStudy_55356_methylation


title: MB_SubtypeStudy_55337_methylation


title: MB_SubtypeStudy_55345_methylation


title: MB_SubtypeStudy_55330_methylation


title: MB_SubtypeStudy_55353_methylation


title: MB_SubtypeStudy_55340_methylation


title: MB_SubtypeStudy_55344_methylation


title: MB_SubtypeStudy_55352_methylation


title: MB_SubtypeStudy_55354_methylation


title: MB_SubtypeStudy_55324_methylation


title: MB_SubtypeStudy_55370_methylation


title: MB_SubtypeStudy_55323_methylation


title: MB_SubtypeStudy_55319_methylation


title: MB_SubtypeStudy_55329_methylation


title: MB_SubtypeStudy_55338_methylation


title: MB_SubtypeStudy_55321_methylation


title: MB_SubtypeStudy_55378_methylation


title: MB_SubtypeStudy_55322_methylation


title: MB_SubtypeStudy_55325_methylation


title: MB_SubtypeStudy_55357_methylation


title: MB_SubtypeStudy_55363_methylation


title: MB_SubtypeStudy_55316_methylation


title: MB_SubtypeStudy_55313_methylation


title: MB_SubtypeStudy_55315_methylation


title: MB_SubtypeStudy_55305_methylation


title: MB_SubtypeStudy_55312_methylation


title: MB_SubtypeStudy_55314_methylation


title: MB_SubtypeStudy_55311_methylation


title: MB_SubtypeStudy_55291_methylation


title: MB_SubtypeStudy_55293_methylation


title: MB_SubtypeStudy_55289_methylation


title: MB_SubtypeStudy_55268_methylation


title: MB_SubtypeStudy_55280_methylation


title: MB_SubtypeStudy_55300_methylation


title: MB_SubtypeStudy_55276_methylation


title: MB_SubtypeStudy_55270_methylation


title: MB_SubtypeStudy_55302_methylation


title: MB_SubtypeStudy_55307_methylation


title: MB_SubtypeStudy_55297_methylation


title: MB_SubtypeStudy_55263_methylation


title: MB_SubtypeStudy_55262_methylation


title: MB_SubtypeStudy_55295_methylation


title: MB_SubtypeStudy_55286_methylation


title: MB_SubtypeStudy_55284_methylation


title: MB_SubtypeStudy_55264_methylation


title: MB_SubtypeStudy_55294_methylation


title: MB_SubtypeStudy_55275_methylation


title: MB_SubtypeStudy_55285_methylation


title: MB_SubtypeStudy_55261_methylation


title: MB_SubtypeStudy_55260_methylation


title: MB_SubtypeStudy_55245_methylation


title: MB_SubtypeStudy_55265_methylation


title: MB_SubtypeStudy_55243_methylation


title: MB_SubtypeStudy_55238_methylation


title: MB_SubtypeStudy_55242_methylation


title: MB_SubtypeStudy_55279_methylation


title: MB_SubtypeStudy_55239_methylation


title: MB_SubtypeStudy_55236_methylation


title: MB_SubtypeStudy_55216_methylation


title: MB_SubtypeStudy_55223_methylation


title: MB_SubtypeStudy_55225_methylation


title: MB_SubtypeStudy_55228_methylation


title: MB_SubtypeStudy_55213_methylation


title: MB_SubtypeStudy_55215_methylation


title: MB_SubtypeStudy_55229_methylation


title: MB_SubtypeStudy_55209_methylation


title: MB_SubtypeStudy_55278_methylation


title: MB_SubtypeStudy_55202_methylation


title: MB_SubtypeStudy_55210_methylation


title: MB_SubtypeStudy_55204_methylation


title: MB_SubtypeStudy_55205_methylation


title: MB_SubtypeStudy_55192_methylation


title: MB_SubtypeStudy_55201_methylation


title: MB_SubtypeStudy_55254_methylation


title: MB_SubtypeStudy_55198_methylation


title: MB_SubtypeStudy_55197_methylation


title: MB_SubtypeStudy_55191_methylation


title: MB_SubtypeStudy_55188_methylation


title: MB_SubtypeStudy_55189_methylation


title: MB_SubtypeStudy_55187_methylation


title: MB_SubtypeStudy_55176_methylation


title: MB_SubtypeStudy_55206_methylation


title: MB_SubtypeStudy_55182_methylation


title: MB_SubtypeStudy_55181_methylation


title: MB_SubtypeStudy_55180_methylation


title: MB_SubtypeStudy_55175_methylation


title: MB_SubtypeStudy_55171_methylation


title: MB_SubtypeStudy_55178_methylation


title: MB_SubtypeStudy_55174_methylation


title: MB_SubtypeStudy_55161_methylation


title: MB_SubtypeStudy_55172_methylation


title: MB_SubtypeStudy_55164_methylation


title: MB_SubtypeStudy_55170_methylation


title: MB_SubtypeStudy_55173_methylation


title: MB_SubtypeStudy_55169_methylation


title: MB_SubtypeStudy_55167_methylation


title: MB_SubtypeStudy_55165_methylation


title: MB_SubtypeStudy_55152_methylation


title: MB_SubtypeStudy_55183_methylation


title: MB_SubtypeStudy_55163_methylation


title: MB_SubtypeStudy_55142_methylation


title: MB_SubtypeStudy_55154_methylation


title: MB_SubtypeStudy_55179_methylation


title: MB_SubtypeStudy_55287_methylation


title: MB_SubtypeStudy_55150_methylation


title: MB_SubtypeStudy_55144_methylation


title: MB_SubtypeStudy_55147_methylation


title: MB_SubtypeStudy_55138_methylation


title: MB_SubtypeStudy_55143_methylation


title: MB_SubtypeStudy_55136_methylation


title: MB_SubtypeStudy_55129_methylation


title: MB_SubtypeStudy_55127_methylation


title: MB_SubtypeStudy_55137_methylation


title: MB_SubtypeStudy_55121_methylation


title: MB_SubtypeStudy_55122_methylation


title: MB_SubtypeStudy_55141_methylation


title: MB_SubtypeStudy_55113_methylation


title: MB_SubtypeStudy_55131_methylation


title: MB_SubtypeStudy_55111_methylation


title: MB_SubtypeStudy_55157_methylation


title: MB_SubtypeStudy_55123_methylation


title: MB_SubtypeStudy_55124_methylation


title: MB_SubtypeStudy_55118_methylation


title: MB_SubtypeStudy_55112_methylation


title: MB_SubtypeStudy_55110_methylation


title: MB_SubtypeStudy_55109_methylation


title: MB_SubtypeStudy_55104_methylation


title: MB_SubtypeStudy_55107_methylation


title: MB_SubtypeStudy_55102_methylation


title: MB_SubtypeStudy_55105_methylation


title: MB_SubtypeStudy_55099_methylation


title: MB_SubtypeStudy_55106_methylation


title: MB_SubtypeStudy_55100_methylation


title: MB_SubtypeStudy_55103_methylation


title: MB_SubtypeStudy_55097_methylation


title: MB_SubtypeStudy_55092_methylation


title: MB_SubtypeStudy_55120_methylation


title: MB_SubtypeStudy_55096_methylation


title: MB_SubtypeStudy_55130_methylation


title: MB_SubtypeStudy_55087_methylation


title: MB_SubtypeStudy_55085_methylation


title: MB_SubtypeStudy_55093_methylation


title: MB_SubtypeStudy_55082_methylation


title: MB_SubtypeStudy_55083_methylation


title: MB_SubtypeStudy_55080_methylation


title: MB_SubtypeStudy_55073_methylation


title: MB_SubtypeStudy_55075_methylation


title: MB_SubtypeStudy_55076_methylation


title: MB_SubtypeStudy_55108_methylation


title: MB_SubtypeStudy_55069_methylation


title: MB_SubtypeStudy_55077_methylation


title: MB_SubtypeStudy_55078_methylation


title: MB_SubtypeStudy_55071_methylation


title: MB_SubtypeStudy_55066_methylation


title: MB_SubtypeStudy_55060_methylation


title: MB_SubtypeStudy_55061_methylation


title: MB_SubtypeStudy_55063_methylation


title: MB_SubtypeStudy_55054_methylation


title: MB_SubtypeStudy_55052_methylation


title: MB_SubtypeStudy_55051_methylation


title: MB_SubtypeStudy_55048_methylation


title: MB_SubtypeStudy_55047_methylation


title: MB_SubtypeStudy_55036_methylation


title: MB_SubtypeStudy_55049_methylation


title: MB_SubtypeStudy_55043_methylation


title: MB_SubtypeStudy_55034_methylation


title: MB_SubtypeStudy_55031_methylation


title: MB_SubtypeStudy_55022_methylation


title: MB_SubtypeStudy_55065_methylation


title: MB_SubtypeStudy_55037_methylation


title: MB_SubtypeStudy_55072_methylation


title: MB_SubtypeStudy_55032_methylation


title: MB_SubtypeStudy_55030_methylation


title: MB_SubtypeStudy_55040_methylation


title: MB_SubtypeStudy_55033_methylation


title: MB_SubtypeStudy_55014_methylation


title: MB_SubtypeStudy_55019_methylation


title: MB_SubtypeStudy_55011_methylation


title: MB_SubtypeStudy_55016_methylation


title: MB_SubtypeStudy_55013_methylation


title: MB_SubtypeStudy_55012_methylation


title: MB_SubtypeStudy_55007_methylation


title: MB_SubtypeStudy_55005_methylation


title: MB_SubtypeStudy_55015_methylation


title: MB_SubtypeStudy_55001_methylation


title: MB_SubtypeStudy_55234_methylation


title: MB_SubtypeStudy_55010_methylation


title: MB_SubtypeStudy_55006_methylation


title: shGLP dex 24h rep1

city: Los Angeles

first: Dai-Ying

last: Wu

state: CA

address: 1441 Eastlake Ave, NOR 6314

institute: University of Southern California

description:
replicate 1
4849554032_D

data_processing: Spatial artifacts removed with BASH, data normalized using neqc with limma in R

source_name: shGLP dex 24h

label_protocol: Labeling, hybridization and scanning was performed by Epigenome Center Core Facility at USC as per their standard protocol.

growth_protocol: Cells were maintained in DMEM and hormone treated cells were plated and grown in phenol red-free medium supplemented with 5% charcoal stripped serum for 3 days prior to hormone treatment

extract_protocol: RNA was extracted using the TRIzol method as per the manufacturer's instructions

treatment_protocol: Cells were treated with 100nM dexamethasone for 24 hours

tag: cell line

value: 100nM dexamethasone

tag: time point

tag: knockdown

value: shGLP


title: shGLP dex 24h rep4

description:
replicate 4
4859453027_H


title: MB_SubtypeStudy_55050_methylation

tag: type

tag: subgroup


title: shGLP dex 0h rep3

description:
replicate 3
4859453027_B

source_name: shGLP dex 0h


title: shGLP dex 24h rep3

description:
replicate 3
4859453027_D


title: mSSCs_rep3

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

description: multipotent spermatogonial stem cells

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were normalized using quantile normalization method with MATLAB

source_name: multipotent spermatogonial stem cells

label_protocol: Refer to the Illumina Gene Expression System Manual

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

value: multipotent spermatogonial stem cells


title: mSSCs_rep2

description: multipotent spermatogonial stem cells