title: 50 μg/L_P3_L_24h

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description: Gene expression in gilthead sea bream liver exposed to 50 μg/L AuNP pool 3

hyb_protocol: The hybridization protocol was carried out according to Agilent's instructions. Briefly, 1.65 μg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 min in a total reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent. On completion of the fragmentation reaction, 55 µl of 2X GEx hybridization buffer was added to the fragmentation mixture and hybridized to S. aurata array (ID 024502, Agilent) at 65°C and 10 rpm for 17 hours in a rotating hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 min at room temperature (RT) with GEWash Buffer 1 (Agilent), 1 min with GE Wash buffer 2 (Agilent) pre-incubated at 37°C, 45 s at RT with Acetonitrile (Sigma, St Louis, MO, USA), and 30 s at RT with stabilization and drying solution (Agilent). Slides were scanned immediately afterwashing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area: 61 x21.6 mm; Scan resolution: 5 µm; Dye channel set to green; Green PMT: 100%). Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent).

data_processing: For microarray analysis, a percentile shift normalization was carried out and then data were filtered by expression (standard deviation) among groups. Then, gene-level analysis was conducted in order to obtain the median of signal intensities from spots within a probe set. Statistical test (t-test unpaired) was done with GeneSpring software GX 14.3 to obtain the differentially expressed genes (p-value < 0.05) between control and treatments.

organism: Sparus aurata

label_protocol: One-color microarray was carried out according to manufacturer’s protocols. Briefly, 200 ng of total RNA was reversed transcribed along with spike-in (Agilent One-Color RNA Spike-In kit, Agilent Technologies, USA). Then, the solution was used as template for Cyanine-3 (Cy3) labeled cRNA synthesis and amplification with the Low Input Quick Amp Labelling kit (Agilent).  Samples of cRNA were purified using the RNeasy micro kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: [test animals] Gilthead sea bream (Sparus aurata) were obtained from an aquatic culture facility (Cádiz, Spain). Once in the laboratory, fish were kept in recirculating aerated 250 L aquaria containing artificial saltwater (salinity 31 g/L) at standard laboratory conditions of 20 °C, under a natural photoperiod during a 10 days acclimatization period. Fish were daily fed with a commercial diet at 1% body weight (Sorgal, Portugal) during the acclimation period.

extract_protocol: Total RNA was extracted from liver using 1 mL of TriReagent (Sigma-Aldrich) per sample, according to the manufacturer's protocol. Total RNA concentration was quantified using a Nanodrop ND-2000 (Thermo Scientific) and RNA integrity checked with the Automated Electrophoresis Station (Bio-Rad Laboratories) using the Experion Standard Sens RNA chip (Bio-Rad Laboratories). Samples with a RNA quality indicator (RQI) >7.0 were included in the analysis.

treatment_protocol: The experimental setup followed the OECD guideline 203 for Fish Acute Toxicity Tests and was in compliance with the Directive 2010/63/EU on the protection of animals used for experimental and other scientific purposes. Test solutions of AuNP (0.5 and 50 µg/L) were prepared by serial dilutions of the stock solution in artificial saltwater. The tested concentrations include a predicted environmental concentration (0.5 µg/L), and a spiking concentration in the same order of magnitude of concentrations tested in previous studies (Teles et al., 2016). After acclimatization, the animals were randomly distributed into duplicated tanks (80 L aquaria filled with 50 L of test solution) (10 fish per tank/1 g of fish per L of test solution) and exposed to 0 (control group), 0.5, or 50 µg/L for 24 h. During the exposure period, fish were subjected to similar laboratory conditions to those used during the acclimation period. After the exposure period, fish (n=10 per experimental group) were sacrificed with tricaine methanesulphonate (MS222, Sigma-Aldrich) and weighed. Blood was quickly collected (less than 3 minutes) from the caudal vasculature using heparinized syringes and blood smear directly prepared. The remaining blood was divided in two aliquots, one used for the Comet assay and the other aliquot centrifuged for plasma isolation. Fish livers were then removed, divided in three replicates, snap frozen in liquid nitrogen and stored at -80 °C until analysed.

value: Liver

value: juveniles, 50 g

tag: agent

value: AuNP

tag: concentration

value: 50 μg/L


title: 50 μg/L_P2_L_24h

status: Public on Jan 24 2017

type: RNA

description: Gene expression in gilthead sea bream liver exposed to 50 μg/L AuNP pool 2

molecule: total RNA

tag: tissue

tag: age


title: corneal_endothelium_control_A32

city: Leuven

first: Joost

middle: J

last: van den Oord

address: Minderbroedersstraat 12, block q, box 1032

department: Department of Imaging & Pathology

country: Belgium

institute: KU Leuven

description:
Control
total RNA (> 200 nucleotides)

data_processing: Data analysis was done through the web portal of Qiagen, according to the manufacturers instructions: http://qiagen.com/geneglobe. The web-based software automatically performed all ΔΔCt based fold-change calculations from the uploaded raw threshold cycle data. For normalization it used the average arithmetic mean of Ct values from three reference genes: RPL13A, RPL19 and RPS5. To calculate p-values it used a two-sided t-statistic. Sample table reports normalized signal (against housekeeping genes). Fold Change file reports FECD/Control ratios.

label: SYBR Green

organism: Homo sapiens

source_name: corneal endothelium control

label_protocol: PCR assays were performed using two complementary Custom RT² Profiler PCR Arrays (CAPH10409 and CAPH104010, Qiagen) following the manufacturer's instructions. Reverse transcription was performed from 100 ng of total RNA per sample for each 96-well plate, using the RT² First Strand Kit (Qiagen). Quantitative real-time PCR was performed (7900 HT Fast Real-Time PCR System; Applied Biosystems, Carlsbad, California) with 40 cycles at 95°C for 15 seconds and 60°C for 60 seconds, using RT² SYBR Green ROX qPCR Mastermix (Qiagen).

extract_protocol: The samples were collected in RNAlater.  Tissues were disrupted and homogenized manually with a Disposable Pestle (VWRTM International, Radnor, Pennsylvania). RNA extraction was performed with RNeasy® Micro Kit (Qiagen, Hilden, Germany), without DNase treatment.

tag: gender

value: Male

value: corneal endothelium with Descemet's membrane

tag: group

value: donor cornea as normal control

tag: phakic or pseudophakic

value: unknown

tag: Cause of death

value: traffic accident

tag: number of cells per mm²


title: corneal_endothelium_FECD_A69

description:
FECD
total RNA (> 200 nucleotides)

source_name: corneal endothelium FECD

extract_protocol: The samples were collected in RNAlater. Tissues were disrupted and homogenized manually with a Disposable Pestle (VWRTM International, Radnor, Pennsylvania). RNA extraction was performed with RNeasy® Micro Kit (Qiagen, Hilden, Germany), without DNase treatment.

value: Fuchs' endothelial corneal dystrophy

tag: inheritance

value: not known

tag: type of surgery

value: Descemet's stripping automated endothelial keratoplasty

value: pseudophakic

tag: time between cataract surgery and keratoplasty (in months)


title: corneal_endothelium_control_A12

description:
Control
total RNA (> 200 nucleotides)

value: trauma


title: GIST-T1_rep1-3

type: genomic

city: Erlangen

first: Evgeny

middle: A.

last: Moskalev

address: Ktankenhausstr. 8-10

department: Institute of Pathology

country: Germany

institute: University of Erlangen-Nuremberg

description:
This Sample represents 3 replicates.
GIST-T1_1, GIST-T1_2, GIST-T1_3

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

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

data_processing: RnBeads version 1.2.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Cell line GIST-T1

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from GIST cell lines using Qiagen DNeasy Kit according to standard instructions.

tag: cell line

tag: cell type

value: gastrointestinal stromal tumour (GIST) cell line

tag: anatomic site of tumour origin

value: stomach


title: corneal_endothelium_FECD_A51

description:
FECD
total RNA (> 200 nucleotides)

value: Female

value: familial FECD


title: corneal_endothelium_control_A62

description:
Control
total RNA (> 200 nucleotides)

value: edema ascites decompensation


title: 50 μg/L_P1_L_24h

description: Gene expression in gilthead sea bream liver exposed to 50 μg/L AuNP pool 1

value: Liver

value: juveniles, 50 g

value: AuNP


title: Severe preeclampsia syncytium 1

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

country: USA

institute: UCSF

hyb_protocol: Sample processing and hybridization were done according to protocols that were devised by the UCSF Gladstone (NHLBI) Genomics Core Facility.

scan_protocol: GeneChips were scanned using a GeneArray Scanner

data_processing: Gene level expression data quality was confirmed, normalized (RMA) and summarized (Affymetrix Expression Console Software). The Sample data tables include transcripts that were annotated and categorized as coding or non-coding (with the non-coding RNAs further broken down into the respective classes lncRNA, microRNA, NATs, pseudogenes, and snoRNA). A coding/noncoding column and an RNA class column are included in the further processed data on the Series record.  Significant differential expression was determined by ANOVA (p < 0.05) and absolute linear fold change >1.5 (Affymetrix Transcriptome Analysis Console Software).

label: biotin

source_name: human placenta, severe preeclampsia

label_protocol: Samples were prepared using the Ambion Whole-Transcript (WT) Expression kit, used in conjunction with the Affymetrix GeneChip  WT Terminal Labeling and Controls Reagent kit

extract_protocol: Total RNA was extracted using Qiagen RNeasy Plus Micro

treatment_protocol: Laser microdissection enabled the isolation of samples that were enriched for syncytiotrophoblasts, invasive cytotrophoblasts or endovascular cytotrophoblasts.

tag: disease state

value: severe preeclampsia

value: syncytium


title: 0.5 μg/L_P3_L_24h

description: Gene expression in gilthead sea bream liver exposed to 0.5 μg/L AuNP pool 3


title: Control_P1_L_24h

description: Gene expression of control group pool 1

source_name: Control,  24h

value: control


title: corneal_endothelium_control_B37

description:
Control
total RNA (> 200 nucleotides)

value: Male

value: corneal endothelium with Descemet's membrane

value: donor cornea as normal control

value: unknown

value: cerebral hemorrhage


title: corneal_endothelium_control_A70

description:
Control
total RNA (> 200 nucleotides)

value: acute myocardial infarction


title: corneal_endothelium_control_A54

description:
Control
total RNA (> 200 nucleotides)

value: cerebrovascular accident


title: corneal_endothelium_FECD_A73

description:
FECD
total RNA (> 200 nucleotides)

value: Fuchs' endothelial corneal dystrophy

value: not known

value: Descemet's stripping automated endothelial keratoplasty

value: pseudophakic


title: 0.5 μg/L_P1_L_24h

description: Gene expression in gilthead sea bream liver exposed to 0.5 μg/L AuNP pool 1

value: Liver


title: corneal_endothelium_FECD_A69

description:
FECD
total RNA (> 200 nucleotides)


title: Control_P2_L_24h

description: Gene expression of control group pool 2

value: juveniles, 50 g


title: corneal_endothelium_FECD_A11

description:
FECD
total RNA (> 200 nucleotides)

value: Female


title: corneal_endothelium_FECD_A51

description:
FECD
total RNA (> 200 nucleotides)

value: familial FECD


title: corneal_endothelium_control_A59

description:
Control
total RNA (> 200 nucleotides)

value: cerebral aneurysm


title: corneal_endothelium_FECD_A68

description:
FECD
total RNA (> 200 nucleotides)


title: 0.5 μg/L_P2_L_24h

description: Gene expression in gilthead sea bream liver exposed to 0.5 μg/L AuNP pool 2

value: AuNP


title: Control_P3_L_24h

description: Gene expression of control group pool 3

value: control


title: corneal_endothelium_FECD_A61

description:
FECD
total RNA (> 200 nucleotides)

value: corneal endothelium with Descemet's membrane


title: corneal_endothelium_FECD_A52

description:
FECD
total RNA (> 200 nucleotides)

value: Male


title: Hippocampus_control_rep1

city: Taiyuan City

first: Tingting

last: Ku

state: Shanxi province

address: 92 Wucheng Road

country: China

institute: Shanxi University

description: miRNA expression after saline exposure

hyb_protocol: Each slide was hybridized with 100ng Cy3‐labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190‐0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55 ℃， 20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188‐5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

organism: Mus musculus

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb, Kit(Cat#5190‐0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) | mirVanaTM PARISTM (Cat#AM1556, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US)

treatment_protocol: MiRNA expression in hippocampi of mice was determined after mice received oropharyngeal aspiration of saline and PM2.5 at 1 and 5 mg/kg every other day for 4 weeks

value: Hippocampus

value: male

tag: treatment

value: saline exposure


title: Hippocampus_PM2.5_1 mg/kg_rep1

description: miRNA expression after PM2.5 at 1 mg/kg exposure

source_name: Hippocampus,PM2.5, 1 mg/kg,replicate1

value: PM2.5 at 1 mg/kg exposure


title: Hippocampus-PM2.5_1 mg/kg_rep3

source_name: Hippocampus,PM2.5, 1 mg/kg,replicate3


title: Hippocampus-PM2.5_5 mg/kg_rep3

description: miRNA expression after PM2.5 at 5 mg/kg exposure

source_name: Hippocampus,PM2.5, 5 mg/kg,replicate3

value: PM2.5 at 5 mg/kg exposure


title: Hippocampus-PM2.5_5 mg/kg_rep1

source_name: Hippocampus,PM2.5, 5 mg/kg,replicate1


title: Hippocampus-PM2.5_5 mg/kg_rep2

source_name: Hippocampus,PM2.5, 5 mg/kg,replicate2


title: Hippocampus_PM2.5_1 mg/kg_rep2

source_name: Hippocampus,PM2.5, 1 mg/kg,replicate2


title: Hippocampus_control_rep2

description: miRNA expression after saline exposure


title: Hippocampus_control_rep3

description: miRNA expression after saline exposure


title: corneal_endothelium_control_A31

description: corneal endothelium control

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Human Gene 1.0 ST Arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were processed with RMA (as implemented in the XPS package of Bioconductor). Reported values are on log2-scale.

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Next the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: The donor cornea was provided in storage medium.

extract_protocol: Tissues were disrupted and homogenized manually with a Disposable Pestle (VWRTM International, Radnor, Pennsylvania). RNA extraction was performed with RNeasy® Micro Kit (Qiagen), without DNase treatment.

treatment_protocol: The sample was collected in RNAlater.

tag: rna integrity number

value: 26 years

value: donor cornea as normal control

value: trauma


title: Tet2 deficient macrophage, biological replicate 5, no pro-inflammatory cytokine stimuli

city: Boston

first: Chia-Ling

last: Wu

state: MA

address: 700Albany St

department: Whitaker Cardiovascular Institute

institute: Boston University

description: Whole-transcript expression profiling

hyb_protocol: Fragmented, biotinylated DNA samples were hybridized on 6 mouse Gene 2.0ST arrays.

scan_protocol: A total of 6 array images were acquired by GeneChip Scanner 3000TG and quality assesed bty Affymetrix Expression Console (Santa Clara, CA)

data_processing:
Mouse Gene 2.0 ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) [1] in the affy package (version 1.36.1) [2] included in the Bioconductor software suite (version 2.12) [3] and an Entrez Gene-specific probeset mapping (17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan [4,5]. Array quality was assessed by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM package (version 1.34.0)
1. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003 4(2):249-64, PubMed ID 12925520, doi:10.1093/biostatistics/4.2.249
2. Gautier L, Cope L, Bolstad BM, Irizarry RA. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004 12;20(3):307-15, PubMed ID 14960456, doi:10.1093/bioinformatics/btg405
3. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 2004;5(10):R80, PubMed ID 15461798, doi:10.1186/gb-2004-5-10-r80
4. Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ, Meng F. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 2005 33(20):e175, PubMed ID 16284200, doi:10.1093/nar/gni179
5. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF
6. Brettschneider J, Collin F, Bolstad BM, and Speed TP. Quality Assessment for Short Oligonucleotide Microarray Data. Technometrics 2008 50(3):241, doi:10.1198/004017008000000334

label: Biotin

source_name: Thioglycollate-elicited macrophages from the peritoneal cavity of mice.

label_protocol: Whole-transcript expresion profiling experiments were carried out by the Boston University Microarray Core Facility. Biotyinated DNA was prepared per manufactureer's recommendaton

growth_protocol: After 4-days of 1mL aged 4% Brewer's thyoglycollate injection (i.p.), peritoneal macrophages were isolated from C57BL/6J Tet2-deficient (Tet2-/-) mice or wildtype littermates, plated on standard cell culture plates in RPMI supplemented with antibiotics and 10% FBS.

extract_protocol: 10hr later, total RNA was extracted with an AllPrep DNA/RNA Mini Kit Print (Qiagen) and treated with Rnase-free Dnase I kit (Qiagen), according to manufacturer’s instructions.

treatment_protocol: No treatment were performed on the isolated macrophages.

tag: strain

tag: genotype/variation

value: Tet2-/- mice


title: Wildtype macrophage, biological replicate 4, no pro-inflammatory cytokine stimuli

description: Whole-transcript expression profiling

value: wildtype littermates


title: Wildtype macrophage, biological replicate 6, no pro-inflammatory cytokine stimuli

description: Whole-transcript expression profiling


title: corneal_endothelium_control_A25

description: corneal endothelium control

tag: age

value: 68 years

tag: tissue

value: malignancy


title: corneal_endothelium_control_A28

description: corneal endothelium control

tag: gender

value: 54 years

tag: group

value: cerebrovascular accident


title: corneal_endothelium_FECD_A39

description: corneal endothelium FECD

growth_protocol: Not applicable.

value: female

value: 78 years

value: Fuchs' endothelial corneal dystrophy

value: Descemet's stripping automated endothelial keratoplasty (DSAEK)

tag: visual acuity

tag: pseudophakic?

value: yes

tag: time between cataract surgery and dsaek

value: 29 months


title: corneal_endothelium_control_A17

description: corneal endothelium control

value: male

value: 63 years

value: corneal endothelium with Descemet's membrane

tag: number of cells per mm²

tag: Cause of death


title: corneal_endothelium_FECD_A13

description: corneal endothelium FECD

value: 70 years

tag: type of surgery

value: 7 months


title: MSC primed with M2MФ 4

city: TOULOUSE

first: Audrey

last: Varin

address: CHU Rangueil, Batiment L1, 2étage , avenue Jean Poulhès

country: France

institute: STROMALab

description: Gene expression datas from human MSC after 24h of co-culture with M2MФ (after magnetic separation of the 2 cell types)

hyb_protocol: Labelled SPIAs cDNA was hybrided for 20h to the human gene ship Human Gene 1.1 ST Array Strip; Affymetrix. Gene ships were washed and stained in the Gene Atlas Fluidic station.

scan_protocol: Arrays were scanned on the GeneAtlas Imaging Station (Affymetrix) and analyzed by using GeneChip Command Console software (Affymetrix)

data_processing: Expression signal values and P-values were obtained for each probe set by use of Partek Genomics suite (Partek) by the robust Multichip Averaging algorythm in normalization. Principal component and gene expression analysis involved use of MeV.

source_name: cultivated bone marrow-derived MSC after 24h co-culture with M2MФ

label_protocol: 27 ng of total RNA was amplified with ovation PicoSL WTA system V2 kit (NuGNEN). 2,5 µg of SPIAs cDNA were labelled with Encore biotin Module kit (NuGEN).

growth_protocol: α-MEM + 10% fœtal calf serum + 1% L-glutamine + 1%  amphotericin/penicillin

extract_protocol: Extraction of RNA with the Rneasy micro kit (Qiagen). Quantification of the RNA by use of Nanodrop ND-2000. Quality of RNA was assayed by the Experion RNA Stdsens analysis kit (Biorad).

treatment_protocol: 24h co-culture alone (MSC) or with pro-inflammatory macrophages (M1MФ) or with anti-inflammatory macrophages (M2MФ). Separation of the MФ and MSCs and microarray analysis of MSC alone (MSC) or M1MФ-primed MSCs (M1-MSC) or M2MФ-primed MSCs (M2-MSCs)

tag: cell type

value: bone-marrow derived mesenchymal stromal cells


title: Wildtype macrophage, biological replicate 5, no pro-inflammatory cytokine stimuli

description: Whole-transcript expression profiling

value: Tet2-/- mice


title: Wildtype macrophage, biological replicate 1

data_processing:
Mouse Gene 2.0 ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) [1] in the affy package (version 1.36.1) [2] included in the Bioconductor software suite (version 2.12) [3] and an Entrez Gene-specific probeset mapping (17.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan [4,5]. Array quality was assessed by computing Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE) using the affyPLM package (version 1.34.0)
References:
1. PMID 12925520; 2. PMID 14960456; 3. PMID 15461798; 4. PMID 16284200
5. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF
6. Brettschneider J, Collin F, Bolstad BM, and Speed TP. Quality Assessment for Short Oligonucleotide Microarray Data. Technometrics 2008 50(3):241, doi:10.1198/004017008000000334

source_name: Wildtype macrophage

extract_protocol: Total RNA was extracted with an AllPrep DNA/RNA Mini Kit Print (Qiagen) and treated with Rnase-free Dnase I kit (Qiagen), according to manufacturer’s instructions.

treatment_protocol: Isolated macrophages were treated with a combination of 10 ng/ml LPS and 2 ng/ml IFNg for 10 hours.

tag: strain background

value: wildtype littermates

value: Thioglycollate-elicited macrophages from the peritoneal cavity of mice.

tag: treated with

value: LPS and IFNg for 10 hr


title: corneal_endothelium_FECD_A41

description: corneal endothelium FECD

value: 75 years


title: MSC primed with M2MФ 2


title: Grass-clump dwarf synthetic wheat-Langdon/Ae.umbellulata KU4052-crown tissue-replicate1

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

country: Japan

institute: Kobe University

description: Gene expression in crown tissues of the 8-week-old plants

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: synthetic hexaploid wheat

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown at 24°C for 50 days under long day (18-h light and 6-h dark) condition

extract_protocol: Total RNA was extracted, using an RNeasy Plant Mini kit (Qiagen). RNA quality was checked using an Agilent 2100 BioAnalyzer.

value: shoot apical meristem

tag: phenotype

value: grass-clump dwarf


title: Tet2 deficient macrophage, biological replicate 6, no pro-inflammatory cytokine stimuli

description: Whole-transcript expression profiling


title: MSC alone 2

description: Gene expression data from human MSC cultivated alone

source_name: cultivated bone marrow-derived MSC


title: MSC alone 1


title: MSC primed with M1MФ 3

description: Gene expression datas from human MSC after 24h of co-culture with M1MФ (after magnetic separation of the 2 cell types)

source_name: cultivated bone marrow-derived MSC after 24h co-culture with M1MФ


title: MSC primed with M1MФ 2


title: MSC primed with M2MФ 1


title: corneal_endothelium_FECD_A22

description: corneal endothelium FECD

tag: rna integrity number

value: female

value: 79 years

value: Fuchs' endothelial corneal dystrophy

value: 14 months


title: Wildtype macrophage, biological replicate 3


title: Tet2 deficient macrophage, biological replicate 4, no pro-inflammatory cytokine stimuli

description: Whole-transcript expression profiling

tag: strain


title: Wildtype macrophage, biological replicate 2

tag: genotype/variation


title: Tet2 deficient macrophage, biological replicate 2

source_name: Tet2 deficient macrophage


title: Tet2 deficient macrophage, biological replicate 3


title: Wild type synthetic wheat-Langdon/Ae. umbellulata KU4103-crown tissue-replicate2

value: wild type


title: Grass-clump dwarf synthetic wheat-Langdon/Ae. umbelluata KU4052-crown tissue-replicate2


title: Shoot meriStem of wild type triploid hybridS-replicate2

source_name: triploid wheat hybrid

growth_protocol: Plants were grown at 24°C for 7 days under long day (18-h light and 6-h dark) condition

tag: age

value: 7-day old


title: Tet2 deficient macrophage, biological replicate 1


title: Shoot meriStem of wild type triploid hybridS-replicate1

tag: tissue


title: MSC alone 3


title: Shoot meriStem of triploid hybridS Showing growth abortion-replicate2

value: severe growth abortion


title: MSC primed with M2MФ 3


title: MSC primed with M1MФ 1


title: Balbc_p53null_2225L_sorted_shRor2_1

status: Public on Jan 23 2017

city: Houston

first: Jeffrey

last: Rosen

state: TX

address: One Baylor Plaza M638

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Samples obtained from Rosen Lab

hyb_protocol: described in Herschkowitz et al., 2007, Genome Biology, 8(5):R76

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

source_name: Whole Mouse Reference RNA

extract_protocol: Total RNA isolated using a Qiagen RNeasy Kit

tag: sample type

value: Reference RNA from C57Bl6/J and 129 male and female Day1 pups

value: P53null 2225L

value: Balbc

tag: lentivirus


title: Wild type synthetic wheat-Langdon/Ae. umbellulata KU4103-crown tissue-replicate1


title: Balbc_p53null_T2_sorted_shRor2_3

description: Samples obtained from Rosen Lab

label_protocol: described in Herschkowitz et al., 2007, Genome Biology, 8(5):R76

value: P53null T2


title: Balbc_p53null_2225L_sorted_shRor2_2

description: Samples obtained from Rosen Lab


title: Shoot meristem of triploid hybrids showing growth abortion-replicate1


title: Balbc_p53null_T2_sorted_shRor2_1

description: Samples obtained from Rosen Lab


title: Balbc_p53null_T2_sorted_shLuc3

description: Samples obtained from Rosen Lab

value: shLuc


title: Balbc_p53null_T1_sorted_shRor2_2

description: Samples obtained from Rosen Lab

value: P53null T1


title: Balbc_p53null_T1_sorted_shRor2_3

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_sorted_shRor2_3

description: Samples obtained from Rosen Lab


title: Balbc_p53null_T2_sorted_shLuc2

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_sorted_shLuc3

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_sorted_shLuc1

description: Samples obtained from Rosen Lab


title: Balbc_p53null_T2_sorted_shLuc1

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_sorted_shLuc2

description: Samples obtained from Rosen Lab


title: Balbc_p53null_T1_sorted_shRor2_1

description: Samples obtained from Rosen Lab


title: Balbc_p53null_T1_sorted_shLuc2

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_shRor2_3

description: Samples obtained from Rosen Lab


title: Balbc_p53null_T2_sorted_shRor2_2

description: Samples obtained from Rosen Lab


title: Balbc_p53null_T1_sorted_shLuc3

description: Samples obtained from Rosen Lab


title: Balbc_p53null_T1_sorted_shLuc1

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_shRor2_2

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_shRor2_1

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_shLuc4

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_shLuc3

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_shRor2_4

description: Samples obtained from Rosen Lab


title: CD19+ B-cell from healthy donor [H9]

city: Heidelberg

first: Katharina

last: Filarsky

address: Im Neuenheimer Feld 580

institute: German Cancer Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Probe Level Quantile Normalization of High Density Oligonucleotide Array Data, Ben Bolstad, Division of Biostatistics, University of California, Berkeley December 2001

source_name: CD19+ B-cell

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was extracted with DNA/RNA all prep Kit (Qiagen) according to the manual. Quality controle was performed with Agilent Bioanalyzer.

tag: gender

tag: ighv status

tag: karyotype


title: CD19+ B-cell from healthy donor [H4]


title: CD19+ B-cell from healthy donor [H3]


title: CD19+ B-cell from healthy donor [H7]


title: CD19+ B-cell from healthy donor [H1]


title: CD19+ B-cell from healthy donor [H6]


title: CD19+ B-cell from healthy donor [H5]


title: CD19+ cells from CLL patient [CLL11]

source_name: CD19+ CLL cell

value: male

value: mutated

value: 13q deletion


title: CD19+ cells from CLL patient [CLL15]


title: CD19+ cells from CLL patient [CLL12]

value: unmutated


title: U3169 cell line

city: Uppsala

first: Sven

last: Nelander

address: Dag Hammarskjölds v. 20

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: Surgical tissue samples and clinical information were obtained from treatment naive patients subjected to brain tumor removal

hyb_protocol: GeneChip® ST Arrays (GeneChip® Human Transcriptome Array 2.0) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were washed and stained using the Fluidics Station 450.

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

data_processing: The raw data was normalized in the free software Expression Console provided by Affymetrix (http://www.affymetrix.com) using the robust multi-array average (RMA) method first suggested by Li and Wong (PNAS, 2001). Only probesets annotated as being in category main were included in further analyses.

source_name: Primary human GBM

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual (P/N 703174 Rev 1 Affymetrix Inc., Santa Clara, CA).

growth_protocol: The cells were cultured in DMEM/F12 Glutamax (Gibco) and Neurobasal medium (Gibco) mixed 1:1 with addition of 1% B27 (Invitrogen), 0.5% N2 (Invitrogen), 1% Penicillin/Streptomycin (Sigma), 10 ng/ml each of EGF and FGF2 (Peprotech) on poly-ornithine/laminin-coated dishes as adherent cells.

extract_protocol: Total mRNA was extracted using the QIAGEN RNeasy kit (QIAGEN)

treatment_protocol: No treatment

value: Glioma stem cells


title: U3180 cell line


title: U3173 cell line


title: CD19+ cells from CLL patient [CLL10]


title: CD19+ cells from CLL patient [CLL14]

value: female


title: U3189 cell line


title: Balbc_p53null_2225L_shLuc1

description: Samples obtained from Rosen Lab


title: Balbc_p53null_2225L_shLuc2

description: Samples obtained from Rosen Lab


title: U3202 cell line


title: CD19+ cells from CLL patient [CLL13]


title: U3172 cell line


title: U3198 cell line


title: U3175 cell line


title: CD19+ B-cell from healthy donor [H8]


title: CD19+ cells from CLL patient [CLL9]


title: CD19+ cells from CLL patient [CLL8]


title: U3167 cell line


title: CD19+ cells from CLL patient [CLL7]

value: normal


title: CD19+ cells from CLL patient [CLL6]


title: CD19+ cells from CLL patient [CLL5]


title: U3155 cell line


title: CD19+ B-cell from healthy donor [H2]


title: U3146 cell line


title: CD19+ cells from CLL patient [CLL4]


title: U3129 cell line


title: U3140 cell line


title: U3137 cell line


title: CD19+ cells from CLL patient [CLL3]


title: KLF4 overexpression in MEC2; 10h

description:
MEC2_10h_KLF4
Mec2_10h_KLF4_9980097070_J mean

source_name: chronic B cell leukemia

growth_protocol: MEC1 and MEC2 cultured in DMEM, 10% FCS, 37°C, 5% CO2; JeKo-1 cultured in RPMI 20% FCS, 37°C, 5% CO2

extract_protocol: Total RNA was extracted with DNA/RNA allprep Kit (Qiagen) according to the manual. Quality controle was performed with Agilent Bioanalyzer.

treatment_protocol: Nucleofection with 2 µg plasmid using Amaxa Nucleofector II device (Lonza); nucleofection solution V; program X-001

tag: cell line

value: chronic B cell leukemia cell line

tag: transfected with

tag: time point

value: 10h after transfection


title: U3123 cell line

tag: cell type


title: U3121 cell line


title: CD19+ cells from CLL patient [CLL1]


title: U3110 cell line


title: empty vector control in MEC2; 10h

description:
MEC2_10h_EVctrl
Mec2_10h_EVctrl_9980097070_D mean


title: U3102 cell line


title: U3118 cell line


title: KLF4 overexpression in MEC2; 3h

description:
MEC2_3h_KLF4
Mec2_3h_KLF4_9980097070_I mean

value: 3h after transfection


title: KLF4 overexpression in MEC1; 3h

description:
MEC1_3h_KLF4
Mec1_3h_KLF4_9980097070_K mean


title: U3104 cell line


title: U3093 cell line


title: U3117 cell line


title: KLF4 overexpression in MEC1; 10h

description:
MEC1_10h_KLF4
Mec1_10h_KLF4_9980097070_F mean


title: empty vector control in MEC2; 3h

description:
MEC2_3h_EVctrl
Mec2_3h_EVctrl_9980097070_G mean


title: U3088 cell line


title: CD19+ cells from CLL patient [CLL2]


title: empty vector control in MEC1; 3h

description:
MEC1_3h_EVctrl
Mec1_3h_EVctrl_9980097070_C mean


title: U3101 cell line


title: U3085 cell line


title: empty vector control in JeKo-1; 10h

description:
JeKo-1_10h_EVctrl
JeKo_10h_EVctrl_9980097070_H mean

source_name: Mantle Cell Lymphoma

value: Mantle Cell Lymphoma cell line


title: U3078 cell line


title: empty vector control in JeKo-1; 3h

description:
JeKo-1_3h_EVctrl
JeKo_3h_EVctrl_9980097070_A mean


title: U3084 cell line


title: KLF4 overexpression in JeKo-1; 10h

description:
JeKo-1_10h_KLF4
JeKo_10h_KLF4_9980097070_B mean


title: KLF4 overexpression in JeKo-1; 3h

description:
JeKo-1_3h_KLF4
JeKo_3h_KLF4_9980097070_E mean


title: U3068 cell line


title: U3053 cell line


title: U3082 cell line


title: U3062 cell line


title: U3164 cell line


title: U3051 cell line


title: U3056 cell line


title: U3071 cell line


title: U3073 cell line


title: empty vector control in MEC1; 10h

description:
MEC1_10h_EVctrl
Mec1_10h_EVctrl_9980097070_L mean


title: U3060 cell line


title: U3065 cell line


title: U3047 cell line


title: U3086 cell line


title: U3039 cell line


title: U3046 cell line


title: U3035 cell line


title: U3037 cell line


title: U3033 cell line


title: U3042 cell line


title: U3029 cell line


title: U3031 cell line


title: U3021 cell line


title: U3034 cell line


title: U3027 cell line


title: U3020 cell line


title: CD19+ B-cell from healthy donor [H8, methylation]

description: MCIp of genomic DNA; high salt fraction

hyb_protocol: hybridization was performed according to protocol number G4170-90012 for Agilent Microarray Analysis of Methylated DNA Immunoprecipitation version 1.0

scan_protocol: arrays were scanned on a Agilent Technologies Scanner G2505C US81503234

data_processing: Images were quantified and analyzed using Agilent Feature Extraction Software (version 10.7.3.1). For the methylation data (1) background correction #according to limma function backgroundCorrect was performed and (2) within-array normalization using intensity-based loess on "least-variant" spots.

label_protocol: BioPrime Total Genomic Labeling System (Invitrogen)

extract_protocol: genomic DNA was isolated using the DNA/RNA allprep kit (Qiagen) and subjectecd to Methyl-CpG-Immunoprecipitation (MCIp); High salt fraction was used for array hybridization

tag: ighv mutation status

source_name: T-cell pool

tag: reference

value: common reference


title: U3002 cell line


title: U3005 cell line


title: U3017 cell line


title: U3013 cell line


title: CD19+ B-cell from healthy donor [H7, methylation]

description: MCIp of genomic DNA; high salt fraction


title: U3009 cell line


title: U3028 cell line


title: U3008 cell line


title: Tumor+Allo/Y (d28) (SAMPLE 12)

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description: CD45+ cells from Tumor+Allo/Y (d28) prostate

hyb_protocol: Biotin-labeled cRNA was hybridized on MouseWG-6 v2.0 Expression BeadChip (harboring probes for ~45k transcript) for 16 hours. The BeadChip underwent a washing and streptavidin-Cy3 (GE Healthcare Bio-Sciences) conjugate staining protocol

scan_protocol: Illumina Bead Array Reader

data_processing: The data were normalized using the quantile algorithm implemented in the Illumina Genome Studio Sofware

label_protocol: Biotinylated cRNA was prepared with the Illumina total Prep Amplification Kit (Ambion Life Technologies)

extract_protocol: Trizol

value: C57Bl/6 (TRAMP)

tag: treatment

value: Tumor+Allo/Y (d28) ACT

value: prostate

value: CD45+ cells


title: CD19+ B-cell from healthy donor [H4, methylation]

description: MCIp of genomic DNA; high salt fraction


title: U3024 cell line


title: CD19+ B-cell from healthy donor [H9, methylation]

description: MCIp of genomic DNA; high salt fraction


title: Tumor+Allo/Y (d28) (SAMPLE 11)

source_name: CD45+ cells from Tumor+Allo/Y (d28) prostate


title: Tumor+Allo/Y (SAMPLE 9)

description: CD45+ cells from Tumor+Allo/Y prostate

source_name: CD45+ cells from Tumor+Allo/Y prostate

value: Tumor+Allo/Y ACT


title: CD19+ cells from CLL patient [CLL11, methylation]

description: MCIp of genomic DNA; high salt fraction

value: male


title: CD19+ cells from CLL patient [CLL8, methylation]

description: MCIp of genomic DNA; high salt fraction

value: mutated


title: CD19+ cells from CLL patient [CLL10, methylation]

description: MCIp of genomic DNA; high salt fraction

value: 13q deletion


title: Tumor+Allo/Y (d28) (SAMPLE 10)


title: Allo/Y (SAMPLE 3)

description: CD45+ cells from Allo/Y prostate

source_name: CD45+ cells from Allo/Y prostate

value: Allo/Y ACT


title: CD19+ cells from CLL patient [CLL9, methylation]

description: MCIp of genomic DNA; high salt fraction

value: unmutated


title: Tumor (SAMPLE 5)

description: CD45+ cells from Tumor prostate

source_name: CD45+ cells from Tumor prostate

value: Tumor ACT


title: Tumor (SAMPLE 4)

description: CD45+ cells from Tumor prostate


title: CD19+ B-cell from healthy donor [H1, methylation]

description: MCIp of genomic DNA; high salt fraction


title: Synechocystis_PCC6803_WT_22h_N_recovery_2

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was normexp background corrected and quantile normalized.

organism: Synechocystis sp. PCC 6803

label_protocol: The DNAse treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: The Synechocystis sp PCC 6803 strain PCC-M (Trautmann, 2012) used in this study was provided by S. Shestakov (Moscow State University) and cultivated on 1% (w/v) agar (Bacto agar; Difco) plates containing BG-11 mineral medium (Rippka, 1979). Liquid cultures of wild-type and mutant strains were grown in BG-11 medium containing 10 mM TES buffer, pH 8.0, under continuous illumination with white light at 80 mmol photons m–2 s–1 at 30 °C, supplemented with a continuous stream of ambient air. BG11 plates for the cultivation of mutant strains were supplemented with 40 µg ml-1 kanamycin (∆ssaA). No antibiotics were added to the liquid cultures to eliminate any influence.

extract_protocol: For the isolation of RNA, samples from discrete stages of cultivation were taken at the indicated times and were immediately put on ice and spun down at 4 °C. The preparation of total RNA from Synechocystis 6803 was essentially performed as described previously (Dienst et al., 2008), using the Hot Trizol method, followed by 2-propanol precipitation.

treatment_protocol: For nitrogen depletion, NaNO3 was omitted from the medium and cells were first washed twice and then resuspended in nitrogen-free medium. Cultures were incubated in nitrogen-depleted medium for 7 days. To induce nitrogen recovery, starved cells were supplemented with 17.6 mM NaNO3. Cells were harvested after cultivation in nitrogen-repleted medium for the indicated times (1h, 4h, 22h, 48h, 144h), to document recovery.

tag: genotype

value: WT

tag: protocol

value: nitrogen recovery

tag: time


title: Tumor (SAMPLE 6)

description: CD45+ cells from Tumor prostate

tag: strain


title: CD19+ cells from CLL patient [CLL15, methylation]

description: MCIp of genomic DNA; high salt fraction


title: CD19+ cells from CLL patient [CLL14, methylation]

description: MCIp of genomic DNA; high salt fraction

value: female


title: Allo/Y (SAMPLE 2)

description: CD45+ cells from Allo/Y prostate

tag: tissue


title: CD19+ cells from CLL patient [CLL7, methylation]

description: MCIp of genomic DNA; high salt fraction

value: normal


title: CD19+ cells from CLL patient [CLL6, methylation]

description: MCIp of genomic DNA; high salt fraction


title: Synechocystis_PCC6803_WT_4h_N_recovery_2


title: Allo/Y (SAMPLE 1)

description: CD45+ cells from Allo/Y prostate


title: CD19+ cells from CLL patient [CLL13, methylation]

description: MCIp of genomic DNA; high salt fraction


title: Synechocystis_PCC6803_WT_4h_N_recovery_1


title: CD19+ cells from CLL patient [CLL5, methylation]

description: MCIp of genomic DNA; high salt fraction


title: Tumor+Allo/Y (SAMPLE 8)

description: CD45+ cells from Tumor+Allo/Y prostate


title: mGC3_CNP biological replicate 3

description: The tumor cells were derived from mouse GBM which were generated by injecting DF-1 cells producing RCAS-PDGFB-HA on to the adult TV-a mouse brain

hyb_protocol: GeneChip® ST Arrays ( GeneChip® Mouse Gene 1.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 2, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450.

source_name: C/tv-a Arf-/- mouse

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression Kit(P/N 4425209 Rev B 05/2009) and Affymetrix GeneChip® WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 3, Affymetrix Inc., Santa Clara, CA).

growth_protocol: The cells were cultured in the medium contains DMEM/F12 GlutaMAX mixed 1:1 (GIBCO-Invitrogen) with addition of 1% penicillin G/streptomycin sulfate (Sigma), B-27 without Vitamin A (1:50; GIBCO-Invitrogen), HEPES (0.2 mM, Sigma) and insulin (20 ng/ml; Sigma). For adherent mouse GC cultures, primary spheres were seeded onto Petri dishes coated with growth factor depleted ECM (Sigma) diluted at a ratio of 1:5.

extract_protocol: Total mRNA was extracted using the QIAGEN RNeasy kit (QIAGEN).

treatment_protocol: No treatment.

value: glioma stem cells


title: Tumor+Allo/Y (SAMPLE 7)

description: CD45+ cells from Tumor+Allo/Y prostate


title: CD19+ cells from CLL patient [CLL4, methylation]

description: MCIp of genomic DNA; high salt fraction

value: common reference


title: Synechocystis_PCC6803_WT_22h_N_recovery_1


title: CD19+ cells from CLL patient [CLL3, methylation]

description: MCIp of genomic DNA; high salt fraction


title: Synechocystis_PCC6803_∆ssaA_22h_N_recovery_1

value: {delta}ssaA


title: mGC2_NES biological replicate 3

source_name: N/tv-a Arf-/- mouse


title: mGC3_CNP biological replicate 2


title: U3048 cell line

value: Glioma stem cells


title: Synechocystis_PCC6803_WT_0h_N_recovery_1

value: control


title: mGC2_NES biological replicate 2


title: Synechocystis_PCC6803_∆ssaA_1h_N_recovery_1


title: Synechocystis_PCC6803_∆ssaA_4h_N_recovery_1


title: Synechocystis_PCC6803_WT_0h_N_recovery_2


title: CD19+ cells from CLL patient [CLL1, methylation]

description: MCIp of genomic DNA; high salt fraction


title: Synechocystis_PCC6803_∆ssaA_4h_N_recovery_2


title: Synechocystis_PCC6803_∆ssaA_22h_N_recovery_2


title: Synechocystis_PCC6803_WT_1h_N_recovery_2


title: Synechocystis_PCC6803_∆ssaA_1h_N_recovery_2


title: mGC2_NES biological replicate 1


title: Synechocystis_PCC6803_∆ssaA_0h_N_recovery_2


title: mGC1_GFAP biological replicate 3

source_name: G/tv-a Arf-/- mouse


title: Synechocystis_PCC6803_∆ssaA_0h_N_recovery_1


title: mNSC_C/tv-a control

description: The NSCs were generated by dissecting, dissociating and  culturing the SVZ of adult TV-a mouse brain

value: normal NSC


title: mGC1_GFAP biological replicate 1


title: mGC3_CNP biological replicate 1


title: mGC1_GFAP biological replicate 2


title: mNSC_G/tv-a control


title: mNSC_N/tv-a control


title: Huh7_control

city: Bunkyo-ku, Tokyo

first: Yasuo

last: Tanaka

address: 7-3-1 Hongo

department: Gastroenterology

institute: The University of Tokyo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 Plus 2.0 Array. Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Liver

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3'IVT Express Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle's medium (DMEM) containing 10% heat-inactivated FBS with puromycin (2 μg/ml) .

extract_protocol: The total RNA of cells was extracted from cultured cells using NucleoSpin® RNAII (Takara, Tokyo, Japan).


title: Huh7_FG-Sharpin

value: Sharpin-expressing


title: Synechocystis_PCC6803_WT_1h_N_recovery_1


title: Aire KO Etopo Topo 1

status: Public on Jan 22 2017

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

source_name: Thymus

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: age

value: 4 Weeks Old

tag: Sex

value: Female

value: Aire-/-

tag: cells

value: MECs

value: Etopo Topo

tag: amplification technique

value: Ambion WT Expression Kit

tag: separation method

value: Dissection / Trimming


title: Aire KO Etopo Topo 2


title: CD19+ B-cell from healthy donor [H3, methylation]

description: MCIp of genomic DNA; high salt fraction

tag: gender

tag: karyotype


title: Aire KO Topo 1

value: 6 Weeks Old

value: Topo


title: Aire KO Topo 3


title: WT Etopo Topo 3

value: Aire+/+


title: Aire KO Etopo 1

value: Etopo


title: Aire KO Etopo 2


title: Aire KO DMSO 3

value: DMSO


title: WT Topo 1


title: WT Etopo 2

value: Male


title: WT Topo 2


title: WT Topo 3


title: Bone marrow_C57B6/J_rep1

city: Oulu

first: Valerio

last: Izzi

state: Select a State or Province

address: Aapistie 7A

country: Finland

institute: University of Oulu

description: Gene expression data from normal adult hematopoietic tissue

hyb_protocol: cRNA was hybridized on Affymetrix GeneChip MG-430.2 array plates according to manufacturer's instructions.

scan_protocol: GeneChips were scanned on Affymetrix GeneChip Scanner 3000

data_processing: Data were normalized at genepattern.org using RMA algorithm with quantile normalization, median scaling and no present/absent call computing. Normalized data were fuether analyzed using GSEA software.

source_name: Flushed bone marrow from femur/tibia_wildtype

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: C57B6/J-Col18a1+/+ and C57B6/J-Col18a1-/- lines were maintained in 12-h light/12-h dark cycle and fed ad libitum with standard chow. Appearence of the vaginal plug after mating was counted as E0.5 (0.5 d.p.c.), and appropriate embryonic staging was confirmed during embryos isolation. All embryos in this study were confirmed to be E14.5 at sacrifice.

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

treatment_protocol: Bone marrows (BM) from femurs and tibias were flushed with phosphate-buffered saline + 4% fetal bovine serum (PBS+FBS) and filtered through a 40-um mesh to obtain single cell suspensions. Fetal livers were isolated from E14.5 embryos under dissection stereomicroscope, and separated into single-cell suspension by pipetting and filtration.

value: bone marrow from femur/tibia

value: 3 months-old


title: WT DMSO 2


title: Bone marrow_Col18a1-/-_rep2

description: Gene expression data from adult hematopoietic tissue perturbed by the lack of Col18a1

source_name: Flushed bone marrow from femur/tibia_Col18a-KO


title: WT Etopo Topo 2


title: Aire KO DMSO 1


title: Fetal liver_C57B6/J_rep1

description: Gene expression data from normal fetal hematopoietic tissue

source_name: E14.5 fetal liver_wildtype

value: Undetermined

value: liver


title: Aire KO Topo 2


title: Fetal liver_Col18a1-/-_rep1

description: Gene expression data from fetal hematopoietic tissue perturbed by the lack of Col18a1

source_name: E14.5 fetal liver_Col18a-KO


title: WT Etopo Topo 1

value: 4 Weeks Old


title: WT DMSO 1


title: Bone marrow_Col18a1-/-_rep1


title: WT Etopo 1

value: Female


title: WT DMSO 3


title: WT Etopo 3


title: Fetal liver_Col18a1-/-_rep2


title: Aire KO DMSO 2

value: Aire-/-


title: Bone marrow_C57B6/J_rep2


title: Fetal liver_C57B6/J_rep2


title: beekeeper_48

status: Public on Jan 21 2017

city: Wroclaw

first: Pawel

last: Karpinski

address: Marcinkowskiego 1

department: Department of Genetics

country: Poland

institute: Wroclaw Medical University

hyb_protocol: The labeled and fragmented aRNA was spiked with cDNA hybridization controls (GeneChip® Hybridization  Control  Kit,  Affymetrix). The spiked aRNA  samples  were  hybridized  at  45°C  for  16  hrs.

scan_protocol: Fluorescent signal intensities  were  detected  with  the  Affymetrix  GeneChip®  3000  Scanner  and  AGCC  Scan Control Software v4.0.0.17 (Affymetrix). Automatic grid was arranged and  raw data  were  processed  to  generate  intensity  files  (*.CEL)  by  the  AGCC Software.

data_processing: Bioconductor's affy and custom cdf BrainArray package (primeviewhsentrezgcdf ver. 20) were used for RMA normalization and raw data processing using default settings for background correction and normalization.

source_name: beekeeper

label_protocol: 200 ng total RNA per sample  were introduced into a reverse transcription with subsequent in vitro  transcription (RT-IVT) reaction. Prior to RT-IVT, the total  RNA samples were spiked with  in  vitro  synthesized  polyadenylated  transcripts  (Gene  Chip®  Poly-A  Control  Kit, Affymetrix  Inc.)  which  serve  as  an  internal  labeling  control. The  spiked  total  RNA  was  reversely  transcribed  into  double  stranded  cDNA  and  then converted  into  Biotin-labeled  aRNA  by  in  vitro  transcription  for  16  hrs  (3´IVT  PLUS Expression  Kit,  Affymetrix  Inc.). The  generated  single  stranded  aRNA  was  purified  and fragmented.

extract_protocol: All blood samples were drawn prior venom injections. 2.5ml of whole lood was collected on PAXgene Blood RNA Tubes. mRNA was isolated using PAXgene Blood miRNA Kit (QIAGEN) according to manufacturer manual.

treatment_protocol: All patients undergone ultra-rush venom immunotherapy (VIT-UR) protocol. VIT-UR  begins with the initial venom dose of 0.1 mcg and the summary dose of 111.1 mcg is reached within 3.5 hours. Maintenance dose of 100 mcg venom was administered every 4 weeks. Standardized lyophilized venom allergen extract (Pharmalgen Alk Abello) was used for build-up phase of VIT, and aluminum hydroxide adsorbed insect venom (Alutard-Alk Abello) for maintenance phase of therapy

tag: condition

value: without signs of HVA

value: male

tag: individual id

tag: group

value: beekeeper

tag: sampling time

value: after beekeeping season (september - october)

tag: blood count (%) [neutrophils / lymohocytes / monocytes / eosinophils / basophils]

value: whole blood


title: beekeeper_47


title: beekeeper_43


title: beekeeper_42


title: after1MonthVIT_46

value: HVA

value: female

value: VIT

value: after 1 Month of VIT


title: beekeeper_41


title: Repeat 1_FaDu cells at 48 h after 4Gy radiation

city: Jinan

first: shengda

last: cao

state: Shandong Province

address: wenhua west road

department: ENT

institute: Qilu hospital

description:
Repeat 1_lncRNA/mRNA expression profiles in FaDu cells at 48 h after 4Gy radiation
F-1

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: FaDu cells, 48 h, 4 Gy radiation

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: Both RS-FaDu and FaDu cells were maintained at 37°C with humidified 5% CO2.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: At 0, 24 and 48 h after 4 Gy radiation, total RNA were extracted from RS-FaDu and FaDu cells in preparation for microarray detection.

tag: cell line

value: FaDu

tag: cell type

value: parental

tag: stress

value: 4Gy radiation

value: 48 h after 4Gy radiation


title: Repeat 3_FaDu cells immediately after 4Gy radiation

description:
Repeat 3_lncRNA/mRNA expression profiles in FaDu cells immediately after 4Gy radiation
M-3

source_name: FaDu cells, 4 Gy radiation

tag: time

value: immediately after 4Gy radiation


title: after1MonthVIT_44

tag: tissue


title: Repeat 3_FaDu cells at 48 h after 4Gy radiation

description:
Repeat 3_lncRNA/mRNA expression profiles in FaDu cells at 48 h after 4Gy radiation
F-3


title: after1MonthVIT_45

tag: age


title: Repeat 1_RS-FaDu cells immediately after 4Gy radiation

description:
Repeat 1_lncRNA/mRNA expression profiles in RS-FaDu cells immediately after 4Gy radiation
MS-1

source_name: RS-FaDu cells, 4 Gy radiation

value: RS-FaDu

value: radioresistant


title: Repeat 1_FaDu cells at 24 h after 4Gy radiation

description:
Repeat 1_lncRNA/mRNA expression profiles in FaDu cells at 24 h after 4Gy radiation
E-1

source_name: FaDu cells, 24 h, 4 Gy radiation

value: 24 h after 4Gy radiation


title: Repeat 3_RS-FaDu cells at 24 h after 4Gy radiation

description:
Repeat 3_lncRNA/mRNA expression profiles in RS-FaDu cells at 24 h after 4Gy radiation
ES-3

source_name: RS-FaDu cells, 24 h, 4 Gy radiation


title: Repeat 2_FaDu cells at 48 h after 4Gy radiation

description:
Repeat 2_lncRNA/mRNA expression profiles in FaDu cells at 48 h after 4Gy radiation
F-2


title: Repeat 2_FaDu cells at 24 h after 4Gy radiation

description:
Repeat 2_lncRNA/mRNA expression profiles in FaDu cells at 24 h after 4Gy radiation
E-2


title: Repeat 1_RS-FaDu cells at 24 h after 4Gy radiation

description:
Repeat 1_lncRNA/mRNA expression profiles in RS-FaDu cells at 24 h after 4Gy radiation
ES-1


title: Repeat 3_FaDu cells at 24 h after 4Gy radiation

description:
Repeat 3_lncRNA/mRNA expression profiles in FaDu cells at 24 h after 4Gy radiation
E-3


title: Repeat 2_FaDu cells immediately after 4Gy radiation

description:
Repeat 2_lncRNA/mRNA expression profiles in FaDu cells immediately after 4Gy radiation
M-2


title: Repeat 2_RS-FaDu cells at 24 h after 4Gy radiation

description:
Repeat 2_lncRNA/mRNA expression profiles in RS-FaDu cells at 24 h after 4Gy radiation
ES-2


title: Repeat 3_RS-FaDu cells at 48 h after 4Gy radiation

description:
Repeat 3_lncRNA/mRNA expression profiles in RS-FaDu cells at 48 h after 4Gy radiation
FS-3

source_name: RS-FaDu cells, 48 h, 4 Gy radiation


title: Repeat 1_RS-FaDu cells at 48 h after 4Gy radiation

description:
Repeat 1_lncRNA/mRNA expression profiles in RS-FaDu cells at 48 h after 4Gy radiation
FS-1


title: Repeat 1_FaDu cells immediately after 4Gy radiation

description:
Repeat 1_lncRNA/mRNA expression profiles in FaDu cells immediately after 4Gy radiation
M-1


title: Repeat 2_RS-FaDu cells at 48 h after 4Gy radiation

description:
Repeat 2_lncRNA/mRNA expression profiles in RS-FaDu cells at 48 h after 4Gy radiation
FS-2


title: Repeat 3_RS-FaDu cells immediately after 4Gy radiation

description:
Repeat 3_lncRNA/mRNA expression profiles in RS-FaDu cells immediately after 4Gy radiation
MS-3


title: Repeat 2_RS-FaDu cells immediately after 4Gy radiation

description:
Repeat 2_lncRNA/mRNA expression profiles in RS-FaDu cells immediately after 4Gy radiation
MS-2


title: Human Tissue Type - Kidney

city: Bethesda

first: Meghali

last: Goswami

state: MD

address: 10 Center Drive

department: Hematology

institute: NHLBI

description: Test

data_processing:
For the normalization the geometric mean of three housekeeping genes: HPRT1, PPIH, TFRC were used
Target gene signals normalized to the geometric mean of housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
For fold change analysis it compares to median of normal donor values (where undetermined values are considered for this purpose to have a CT of 35)
Fold Change worksheet reports healthy human gene expression as compared to the median normal donor expression of that gene

source_name: 40-year-old female Caucasian

label_protocol: 400ng of total RNA was reverse-transcribed into cDNA using RT2 First Strand Kit (Qiagen).   PCR assays were performed using SABiosciences custom panel CAPH11327E

extract_protocol: Total RNA was extracted using Qiagen All-Prep Kit from ficoll purified bone marrrow aspirate (BMC).

tag: disease state

value: healthy

value: Kidney


title: Human Tissue Type - Spleen

description: Test

source_name: pooled from 15 male/female Caucasians; ages 22-69

value: Spleen


title: Human Tissue Type - Intestine

description: Test

source_name: pooled from 5 male/female Caucasians; ages 20-61

value: Intestine


title: after1MonthVIT_40

value: whole blood


title: Human Tissue Type - Prostate

description: Test

source_name: pooled from 12 Caucasians; ages 20-58

value: Prostate


title: Human Tissue Type - Muscle

description: Test

source_name: pooled from 2 male/female Caucasians; ages 43-63

value: Muscle


title: after1MonthVIT_38

value: HVA

value: female

value: VIT


title: Human Tissue Type - Colon

description: Test

source_name: pooled from 5 male Asians; ages: 20-44, cause of death: sudden death

value: Colon


title: after1MonthVIT_39

value: male

value: after 1 Month of VIT


title: Human Tissue Type - Cerebellum

description: Test

source_name: pooled from 10 male/female Caucasians, ages: 22-68

value: Cerebellum


title: Human Tissue Type - Thyroid

description: Test

source_name: pooled from 64 male/female Caucasians; ages 15-61

value: Thyroid


title: Human Tissue Type - Heart

description: Test

source_name: pooled from 3 male Caucasians; ages: 30-39

value: Heart


title: beekeeper_36

value: without signs of HVA

value: beekeeper

value: after beekeeping season (september - october)


title: Human Tissue Type - Whole Brain

description: Test

source_name: 43-year-old male Caucasian

value: healthy

value: Whole brain


title: Human Tissue Type - Lung

description: Test

source_name: pooled from 3 male/female Caucasians, ages: 32-61

value: Lung


title: Human Tissue Type - Liver

description: Test

source_name: 51-year-old male Caucasian

value: Liver


title: after1MonthVIT_37

value: whole blood


title: beekeeper_35

source_name: beekeeper


title: beekeeper_34


title: beekeeper_33


title: beekeeper_30


title: beekeeper_31


title: Normal Donor #6

description: Control

data_processing:
For the normalization the geometric mean of three housekeeping genes: HPRT1, PPIH, TFRC were used
Target gene signals normalized to the geometric mean of housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
For fold change analysis it compares to median of normal donor values (where undetermined values are considered for this purpose to have a CT of 35)
Fold Change data in  Series supplementary file report AML sample gene expression as compared to the median normal donor expression of that gene

source_name: BMC

extract_protocol: Total RNA was extracted using Qiagen All-Prep Kit from ficoll purified bone marrrow aspirate (BMC). 400ng of total RNA was reverse-transcribed into cDNA using RT2 First Strand Kit (Qiagen).   PCR assays were performed using SABiosciences custom panel CAPH11327E.

value: purified bone marrrow aspirate

tag: phenotype

value: normal


title: beekeeper_32

value: female


title: after1MonthVIT_29

value: HVA

value: VIT


title: Normal Donor #7

description: Control


title: Normal Donor #4

description: Control


title: Normal Donor #3

description: Control


title: Normal Donor #5

description: Control


title: after1MonthVIT_28

value: after 1 Month of VIT


title: Normal Donor #2

description: Control


title: Normal Donor #1

description: Control


title: after1MonthVIT_26

value: male


title: control_24

source_name: control

value: control


title: after1MonthVIT_27


title: AML Patient #48

description: Test

value: AML


title: RNF125 mutated individual OGS21

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

source_name: RNF125 mutated individual

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

value: Male

tag: genotype

value: RNF125 mutation

tag: health state

value: Diseased donor


title: after1MonthVIT_25

tag: gender


title: AML Patient #45

description: Test


title: control_22

value: without signs of HVA


title: AML Patient #46

description: Test


title: control_20


title: control_21


title: control_23


title: AML Patient #44

description: Test


title: after12monthsVIT_18

value: after 12 months of VIT


title: AML Patient #43

description: Test


title: AML Patient #42

description: Test


title: control_19


title: AML Patient #47

description: Test


title: after12monthsVIT_17


title: RNF125 mutated individual OGS009


title: AML Patient #40

description: Test


title: AML Patient #39

description: Test


title: RNF125 mutated individual OGS836


title: AML Patient #41

description: Test


title: RNF125 mutated individual OGS837

value: Female


title: AML Patient #37

description: Test


title: AML Patient #38

description: Test


title: priorVIT_18

source_name: priorVIT

value: prior to VIT

value: prior VIT


title: priorVIT_17

value: whole blood


title: AML Patient #36

description: Test

value: purified bone marrrow aspirate


title: AML Patient #35

description: Test


title: after12monthsVIT_16


title: after12monthsVIT_15


title: AML Patient #33

description: Test


title: AML Patient #34

description: Test


title: priorVIT_16


title: priorVIT_13

value: female


title: AML Patient #31

description: Test


title: control_12


title: priorVIT_15

value: HVA


title: after12monthsVIT_14

value: VIT


title: control_10


title: AML Patient #11

description: Test


title: priorVIT_14


title: AML Patient #10

description: Test


title: AML Patient #9

description: Test


title: AML Patient #32

description: Test


title: control_8


title: after12monthsVIT_13


title: after12monthsVIT_5


title: control_7


title: priorVIT_4


title: control_11


title: AML Patient #12

description: Test


title: after12monthsVIT_3


title: control_9


title: after12monthsVIT_4


title: priorVIT_3


title: after12monthsVIT_2


title: priorVIT_2


title: after12monthsVIT_1


title: priorVIT_6


title: after12monthsVIT_6


title: priorVIT_1


title: DG_ECS-10times-48h

city: Tokyo

first: Eri

last: Segi-Nishida

state: Tokyo

address: Niijuku 6-3-1

institute: Tokyo University of Science

description: Gene expression data from vehicle-treated mouse DG

hyb_protocol: Following fragmentation, 5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by GeneChip Scanner 3000.

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

source_name: mouse dentate gyrus of hippocampus, ECS 10 times, 48 h

label_protocol: The total RNA samples of the same groups were put together. From each group, 100 ng of total RNA was amplified with 3’IVT Express kit (Affymetrix, Inc., Santa Clara, CA, USA).

extract_protocol: Total RNA was extracted from the dentate gyrus dissected by using an RNeasy micro kit (Qiagen) .

treatment_protocol: Bilateral ECS (current, 25 mA; shock duration, 1 sec; frequency, 100 pulse/sec; pulse width, 0.5 msec) was administered via moistened, spring-loaded ear-clip electrodes with a pulse generator (ECT Unit; Ugo Basile, Comeria, Italy) to mice that were anesthetized with isoflurane (1.5 to 2%) in order to avoid sudden unexpected death associated with seizures.ECS was administered 4 times a week for 3 weeks. The Sham-treated animals were handled in an identical manner to the ECS-treated animals, without the administration of shock. For chronic SSRI administration, fluoxetine hydrochloride was dissolved in drinking water and orally applied at a dose of 22 mg/kg/day for 4 weeks. The fluoxetine solutions were prepared everyday, and daily fluoxetine intake was determined for individual mice on the basis of the water consumption during the preceding 24 h and the body weight measured every other day. Saccharin (0.2%) was included in the fluoxetine solution to keep water intake comparable to the baseline.

tag: strain

value: hippocampus

tag: treatment

value: ESC, 10 times, 48 hr

tag: sample type

value: chronic

tag: response

value: long-lasting response


title: DG_ESC-1time-1h

description: Gene expression data from chronic ECS-treated mouse DG

source_name: mouse dentate gyrus of hippocampus, ECS, 1 time, 1 h

value: ESC, 1 time, 1 hr

value: single

value: acute response


title: DG_ECS-11times-1h

description: Gene expression data from chronic fluoxetine-treated mouse DG

source_name: mouse dentate gyrus of hippocampus, ECS 11 times, 1 h

value: ESC, 11 times, 1 hr


title: DG_sham-1time-1h

description: Gene expression data from sham-treated mouse DG

source_name: mouse dentate gyrus of hippocampus, sham, 1 time, 1 h

value: sham

value: control


title: Mll1 KO, rep2

status: Public on Jan 20 2017

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

description:
PE6
Gene expression data with or without Mll1 deletion in LSC-enriched MLL-AF9 leukemia cells.
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.

hyb_protocol: The labeled products were hybridized to Affymetrix mouse 430 2.0 Arrays at the Dartmouth Genomics and Microarray Laboratory.

scan_protocol: Arrays were scanned using the GeneChip 3000 7G scanner and exported as standard .CEL files.

data_processing: Expression was extracted from the CEL files using Bioconductor in R using the GCRMA package.

source_name: LSC-enriched MLL-AF9 leukemia cells, Mll1 KO

label_protocol: Input RNA was 250ng and labeled using the Affymetrix GeneChip 3' IVT PLUS Reagent Kit.

growth_protocol: Primary MLL-AF9 leukemia mice transformed from Lin-/Sca1+/c-Kit+ (LSK) cells with the genotype of Cre+;Mll1F/+ or Cre+;Mll1F/F.

extract_protocol: Trizol extraction of total RNA was performed with Qiagen RNeasy Mini Kit.

treatment_protocol: Leukemia mice were injected with two doses of tamoxifen (TAM) every other day to induce Mll1 deletion. Three days after the last TAM injection, YFP+/Lin-/c-Kit+ leukemia cells were sorted for RNA extraction.

value: bone marrow

value: LSC-enriched MLL-AF9 leukemia cells

tag: genotype/variation

value: tamoxifen


title: Mll1 KO, rep1

description:
PE5
Gene expression data with or without Mll1 deletion in LSC-enriched MLL-AF9 leukemia cells.
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: Control, rep2

description:
PE2
Gene expression data with or without Mll1 deletion in LSC-enriched MLL-AF9 leukemia cells.
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.

source_name: LSC-enriched MLL-AF9 leukemia cells, control


title: Mll1 KO, rep3

description:
PE7
Gene expression data with or without Mll1 deletion in LSC-enriched MLL-AF9 leukemia cells.
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: Control, rep4

description:
PE4
Gene expression data with or without Mll1 deletion in LSC-enriched MLL-AF9 leukemia cells.
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: CGNs with ICRF193, biological replicate 4

first: Haikun

last: Liu

address: INF 581

institute: DKFZ

description:
CGNs obtained from P7 Bl6 pups
ICRF4

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

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

data_processing: The data were analyzed with R pacage “affy” with algoritm Mas5

source_name: Granule Neuron Progenitors

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

growth_protocol: CGNs were cultured as standard condition

extract_protocol: RNA was extracted with a protocol combined with Tri-reagent and RNAeasy-mini Kit.

treatment_protocol: CGNs were treated either with ICRF-193 10 uM or DMSO for 12 hours. CGNs were cultured in the presense of Smo2 as indicated.

value: cerebellum

tag: developmental stage

value: Granule Neuron Progenitors


title: Control, rep3

description:
PE3
Gene expression data with or without Mll1 deletion in LSC-enriched MLL-AF9 leukemia cells.
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: CGNs (Smo2_con), biological replicate 2

description:
CGNs obtained from P7 Bl6 pups
Smo2_con2


title: CGNs (ICRF_con) with DMSO, biological replicate 2

description:
CGNs obtained from P7 Bl6 pups
ICRF_con2

value: DMSO


title: CGNs (Smo2_con), biological replicate 1

description:
CGNs obtained from P7 Bl6 pups
Smo2_con1


title: Control, rep1

description:
PE1
Gene expression data with or without Mll1 deletion in LSC-enriched MLL-AF9 leukemia cells.
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: CGNs (ICRF_con) with DMSO, biological replicate 3

description:
CGNs obtained from P7 Bl6 pups
ICRF_con3


title: CGNs with Smo2, biological replicate 3

description:
CGNs obtained from P7 Bl6 pups
Smo2_3


title: CGNs (ICRF_con) with DMSO, biological replicate 4

description:
CGNs obtained from P7 Bl6 pups
ICRF_con4


title: CGNs with ICRF193, biological replicate 1

description:
CGNs obtained from P7 Bl6 pups
ICRF1


title: CGNs with Smo2, biological replicate 1

description:
CGNs obtained from P7 Bl6 pups
Smo2_1


title: CGNs with ICRF193, biological replicate 3

description:
CGNs obtained from P7 Bl6 pups
ICRF3


title: Mll1 KO, rep4

description:
PE8
Gene expression data with or without Mll1 deletion in LSC-enriched MLL-AF9 leukemia cells.
Animal studies were conducted in accordance with IACUC-approved animal protocols at Dartmouth College, University of Colorado, Denver and in accordance with German animal welfare legislation. The Mll1F/F (Jude et al., 2007 (PMID 18371366)) and Men1F/F (Hughes et al., 2004 (PMID 14992727)) mice were intercrossed with R26CreER strain (stock no. 004847, Jackson Laboratory, USA or Artemis Pharmaceuticals, Germany) to generate conditional knockout mice. For transplantation recipients, C57BL/6 (#000664) and B6.SJL strains (B6.SJL-Ptprca Pep3b /BoyJ, #002014) female mice between 8 and 12 weeks of age were purchased from the Jackson Laboratory.


title: Chd7 mutant CGNs, biolgoical replicate 4

description:
CGNs obtained from P7 Bl6 pups
CHD7_mutant4

value: Chd7 mutant


title: CGNs with Smo2, biological replicate 2

description:
CGNs obtained from P7 Bl6 pups
Smo2_2


title: Chd7 mutant CGNs, biolgoical replicate 2

description:
CGNs obtained from P7 Bl6 pups
CHD7_mutant2


title: Chd7 mutant CGNs, biolgoical replicate 3

description:
CGNs obtained from P7 Bl6 pups
CHD7_mutant3


title: CGNs (ICRF_con) with DMSO, biological replicate 1

description:
CGNs obtained from P7 Bl6 pups
ICRF_con1


title: CGNs (Smo2_con), biological replicate 3

description:
CGNs obtained from P7 Bl6 pups
Smo2_con3


title: CGNs with ICRF193, biological replicate 2

description:
CGNs obtained from P7 Bl6 pups
ICRF2


title: Chd7 mutant CGNs, biolgoical replicate 1

description:
CGNs obtained from P7 Bl6 pups
CHD7_mutant1


title: CGNs (CHD7_con), biological replicate 3

description:
CGNs obtained from P7 Bl6 pups
CHD7_con3

value: wild type


title: CGNs (CHD7_con), biological replicate 4

description:
CGNs obtained from P7 Bl6 pups
CHD7_con4


title: CGNs (CHD7_con), biological replicate 1

description:
CGNs obtained from P7 Bl6 pups
CHD7_con1


title: Sample4_WA09_Mutant_2

city: La Jolla

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

description: Mutant 2

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting

data_processing:
Genotyping calls were made with GenomeStudio (Illumina, Inc.) via the cluster files provided by the manufacturer. The GenCall (v. 6.3.0) threshold was set to 0.15, and the call rates were greater than 0.998. Reproducibility and heritability were calculated in GenomeStudio (Illumina, Inc.). CNVs were identified using the cnvPartition Plug-in v 3.2.0 in GenomeStudio (Illumina, Inc.). The cnvPartition confidence threshold was set at 35, with a minimum number of SNPs per CNV region of 3. All CNVs were visually verified by assessing both the B-allele-frequency and Log R ratios.
Name is the SNP ID, Chr (Chromosome), Position (location on Chr), Genotype: AA,AB,BB,or NC (No Call), Score, Thera, R, B Allele, Log R Ratio

label: Cy3 and Cy5

source_name: WA09 Human Embryonic Stem Cell

label_protocol: Standard Illumina Protocol

growth_protocol: The four WA09 clones (2 wild-type and 2 mutant) were initially grown on MEF feeder layers in standard hPSC medium. These initial cultures were transitioned to feeder-free conditions in a stepwise fashion by passaging them with Accutase onto Geltrex (Gibco) with MEF-conditioned medium (MEF-CM) supplemented with 12 ng/ml basic FGF. After one passage in MEF-CM, the cultures were either continued in MEF-CM or passaged into E8 medium (Life Technologies). For all cultures, cells were grown at 37°C and 5% CO2 and passaged every three to four days, when they were ~80% confluent. At each passage, 150,000 cells were seeded per well of a 6-well plate (equivalent to a cell plating density of ~15,600 cells/ cm2). The medium was changed daily.

extract_protocol: DNA was extracted from hESC samples using the DNeasy Blood and Tissue Genomic DNA Purification Kit (QIAGEN), and quantified (Qubit dsDNA BR Assay Kits, Life Technologies, Inc.) according to the manufacturer’s protocol.

treatment_protocol: Single-cell cloning was used to derive pure subpopulations of mutant and wild-type cells from the original mosaic MefEnz culture. MefEnz cells cultured on irradiated mouse embryonic fibroblasts (MEFs) in standard hPSC medium, consisting of Dulbecco’s modified eagle medium DMEM/F12 (Life Technologies) with 20% Knockout Serum Replacement (Life Technologies), 1 mM GlutaMAX (Life Technologies), 0.1 mM nonessential amino acids (NEAA, Life Technologies), 0.1 mM -mercaptoethanol, and 12 ng/ml basic FGF (Life Technologies), were treated for 1 hour with 10 M ROCK inhibitor Y-27632 (Calbiochem) before dissociation. The medium was supplemented with SMC4 (0.58 l SMC4/ 1 ml medium) (BD Biosciences) for one day.

value: ch17p13.1 deletion

value: WA09 Human Embryonic Stem Cell


title: Sample3_WA09_Mutant_1

description: Mutant 1


title: Sample1_WA09_Wild_Type_1

description: Wild-type 1

value: wildtype


title: Sample2_WA09_Wild_Type_2

description: Wild-type 2


title: BaF3-EpoR-PTEN-5h.CEL

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: 1.5 µg labelled cRNA were hybridized onto the Mouse Genome 2.0 GeneChip® Arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor

source_name: Ba/F3 cell line overexpressing EpoR and Pten

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: Retroviral expression vectors were pMOWS-puro-MCS/M2. For stable transfection of BaF3cells with murine EpoR, pMOWS-Kz-HA-EpoR was generated in our laboratory (Becker et al., 2008). Human PTEN cDNAs were cloned into pMOWSnr-MCS/M2, in which the puromycin resistance gene was replaced by the LNGFR cDNA (Miltenyi Biotech) that allowed magnetic bead selection of transduced cells (Ketteler et al., 2002). Transient transfection of Phoenix-eco cells with retroviral expression vectors were performed by calcium-phosphate precipitation. To ensure an efficient uptake of DNA, Phoenix cells were incubated for 6 h in DMEM medium supplemented with 25 µM chloroquine and 10% FCS. Subsequently the medium was replaced by IMDM containing 50 µM β-mercaptoethanol and 30% FCS. 1x10^5 BaF3 cells were transduced using 250µl retroviral supernatant of pMOWS-Kz-HA-EpoR supplemented with 8 µg/ml polybrene and centrifuged for 2 h at 340g and 37C. Selection with 1.5 µg/ml puromycine (Sigma-Aldrich) started 48 h after transduction resulting in BaF3-EpoR cells. Surface expression of EpoR in BaF3 cells was verified by flow cytometry using an antibody against HA (Roche) and a CY-5 labeled anti-rat antibody (Jackson Immuno Research).   For overexpression experiments, 5x10^6 cells were transduced using 4.5 ml retroviral supernatant supplemented with 8 µg/ml polybrene in a 6-well plate and centrifuged for 3 h at 340g and 37C. Following spin-infection, cells were cultured for 14 - 16h in the standard media. Positively transduced cells were selected using MACSelect LNGFR selection kit (Miltenyi Biotech) according to manufacturer’s instructions. Level of overexpression was always verified at the day of experiment using immunoblotting.

extract_protocol: Per time point total RNA from 2-4 x 10^6 BaF3-EpoR cells was isolated using the RNeasy Mini Plus Kit (Qiagen).

treatment_protocol: After washing with serum free medium, BaF3-EpoR cells were were growth factor deprived for 5 h and resuspended in RPMI supplemented with 1mg/ml BSA. RNA samples were taken at 0, 1, 2, 3, 4, 5, 7, 18.5h after 1 U/ml Epo stimulation.

tag: cell line

value: Ba/F3 Bone marrow-derived pro-B-cell line

value: male


title: BaF3-EpoR-PTEN-2h.CEL


title: BaF3-EpoR-PTEN-18.5h.CEL


title: BaF3-EpoR-Ctl-18.5h.CEL

source_name: Ba/F3 cell line overexpressing EpoR


title: BaF3-EpoR-PTEN-7h.CEL


title: CGNs (CHD7_con), biological replicate 2

description:
CGNs obtained from P7 Bl6 pups
CHD7_con2

tag: cell type


title: BaF3-EpoR-Ctl-0h.CEL


title: BaF3-EpoR-PTEN-1h.CEL


title: BaF3-EpoR-PTEN-3h.CEL


title: BaF3-EpoR-PTEN-4h.CEL


title: BaF3-EpoR-Ctl-5h.CEL


title: BaF3-EpoR-PTEN-0h.CEL


title: BaF3-EpoR-Ctl-3h.CEL


title: BaF3-EpoR-Ctl-1h.CEL


title: 24hr_UC_PO

city: Sagamihara

first: TAKAYUKI

last: MINESHIGE

state: Kanagawa

address: Chuo-ku, Kyowa 4-22-6

institute: Azabu University

description: Sampling time_24hr

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent SureScan G4900DA at 5 micron resolution. Images werequantified using Agilent Feature Extraction software version 11.5.1.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

organism: Canis lupus familiaris

source_name: stimulated by 4µg/mL recombinant human periostin for 24 hrs

label_protocol: Agilent two-color Low Input Quick Amp Labeling Kit labeling protocol

extract_protocol: Total RNA was extracted from cell cultures using the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany).

value: Canine keratinocyte cell line (CPEK)

source_name: unstimulated control


title: BaF3-EpoR-Ctl-4h.CEL


title: BaF3-EpoR-Ctl-7h.CEL


title: 6hr_UC_PO

description: Sampling time_6hr

source_name: stimulated by 4µg/mL recombinant human periostin for 6 hrs


title: BaF3-EpoR-Ctl-2h.CEL


title: HDF siU_day4

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12  Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2

source_name: HDF

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

extract_protocol: RNA was extracted with Trizol reagent(Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. Quality control was performed with Agilent Bioanalyser.

value: human diploid fibroblast (HDF)

tag: sirna-mediated knockdown


title: HDF siU_day3


title: HDF siD_day4


title: HDF H2O2_2d

description: HDF H2O2_2d.AVG_Signal

tag: treated with

value: hydrogen peroxide for 2 days


title: HDF H2O2_5d

description: HDF H2O2_5d.AVG_Signal

value: hydrogen peroxide for 5 days


title: HDF siD_day3


title: HDF H2O2_6d

description: HDF H2O2_6d.AVG_Signal

value: hydrogen peroxide for 6 days


title: HDF H2O2_4d

description: HDF H2O2_4d.AVG_Signal

value: hydrogen peroxide for 4 days


title: HDF siNC

value: siRNA Negative Control


title: HDF H2O2_1d

description: HDF H2O2_1d.AVG_Signal

value: hydrogen peroxide for 1 day


title: epidermis_D113_young_20y

city: Zürich

first: Nicola

last: Zamboni

state: Zurich

address: Auguste-Piccard-Hof 1

department: Institute for Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

hyb_protocol: done by Genomics Services from Miltenyi Biotec

data_processing: Agilent Feature Extraction Software; data processing using LIMMA for R

source_name: human epidermis, inner forearm

label_protocol: Agilent Whole Human Genome Oligo Microarrays 8x60K V2 Kit

extract_protocol: Suction blisters were obtained as described previously from the inner forearms of 28 young (20 to 25 years) and 54 old (aged between 55 and 66 years) healthy female volunteers (Sudel et al Photochem Photobiol 2003). Suction blister roofs were taken and immediately stored at -80°C . For transcriptomics analysis the suction blister epidermis samples were homogenized using a ball mill. RNA was extracted using RNeasy Fibrous Tissue Mini Kit  (Qiagen) according to manufacturer's instructions

treatment_protocol: no treatment

tag: tissue

value: epidermis

value: female

tag: group

value: young


title: epidermis_D27_young_24y

scan_protocol: done by Genomics Services from Miltenyi Biotec

tag: age


title: Ground_BLM_1.0_rep4

city: Houston

first: Tao

last: Lu

state: Texas

address: 2101 E NASA Pkwy

department: Radiation Research

institute: NASA Johnson Space Center

description:
Gene expression after 3 hours of 1.0 micrg/mlbleomycin treatment.
gHB-10

hyb_protocol: Followed Agilent protocol for SurePrint G3 Human Gene Expression v3 8x60K Microarray Kit (G4851). 50 ng of total RNA was used for RNA amplification and labeling according to the Agilent Quick Amp Labeling Kit (for one-color) Protocol Version 6.7, using Agilent Labeling Kit along with an Agilent’s RNA Spike-In Kit (Agilent).  The resulting cRNAs were purified using Qiagen RNeasy mini spin columns and measured again on the Nanodrop for yields (1.1 to 1.5 g per sample) and dye incorporation (average 13.2 pmol/g, with 2 of the 15 samples at 7.7 and 9.9 pmol/g). The samples were then fragmented and 0.6 µg of each hybridization mixture was loaded onto the arrays.

scan_protocol: The slides were scanned with Agilent Scanner (G2565BA) using Scanner Version C and Scan Control software version A.8.5.1.

data_processing: The scanned images were processed with Agilent Feature Extraction Software Version 11.0.1.1 to obtain background subtracted and spatially detrended Processed Signal intensities..

source_name: Confluent human fibroblast, 3hr, BLM_1.0 microgram, ground, replicate 4

label_protocol: Single color labeling with Cyanine-3 (Cy3), using Agilent kit and protocol.

growth_protocol: Human fibroblasts AG01522 were cultured at 37ºC in alpha-MEM supplemented with 10% heat-inactivated fetal bovine serum and Penicillin and Streptomycin to conflence.

extract_protocol: Total RNA was extracted using Qiagen miRNeasy Mini kits. RNA quality was verified by Nanodrop Spectophotometer and Agilent Bioanalyzer.

treatment_protocol: After in Space on ISS for three daya, the cells were treated with 1.0 microgram/ml of bleomycin for 3 hours and with no drug control.

value: fibroblast

value: Male


title: Ground_Ctrl_rep4

description:
Gene expression after 3 hours of 10.0 micrg/mlbleomycin treatment.
gHA-05

source_name: Confluent human fibroblast, 3hr, BLM_0 microgram, ground, replicate 4


title: HDF H2O2_3d

description: HDF H2O2_3d.AVG_Signal

value: hydrogen peroxide for 3 days


title: epidermis_D87_old_63y

value: old


title: Ground_BLM_1.0_rep3

description:
Gene expression after 3 hours of 10.0 micrg/mlbleomycin treatment.
gHB-09

source_name: Confluent human fibroblast, 3hr, BLM_1.0 microgram, ground, replicate 3


title: epidermis_D56_old_61y


title: Ground_BLM_1.0_rep2

description:
Gene expression after 3 hours of 10.0 micrg/mlbleomycin treatment.
gHB-08

source_name: Confluent human fibroblast, 3hr, BLM_1.0 microgram, ground, replicate 2


title: epidermis_D109_young_21y


title: epidermis_D85_old_64y