title: Wap-Cre:PTEN tumor PW28

type: genomic

city: Toronto

first: Sharon

state: Ontario

address: 67 College Street Room 456

country: Canada

institute: University of Toronto

description:
PW28
Raw data file contains duplicated feature numbers 749537-750823 and 804148-805434.

data_processing:
Mouse 1X1M CGH  experiment were performed by the Centre of Applied Genomics (HSC, Toronto)
normalized values are represented by normalized log10 ratio (Cy5/Cy3) representing test/reference

source_name: Mouse Mammary Tumor

growth_protocol: Samples from independent primary mammary tumors were frozen and kept in -80 degree.

extract_protocol: Total DNA was extracted using QIAGEN DNeasy Blood & Tissue Kits

treatment_protocol: Total DNA obtained from primary tumors were used for arrayCGH analysis to determine changes in copy number

value: mammary tumor

tag: histology

value: Poorly differentiated

tag: sample dimension

value: Mammary Tumor less than 1.0 cm diameter

source_name: pooled mouse DNA for reference

value: pooled mouse DNA


title: Wap-Cre:PTEN tumor PW83

status: Public on Aug 18 2017

last: Wang

hyb_protocol: Mouse 1X1M CGH  experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: sample type


title: HEK293_SnxA_90min_Rep1

type: RNA

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

country: USA

institute: University of South Carolina

hyb_protocol: 300 ng of Cy3-labelled cRNA and 300 ng of Cy5-labelled cRNA was mixed and fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent SurePrint G3 Human Gene Expression 8x60K Microarrays (G4851A-28004) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channels set to 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data was uploaded into Genespring version 11.5.1 where was thresholded to 1.0, log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filtered by flags in a way that at least 75% of the samples in any of the 2 experimental groups had DETECTED flags. Then, differentially expressed genes were determined using a moderated t-test statistics with p-value 0.01 and fold change 1.5 as cutoffs.

molecule: total RNA

organism: Homo sapiens

source_name: HEK293 cells, treated with 5μM Senexin A for 90 minutes, Rep-1

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: HEK293 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well 24 hours prior to treatment.

extract_protocol: Total RNA was extracted using RNAeasy Mini Kit (Qiagen) and RNA quality was tested using Bioanalyser.

treatment_protocol: Cells were first pre-treated with 5μM Senexin A or 0.1% DMSO (control) for 1 hour and then treated with or without 10 ng/mL TNFα for 30min.

tag: cell line


title: HEK293_DMSO_90min_Rep4

source_name: HEK293 cells, treated with 0.1% DMSO for 90 minutes, Rep-4


title: Wap-Cre:PTEN tumor PW96

scan_protocol: Mouse 1X1M CGH  experiment were performed by the Centre of Applied Genomics (HSC, Toronto)

value: Well differentiated


title: Wap-Cre:PTEN tumor PW104

description:
PW104
Raw data file contains duplicated feature numbers 570279-571551 and missing feature numbers 624924-626197.

label_protocol: Mouse 1X1M CGH  experiment were performed by the Centre of Applied Genomics (HSC, Toronto)


title: HEK293_DMSO_90min_Rep3

source_name: HEK293 cells, treated with 0.1% DMSO for 90 minutes, Rep-3


title: Wap-Cre:PTEN tumor PW105


title: Wap-Cre:PTEN tumor PW152L2

description:
PW152L2
Raw data file contains duplicated feature numbers 167597-168863, 223550-224809, 503182-504472 and triplicates of 559100-574389. Missing feature numbers are: 222231-223497, 278182-279441, 557796-559085, and 584425-615006.


title: HEK293_DMSO_90min_Rep2

source_name: HEK293 cells, treated with 0.1% DMSO for 90 minutes, Rep-2


title: Wap-Cre:PTEN tumor PW19


title: HEK293_DMSO_90min_Rep1

source_name: HEK293 cells, treated with 0.1% DMSO for 90 minutes, Rep-1


title: [Mj]-[IFX]-[donor11+12]

city: Amsterdam

first: Felica

last: Bloemendaal

address: Meibergdreef 69-71

department: Experimental Gastroenterology

country: Netherlands

institute: AMC

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio.

source_name: macrophages

label_protocol: Biotinylated cRNA were prepared with the Invitrogen Illumina Totalprep RNA amplification kit for Illumina arrays.

growth_protocol: Peripheral blood mononuclear cells (PBMC) from healthy volunteers were isolated by Ficoll Paque density-gradient centrifugation. Monocytes were isolated by Percoll density-gradient centrifugation.

extract_protocol: Qiagen RNeasy

treatment_protocol: Anti-TNF 10 µg/ml, IFNγ 50 ng/ml, IL-4 40 ng/ml, IL-10 50 ng/ml.

tag: disease status

value: healthy

tag: cell type

value: macrophages

tag: treatment

value: Infliximab (IFX; anti-TNF)

tag: donor


title: Wap-Cre:PTEN tumor PW191


title: [Mj]-[IFX]-[donor1+2]


title: [Mj]-[IL-IFN]-[donor5]

value: IFN


title: Wap-Cre:PTEN tumor PW266


title: Wap-Cre:PTEN tumor PW293R5

description:
PW293R5
Raw data file contains duplicated feature numbers 33743-35042 and 90062-91378 and missing feature numbers 88762-90061 and 144744-146055.


title: [Mj]-[IL-IFN]-[donor6]


title: [Mj]-[IFN]-[donor3]


title: [Mj]-[IFX]-[donor3+4]


title: [Mj]-[IL-10]-[donor6]


title: [Mj]-[IL-4]-[donor6]


title: [Mj]-[IL-10]-[donor1]


title: [Mj]-[IL-10]-[donor4]


title: [Mj]-[IL-10]-[donor3]


title: [Mj]-[IFX]-[donor9+10]


title: [Mj]-[IFX]-[donor7+8]


title: [Mj]-[IFX]-[donor5+6]


title: [Mj]-[IL-IFN]-[donor2]


title: [Mj]-[IL-4]-[donor5]


title: [Mj]-[IL-4]-[donor3]


title: [Mj]-[IL-4]-[donor1]


title: [Mj]-[IFN]-[donor4]


title: WT-LPS-42

status: Public on Aug 17 2017

city: Kingston

first: Xinzhi

last: Li

address: 18 Stuart Street

department: Biomedical and Molecular Sciences

institute: Queen's University

description: WT-LPS

hyb_protocol: Procedures were performed according to the manufacturer’s protocol (Nanostring Technologies, Seattle, WA, USA). In brief, reactions were hybridized for about 18 h at 65°, after which the products were run through the nCounter preparation station for removal of excess probes.

scan_protocol: Raw data were generated with the nCounter digital analyzer by counting individual barcodes.

data_processing: Collected data were imported into nSolver 3.0 software (Nanostring Technologies). Annotated genotypes （WT，COX-2>COX-1, COX-1>COX-2, and Reversa, n=6, each) and treatments (Control or LPS) were used to group the data. Grouped data then were normalized to the geometric means of spiked-in positive controls (controls for assay efficiency) and spiked-in negative controls (normalized for background).

source_name: peritoneal macropohage

extract_protocol: Total RNA was extracted from LPS-elicited macrophages using the RNeasy Mini Kit (Cat#74104, QIAGEN, Maryland, USA). The quality of the isolated RNA was checked with Agilent RNA 6000 Nano Assay kit reagents using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples with a RNA Integrity Number (RIN) of 7.0 or higher were used for Nanostring analysis. The RNA samples were quantified using a standard Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA). The RNA concentrations were then adjusted to 20 ng/µl.

treatment_protocol: A dose of 2 mg/kg lipopolysaccharide (LPS) (body weight), diluted in sterile PBS, was injected intraperitoneally into WT (annotated as WT+LPS), COX-2>COX-1, COX-1>COX-2, and Reversa mice (12-16 wk; n=6 each group). An equivalent volume of PBS alone was given to another group of WT mice (Control group, annotated as WT-LPS).

tag: strain

tag: agent

value: PBS

tag: genotype/variation

value: WT


title: Ws-2, water-treated, biological replicate 2

city: Sophia Antipolis

first: Harald

last: Keller

address: 400 route des Chappes

department: UMR-ISA

country: France

institute: INRA

description: wild-type expression in the absence of infection

hyb_protocol: Operated by the NASC's International Affymetrix Service

data_processing: Background adjustment, quantile normalization, and summarization of raw data were performed with the Affymetrix Power Tools APT1.14.4 software package.

label: biotin

organism: Arabidopsis thaliana

source_name: Ws-2 treated with water

growth_protocol: Seeds from A. thaliana ecotype Wassilewskija (Ws-2) were sown on a soil/sand mixture, stratified for 3 days at 4 °C, and then grown under a 12 h photoperiod in a growth chamber at 20 °C.

extract_protocol: In two independent experiments, cotyledons from the ecotype Wassilewskija (Ws-2) wild-type or clv1 mutant plants were treated with water, or inoculated with H. arabidopsidis to establish a compatible interaction. Total RNA was extracted from about 100 mg of these tissues according to a procedure described (Laroche-Raynal et al., Plant Science Letters 35, 139-146,1984).

treatment_protocol: For infection, 10-day-old plants were spray-inoculated to saturation with a spore suspension of 40,000 spores/ml (strain  Emwa1)

value: Cotyledons

tag: ecotype

tag: genotype

tag: infection

value: control


title: clv1.13, water-treated, biological replicate 1

description: mutant expression in the absence of infection

scan_protocol: Operated by the NASC's International Affymetrix Service

source_name: clv1.13 treated with water


title: WT-LPS-41

description: WT-LPS


title: [Mj]-[IL-4]-[donor2]


title: WT-LPS-39

description: WT-LPS


title: clv1.12, inoculated cotyledons at 3 dpi, biological replicate 2

description: mutant expression after infection

source_name: clv1.12 Hpa-inoculated

label_protocol: Operated by the NASC's International Affymetrix Service


title: clv1.12, water-treated, biological replicate 1

source_name: clv1.12 treated with water


title: clv1.13, inoculated cotyledons at 3 dpi, biological replicate 1

description: mutant expression after infection

source_name: clv1.13 Hpa-inoculated


title: clv1.12, water-treated, biological replicate 2


title: [Mj]-[IL-10]-[donor2]


title: clv1.13, inoculated cotyledons at 3 dpi, biological replicate 2

description: mutant expression after infection


title: [Mj]-[IL-10]-[donor5]


title: clv1.13, water-treated, biological replicate 2


title: WT+LPS-56

description: WT+LPS

value: LPS challenged


title: Ws-2, water-treated, biological replicate 1


title: Ws-2, inoculated cotyledons at 3 dpi, biological replicate 2

description: wild-type expression after infection

source_name: Ws-2 Hpa-inoculated


title: clv1.12, inoculated cotyledons at 3 dpi, biological replicate 1

description: mutant expression after infection


title: Ws-2, inoculated cotyledons at 3 dpi, biological replicate 1

description: wild-type expression after infection


title: WT+LPS-54

description: WT+LPS


title: [Mj]-[IL-IFN]-[donor1]


title: WT+LPS-51

description: WT+LPS


title: [Mj]-[IL-4]-[donor4]


title: WT-LPS-40

description: WT-LPS


title: WT-LPS-38

description: WT-LPS


title: WT+LPS-55

description: WT+LPS


title: WT+LPS-52

description: WT+LPS


title: WT+LPS-53

description: WT+LPS


title: Rev-52+LPS

description: Reversa

value: Reversa


title: COX2-55+LPS


title: COX2-51+LPS


title: WT-LPS-37

description: WT-LPS


title: Rev-55+LPS

description: Reversa


title: COX2-56+LPS


title: COX2-52+LPS


title: COX2-53+LPS


title: COX2-54+LPS


title: Rev-56+LPS

description: Reversa


title: COX1-58+LPS


title: COX1-60+LPS


title: Rev-54+LPS

description: Reversa


title: COX1-57+LPS


title: Rev-53+LPS

description: Reversa


title: COX1-55+LPS


title: Rev-51+LPS

description: Reversa


title: COX1-33+LPS


title: COX1-59+LPS


title: LMNB1 RNAitransfected following induction of SHM passage 2

status: Public on Aug 16 2017

city: Ulm

first: Johannes

last: Bloehdorn

address: Albert-Einstein-Allee 23

country: Germany

institute: University of Ulm

description: Gene expression data from BL2 cells passage 2 after LMNB1 RNAi transfection following induction of SHM

hyb_protocol: Array hybridization was performed at 45°C for 16-18h in the Affymetrix GeneChip® Hybridization Oven 640, arrays were subsequently washed in the Fluidics Station 450.

scan_protocol: Arrays were scanned on the GeneChip scanner 3000 7G.

data_processing: Raw Affymetrix Human Exon array (HuEx-1_0-st-v2) data files have been normalized using the RMAsketch normalization of the Affymetrix Expression Console Software V1.4.1

label: Biotin

source_name: BL2 cell line after transfection

label_protocol: Samples from functional studies on BL2 cells were analyzed for mRNA expression using the Affymetrix GeneChip® Human Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). The experiment was conducted according to the manufacturer’s protocol. In brief, 250 ng RNA per sample were amplified, transcribed to cDNA, fragmented and subsequently labeled with Biotin.

growth_protocol: BL2 cell line was obtained from the German Collection of Microorganisms and Cell culture (ACC 625. Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ).  Cells were maintained in antibiotic-free RPMI 1640 medium with FCS (10%; Sigma-Aldrich) and glutamine (2 mM; Gibco, Invitrogen) at 37°C, 5% CO2, and were routinely screened for mycoplasma contamination.

extract_protocol: Total RNA for mRNA profiling was extracted from whole cell lysates of treated BL2 cells according to the Allprep DNA/RNA mini kit (Qiagen). Quality control was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip (Agilent Technologies). RNA for gene expression profiling on BL2 cell line functional studies had a RIN of 10.

treatment_protocol: For in vitro SHM cells were incubated at 2x10^6 cells/ml in RPMI medium, containing 2.5 µg/ml of biotinylated anti−human IgM (clone UCHB1 Caltag Laboratories, Buckingham, UK), 10ug/ml of anti-CD19 (clone RFB9, in-house, Southampton, UK) and 10ug/ml of anti-CD21 (clone HB135, in-house, Southampton, UK) for 20 min at 4 °C. Cells were washed and then resuspended in RPMI medium containing streptavidin-conjugated magnetic beads (5−7 beads/cell) (Dynabeads M280, Thermo-Fisher, UK) and incubated with agitation at 4 °C for 20 min. Complete RPMI medium containing 10% FBS was added to the activated cells to a final density of 1x106, followed by incubation at 37 °C for 24h, 48h or 72h. For LMNB1 RNAi transfections, 50 nM siRNA was electroporated into 106 of logarithmically growing BL2 cells using Lonza Nucleofector 2b device (Basel, Switzerland), nucleofection solution T and C009 programme. After electroporation, cells were resuspended and immediately seeded into a pre-warmed fresh growth medium at 0.25x106 cells/ml concentration. Total and incorporated Lamin B1 levels were assessed by WB or ImageStream cytometry 48 hours after electroporation. siRNAs used for this study: siGENOME siRNAs were received from Dharmacon (GE Healthcare, Roserberg, Sweden) and target sequences were the following: siRNA1 – GAAGGAAUCUGAUCUUAAU, siRNA2 – CAACUGACCUCAUCUGGAA, siRNA3 – GAAAGAGUCUAGAGCAUGU. GCAUGAAACGCGCUUGGUA. ON-TARGETplus Non-targeting Control siRNA Pool (D-001810-10-05, Dharmacon) was used at 50 nM as an off-target siRNA control.


title: LMNB1 RNAitransfected following induction of SHM passage 1

description: Gene expression data from BL2 cells passage 1 after LMNB1 RNAi transfection following induction of SHM


title: IPF sample circRNA 3

city: Yan tai

first: Jin

middle: jin

last: Zhang

address: Laishan District

country: China

institute: binzhou medical university

description: circRNA expression from IPF patient

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μL 10× blocking agent and 1 μL 25× fragmentation buffer. The mixture was then heated at 60 °C for 30 min and finally 25 μL 2× hybridization buffer was added to dilute the labeled cRNA. Then 50 μL of the hybridization solution was dispensed into the gasket slide and assembled into Arraystar circRNA expression microarray slide. The slides were incubated for 17 h at 65°C in Agilent hybridization oven.

scan_protocol: The slides were washed and then the hybridized arrays were scanned usingAgilent G2505C scanner.

data_processing: The scanned images were imported into Agilent feature extraction software to extract raw data.The quantile normalization of raw data and the subsequent data processing were performed using R limma package. After the quantile normalization of raw data, low intensity filtering was performed and circRNA with at least 1 out of 6 samples with flags in “present” or “marginal” (“all target values”) were retained for further analyses. While comparing the two groups that is disease versus normal controls, the “fold change” (the ratio of group average values) among the groups was computed for each circRNA. The statistical significance of the difference was estimated via t-test. circRNA with fold changes of 1.5 and p values of 0.05 was selected as significantly differentially expressed. The final outputs were filtered and the differentially expressed circRNA was ranked based on fold change and p value, among others, by using the “Data/Sort” and“Filter”functions of Microsoft Excel.To facilitate researcher’s study, the circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software based on TargetScan & miRanda, and the differentially expressed circRNAs within all the comparisons were annotated in detail with the circRNA/miRNA interaction information.

source_name: IPF sample

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol.

growth_protocol: IPF and matched non-fibrotic plasma samples

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

treatment_protocol: Fresh peripheral blood samples were collected in ethylene diaminetetraacetic acid tubes and then centrifuged for the isolation of plasma.

tag: disease

value: idiopathic pulmonary fibrosis (IPF)

tag: gender

value: male

value: plasma


title: IPF sample circRNA 2

description: circRNA expression from IPF patient


title: control sample circRNA 1

description: circRNA expression data from healthy person

source_name: normal sample


title: LMNB1 RNAi transfected passage 2

description: Gene expression data from BL2 cells passage 2 after LMNB1 RNAi transfection


title: control with non-targeting siRNA after induction of SHM passage 1

description: Gene expression data from BL2 cells passage 1 after non-targeting siRNA transfection after induction of SHM


title: control with non-targeting siRNA passage 1

description: Gene expression data from BL2 cells passage 1 after non-targeting siRNA transfection


title: IPF sample circRNA 1

description: circRNA expression from IPF patient

value: female


title: control sample circRNA 2


title: H1975_50%

city: Tokyo

first: Junko

last: Hamamoto

address: 35 Shinanomachi, Shinjuku-ku

department: Pulmonary Medicine

country: Japan

institute: School of Medicine, Keio University

description: Gene expression after 24hr in hyperxia human lung cancer cell line H1975

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 8x60K human array (G4851A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Lung cancer cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 175 ng RNA using Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cell lines were cultured in RPMI-1640 growth medium, supplemented with 10% FBS at 37°C in a humidified 5% CO2 incubator.

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

treatment_protocol: Lung cancer cell lines, H1975 and SK-MES-1 were exposed to 50% O2 for 24h at 37°C in a humidified 5% CO2 incubator.

value: lung

value: lung cancer


title: control sample circRNA 3


title: control with non-targeting siRNA passage 2

description: Gene expression data from BL2 cells passage 2 after non-targeting siRNA transfection


title: LMNB1 RNAi transfected passage 1

description: Gene expression data from BL2 cells passage 1 after LMNB1 RNAi transfection


title: control with non-targeting siRNAafter induction of SHM passage 2

description: Gene expression data from BL2 cells passage 2 after non-targeting siRNA transfection after induction of SHM


title: SK-MES-1_50%

description: Gene expression after 24hr in hyperxia human lung cancer cell line SK-MES-1


title: H1975_20%

description: Gene expression after 24hr in normoxia human lung cancer cell line H1975


title: SK-MES-1_20%

description: Gene expression after 24hr in normoxia human lung cancer cell line SK-MES-1


title: Th17 T cell clone_1

city: Munich

first: Stefanie

last: Eyerich

address: Biedersteinderstrasse 29

institute: Center of Allergy and Environment

description: isolated by limiting dilution

hyb_protocol: Agilent gene expression hybridization kit, 17h, 65°C

scan_protocol: Agilent Microarray scanner system and Feature Extraction Software

data_processing: Genespring software

source_name: skin derived T cell clone

label_protocol: Cy3 labeling using the Low input RNA linear AMP kit from Agilent

growth_protocol: clone generation by limiting dilution

extract_protocol: RNA extraction using the Qiagen RNA Mini kit

treatment_protocol: stimulation with plate-bound aCD3 and soluble aCD28 (both 0.75µg/ml)

value: stimulated, 6 hours aCD3/aCD28


title: Th17 T cell clone_2

description: isolated by limiting dilution


title: Th2 T cell clone_2

description: isolated by limiting dilution


title: Th2 T cell clone_1

description: isolated by limiting dilution


title: gpa1-2 ATP treated root, biological rep2

city: Shijiahzuang

first: Zhonglin

last: Shang

state: Hebei Province

address: Nanerhuan East Road 20

department: College of Life Sciences

institute: Hebei Normal University

description: Gene expression data from root cells after ATP treatment

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

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

data_processing: The data were analyzed with Microarray Suite version 5.1 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: root

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: seedlings were growing in 1/2 MS medium for 4 days, 16/8 L/D cycle, 22 C

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

treatment_protocol: seedlings were transplanted onto a ATP-containg 1/2 MS medium, growing for 60 min, 22 C

tag: condition

value: after ATP treatment

value: G[alpha] null mutant


title: ws ATP treated root, biological rep2

value: wild type, WS ecotype


title: gpa1-2 untreated root, biological rep1

description: Gene expression data from root cells before ATP treatment

value: before ATP treatment


title: Th1 T cell clone_1

description: isolated by limiting dilution


title: gpa1-2 ATP treated root, biological rep1


title: ws untreated root, biological rep1


title: Th22 T cell clone_3_unstim

description: isolated by limiting dilution

value: unstimulated


title: Th22 T cell clone_1_stim

description: isolated by limiting dilution


title: Th22 T cell clone_2_stim

description: isolated by limiting dilution


title: Pregnant_3rd tri_MR_2

status: Public on Aug 14 2017

city: Los Angeles

first: Suan-Sin

last: Foo

state: California

address: 1501 San Pablo St

department: Molecular Microbiology and Immunology

institute: University of Southern California

scan_protocol: Sample Cartridges are placed in the Digital Analyzer for data collection. Color codes on the surface of the cartridge are counted and tabulated for each target molecule. The data produced by the nCounter Digital Analyzer are exported as a Reporter Code Count (RCC) file.

data_processing: Data collection is performed using epifluorescence microscopy and CCD capture technology on an nCounter instrument to yield hundreds of thousands of target molecule counts. Digital images are processed within the nCounter instrument, and the Reporter Probe counts are tabulated in a comma-separated value (CSV) format or RCC file for downstream data analysis with NanoString’s nSolverTM Analysis Software.

source_name: Whole blood

extract_protocol: 10,000 CD14+ sorted monocytes were lysed in RLT buffer at a concentration of 6500 cells/ul.

treatment_protocol: In vitro whole blood infection was performed using different strains of ZIKV. At 40 hpi, peripheral blood mononuclear cells (PBMCs) were isolated using density gradient centrifugation using SepMate and lymphocyte separation medium. Total monocytes were further isolated from PBMCs using Pan Monocyte Isolation Kit.

tag: Sex

value: Female

tag: pregnancy status

value: Pregnant - 3rd trimester

value: African ZIKV (MR766)

value: CD14+ monocytes


title: Pregnant_3rd tri_HPF_1

value: Asian ZIKV (H/PF/2013)


title: Th22 T cell clone_2_unstim

description: isolated by limiting dilution


title: Th22 T cell clone_3_stim

description: isolated by limiting dilution


title: Pregnant_3rd tri_MR_1


title: Pregnant_3rd tri_Mock_2

value: Mock


title: ws untreated root, biological rep2


title: gpa1-2 untreated root, biological rep2


title: ws ATP treated root, biological rep1


title: Pregnant_3rd tri_Mock_1


title: Th22 T cell clone_1_unstim

description: isolated by limiting dilution


title: pES6_5aza_2uM

city: Pardess hana

first: Uri

last: Weissbein

state: Please Select

address: Haalon 4

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem

hyb_protocol: Standard Illumina protocol.

scan_protocol: HumanMethylation450 BeadChips were scanned with Illumina's iScan System.

data_processing: IDAT files were processed and normalized by subset-quantile within array normalization (SWAN) and adjusted for batch effects using the R package ChAMP (version 1.4.0).

label: Cy5 and Cy3

source_name: Human embryonic stem cells

label_protocol: Standard Illumina protocol.

growth_protocol: ES medium.

extract_protocol: Genomic DNA was isolated (NucleoSpin Tissue Kit, MACHEREY-NAGEL) and bisulfite converted (EZ DNA Methylation Kit, Zymo Research) according to the manufacturer's protocol.

treatment_protocol: 2µM 5-aza-2'-deoxycytidine was supplemented to the growth medium for 5 days.

value: Embryonic stem cell line

tag: differentiation status

value: Undifferentiated


title: Pregnant_3rd tri_HPF_2


title: Pregnant_2nd tri_HPF_2

value: Pregnant - 2nd trimester


title: Pregnant_2nd tri_Mock_2


title: Pregnant_2nd tri_HPF_1


title: pES6_control

description: Control cells

tag: cell line

value: Control


title: Pregnant_1st tri_MR_2

value: Pregnant - 1st trimester


title: Pregnant_2nd tri_Mock_1


title: Pregnant_1st tri_HPF_2


title: Pregnant_2nd tri_MR_1


title: Pregnant_2nd tri_MR_2


title: Pregnant_1st tri_Mock_2


title: Human metastatic melanoma G361 cells_rep1

status: Public on Aug 13 2017

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v4 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed using RMA

source_name: Human metastatic melanoma G361 cells

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: mid-log phase cell cultures collected with EDTA and washed PBS

extract_protocol: RNA was isolated using RNAEasy Mini Kit (Qiagen #74104) according to the manufacturers protocol

value: metastatic melanoma G361 cells


title: Human metastatic melanoma A375 cells_rep1

source_name: Human metastatic melanoma A375 cells

value: metastatic melanoma A375 cells


title: Primary normal human epidermal melanocytes_adult

description:
NHEMadult
PromoCell GmbH, Inc.

source_name: Primary normal human epidermal melanocytes, adult

growth_protocol: primary cultures

value: Primary normal epidermal melanocytes

tag: developmental stage

value: adult


title: Non-pregnant_MR_2

value: Non-pregnant

tag: cell type


title: Non-pregnant_HPF_2


title: Pregnant_1st tri_Mock_1


title: Pregnant_1st tri_MR_1


title: Non-pregnant_Mock_2


title: Non-pregnant_HPF_1


title: Human metastatic melanoma A375 cells_rep2


title: Human metastatic melanoma G361 cells_rep2


title: Primary normal human epidermal melanocytes_juvenile

description:
NHEMjuve
PromoCell GmbH, Inc.

source_name: Primary normal human epidermal melanocytes, juvenile

value: juvenile


title: Non-pregnant_MR_1

value: Female


title: Pregnant_1st tri_HPF_1


title: Tumor Nephrectomy [H7-Glom-TN997]

status: Public on Aug 12 2017

city: Ann Arbor

first: Jennifer

last: Harder

state: Michigan

address: 1150 W. Medical Center Drive

department: Division of Nephrology

institute: The University of Michigan

description: Gene Expression data from the glomeruli of human Tumor Nephrectomy

hyb_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

scan_protocol: The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 18 was used for the normalization

data_processing: Each of the hybridization was normalized seperately and the last sheet contains the batchcorrected data using Combat. Background data was filtered by excluding all genes that did not have at least one expression value exceeding the median plus 2 standard deviations of the Affymetrix negative control expression.

source_name: Kidney biopsy

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

extract_protocol: Total RNA was isolated using Rneasy kit (Qiagen) following manufacturer's protocol

tag: tissue

value: glomeruli from kidney biopsy

tag: batch


title: Tumor Nephrectomy [H7-Glom-TN996]


title: Tumor Nephrectomy [H7-Glom-TN995]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN939]

description: Gene Expression data from the glomeruli of human Rapidly Progressive Glomerulonephritis


title: Non-pregnant_Mock_1


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN946]


title: genomic DNA from CTR 1

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

description:
Whole blood from CTR
X200477510076_R05C01

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IInfinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: HiScan SQ scanner (Illumina)

data_processing: Signal intensities files were extracted using the minfi Bioconductor package. Normalization was performed using the Functional Normalization function implemented in minfi.

source_name: CTR 1

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood using the Duplica® Blood DNA Kit (Euroclone) on Duplica® Prep Platform (Euroclone).

value: Whole blood

value: normal

tag: age

value: Male


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN942]


title: genomic DNA from WS patient 2

description:
Whole blood from WS patient
X200477510076_R06C01

source_name: WS patient 2

value: Werner Syndrome


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN943]


title: genomic DNA from CTR 3

description:
Whole blood from CTR
X200477510169_R08C01

source_name: CTR 3


title: genomic DNA from WS patient 3

description:
Whole blood from WS patient
X200477510076_R08C01

source_name: WS patient 3


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN934]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN937]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN909]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN936]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN908]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN938]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN928]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN935]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN924]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN911]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN913]


title: genomic DNA from WS patient 1

description:
Whole blood from WS patient
X200477510076_R04C01

source_name: WS patient 1


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN929]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN930]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN926]


title: genomic DNA from CTR 2

description:
Whole blood from CTR
X200477510076_R07C01

source_name: CTR 2


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN925]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN904]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN907]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN902]


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS971]

description: Gene Expression data from the glomeruli of human Focal and Segmental Glomerulosclerosis


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS972]


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS912]


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS933]


title: Rapidly Progressive Glomerulonephritis [H7-Glom-RPGN906]


title: Minimal Change Disease [H7-Glom-MCD921]

description: Gene Expression data from the glomeruli of human Minimal Change Disease


title: Minimal Change Disease [H7-Glom-MCD903]


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS927]


title: Minimal Change Disease [H7-Glom-MCD973]


title: Minimal Change Disease [H7-Glom-MCD919]


title: Minimal Change Disease [H7-Glom-FSGS&MCD940]


title: Minimal Change Disease [H7-Glom-FSGS&MCD944]


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS915]


title: Minimal Change Disease [H7-Glom-MCD945]


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS920]


title: Diabetic Nephropathy [H7-Glom-DN932]

description: Gene Expression data from the glomeruli of human Diabetic Nephropathy


title: Diabetic Nephropathy [H7-Glom-DN916]


title: Diabetic Nephropathy [H7-Glom-DN941]


title: Diabetic Nephropathy [H7-Glom-DN947]


title: Diabetic Nephropathy [H7-Glom-DN914]


title: Minimal Change Disease [H7-Glom-FSGS&MCD905]


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS917]


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS970]


title: Minimal Change Disease [H7-Glom-FSGS&MCD922]


title: Diabetic Nephropathy [H7-Glom-DN910]


title: Focal and Segmental Glomerulosclerosis [H7-Glom-FSGS918]


title: Minimal Change Disease [H7-Glom-FSGS&MCD931]


title: Minimal Change Disease [H7-Glom-FSGS&MCD923]


title: Tumor Nephrectomy [H7-Tub-TN1187]

description: Gene Expression data from the tubulointerstitial compartment of human Tumor Nephrectomy [H7-Tub-TN1187]

scan_protocol: The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 18 was used for the normalization. Background data was filtered by excluding all genes that did not have at least one expression value exceeding the median plus 2 standard deviations of the Affymetrix negative control expression.

data_processing: Each of the hybridization was normalized seperately and the last sheet contains the batchcorrected data using Combat

source_name: Kidney Biopsy from Tumor Nephrectomy

value: tubulo interstitium from kidney biopsy


title: Tumor Nephrectomy [H7-Tub-TN1186]

description: Gene Expression data from the tubulointerstitial compartment of human Tumor Nephrectomy [H7-Tub-TN1186]


title: Tumor Nephrectomy [H7-Tub-TN1185]

description: Gene Expression data from the tubulointerstitial compartment of human Tumor Nephrectomy [H7-Tub-TN1185]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1135]

source_name: Kidney Biopsy from Rapidly Progressive Glomerulonephritis


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1138]


title: Diabetic Nephropathy [H7-Glom-DN901]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1120]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1134]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1131]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1119]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1118]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1126]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1121]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1113]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1109]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1127]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1123]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1130]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1102]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1128]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1103]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1122]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1129]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1107]


title: Minimal Change Disease [H7-Tub-MCD1116]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H7-Tub-MCD1116]

source_name: Kidney Biopsy from Minimal Change Disease


title: Minimal Change Disease [H7-Tub-MCD1137]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H7-Tub-MCD1137]


title: Minimal Change Disease [H7-Tub-MCD1163]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H7-Tub-MCD1163]


title: Minimal Change Disease [H7-Tub-MCD1112]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H7-Tub-MCD1112]


description: Gene Expression data from the tubulointerstitial compartment of human Rapidly Progressive Glomerulonephritis [H7-Tub-RPGN1106]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H7-Tub-FSGS1162]

source_name: Kidney Biopsy from Focal and Segmental Glomerulosclerosis


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis and Minimal Change Disease [H7-Tub-FSGS&MCD1136]

source_name: Kidney Biopsy from Focal and Segmental Glomerulosclerosis and Minimal Change Disease


title: Minimal Change Disease [H7-Tub-MCD1111]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H7-Tub-MCD1111]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis and Minimal Change Disease [H7-Tub-FSGS&MCD1124]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis and Minimal Change Disease [H7-Tub-FSGS&MCD1117]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H7-Tub-FSGS1125]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H7-Tub-FSGS1115]


title: HK2, hypoxia, HIF2kd [HK2_H1_HIF2kd_c]

description: human proximal tubular epithelial cells (HK2)

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The raw data was normalized using Robust Multichip Algorithm (RMA), annotated by  Human Entrez Gene custom CDF annotation version 18 and batch-corrected using ComBat from the GenePattern pipeline

label_protocol: Fragmentation and biotin labelling of each amplified cDNA was processed with the NuGen Encore Biotin Module (NuGen Inc.) and according to manufacturer's protocol

growth_protocol: HK-2 cells were cultured in DMEM/F-12 supplemented with 10% fetal calf serum (FCS), 1% ITS, hydrocortisone (36 ng/ml), penicillin (100 U/ml) and streptomycin (100 µg/ml). The cells were incubated at 37°C.

treatment_protocol: Proximal tubular epithelial cells were treated with hypoxia (1% O2) for 24h.

value: hypoxia


title: HK2, normoxia, HIF1kd [HK2_N2_HIF1kd_b]

source_name: human proximal tubular epithelial cells (HK2)

value: normoxia


title: HK2, normoxia, wild type [HK2_N2_WT_c]

value: wt


title: HK2, hypoxia, HIF12kd [HK2_H1_HIF12kd_a]


title: HK2, normoxia, wild type [HK2_N2_WT_b]


title: HK2, hypoxia, HIF12kd [HK2_H1_HIF12kd_b]


title: HK2, normoxia, HIF2kd [HK2_N2_HIF2kd_a]


title: HK2, normoxia, HIF1kd [HK2_N2_HIF1kd_a]


title: HK2, normoxia, HIF2kd [HK2_N2_HIF2kd_c]


title: HK2, normoxia, HIF2kd [HK2_N2_HIF2kd_b]


title: HK2, normoxia, wild type [HK2_N1_WT_b]


title: HK2, hypoxia, HIF1kd [HK2_H1_HIF1kd_c]


title: HK2, normoxia, wild type [HK2_N1_WT_a]


title: HK2, normoxia, wild type [HK2_N1_WT_c]


title: HK2, hypoxia, HIF12kd [HK2_H1_HIF12kd_c]


title: HK2, normoxia, wild type [HK2_N2_WT_a]


title: HK2, normoxia, HIF12kd [HK2_N2_HIF12kd_a]


title: HK2, normoxia, HIF1kd [HK2_N2_HIF1kd_c]


title: HK2, hypoxia, HIF2kd [HK2_H1_HIF2kd_a]


title: HK2, normoxia, HIF12kd [HK2_N2_HIF12kd_c]


title: HK2, normoxia, HIF12kd [HK2_N2_HIF12kd_b]


title: HK2, hypoxia, HIF2kd [HK2_H1_HIF2kd_b]


title: HK2, hypoxia, HIF1kd [HK2_H1_HIF1kd_b]


title: HK2, hypoxia, HIF1kd [HK2_H1_HIF1kd_a]


title: HK2, hypoxia, wild type [HK2_H1_WT_b]


title: HK2, hypoxia, wild type [HK2_H1_WT_a]


title: AB81, normoxia, HIF12kd, a

description: Gene expression data from conditionally immortalized podocytes (AB81)

data_processing: The raw data was normalized using Robust Multichip Algorithm (RMA) using CustomCDF v 18 ENTREZG

source_name: conditionally immortalized human podocytes (AB81)

label_protocol: Fragmentation and biotin labelling of each amplified cDNA was processed with the NuGen Encore Biotin Module (NuGen Inc.) and according to manufacturer's protocol.

growth_protocol: Conditionally immortalized human podocytes were cultured under permissive conditions (33°C) in RPMI-1640 supplemented with 10% FBS, penicillin (100 U/ml)/streptomycin (100 µg/ml), and 1% ITS. Differentiation was induced by thermoshift to 37°C.

treatment_protocol: Differentiated human podocytes were treated with hypoxia (1% O2) for 24h.


title: AB81, normoxia, HIF12kd, c


title: HK2, hypoxia, wild type [HK2_H1_WT_c]


title: AB81, normoxia, HIF2kd, b


title: AB81, normoxia, HIF1kd, c


title: AB81, normoxia, HIF2kd, c


title: AB81, normoxia, HIF12kd, b


title: AB81, normoxia, wild type, b


title: AB81, normoxia, wild type, a


title: AB81, normoxia, HIF1kd, a


title: AB81 hypoxia, HIF1kd, b


title: AB81, normoxia, HIF1kd, b


title: AB81 hypoxia, wild type, b


title: AB81, normoxia, HIF2kd, a


title: AB81, hypoxia, HIF12kd, a


title: AB81, hypoxia, HIF2kd, b


title: AB81, normoxia, wild type, c


title: AB81 hypoxia, HIF1kd, a


title: AB81 hypoxia, wild type, c


title: AB81, hypoxia, HIF2kd, a


title: AB81, hypoxia, HIF2kd, c


title: AB81 hypoxia, HIF1kd, c


title: AB81, hypoxia, HIF12kd, b


title: AB81, hypoxia, HIF12kd, c


title: AB81 hypoxia, wild type, a


title: Mutant calvaria at P10, biological rep1

city: Hong Kong

first: Kwok Yeung

last: Tsang

address: 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: Transgenic mice expressing a Col10a1-13del transgene

hyb_protocol: Mouse Genome 430 2.0 GeneChip (Affymetrix)

scan_protocol: Scanner Type M10 (Affymetrix)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings (ExpressionStat 5.0). Statistical analyses was performed using geWorkbench.

source_name: Mutant calvaria at P10, biological rep1

label_protocol: RNA was taken to generate antisense RNA using MessageAmpTM II-Biotin Enhanced Kit

growth_protocol: Mice kept in Minimal Disease Area

extract_protocol: Parietal bones dissected and embedded in OCT compound, 5um cryosectioned, and then TRIZOL extraction for RNA

value: calvaria

value: 13del-tg mutant with bone overgrowth


title: Mutant calvaria at P10, biological rep2

source_name: Mutant calvaria at P10, biological rep2


title: Mutant calvaria at P10, biological rep3

source_name: Mutant calvaria at P10, biological rep3


title: Control calvaria at P10, biological rep3

description: control

value: wild type


title: Systemic Lupus Erymthematosus [H5-Glom-SLE467]

description: Gene Expression data from the glomeruli of human Systemic Lupus Erymthematosus

source_name: Kidney biopsy


title: Control calvaria at P10, biological rep2

description: control


title: Control calvaria at P10, biological rep1

description: control


title: Systemic Lupus Erymthematosus [H5-Glom-SLE464]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE466]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE465]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE430]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE445]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE419]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE423]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE462]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE440]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE450]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE418]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE463]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE414]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE411]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE451]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE410]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE438]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE442]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE413]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE406]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE404]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE454]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE412]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE408]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE401]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE407]


title: Membranous Glomerulonephritis [H5-Glom-MGN461]

description: Gene Expression data from the glomeruli of human Membranous Glomerulonephritis


title: Membranous Glomerulonephritis [H5-Glom-MGN460]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE409]


title: Membranous Glomerulonephritis [H5-Glom-MGN455]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE402]


title: Membranous Glomerulonephritis [H5-Glom-MGN453]


title: Systemic Lupus Erymthematosus [H5-Glom-SLE405]


title: Membranous Glomerulonephritis [H5-Glom-MGN439]


title: Membranous Glomerulonephritis [H5-Glom-MGN432]


title: Membranous Glomerulonephritis [H5-Glom-MGN456]


title: Membranous Glomerulonephritis [H5-Glom-MGN437]


title: Membranous Glomerulonephritis [H5-Glom-MGN452]


title: Membranous Glomerulonephritis [H5-Glom-MGN431]


title: Membranous Glomerulonephritis [H5-Glom-MGN434]


title: Membranous Glomerulonephritis [H5-Glom-MGN436]


title: Membranous Glomerulonephritis [H5-Glom-MGN417]


title: Membranous Glomerulonephritis [H5-Glom-MGN422]


title: Membranous Glomerulonephritis [H5-Glom-MGN403]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS459]

description: Gene Expression data from the glomeruli of human Focal and Segmental Glomerulosclerosis


title: Membranous Glomerulonephritis [H5-Glom-MGN416]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS458]


title: Membranous Glomerulonephritis [H5-Glom-MGN421]


title: Membranous Glomerulonephritis [H5-Glom-MGN425]


title: Membranous Glomerulonephritis [H5-Glom-MGN424]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS446]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS449]


title: Membranous Glomerulonephritis [H5-Glom-MGN415]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS457]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS427]


title: Membranous Glomerulonephritis [H5-Glom-MGN435]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS447]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS426]


title: IgA Nephropathy [H4-Glom-IgA25]

description: Gene Expression data from the glomeruli of human IgA Nephropathy


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS441]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS428]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS420]


title: IgA Nephropathy [H4-Glom-IgA27]


title: Focal and Segmental Glomerulosclerosis [H5-Glom-FSGS443]


title: IgA Nephropathy [H4-Glom-IgA20]


title: IgA Nephropathy [H4-Glom-IgA15]


title: IgA Nephropathy [H4-Glom-IgA24]


title: IgA Nephropathy [H4-Glom-IgA17]


title: IgA Nephropathy [H4-Glom-IgA11]


title: IgA Nephropathy [H4-Glom-IgA22]


title: IgA Nephropathy [H4-Glom-IgA4]


title: IgA Nephropathy [H4-Glom-IgA2]


title: IgA Nephropathy [H4-Glom-IgA12]


title: IgA Nephropathy [H4-Glom-IgA5]


title: IgA Nephropathy [H4-Glom-IgA8]


title: IgA Nephropathy [H4-Glom-IgA21]


title: IgA Nephropathy [H4-Glom-IgA9]


title: Tumor Nephrectomy [H3-Glom-TN33]

description: Gene Expression data from the glomeruli of human Tumor Nephrectomy


title: IgA Nephropathy [H4-Glom-IgA19]


title: IgA Nephropathy [H4-Glom-IgA18]


title: IgA Nephropathy [H4-Glom-IgA10]


title: IgA Nephropathy [H4-Glom-IgA7]


title: IgA Nephropathy [H4-Glom-IgA14]


title: IgA Nephropathy [H4-Glom-IgA16]


title: IgA Nephropathy [H4-Glom-IgA3]


title: Tumor Nephrectomy [H3-Glom-TN34]


title: IgA Nephropathy [H4-Glom-IgA1]


title: IgA Nephropathy [H4-Glom-IgA26]


title: IgA Nephropathy [H4-Glom-IgA6]


title: Tumor Nephrectomy [H3-Glom-TN6]


title: IgA Nephropathy [H4-Glom-IgA13]


title: Tumor Nephrectomy [H3-Glom-TN2]


title: Minimal Change Disease [H3-Glom-MCD10]

description: Gene Expression data from the glomeruli of human Minimal Change Disease


title: Tumor Nephrectomy [H3-Glom-TN1]


title: Minimal Change Disease [H3-Glom-MCD9]


title: Hypertensive Nephropathy [H2-Glom-TN3]

description: Gene Expression data from the glomeruli of human Hypertensive Nephropathy


title: Minimal Change Disease [H3-Glom-MCD12]


title: Minimal Change Disease [H3-Glom-MCD8]


title: Hypertensive Nephropathy [H2-Glom-TN1]


title: Hypertensive Nephropathy [H2-Glom-HT20]


title: Hypertensive Nephropathy [H2-Glom-TN2]


title: Hypertensive Nephropathy [H2-Glom-HT7]


title: Hypertensive Nephropathy [H2-Glom-HT11]


title: ms188 vs Col Replicate 3

city: Shanghai

first: Zhong-Nan

last: Yang

address: Shanghai Guilin Road No.100

institute: Shanghai Normal University

description:
Biological replicate 3 of 3.
ms188-3 vs Col-3

hyb_protocol: Each Slide was hybridized with 825ng Cy3-labeled cRNA and 825ng Cy-5 labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US)with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

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. Raw data were normalized by Lowess(locally weighted scatter plot smoothing) algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
Normalized signal log2 ratio (Cy3/Cy5) representing test/reference

source_name: Inflorescence of ms188

label_protocol: Total RNA were amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX, US), Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US) ，Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US)followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Arabidopsis, ecotype Columbia-0, was the source of both the wild-type and mutant plants. Plants were grown under long-day conditions (16-hour of light / 8-hour of dark) in a growth room at approximately 22°C.

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

value: closed buds (before flower stage 12)

source_name: Inflorescence of col


title: Hypertensive Nephropathy [H2-Glom-HT15]


title: Hypertensive Nephropathy [H2-Glom-HT13]


title: Hypertensive Nephropathy [H2-Glom-HT14]


title: Hypertensive Nephropathy [H2-Glom-HT5]


title: Hypertensive Nephropathy [H2-Glom-HT16]


title: Hypertensive Nephropathy [H2-Glom-HT6]


title: Tumor Nephrectomy [H1-Glom-TN2]


title: Hypertensive Nephropathy [H2-Glom-HT8]


title: Hypertensive Nephropathy [H2-Glom-HT18]


title: Hypertensive Nephropathy [H2-Glom-HT4]


title: Tumor Nephrectomy [H1-Glom-TN3]


title: Hypertensive Nephropathy [H2-Glom-HT12]


title: Hypertensive Nephropathy [H2-Glom-HT2]


title: Tumor Nephrectomy [H1-Glom-TN1]


title: Thin Membrane Disease [H1-Glom-TMD5]

description: Gene Expression data from the glomeruli of human Thin Membrane Disease


title: Thin Membrane Disease [H1-Glom-TMD2]


title: Hypertensive Nephropathy [H2-Glom-HT1]


title: Thin Membrane Disease [H1-Glom-TMD1]


title: Minimal Change Disease [H1-Glom-MCD5]


title: ms188 vs Col Replicate 1

description:
Biological replicate 1 of 3.
ms188-1 vs Col-1


title: Minimal Change Disease [H1-Glom-MCD3]


title: ams vs Col Replicate 3

description:
Biological replicate 3 of 3.
ams-3 vs Col-3

source_name: Inflorescence of ams


title: Minimal Change Disease [H1-Glom-MCD2]


title: ms188 vs Col Replicate 2

description:
Biological replicate 2 of 3.
ms188-2 vs Col-2


title: ams vs Col Replicate 1

description:
Biological replicate 1 of 3.
ams-1 vs Col-1


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis and Minimal Change Disease [H7-Tub-FSGS&MCD1104]


title: ams vs Col Replicate 2

description:
Biological replicate 2 of 3.
ams-2 vs Col-2


title: tdf1 vs Col Replicate 1

description:
Biological replicate 1 of 3.
tdf1-1 vs Col-1

source_name: Inflorescence of tdf1


title: tdf1 vs Col Replicate 2

description:
Biological replicate 2 of 3.
tdf1-2 vs Col-2


title: Diabetic Nephropathy [H1-Glom-DN10]

description: Gene Expression data from the glomeruli of human Diabetic Nephropathy


title: tdf1 vs Col Replicate 3

description:
Biological replicate 3 of 3.
tdf1-3 vs Col-3


title: dyt1 vs Col Replicate 1

description:
Biological replicate 1 of 3.
dyt1-1 vs Col-1

source_name: Inflorescence of dyt1


title: Diabetic Nephropathy [H1-Glom-DN8]


title: Diabetic Nephropathy [H7-Tub-DN1108]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H7-Tub-DN1108]

source_name: Kidney Biopsy from Diabetic Nephropathy


title: Diabetic Nephropathy [H7-Tub-DN1101]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H7-Tub-DN1101]


title: Diabetic Nephropathy [H7-Tub-DN1110]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H7-Tub-DN1110]


title: Diabetic Nephropathy [H1-Glom-DN5]


title: Diabetic Nephropathy [H1-Glom-DN6]


title: Minimal Change Disease [H1-Glom-MCD1]

description: Gene Expression data from the glomeruli of human Minimal Change Disease


title: Diabetic Nephropathy [H7-Tub-DN1114]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H7-Tub-DN1114]


title: dyt1 vs Col Replicate 2

description:
Biological replicate 2 of 3.
dyt1-2 vs Col-2


title: Diabetic Nephropathy [H7-Tub-DN1133]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H7-Tub-DN1133]


title: Diabetic Nephropathy [H7-Tub-DN1139]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H7-Tub-DN1139]


title: Diabetic Nephropathy [H1-Glom-DN1]


title: dyt1 vs Col Replicate 3

description:
Biological replicate 3 of 3.
dyt1-3 vs Col-3


title: Diabetic Nephropathy [H1-Glom-DN16]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE358]

source_name: Kidney Biopsy from Systemic Lupus Erythematosus


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE357]


title: Diabetic Nephropathy [H7-Tub-DN1132]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H7-Tub-DN1132]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE352]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE361]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE359]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE340]


title: Diabetic Nephropathy [H1-Glom-DN2]

description: Gene Expression data from the glomeruli of human Diabetic Nephropathy


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE362]


title: wild type, rep2

city: Stockholm

first: Christos

last: Samakovlis

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

country: Sweden

institute: Stockholm University

hyb_protocol: Samples were hybridized to the Affymetrix GeneChIP Drosophila Genome 2.0 Array at the Genomic Core Laboratory at Memorial Sloan-Kettering Cancer Center.

scan_protocol: Samples were scanned at the Genomic Core Laboratory at Memorial Sloan-Kettering Cancer Center.

data_processing: Data were normalized using the GCRMA frunction (R/bioconductor) with default settings. In addition MAS5 present/absent calls were computed (also using R/bioconductor)

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Stage 16 embryos

label_protocol: Samples were labeled at the Genomic Core Laboratory at Memorial Sloan-Kettering Cancer Center.

growth_protocol: Embryos were aged to stage 16

extract_protocol: RNA was extracted with Trizol and was incubated with Turbo DNAse. Four μg of total RNA was reverse transcribed with Superscript III reverse transcriptase (RT) using random primers.

value: wildtype (w1118)

value: Stage 16 embryos


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE338]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE336]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE360]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE323]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE349]


title: wild type, rep1


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE343]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE329]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE348]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE319]


title: grh mutant, rep1

value: grhB37 mutant


title: grh overexpression, rep1

value: 69B>grh overexpression


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE311]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE318]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE313]


title: grh mutant, rep2


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE309]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE308]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE305]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE306]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN356]

source_name: Kidney Biopsy from Membranous Glomerulonephritis


title: grh overexpression, rep2


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN354]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN355]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN335]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE310]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN351]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE312]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE314]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE301]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE302]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN337]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN331]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE304]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN333]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN334]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN324]


description: Gene Expression data from the tubulointerstitial compartment of human Systemic Lupus Erythematosus [H5-Tub-SLE307]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN330]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN317]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN325]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN322]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H5-Tub-FSGS327]

source_name: Kidney Biopsy from Focal and Segmental Glomerulosclerosis


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H5-Tub-FSGS339]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN315]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN321]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H5-Tub-FSGS347]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN316]


description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis [H5-Tub-MGN303]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H5-Tub-FSGS345]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H5-Tub-FSGS344]


title: IgA nephropathy [H4-Tub-IgA27]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA27]

source_name: Kidney Biopsy from


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H5-Tub-FSGS341]


title: IgA nephropathy [H4-Tub-IgA26]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA26]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H5-Tub-FSGS326]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H5-Tub-FSGS320]


title: Rat 2 C2

city: Changsha

first: Qiquan

last: Wan

address: No 138 Tongzipo Road

institute: Central South University

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

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 2 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed circRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

organism: Rattus norvegicus

source_name: normal lung samples

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, total RNA was treated with Rnase R (Epicenter, Madison, WI, USA) to remove linear RNAs. Thereafter, enriched circRNAs from each sample were amplified and transcribed into fluorescent cRNA utilizing a random priming method according to Arraystar Super RNA Labeling protocol  (Arraystar Inc.) The labelled cRNAs were purified with an RNeasy Mini Kit (Qiagen, Suzhou, China). After being measured for the concentration and specific activity with a NanoDrop ND-1000, the labelled cRNAs (pmol Cy3/microg cRNA) were then hybridized onto the Arraystar Rat circRNA Arrays (8x15K, Arraystar).

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: lung

value: Adult


title: Rat 3 C3

value: normal


title: Rat 4 L1

source_name: ARDS lung samples

value: Acute respiratory distress syndrome (ARDS)

value: Male


title: IgA nephropathy [H4-Tub-IgA22]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA22]

value: tubulo interstitium from kidney biopsy


title: IgA nephropathy [H4-Tub-IgA24]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA24]


title: IgA nephropathy [H4-Tub-IgA25]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA25]


description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis [H5-Tub-FSGS328]


title: Rat 6 L3


title: Rat 5 L2


title: Caco-2 cells non-infected 24h,rep4

city: chongqing

first: bin

last: tang

state: chongqing

address: Southwest Hospital &College of Medical Laboratory Science; Third Military Medical University

department: Department of Clinical Microbiology and Immunology

description: expression data from Caco-2 cells with non-infected for 24 hours

hyb_protocol: The Fluidics Station 450/250 is used to wash and stain the probe arrays. It is operated using Affymetrix GeneChip Command Console (GeneChip® Expression Wash, Stain and Scan User Manual, Affymetrix).

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

data_processing: Affymetrix GeneChip® Command Console® Software (AGCC)

source_name: Caco-2 cells non-infected 24h

label_protocol: cRNA were prepared according to the standard Affymetrix protocol with GeneChip IVT Labeling Kit from 6 ug total RNA (GeneChip® Expression Wash, Stain and Scan User Manual, Affymetrix).

growth_protocol: Caco-2 cells were grown in DMEM medium (Gibco, 11965-092) containing 10% fetal bovine serum (Gibco, 10099-141) and 100 U/ml penicillin/streptomycin (Gibco, 15140-122) at 37 °C in 5% CO2.

extract_protocol: Total RNA of cells was extracted using the TRIzol® Reagent (Life Technologies) and cRNA was generated using the PimeScript TMRT Reagent Kit (Takara).

treatment_protocol: Caco-2 cells were infected with F. nucleatum (MOI=100:1) or non-infected (control) for 24 hours.

value: Human colorectal adenocarcinoma


title: IgA nephropathy [H4-Tub-IgA20]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA20]


title: IgA nephropathy [H4-Tub-IgA16]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA16]


title: Caco-2 cells non-infected 24h,rep5

institute: Southwest Hospital &College of Medical Laboratory Science; Third Military Medical University


title: IgA nephropathy [H4-Tub-IgA14]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA14]


title: Caco-2 cells non-infected 24h,rep3


title: IgA nephropathy [H4-Tub-IgA11]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA11]


title: Caco-2 cells non-infected 24h,rep2


title: IgA nephropathy [H4-Tub-IgA21]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA21]


title: IgA nephropathy [H4-Tub-IgA8]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA8]


title: Rat 1 C1


title: IgA nephropathy [H4-Tub-IgA19]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA19]


title: IgA nephropathy [H4-Tub-IgA18]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA18]


title: IgA nephropathy [H4-Tub-IgA12]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA12]


title: IgA nephropathy [H4-Tub-IgA10]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA10]


title: Caco-2 cells F. nucleatum 24h,rep3

description: expression data from Caco-2 cells infected with F. nucleatum for 24 hours

source_name: Caco-2 cells F. nucleatum 24h


title: IgA nephropathy [H4-Tub-IgA6]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA6]


title: Caco-2 cells F. nucleatum 24h,rep4


title: IgA nephropathy [H4-Tub-IgA5]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA5]


title: IgA nephropathy [H4-Tub-IgA3]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA3]


title: Caco-2 cells F. nucleatum 24h,rep5


title: IgA nephropathy [H4-Tub-IgA13]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA13]


title: IgA nephropathy [H4-Tub-IgA2]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA2]


title: Caco-2 cells F. nucleatum 24h,rep2


title: IgA nephropathy [H4-Tub-IgA7]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA7]


title: Caco-2 cells non-infected 24h,rep1

description: expression data from Caco-2 cells with non-infected for 24 hours


title: IgA nephropathy [H4-Tub-IgA9]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA9]


title: Caco-2 cells F. nucleatum 24h,rep1


title: IgA nephropathy [H4-Tub-IgA4]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA4]


title: Tumor Nephrectomy [H3-Tub-TN1]

description: Gene Expression data from the tubulointerstitial compartment of human Tumor Nephrectomy [H3-Tub-TN1]

source_name: Kidney Biopsy from Tumor Nephrectomy


title: IgA nephropathy [H4-Tub-IgA1]

description: Gene Expression data from the tubulointerstitial compartment of human IgA nephropathy [H4-Tub-IgA1]


title: Minimal Change Disease [H3-Tub-MCD9]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H3-Tub-MCD9]

source_name: Kidney Biopsy from Minimal Change Disease


title: Hypertensive Nephropathy [H2-Tub-HT20]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT20]

source_name: Kidney Biopsy from Hypertensive Nephropathy


title: Hypertensive Nephropathy [H2-Tub-HT19]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT19]


title: Tumor Nephrectomy [H3-Tub-TN6]

description: Gene Expression data from the tubulointerstitial compartment of human Tumor Nephrectomy [H3-Tub-TN6]


title: Minimal Change Disease [H3-Tub-MCD11]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H3-Tub-MCD11]


title: Tumor Nephrectomy [H3-Tub-TN2]

description: Gene Expression data from the tubulointerstitial compartment of human Tumor Nephrectomy [H3-Tub-TN2]


title: Hypertensive Nephropathy [H2-Tub-HT16]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT16]


title: Hypertensive Nephropathy [H2-Tub-HT15]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT15]


title: Hypertensive Nephropathy [H2-Tub-HT14]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT14]


title: Minimal Change Disease [H3-Tub-MCD8]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H3-Tub-MCD8]


title: Hypertensive Nephropathy [H2-Tub-HT8]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT8]


title: Hypertensive Nephropathy [H2-Tub-HT9]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT9]


title: Hypertensive Nephropathy [H2-Tub-HT17]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT17]


title: Hypertensive Nephropathy [H2-Tub-HT6]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT6]


title: Hypertensive Nephropathy [H2-Tub-HT7]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT7]


title: Hypertensive Nephropathy [H2-Tub-HT10]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT10]


title: Hypertensive Nephropathy [H2-Tub-HT5]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT5]


title: Hypertensive Nephropathy [H2-Tub-HT13]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT13]


title: Thin Membrane Disease [H1-Tub-TMD5]

description: Gene Expression data from the tubulointerstitial compartment of human Thin Membrane Disease [H1-Tub-TMD5]

source_name: Kidney Biopsy from Thin Membrane Disease


title: Hypertensive Nephropathy [H2-Tub-HT12]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT12]


title: Hypertensive Nephropathy [H2-Tub-HT18]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT18]


title: Hypertensive Nephropathy [H2-Tub-HT11]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT11]


title: Hypertensive Nephropathy [H2-Tub-HT3]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT3]


title: Hypertensive Nephropathy [H2-Tub-HT1]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT1]


title: Hypertensive Nephropathy [H2-Tub-HT2]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT2]


title: Thin Membrane Disease [H1-Tub-TMD4]

description: Gene Expression data from the tubulointerstitial compartment of human Thin Membrane Disease [H1-Tub-TMD4]


title: Thin Membrane Disease [H1-Tub-TMD1]

description: Gene Expression data from the tubulointerstitial compartment of human Thin Membrane Disease [H1-Tub-TMD1]


title: Minimal Change Disease [H1-Tub-MCD3]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H1-Tub-MCD3]


title: Thin Membrane Disease [H1-Tub-TMD6]

description: Gene Expression data from the tubulointerstitial compartment of human Thin Membrane Disease [H1-Tub-TMD6]


title: Minimal Change Disease [H1-Tub-MCD4]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H1-Tub-MCD4]


title: Hypertensive Nephropathy [H2-Tub-HT4]

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive Nephropathy [H2-Tub-HT4]


title: Thin Membrane Disease [H1-Tub-TMD2]

description: Gene Expression data from the tubulointerstitial compartment of human Thin Membrane Disease [H1-Tub-TMD2]


title: Thin Membrane Disease [H1-Tub-TMD3]

description: Gene Expression data from the tubulointerstitial compartment of human Thin Membrane Disease [H1-Tub-TMD3]


title: Minimal Change Disease [H1-Tub-MCD2]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H1-Tub-MCD2]


title: SLE without nephritis 1

city: Hefei, Anhui

first: Guo-Cui

last: Wu

address: 81 Meishan Road

department: Department of Epidemiology and Biostatistics, School of Public Health

institute: Anhui Medical University

description: LncRNAs and mRNAs expression profiles in the plasma of SLE without nephritis patients

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

scan_protocol: Slides were scanned immediately after washing with using the Agilent DNA Microarray Scanner (Agilent p/n G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 9 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Plasma, replicate 1

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The TRIzol LS (Invitrogen) was used to isolate RNA with EDTA-plasma from 12 SLE without nephritis, 12 LN and 12 healthy controls. Four RNA samples were mixed together as a pool of sample for microarray analysis. Accordingly, there were each three pooled RNA samples from 12 SLE without nephritis, 12 LN and 12 healthy controls for microarray analysis. Total RNAs Clean-up is used the RNeasy kit (Qiagen) according to manufacturer’s instructions.

value: Plasma

value: 3 female, 1 male


title: SLE without nephritis 3

source_name: Plasma, replicate 3

value: 4 female


title: LN 3

description: LncRNAs and mRNAs expression profiles in the plasma of LN patients


title: SLE without nephritis 2

source_name: Plasma, replicate 2


title: Diabetic Nephropathy [H1-Tub-DN11]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN11]

source_name: Kidney Biopsy from Diabetic Nephropathy


title: LN 2


title: Diabetic Nephropathy [H1-Tub-DN9]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN9]


title: Minimal Change Disease [H1-Tub-MCD1]

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease [H1-Tub-MCD1]


title: Diabetic Nephropathy [H1-Tub-DN8]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN8]


title: Diabetic Nephropathy [H1-Tub-DN6]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN6]


title: Diabetic Nephropathy [H1-Tub-DN7]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN7]


title: Diabetic Nephropathy [H1-Tub-DN10]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN10]


title: Cadaveric Donor [H1-Tub-CD4]

description: Gene Expression data from the tubulointerstitial compartment of human Cadaveric Donor [H1-Tub-CD4]

source_name: Kidney Biopsy from Cadaveric Donor


title: Diabetic Nephropathy [H1-Tub-DN5]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN5]


title: Diabetic Nephropathy [H1-Tub-DN4]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN4]


title: LN 1


title: Diabetic Nephropathy [H1-Tub-DN3]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN3]


title: control 3

description: LncRNAs and mRNAs expression profiles in the plasma of healthy controls


title: control 1


title: control 2


title: Diabetic Nephropathy [H1-Tub-DN1]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN1]


title: Diabetic Nephropathy [H1-Tub-DN2]

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy [H1-Tub-DN2]


title: Cadaveric Donor [H1-Tub-CD3]

description: Gene Expression data from the tubulointerstitial compartment of human Cadaveric Donor [H1-Tub-CD3]


title: Grh_mouse_ab_ChIP

type: SRA

description:
V087
Raw data for this sample are available as a FASTA file included as a supplementary file.

library_source: genomic

data_processing:
Alignement: Bowtie, with parameters –v 2 –m 1
Peak calling: Quest with the following parameters: bandwidth, 30; region size, 300; ChIP enrichment, 5; ChIP to background enrichment, 2; and ChIP extension enrichment, 2.
Genome_build: dm3
Supplementary_files_format_and_content: bed file with called peaks

source_name: 13-16h embryos

growth_protocol: Embryos were aged to 13-16h

extract_protocol:
Embryos were homogenized and fixed in 1.8% formaldehyde at room temperature. After several washes, chromatin in lysis buffer was sonicated to a length range of 0.1kb-0.5kb. For each immunoprecipitation, sheared chromatin was precleared with Gammabind G agarose coated with BSA and incubated with pre-absorbed rabbit anti-Grh antibody, mouse anti-Grh antibody or rabbit IgG. Precipitated complexes were washed, eluted, and cross-links were reversed at 65°C. After Proteinase K treatment, DNA was purified using QIAprep Spin columns and recovered in 50 μl of elution buffer containing RNase A.
DNA libraries were made using the Illumina ChIP-seq library kit

tag: strain

value: 13-16h embryos

tag: chip antibody

value: mouse anti-Grh antibody


title: Cadaveric Donor [H1-Tub-CD2]

description: Gene Expression data from the tubulointerstitial compartment of human Cadaveric Donor [H1-Tub-CD2]


title: Cadaveric Donor [H1-Tub-CD1]

description: Gene Expression data from the tubulointerstitial compartment of human Cadaveric Donor [H1-Tub-CD1]


title: Salmonella Typhimurium ATCC14028 fimZ mutant

city: Taipei

first: Chang

last: Chieh-Hsiang

address: No. 1, Sec. 4, Roosevelt Rd

country: Taiwan

institute: National Taiwan University

hyb_protocol: The labeled cDNA was then pooled and hybridized to microarrays at 65° C for 17 h.

scan_protocol: Microarrays were scanned with an Agilent microarray scanner at 535 nm for Cy3-CTP and 625 nm for Cy5-CTP.

data_processing: Scanned images were then analyzed by Feature Extraction 10.5.1.1 software (Agilent). Image analysis and normalization software was used to quantify signal and background intensity for each feature and substantially normalized the data by rank-consistant .

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

source_name: Mutant Salmonella Typhimurium ATCC14028

label_protocol: The total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: Bacterial cells were cultured on static LB broth

extract_protocol: Total RNA were harvested in TRIzole reagent and disrupted using the MagNA Lyser System.

treatment_protocol: Bacterial cells were cultured 37℃for 48 hr

tag: background strain

tag: genotype/variation

value: fimZ mutant

source_name: Wild-type Salmonella Typhimurium ATCC14028

value: Wild-type


title: Breast cancer tissue 677

status: Public on Aug 11 2017

first: Hung-Chun

last: Cheng

state: Taiwan

address: 125 Lih-Der Road, Peitou District

department: Research

institute: Koo Foundation SYS Cancer Center

description:
Breast cancer data.
B270-141238

hyb_protocol: A cocktail was prepared by combining the specific amounts of fragmented cRNA, probe array controls, bovine serum albumin, and herring sperm DNA according to the protocol of the manufacturer. The cRNA cocktail was hybridized to oligonucleotide probes on the U133 Plus 2.0 array for 16 hours at 45˚C according to the Affymetrix protocol. Immediately following hybridization, the hybridized probe array underwent an automated washing and staining in an Affymetrix GeneChip Fluidics Station 450 using the protocol EukGE-WS2v5.

scan_protocol: U133 Plus 2.0 arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings, and normalized using quantile normalization.

source_name: primary breast cancer tissue

label_protocol: Biotin-labeled complementary RNA (cRNA) hybridization targets were prepared from 5 ug total RNA by in vitro transcription from cDNA templates according to the Affymetrix protocol. The cRNA was purified and chemically fragmented before hybridization.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA) and purified with the RNeasy Mini Kit (Qiagen, Valencia, CA).

value: primary breast cancer

value: female

tag: age at diagnosis

tag: surgery

value: BCT

tag: Stage

tag: t stage

tag: n stage

tag: 18-gene score


title: Breast cancer tissue 679

description:
Breast cancer data.
B270-141246

tag: gender


title: Breast cancer tissue 676

description:
Breast cancer data.
B270-141187

value: MRM


title: Breast cancer tissue 682

description:
Breast cancer data.
T08-0538T


title: Breast cancer tissue 680

description:
Breast cancer data.
B270-141254


title: Breast cancer tissue 683

description:
Breast cancer data.
T08-1080T


title: Breast cancer tissue 681

description:
Breast cancer data.
B270-141258


title: Breast cancer tissue 672

description:
Breast cancer data.
B270-141140


title: Breast cancer tissue 678

description:
Breast cancer data.
B270-141240


title: Breast cancer tissue 673

description:
Breast cancer data.
B270-141146


title: Breast cancer tissue 675

description:
Breast cancer data.
B270-141172


title: Breast cancer tissue 669

description:
Breast cancer data.
B270-141094


title: Breast cancer tissue 674

description:
Breast cancer data.
B270-141152


title: Breast cancer tissue 666

description:
Breast cancer data.
B270-141069


title: Breast cancer tissue 671

description:
Breast cancer data.
B270-141121


title: Breast cancer tissue 665

description:
Breast cancer data.
B270-141066


title: Breast cancer tissue 667

description:
Breast cancer data.
B270-141071


title: Breast cancer tissue 670

description:
Breast cancer data.
B270-141111


title: Breast cancer tissue 657

description:
Breast cancer data.
B270-140942


title: Breast cancer tissue 661

description:
Breast cancer data.
B270-140964


title: Breast cancer tissue 663

description:
Breast cancer data.
B270-141021


title: Breast cancer tissue 654

description:
Breast cancer data.
B270-140906


title: Breast cancer tissue 656

description:
Breast cancer data.
B270-140938


title: Breast cancer tissue 658

description:
Breast cancer data.
B270-140943


title: Breast cancer tissue 662

description:
Breast cancer data.
B270-140972


title: Breast cancer tissue 668

description:
Breast cancer data.
B270-141078


title: Breast cancer tissue 664

description:
Breast cancer data.
B270-141052


title: Breast cancer tissue 659

description:
Breast cancer data.
B270-140948


title: Breast cancer tissue 650

description:
Breast cancer data.
B270-140881


title: Breast cancer tissue 652

description:
Breast cancer data.
B270-140899


title: Breast cancer tissue 649

description:
Breast cancer data.
B270-140880