title: male 51.80013689y #102


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(2)-24.2]

status: Public on May 31 2013

type: RNA

city: Maastricht

first: Lize

last: Deferme

state: Limburg

address: Universiteitssingel 50

department: TGX

country: Netherlands

institute: Maastricht University

hyb_protocol: 12.5µg of cRNA was used. The GeneTitan arrays were hybridized, washed and stained using the GeneTitan hybridization, wash and stain kit for 3’ IVT Arrays and GeneTitan Operating Software and scanned by means of an Affymetrix GeneTitan scanner

scan_protocol: Arrays were scanned with the GeneTitan scanner

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/entrezg.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Qiazol extraction was performed using the miRNAeasy kit from Qiagen according to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing, or fresh medium containing either 100µM menadione, 200µM TBH or 50µM H2O2

tag: cell line

tag: compound, dose

value: Control

tag: time (h)


title: Effect of menadione on mRNA levels in HepG2 cells [men100(1)-24.5]

value: 100µM Men


title: male 67.38945927y #108

city: ROTTERDAM

first: Marjolein

middle: J.

last: Peters

address: Wytemaweg 80

department: Internal Medicine

institute: Erasmus MC

hyb_protocol: RNA was hybridized to the Illumina Whole-Genome Expression Beadchips (HT12-v4), using the standard Illumina Hybridization Protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Missing intensities were not imputed but deleted. Background values were not substracted. Raw intensities were quantile normalized, log2-transformed, and centered. Samples were standardized. We used the software-pipeline AssociationGG (www.genenetwork.nl/associationgg).

label_protocol: The isolated RNAs were amplified and labelled using the Ambion TotalPrep RNA Protocol.

extract_protocol: RNA was stabilized using PAXgene Tubes (Becton Dickinson) and RNA was isolated using the Qiagen PAXgene Blood RNA kit. Quality Control was performed with the Caliper Life Sciences LabChip GX system.

tag: gender

value: male

tag: age (y)

tag: tissue

value: blood


title: male 48.93634497y #103


title: female 78.32991102y #100

value: female


title: male 62.09445585y #104


title: male 60.57768652y #106


title: male 60.64065708y #101


title: RORA1-ChIP_vs_IgG-ChIP

type: genomic

city: Washington

first: Valerie

middle: Wailin

last: Hu

state: DC

department: Biochemistry and Molecular Medicine

country: USA

institute: The George Washington University School of Medicine and Health Sciences

description:
RORA1 ChIP Rep 1-3, promoter
ChIP (test) CEL files are R1, R2, R3 and control are G1, G2, G3

hyb_protocol: Approximately 7.5μg of ChIP DNA was hybridzed per array using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit. All arrays were hybridized for 16 hours at 45°C at 60rpm using the Affymetrix Hybridization Oven.

scan_protocol: All arrays were scanned using the GeneChip Scanner 3000 with AutoLoader (Affymetrix).

data_processing:
Microarray data were quantile normalized and analyzed using the Partek Genomics Suite following the "Analysis of a Tiling Regulation Study in Partek Genomics Suite" protocol.
Enriched genes in Result file.xls was generated by Partek Genomics Suite version 6.12.0420. It contains gene symbol, p-value, MAT-score, and fold change (RORA1-ChIP/IgG-ChIP) for each region.

molecule: genomic DNA

source_name: RORA1-ChIP DNA from SH-SY5Y nuclear lysates

label_protocol: ChIP DNA was enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.

growth_protocol: The human neuroblastoma cells SH-SY5Y (ATCC, Manassas,VA) were cultured in 1:1 Modified Eagle’s Medium (MEM) and Ham’s F12 media (MediaTech, Manassas, VA) supplemented with 15% (v/v) fetal bovine serum (Atlanta Biologicals, Lawrenceville, GA) and 1% penicillin/streptomycin (P/S; MediaTech). Cells were maintained at 37°C with 5% CO2, and split 1:2 every 3–4 days when the cells reached ~80% confluency.

extract_protocol: Chromatin immunoprecipitation (ChIP) for promoter array analysis was performed using the Millipore EZ-ChIP Chromatin Immunoprecipitation Kit (Millipore, Billerica, MA) according to the manufacturer's protocol. Briefly, the human neuronal cell line SH-SY5Y was cultured in complete growth medium in a T-175 flask until ~80% confluency (approximately 1.5 × 107 cells). The medium was then carefully removed without disturbing the cells. The cells were fixed with 37% formaldehyde for exactly 10 min to crosslink chromatin. The crosslinking reaction was terminated by addition of 10% glycine, then ice-cold PBS supplemented with protease inhibitor cocktail was added to the culture flask to wash and chill the cells. The crosslinked cells were dislodged from the flask by scraping gently with a cell scraper and then transferred to a pre-chilled centrifuge tube. Crosslinked cells were pelleted and nuclear extraction was performed using the Active Motif Nuclear Extract Kit (Active Motif, Carlsbad, CA) according to the manufacturer's protocol. Nuclear pellets were resuspended in SDS Lysis Buffer and sonicated on wet ice to shear crosslinked chromatin to 200-1,000 bp using a Heat Systems-Ultrasonics W-380 sonicator (Heat Systems-Ultrasonics/Misonix, Farmingdale, NY) set to 30% of maximum output power for 20 × 10 seconds with 1 min interval. Sonicated chromatin was divided into several aliquots for immunoprecipitation reactions and stored at -80°C until use. Each immunoprecipitation reaction was conducted using 1µg of goat anti-RORA1 (SC-26377) or normal goat IgG (SC-2028) antibody (Santa Cruz Biotechnology, Santa Cruz, CA). Immunoprecipitated chromatin was then reverse-crosslinked by adding 5 M NaCl to the final concentration of 0.2 M and incubated at 65°C overnight. DNA from the immunoprecipitated chromatin was isolated and purified using Millipore DNA purification columns (Millipore). Purified DNA from the chromatin immunoprecipitated with anti-RORA1 or IgG antibodies was amplified using the Whole Genome Amplification 2 Kit (Sigma Aldrich) according to the manufacturer’s protocol.

tag: cell type

value: human neuroblastoma cell line

source_name: IgG-ChIP DNA from SH-SY5Y nuclear lysates

extract_protocol: Chromatin immunoprecipitation (ChIP) for promoter array analysis was performed using the Millipore EZ-ChIP Chromatin Immunoprecipitation Kit (Millipore, Billerica, MA) according to the manufacturer's protocol. Briefly, the human neuronal cell line SH-SY5Y was cultured in complete growth medium in a T-175 flask until ~80% confluency (approximately 1.5 × 107 cells). The medium was then carefully removed without disturbing the cells. The cells were fixed with 37% formaldehyde for exactly 10 min to crosslink chromatin. The crosslinking reaction was terminated by addition of 10% glycine, then ice-cold PBS supplemented with protease inhibitor cocktail was added to the culture flask to wash and chill the cells. The crosslinked cells were dislodged from the flask by scraping gently with a cell scraper and then transferred to a pre-chilled centrifuge tube. Crosslinked cells were pelleted and nuclear extraction was performed using the Active Motif Nuclear Extract Kit (Active Motif, Carlsbad, CA) according to the manufacturer's protocol. Nuclear pellets were resuspended in SDS Lysis Buffer and sonicated on wet ice to shear crosslinked chromatin to 200-1,000 bp using a Heat Systems-Ultrasonics W-380 sonicator (Heat Systems-Ultrasonics/Misonix, Farmingdale, NY) set to 30% of maximum output power for 20 × 10 seconds with 1 min interval. Sonicated chromatin was divided into several aliquots for immunoprecipitation reactions and stored at -80°C until use. Each immunoprecipitation reaction was conducted using 1µg of goat anti-RORA1 (SC-26377) or normal goat IgG antibody (Santa Cruz Biotechnology, Santa Cruz, CA). Immunoprecipitated chromatin was then reverse-crosslinked by adding 5 M NaCl to the final (SC-2028) concentration of 0.2 M and incubated at 65°C overnight. DNA from the immunoprecipitated chromatin was isolated and purified using Millipore DNA purification columns (Millipore). Purified DNA from the chromatin immunoprecipitated with anti-RORA1 or IgG antibodies was amplified using the Whole Genome Amplification 2 Kit (Sigma Aldrich) according to the manufacturer’s protocol.


title: female 56.57768652y #98


title: Effect of menadione on mRNA levels in HepG2 cells [men100(3)-8.8]


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(1)-24.1]


title: male 48.44626968y #99


title: female 59.85489391y #97


title: male 75.16221766y #95


title: female 48.3449692y #96


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(3)-8.7]


title: female 57.68651608y #93


title: female 49.92197125y #92


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(2)-8.2]


title: Effect of menadione on mRNA levels in HepG2 cells [men100(2)-8.6]


title: Effect of menadione on mRNA levels in HepG2 cells [men100(1)-8.5]


title: male 57.32238193y #94


title: male 81.50855578y #91


title: female 60.79945243y #90


title: female 53.84804928y #87


title: PC-3_basalhTERT_LongTelomeres_LhTERTLcre_4

city: Koto-ku

first: kyotaro

last: HIRASHIMA

state: Tokyo

address: 3-8-31 Ariake

department: Cancer Chemotherapy Center

country: Japan

institute: The JFCR-Cancer Inst.

description: LhTERTL/cre+

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Gene-level expression signals were obtained by processing of raw data with the RMA procedure using GeneSpring GX (Agilent Technologies).

source_name: Human prostate cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: 1x10^6 cells were subcutaneously injected into five-week-old female nude mice with a BALB/c genetic background. When the tumor size reached at least 5 mm in diameter, mice were euthanized and tumor tissue was collected.

extract_protocol: RNA extraction from tumor xenografts were performed by using the RNeasy kit and Tissue Lyser (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: no treatment.

value: prostate cancer cell line PC-3

tag: telomere status

value: Long

tag: exogenous htert

value: absent


title: Ptbp2 KO cortex 1 [Exon]

city: Cleveland

first: Donny

middle: D

last: Licatalosi

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve University

description: Ptbp2 KO cortex 1

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Expression Console; exon level data processed using core and extended probesets (RMA, DABG (p<0.05))
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.extended.mps

organism: Mus musculus

source_name: mouse Ptbp2 knockout cortex

label_protocol: Affymetrix WT Sense Target Labeling Assay

growth_protocol: Animals housed and timed matings performed following standard procedures.  Day when copulatory plug is observed is considered embryonic day 0.5.  Embryos collected at day 18.5 by caesarian section.  Animals have a mixed background (CD1 and C57BL/6).

extract_protocol: Trizol Extraction

value: cortex

tag: strain

value: CD1 and C57BL/6 mixed background

tag: developmental stage

value: embryonic day 18.5


title: PC-3_basalhTERT_LongTelomeres_LhTERTLcre_3

description: LhTERTL/cre+


title: Ptbp2 KO cortex 2 [Exon]

description: Ptbp2 KO cortex 2


title: female 61.28405202y #85


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(1)-8.1]


title: Effect of menadione on mRNA levels in HepG2 cells [men100(3)-6.8]


title: male 62.01779603y #89


title: PC-3_basalhTERT_LongTelomeres_LhTERTLcre_1

description: LhTERTL/cre+


title: Effect of menadione on mRNA levels in HepG2 cells [men100(1)-6.5]


title: PC-3_basalhTERT_ShortTelomeres_mockcre_3

description: mock/cre+

value: Short


title: PC-3_basalhTERT_ShortTelomeres_mockcre_4

description: mock/cre+


title: female 55.43052704y #86


title: male 56.09856263y #88


title: female 57.82340862y #83


title: Effect of menadione on mRNA levels in HepG2 cells [men100(2)-6.6]


title: Ptbp2 KO cortex 4 [Exon]

description: Ptbp2 KO cortex 4


title: PC-3_basalhTERT_LongTelomeres_LhTERTLcre_2

description: LhTERTL/cre+


title: male 76.77207392y #82


title: Wild type cortex 1 [Exon]

description: Wild type cortex 1

source_name: mouse wild type cortex


title: Wild type cortex 2 [Exon]

description: Wild type cortex 2


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(3)-6.7]


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(2)-6.2]


title: Wild type cortex 4 [Exon]

description: Wild type cortex 4


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(1)-6.1]


title: female 71.42231348y #81


title: Wild type cortex 3 [Exon]

description: Wild type cortex 3


title: PC-3_basalhTERT_ShortTelomeres_mockcre_2

description: mock/cre+


title: PC-3_overexpresshTERT_LongTelomeres_LhTERTL_4

description: LhTERTL

value: present


title: Effect of menadione on mRNA levels in HepG2 cells [men100(2)-4.6]


title: female 54.11909651y #78


title: Plant inoculated with PsJN inactivated, biological rep 3

city: Santiago

first: Andrea

last: Vega

address: Vicuña Mackenna 4860

department: Ciencias Vegetales

country: Chile

institute: Pontificia Universidad Catolica de Chile

description: Gene expression data from plants inoculated with PsJN heated at 13 DAS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Array scanning was carried out with the GeneChip® scanner 300 and image analysis was performed using the GeneChip® Operating Software

data_processing: The data were processed and normalized by RMA using the R package known as “affy”.

organism: Arabidopsis thaliana

source_name: Plant inoculated with PsJN inactivated (104 colony forming units (CFU)/ml) at 13 DAS

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (GeneChip® 3’ IVT Express Kit User Manuall, 2008, Affymetrix).

growth_protocol: Col-0 A. thaliana seedswere surface sterilized with 50% sodium hypochlorite (100% commercial laundry bleach) containing 0.1% Tween 20, rinsed three times with sterile water, and kept at 4°C for 4 days to synchronize germination. Then, seeds were sown on square Petri dishes with half strength Murashige and Skoog medium (MS) 0.8% agar, inoculated or not with of strain PsJN (104 CFU/ml). To assess the effect of inactivated bacteria, an inoculum was heated at 95°C for 20 min and then was used at a dilution of 104 CFU/ml. Mortality was corroborated by plate counting. Plates were placed vertically in a growth chamber at 22°C with a photoperiod of 12 h of light and 12 h of dark. At day 13 after sowing (13 DAS) transcriptional profiles were determined.

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

treatment_protocol: For treatment, B. phytofirmans PsJN, kindly provided by A. Sessitsch (AIT, Austria), was routinely grown in minimal saline medium, containing 10 mM fructose, in an orbital shaker (150 rpm) at 30°C. Cell suspensions from each inoculum were then collected and adjusted to approximately 108 colony forming units per millilitre (CFU/ml), as determined by plate counting

tag: ecotype

value: Plantlet

tag: time

value: 13 days after sowing (DAS)

tag: develomental stage

value: plantlets with 4 rosette leaves


title: Plant inoculated with PsJN inactivated, biological rep 1


title: Plant inoculated with PsJN, biological rep 2

description: Gene expression data from plants inoculated with PsJN at 13 DAS

source_name: Plant inoculated with PsJN (104 colony forming units (CFU)/ml) at 13 DAS


title: Plant inoculated with PsJN, biological rep 3


title: Ptbp2 KO cortex 3 [Exon]

description: Ptbp2 KO cortex 3


title: Effect of menadione on mRNA levels in HepG2 cells [men100(1)-4.5]


title: Plant inoculated with PsJN inactivated, biological rep 2


title: female 51.01437372y #79


title: male 58.37919233y #84


title: Plant inoculated with PsJN, biological rep 1


title: PC-3_overexpresshTERT_LongTelomeres_LhTERTL_1

description: LhTERTL


title: PC-3_basalhTERT_ShortTelomeres_mockcre_1

description: mock/cre+


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(3)-4.7]

value: Control


title: male 52.862423y #75


title: female 57.9247091y #77


title: PC-3_overexpresshTERT_LongTelomeres_LhTERTL_3

description: LhTERTL


title: PC-3_overexpresshTERT_LongTelomeres_LhTERTL_2

description: LhTERTL


title: female 69.11430527y #76


title: female 49.78234086y #74


title: Effect of menadione on mRNA levels in HepG2 cells [men100(3)-4.8]

value: 100µM Men


title: Plants not inoculated, biological rep 3

description: Gene expression data from plants not inoculated at 13 DAS

source_name: Plants not inoculated with bacterium at 13 DAS


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(1)-4.1]


title: female 65.88364134y #73


title: female 62.49691992y #80


title: Plants not inoculated, biological rep 2


title: PC-3_basalhTERT_ShortTelomeres_mock_4

description: mock


title: female 66.98973306y #72


title: Plants not inoculated, biological rep 1


title: PC-3_basalhTERT_ShortTelomeres_mock_2

description: mock


title: PC-3_basalhTERT_ShortTelomeres_mock_3

description: mock


title: Effect of menadione on mRNA levels in HepG2 cells [men100(3)-2.8]


title: PC-3_basalhTERT_ShortTelomeres_mock_1

description: mock


title: Effect of menadione on mRNA levels in HepG2 cells [men100(2)-2.6]


city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

country: Germany

institute: Hannover Medical School

description: Gene expression data FPV-infected HUVEC in the presence of SB 202190, biological rep2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with (GCOS) version 1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: cRNA were prepared and biotin-labeled according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) from 5 ug total RNA.

extract_protocol: Total RNA was isolated using the RNeasy Kit (Qiagen) according to the manufacturer's instruction.

value: human umbilical vein endothelial cells


description: Gene expression data FPV-infected HUVEC in the presence of SB 202190, biological rep3


title: male 49.47843943y #71

value: male

value: blood


title: Effect of menadione on mRNA levels in HepG2 cells [men100(1)-2.5]


title: female 62.63107461y #70

value: female


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(3)-2.7]


title: Sample 59_left_treated

city: Oslo

first: Syed

last: Nuruddin

address: Ullevalsveien 72

department: Production animal clinical sciences

country: Norway

institute: Norwegian school of veterinary science

description: Sample 59

hyb_protocol: Hybridization was performed following protocols from Agilent; in brief, 300 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 X 15 K array slide (Agilent 019921) containing eight arrays with 15,208 oligomers with a length 60 bases corresponding to 15,208 sheep probes and hybridized at 650 C for 17h at 10 rpm. The arrays were washed, dried, and stabilized.

scan_protocol: Scanned with a GenePix® 4000B two-color scanner (Axon instrument, Foster City, CA).

data_processing: Two channel images were imported into the Agilent's Feature Extraction 9.1 software for feature (spot) finding and alignment. Total analysis was done in R-statistical software by using Bioconductor package LimmaGUI. For within-array and between array normalization, print tip Loess and simple scale normalization were used, respectively (Smyth, G.K., Speed, T., 2003. Normalization of cDNA microarray data. Methods 31, 265-273).

organism: Ovis aries

source_name: Amygdala, female, left, GnRHa treated

label_protocol: A dye-swap design was applied. This means that within each group, DNase-treated RNA was labeled with Cyanine 3 (Cy3) CTP and Cyanine 5 (Cy5) CTP to exclude effects due to the dyes with the Quick Amp Labeling Kit, two-color (5190-0444, New Castle, DE) according to their methodology, purified with the Qiagen RNeasy kit (Valencia, CA) according to Agilent's revision of the Qiagen protocol as shown in the Quick Amp kit protocol except that the microcentrifugation spins were performed at room temperature instead of 4oC. The resulting labeled cRNA was analyzed with the NanoDrop spectrophotometer, and the specific activities and the yields of cRNAs were calculated; these ranged from 9.25 to 28.54 pmol pmol Cy3/Cy5 µg cRNA RNA and from 1.1 to11.65 µg, respectively. The labeled cRNA was stored at -80o C until use.

growth_protocol: Lambs were born between 17th March and 1st April 2008 and remained with their dams until weaned at about 12 weeks of age. Males and females were maintained separately during the entire study period. Within each set of twins, one was randomly assigned, at birth, to the control (C) and the other to the treatment (T) group.

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

treatment_protocol: Animals in the treatment group received subcutaneous implants of the GnRH analog Goserelin acetate (Zoladex; kindly donated by Astra Zeneca; Macclesfield, UK 3.6 mg) every 4 weeks from 8 weeks of age in males and 28 weeks of age in females. The differences in the timing of treatment initiation between males and females was instigated as puberty in sheep, as in humans, is sexually dimorphic, and this treatment paradigm was designed so that the pharmacological inhibition of GnRH action should begin approximately 2 weeks before the predicted time of onset of pubertal development in both rams and ewes.

tag: breed

value: Scottish Mule Texel Cross Breed

tag: age

value: 50 weeks

value: amygdala

tag: side of amygdala

value: left

tag: treatment

value: gonadotropin-releasing hormone agonist (GnRHa)

tag: twin pair

value: same twin pair as samples 45 and 46

source_name: Pooled RNA from amygdala samples of all sexes and sides

value: male, female

value: left, right

value: GnRHa, none

tag: sample type

value: reference


title: female 59.42505133y #68

tag: gender


title: Sample 60_right_treated

description: Sample 60

source_name: Amygdala, female, right, GnRHa treated

value: right


title: female 52.07392197y #69

tag: age (y)


title: FPV-infected HUVEC, biological rep3

description: Gene expression data FPV-infected HUVEC, biological rep3

source_name: FPV-infected HUVEC, biological rep3


title: KG1_TatSF2G48R57A [array 1 of 2]

city: BOSTON

first: NAYOUNG

last: KIM

state: MA

address: 61 BINNEY

department: MEDICINE

institute: BOSTON CHILDREN'S HOSPITAL

description: comparison of enrichment ratio of IP samples from cells infected with Ad-TatSF2G48R57A and input DNA in KG-1 cells

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols.

scan_protocol: The microarrays (Design ID - 014706 and 014707) have probes for about 17,000 human promoters. Arrays were then washed using standard Agilent protocols and scanned using an Agilent DNA microarray scanner BA.

data_processing: The value is log2R normalized using loess.  The limma package in Bioconductor (R) was used for loess normalization.

source_name: Tat ChIP DNA from KG-1 cells

label_protocol: Amplified DNA was labeled and purified using Bioprime random primer labeling kits (Invitrogen, immunoenriched DNA was labeled with Cy5 fluorophore, whole cell extract DNA was labeled with Cy3 fluorophore). Labeled DNA was mixed and hybridized to Agilent Human Promoter ChIP-on-chip Microarray Set for 20 hours at 40°C.

growth_protocol: KG-1 cells were differentiated into dendritic cells with GM-CSF, IL-4 and TNF-alpha

extract_protocol: 5x10E7 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in nanodrop UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and incubated overnight with with protein G magnetic beads (Invitrogen) coupled to anti-FLAG (Sigma M2) monoclonal antibodies at 4C. The immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 200 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

treatment_protocol: KG-1 cells were infected with adeno virus expressing TatSF2G48R57A tagged with FLAG

tag: genotype/variation

value: Ad-TatSF2G48R57A, the mutant that does not go to the nucleus (via infection with adenovirus construct)

tag: cell line

value: CD34+ myelomonocytic cell line KG-1

tag: growth protocol

value: KG-1 cells were differentiated into DCs

tag: chip antibody

value: FLAG (Sigma M2)

source_name: Input DNA from KG-1 cells

treatment_protocol: KG-1 cells were not infected

value: control (no infection)

value: none (input DNA)


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(2)-2.2]

tag: compound, dose

value: Control

tag: time (h)


title: FPV-infected HUVEC, biological rep2

description: Gene expression data FPV-infected HUVEC, biological rep2

source_name: FPV-infected HUVEC, biological rep2

tag: cell type

value: human umbilical vein endothelial cells


description: Gene expression data FPV-infected HUVEC in the presence of SB 202190, biological rep1


title: Effect of menadione on mRNA levels in HepG2 cells [Men100(2)-1.6]

value: 100µM Men


title: Sample 58_right_treated

description: Sample 58

value: Scottish Mule Texel Cross Breed

value: 50 weeks

value: female

tag: tissue

value: amygdala

value: same twin pair as samples 43 and 44


title: Effect of menadione on mRNA levels in HepG2 cells [men100(3)-1.8]


title: FPV-infected HUVEC, biological rep1

description: Gene expression data FPV-infected HUVEC, biological rep1

source_name: FPV-infected HUVEC, biological rep1


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(1)-2.1]

source_name: hepatocellular carcinoma cell line


title: male 61.71937029y #63

value: male

value: blood


title: female 60.7008898y #66


title: female 51.23066393y #65


title: Sample 54_right_treated

description: Sample 54

value: right

value: gonadotropin-releasing hormone agonist (GnRHa)

value: same twin pair as samples 39 and 40

value: male, female

value: left, right

value: GnRHa, none

value: reference


title: Sample 56_right_treated

description: Sample 56

value: same twin pair as samples 41 and 42


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(3)-1.7]

value: Control


title: Sample 57_left_treated

description: Sample 57

value: left


title: KG1_tTA [array 1 of 2]

description: comparison of enrichment ratio of IP samples from cells infected with Ad-tTA control and input DNA in KG-1 cells

treatment_protocol: KG-1 cells were infected with adeno virus expressing tTA tagged with FLAG

value: Ad-tTA control (via infection with adenovirus construct)

value: CD34+ myelomonocytic cell line KG-1

value: KG-1 cells were differentiated into DCs

value: FLAG (Sigma M2)

value: control (no infection)

value: none (input DNA)


title: Sample 53_left_treated

description: Sample 53

value: Scottish Mule Texel Cross Breed

value: 50 weeks

value: female

value: amygdala


title: control HUVEC biological rep3

description: Gene expression data control HUVEC biological rep3

source_name: control HUVEC biological rep3

value: human umbilical vein endothelial cells


title: control HUVEC biological rep1

description: Gene expression data control HUVEC biological rep1

source_name: control HUVEC biological rep1


title: female 58.08350445y #67

value: blood


title: Sample 52_right_treated

description: Sample 52

value: right

value: gonadotropin-releasing hormone agonist (GnRHa)

value: same twin pair as samples 35 and 36

value: male, female

value: left, right

value: GnRHa, none


title: Effect of menadione on mRNA levels in HepG2 cells [Men_contr(2)-1.2]

value: Control


title: Effect of menadione on mRNA levels in HepG2 cells [Men100(1)-1.5]

value: 100µM Men


title: Sample 55_left_treated

description: Sample 55

value: left

value: same twin pair as samples 41 and 42

value: reference


title: control HUVEC biological rep2

description: Gene expression data control HUVEC biological rep2

source_name: control HUVEC biological rep2


title: male 53.64271047y #64

value: male


title: Effect of menadione on mRNA levels in HepG2 cells [Men100(2)-30.6]


title: Effect of menadione on mRNA levels in HepG2 cells [men100(3)-30.8]


title: male 47.55099247y #61


title: male 51.31827515y #62


title: Sample 51_left_treated

description: Sample 51

value: Scottish Mule Texel Cross Breed

value: 50 weeks


title: PC-3_basalhTERT_LongTelomeres [LhTERTL/cre+]

description: LhTERTL/cre+

source_name: Human prostate cancer cell line

growth_protocol: The cell line was cultured in vitro in 10cm dishes until 80-90% confluency and then total RNA was isolated.

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

value: PC-3 prostate cancer cell line

tag: htert status

value: basal hTERT

tag: telomere status

value: Long telomeres


title: Effect of menadione on mRNA levels in HepG2 cells [Men_contr(1)-1.1]


title: PC-3_basalhTERT_ShortTelomeres [mock/cre+]

description: mock/cre+

value: Short telomeres


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(2)-4.2]


title: female 82.44490075y #60

value: female

value: blood


title: PC-3_basalhTERT_ShortTelomeres [mock]

description: mock


title: PC-3_overexpresshTERT_LongTelomeres [LhTERTL]

description: LhTERTL

value: overexpress hTERT


title: Sample 48_right_treated

description: Sample 48

tag: breed

tag: age

value: amygdala

value: right

value: gonadotropin-releasing hormone agonist (GnRHa)

value: same twin pair as samples 31 and 32

value: male, female

value: left, right


title: Effect of menadione on mRNA levels in HepG2 cells [Men_contr(2)-30.2]

value: Control


title: female 53.5523614y #58


title: Effect of menadione on mRNA levels in HepG2 cells [Men100(1)-30.5]

value: 100µM Men


title: Sample 49_left_treated

description: Sample 49

value: Scottish Mule Texel Cross Breed

tag: side of amygdala

value: left

tag: treatment

value: same twin pair as samples 33 and 34

value: GnRHa, none

value: reference


title: Effect of menadione on mRNA levels in HepG2 cells [Men_contr(1)-30.1]


title: Effect of menadione on mRNA levels in HepG2 cells [men_contr(3)-30.7]


title: female 57.20465435y #59


title: Sample 47_left_treated

description: Sample 47

value: 50 weeks

tag: twin pair

tag: sample type


title: female 75.3100616y #57

tag: gender

value: female

tag: age (y)


title: High POP Exposure, Sample 4

city: Washington DC

first: Sisir

middle: K.

last: Dutta

address: 415 College Street, NW

department: Biology

institute: Howard University

description: Gene expression data from the Child with high exposure of POPs.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human 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 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: 45-month-old Slovak child, high POP exposure

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

extract_protocol:
Child blood (2.5cc) drawn by venipuncture and directly collecetd in the Collection Tube of PAXgene Blood RNA Kit IVD.
Extraction of total RNA was performed by Qiagen PAXgene Blood RNA Kit IVD according to the manufacturer's instructions.

treatment_protocol: Child with High POPs Exposure

tag: ethnicity

value: Slovak

value: 45 months

value: blood

tag: exposure

value: high POP exposure


title: Sample 46_right_control

description: Sample 46

source_name: Amygdala, female, right, untreated control

value: amygdala

value: right

value: same twin pair as samples 59 and 60


title: Sample 45_left_control

description: Sample 45

source_name: Amygdala, female, left, untreated control

value: male, female

value: left, right


title: female 60.94182067y #55


title: High POP Exposure, Sample 5


title: High POP Exposure, Sample 1


title: High POP Exposure, Sample 3


title: male 59.6440794y #54

value: male


title: female 64.17522245y #53


title: Sample 43_left_control

description: Sample 43

value: Scottish Mule Texel Cross Breed

value: same twin pair as samples 57 and 58


title: Pig 23

city: Winnipeg

first: Charles

middle: K

last: Nfon

state: Manitoba

address: 1015Arlington Street

department: Science Branch

country: Canada

institute: Canadian Food Inspection Agency

description: Gene expression in lungs at DPI29

hyb_protocol: 1.0 ug of Cy3-labelled cRNA (specific activity 6.0 pmol Cy3/ug cRNA)

scan_protocol: Microarray slides were scanned on G2565C DNA scanner

data_processing:
The scanned images were analyzed with Agilent Feature Extraction software version 10.7
R version 2.10.0 (2009-10-26) with arrayQualityMetrics_2.4.3
GeneSpring GX 11.0.1
QC:
Intensity files were loaded into R using gMeanSignal as green channel foreground, gBGUsed as green
channel background.
Density plot was generated called 'Gdensities.png'
log2 intensity boxplot was generated called 'Gboxplot.png'
Analysis:
Intensity files were loaded into GeneSpring.
Threshold: 1.0
Logbase: 2
Normalization: Quantile
Baseline Transformation: median of all samples

organism: Sus scrofa

source_name: Lung from Zaire ebolavirus-infected pig euthanized at day 29 post infection (DPI29)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500ug RNA, Labelling protocol version GE1 v6.0

extract_protocol: Lung sections from euthanized control and Zaire ebolavirus-infected pigs were homogenized in MEM using a bead mill homogenizer and total RNA using Tripure Reagent (Roche; Laval, QC, Canada) according to manufacturer’s protocol.

value: lung section

tag: age at infection

value: 3 weeks


title: Sample 44_right_control

description: Sample 44

value: GnRHa, none

value: reference


title: male 61.95208761y #51


title: KG1_TatSF2 [array 1 of 2]

description: comparison of enrichment ratio of IP samples from cells infected with Ad-TatSF2 and input DNA in KG-1 cells

treatment_protocol: KG-1 cells were infected with adeno virus expressing TatSF2 tagged with FLAG

tag: genotype/variation

value: Ad-TatSF2 (via infection with adenovirus construct)

tag: cell line

value: CD34+ myelomonocytic cell line KG-1

tag: growth protocol

value: KG-1 cells were differentiated into DCs

tag: chip antibody

value: FLAG (Sigma M2)

value: control (no infection)

value: none (input DNA)


title: Pig 22

description: Gene expression in lungs at DPI29

tag: tissue


title: female 64.41889117y #52

value: female

value: blood


title: Pig 19

description: Gene expression in lungs at DPI28

source_name: Lung from Zaire ebolavirus-infected pig euthanized at day 28 post infection (DPI28)


title: High POP Exposure, Sample 2

value: Slovak

value: 45 months

value: high POP exposure


title: female 61.97125257y #50


title: male -9y #49

source_name: male -9y

value: male


title: Pig 17

description: Gene expression in lungs at DPI28


title: Sample 42_right_control

description: Sample 42

value: Scottish Mule Texel Cross Breed

value: 50 weeks

value: amygdala

value: right

value: same twin pair as samples 55 and 56

source_name: Pooled RNA from amygdala samples of all sexes and sides

value: male, female

value: left, right


title: Pig 20

description: Gene expression in lungs at DPI21

source_name: Lung from Zaire ebolavirus-infected pig euthanized at day 21 post infection (DPI21)

value: lung section

value: 3 weeks


title: Pig 21

description: Gene expression in lungs at DPI21


title: male 73.11704312y #48


title: male 57.50581793y #56


title: male 48.84325804y #47


title: Sample 37_left_control

description: Sample 37

source_name: Amygdala, male, left, untreated control

value: left

value: same twin pair as samples 27 and 28

value: GnRHa, none

value: reference


title: Sample 39_left_control

description: Sample 39

value: female

value: same twin pair as samples 53 and 54


title: Sample 41_left_control

description: Sample 41


title: Sample 36_right_control

description: Sample 36

value: same twin pair as samples 51 and 52


title: Pig 18

description: Gene expression in lungs at DPI7

source_name: Lung from Zaire ebolavirus-infected pig euthanized at day 7 post infection (DPI7)

value: 5 weeks


title: Sample 40_right_control

description: Sample 40

value: Scottish Mule Texel Cross Breed


title: female 52.183436y #46

value: blood


title: Sample 32_right_control

description: Sample 32

value: 50 weeks

value: amygdala

value: same twin pair as samples 47 and 48


title: Pig 13

description: Gene expression in lungs at DPI5

source_name: Lung from Zaire ebolavirus-infected pig euthanized at day 5 post infection (DPI5)


title: Sample 38_right_control

description: Sample 38

source_name: Amygdala, male, right, untreated control

value: male

value: right

value: male, female


title: Sample 33_left_control

description: Sample 33

value: same twin pair as samples 49 and 50

value: left, right


title: Pig 12

description: Gene expression in lungs at DPI7

value: lung section


title: female 59.93976728y #45


title: Pig 14

description: Gene expression in lungs at DPI7


title: male 78.73511294y #43


title: Pig 11

description: Gene expression in lungs at DPI5


title: Pig 10

description: Gene expression in lungs at DPI3

source_name: Lung from Zaire ebolavirus-infected pig euthanized at day 3 post infection (DPI3)


title: male 47.22792608y #40


title: female 58.9486653y #44


title: Sample 35_left_control

description: Sample 35

value: left

value: GnRHa, none


title: female 81.86173854y #42

value: female


title: Pig 9

description: Gene expression in lungs at DPI3


title: Sample 29_left_control

description: Sample 29

value: same twin pair as samples 25 and 26

value: reference


title: female 55.59479808y #39


title: Sample 31_left_control

description: Sample 31


title: male 72.3449692y #41


title: ctrl Pig 3

description: Gene expression in naïve lungs

source_name: Lung from mock-infected control pig

value: 5 weeks


title: Sample 30_right_control

description: Sample 30

value: Scottish Mule Texel Cross Breed


title: ctrl Pig 1

description: Gene expression in naïve lungs


title: female 57.63449692y #38

value: blood


title: Sample 34_right_control

description: Sample 34

value: 50 weeks


title: Sample 28_right_treated

description: Sample 28

source_name: Amygdala, male, right, GnRHa treated

value: amygdala

value: gonadotropin-releasing hormone agonist (GnRHa)

value: same twin pair as samples 37 and 38


title: male 80.72826831y #37

value: male


title: ctrl Pig 2

description: Gene expression in naïve lungs


title: male 53.79876797y #36


title: Sample 27_left_treated

description: Sample 27

source_name: Amygdala, male, left, GnRHa treated

value: male, female


title: Sample 26_right_treated

description: Sample 26

value: right

value: same twin pair as samples 29 and 30


title: Sample 50_right_treated

description: Sample 50

source_name: Amygdala, female, right, GnRHa treated

value: same twin pair as samples 33 and 34

value: left, right


title: Sample 25_left_treated

description: Sample 25

value: left

value: GnRHa, none


title: V. campbellii, WT, biological rep3

first: Baochuan

last: Lin

address: 4555 Overlook Avenue, S. W.

department: Center for Bio/Molecular Science & Engineering

institute: US Naval Research Laboratory

hyb_protocol: The cocktail was hybridized onto the Custom design Vharveyi520694 arrays (affymetrix). Hybridization was carried out for 16 h at 49 °C with rotation at 60 rpm. The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip 7G Scanner.

scan_protocol: The microarrays were then washed and stained using the Affymetrix GeneChip Fluidics Station 450 and scanned using the GeneChip Scanner 3000.   GeneChip® Operating Software 1.2 (GCOS 1.2) (Affymetrix) was used to acquire and process array images, determine the quantity and presence or absence of a transcript using the Microarray Suite 5.0 (MAS5) algorithm, and generated the Report files summarizing the quality of target detection for each microarray.

data_processing: CEL files were processed using the Bioconductor affy package.

organism: Vibrio campbellii

source_name: ATCC® BAA-1116

label_protocol: Target Preparation and Hybridization to Arrays: 600ng of mRNA contained PolyA RNA controls (Affymetrix, Santa Clara, CA) with known concentrations to monitor the quality of the procedures. The labeling reaction is carried out in 30 uL reaction volume using KREATECH’s aRNA Labeling Kit (KREATECH Biotechnology, Amsterdam, the Netherlands) according to the manufacture’s recommended protocol. Labeled mRNAs were purified and fragmented using fragmentation buffer from Ambion (Austin, TX). Fragmentation from reaction was carried out in a reaction volume of 33 uL containing 1x fragmentation buffer (Ambion), labeled mRNA, and incubated at 70oC for 15 minutes. After incubation, the reaction is stopped by adding 1 uL stop solution.

growth_protocol: Six total cultures (three biological replicates of the wild type (STR) V. campbellii BAA-1116 and hmgA mutanats were seeded with 1.0E+5 mid-log phase bacteria/mL in 50 mL of LM medium and 125 mL baffled Erlenmeyer flasks. Cultures were incubated at 30°C and 200 rpm for 48 h and then harvested for total RNA extraction.

extract_protocol: Total RNA were extracted using RiboPure Bacteria Kit (Ambion Inc., Austin, TX) according to the manufacturer's instructions.  The quality and quantity of RNA samples were determined using RNA 6000 Nano kit with 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA) and NanoDrop ND2000 (Thermo Scientific Inc., Waltham, MA) spectrophotometer.  The RNA samples were accepted for mRNA enrichment if the A260/A280 ratios were between 1.9-2.1, the ratio of intensities of the 23S and 16S rRNA were 1.5-2.5: 1 and the RNA integrity no. is between 7 and 10.    mRNA enrichment were performed with 10 ug total RNA using using the MICROBExpress kit (Ambion) according to the manufacturer’s protocol. The quantity of mRNA samples were determined by NanoDrop ND2000 (Thermo Scientific Inc., Waltham, MA) spectrophotometer.

treatment_protocol: Compare wild type versus mutant, no treatment difference

tag: growth phase

value: Log phase

value: wild type


title: female 63.19780972y #35

value: female


title: V. campbellii, hmg mutant, biological rep1

description: Vcampbellii_BAA1116_hmg mutant_1

value: hmg mutant


title: Sample 23_left_treated

description: Sample 23

tag: breed

value: Scottish Mule Texel Cross Breed

value: same two pair as samples 11 and 12 (sample 11 was not used as RIN number was too low)

value: reference


title: JHH-4 microRNA

city: Tokyo

first: Johji

last: Inazawa

address: 1-5-45 Yushima, Bunkyo-ku

institute: Tokyo Medical & Dental University

description: Endogeneous miRNA expression

hyb_protocol: Each Cy3-labelled cRNAs were dried up and resuspended in 18 ul of DNase/RNase free water, 4.5 ul of 10× Gene Expression Blocking Agent and 22.5 ul of 2×Hi-RPM Hybridization Buffer, and incubate at 100°C for 5 min and hybridized to AgilentHuman miRNA microarray 8×15K Version 3, miRBase 12.0 (GA4471A) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 021827_D_F_20100604) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNAs were prepared from 100 ng RNA using the Agilent miRNA Complete Labeling and Hyb kit (Agilent according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: cell lines were maintained in appropriate media, D-MEM medium  or RPMI-1640 medium supplemented with 10%fetal bovine serum.

extract_protocol: Total RNAs were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. The protocol includes clean up step after DNaseI (TaKaRa, Shiga, Japan) digestion. RNAs were quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: normal coditioned cell lines and normal liver samples derived from frozen primary tumors were used.

value: HCC cell line


title: V. campbellii, hmg mutant, biological rep2

description: Vcampbellii_BAA1116_hmg mutant_2


title: V. campbellii, hmg mutant, biological rep3

description: Vcampbellii_BAA1116_hmg mutant_3


title: V. campbellii, WT, biological rep1

description: V campbellii-BAA1116_1


title: male 53.37166324y #34

value: blood


title: female 59.78918549y #33


title: V. campbellii, WT, biological rep2


title: Huh7 microRNA

description: Endogeneous miRNA expression


title: male 70.21218344y #31

value: male


title: Sample 20_right_treated

description: Sample 20

tag: age

value: 50 weeks

value: amygdala

value: gonadotropin-releasing hormone agonist (GnRHa)

value: same twin pair as samples 7 and 8

value: male, female


title: HLE microRNA

description: Endogeneous miRNA expression

source_name: HLE

value: HLE


title: Sample 17_left_treated

description: Sample 17

tag: side of amygdala

value: left

value: same twin pair as samples 5 and 6

value: left, right

value: GnRHa, none


title: male 65.19917864y #32


title: male 53.71389459y #29


title: Sample 21_left_treated

description: Sample 21

tag: treatment

value: same two pair as samples 9 and 10 (sample 10 was not used as RIN number was too low)


title: sK-Hep-1 microRNA

description: Endogeneous miRNA expression


title: Sample 19_left_treated

description: Sample 19

value: Scottish Mule Texel Cross Breed

tag: twin pair


title: C40 microRNA

description: Endogeneous miRNA expression

tag: sample type

value: normal liver tissue

value: normal liver


title: male 51.17043121y #28

tag: gender


title: Sample 24_right_treated

description: Sample 24

value: right

value: same two pair as samples 11 and 12 (sample 11 was not used as RIN number was too low)

value: reference


title: male 55.76728268y #30

value: male

tag: age (y)

value: blood


city: Detroit

first: Aliccia

middle: B

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

institute: Karmanos Cancer Inst., Wayne State University

hyb_protocol: Hybridization to 4x44k expression arrays (Agilent slide bar codes: 252665214416 and 252665214415) used the Agilent Gene Expression Hybridization Kit reagents and recommended protocol, and Agilent SureHyb chambers

scan_protocol: GE2-v5_95_Feb07 Agilent G2505B microarray scanner system

data_processing:
Data quality were assessed and data were processed with Agilent Feature Extraction software (version A.9.5.1.1) producing expression data measures including Log10 Ratio expression levels (background subtracted, lowess normalizd), LogRatioError and PValueLogRatio.
lowess normalized log10 ratio test(GN-25 treated) Cy5/reference (vehicle treated) Cy3, LogRatioError and PValueLogRatio

source_name: GN-25 treated Kras-SNAIL-HMLE cell line biological replicate 4 of 4

label_protocol: Labeling reaction used the Low Input Quick Amp Labeling Kit from Agilent Technologies, Inc. following the recommended protocol to produce cRNA for a two-color microarray experiment

growth_protocol: Kras-HMLE or K-ras-HMLE-SNAIL cells were plated so that they reached 75% confluence after 3 days.

extract_protocol: Total RNA was extracted from cell pellets using the Qiagen EZ1 instrument and RNA extraction kit. Total RNA quantity and quality was determined by analysis with the NanoDrop 1000 and Agilent Bioanalyzer (Agilent Technologies,). All analyzed samples had RIN scores ≥ 7.

treatment_protocol: Cell cultures at 75% confluence were treated with or without GN-25 (15 μM). For each cell line, HMLE or HMLE-SNAIL RNA was isolated from four sets of parallel plated plates, treated with or without GN-25, at 24 hours after addition of inhibitor. Media was changed the day after plating and at the start of treatment.

value: breast cell line

source_name: vehicle treated Kras-SNAIL-HMLE cell line biological replicate 4 of 4


title: Hep G2 microRNA

description: Endogeneous miRNA expression

source_name: Hep G2

value: HCC cell line

value: Hep G2


source_name: GN-25 treated Kras-SNAIL-HMLE cell line biological replicate 2 of 4

source_name: vehicle treated Kras-SNAIL-HMLE cell line biological replicate 2 of 4


source_name: GN-25 treated Kras-SNAIL-HMLE cell line biological replicate 3 of 4

source_name: vehicle treated Kras-SNAIL-HMLE cell line biological replicate 3 of 4


title: Sample 16_right_treated

description: Sample 16

value: 50 weeks

value: amygdala

value: gonadotropin-releasing hormone agonist (GnRHa)

value: same twin pair as samples 3 and 4

source_name: Pooled RNA from amygdala samples of all sexes and sides

value: male, female


title: Hep 3B microRNA

description: Endogeneous miRNA expression

source_name: Hep 3B

value: Hep 3B


title: Sample 15_left_treated

description: Sample 15

value: Scottish Mule Texel Cross Breed

value: left

value: left, right

value: GnRHa, none


title: Sample 22_right_treated

description: Sample 22

value: right

value: same two pair as samples 9 and 10 (sample 10 was not used as RIN number was too low)


title: female 48.94455852y #27

value: female


source_name: GN-25 treated Kras-SNAIL-HMLE cell line biological replicate 1 of 4

source_name: vehicle treated Kras-SNAIL-HMLE cell line biological replicate 1 of 4


title: Sample 12_right_control

description: Sample 12

source_name: Amygdala, male, right, untreated control

value: male

value: same two pair as samples 23 and 24

value: reference


title: female 47.32375086y #23

value: blood


title: female 57.62354552y #22


title: male 64.94182067y #24


title: Sample 7_left_control

description: Sample 7

source_name: Amygdala, male, left, untreated control

value: 50 weeks

value: same twin pair as samples 19 and 20


title: female 80.74469541y #26


title: Sample 9_left_control

description: Sample 9

value: amygdala

value: same two pair as samples 21 and 22


title: Sample 14_right_treated

description: Sample 14

source_name: Amygdala, male, right, GnRHa treated

value: gonadotropin-releasing hormone agonist (GnRHa)

value: same twin pair as samples 1 and 2

value: male, female


title: male 48.74195756y #25


title: C20 microRNA

description: Endogeneous miRNA expression

value: normal liver tissue

value: normal liver


title: female 62.13552361y #21


source_name: GN-25 treated Kras-HMLE cell line biological replicate 3 of 4

value: breast cell line

source_name: vehicle treated Kras-HMLE cell line biological replicate 3 of 4


source_name: GN-25 treated Kras-HMLE cell line biological replicate 4 of 4

source_name: vehicle treated Kras-HMLE cell line biological replicate 4 of 4


source_name: GN-25 treated Kras-HMLE cell line biological replicate 2 of 4

source_name: vehicle treated Kras-HMLE cell line biological replicate 2 of 4


source_name: GN-25 treated Kras-HMLE cell line biological replicate 1 of 4

source_name: vehicle treated Kras-HMLE cell line biological replicate 1 of 4


title: Patient 10 Rec

city: Namur

first: jean-pierre

last: gillet

address: 61 Rue de Bruxelles

department: URPhyM

country: Belgium

institute: University of Namur

description: Two samples: taken at diagnosis and at relapse after treatment

scan_protocol: ABI Prism 7900 HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA)

data_processing: SDS files were processed in RQ manager software and raw data were then exported in XLS file

label: FAM

source_name: Acute Myeloid Leukemic Blasts

label_protocol: cDNA was prepared using the High Capacity cDNA kit with RNAse inhibitor (Applied Biosystems, Foster City, CA, USA) as per the manufacturer’s instructions, but no labelling was performed as TaqMan-based qRT-PCR was performed subsequently.

growth_protocol: Clinical samples

extract_protocol: Total RNA was prepared using the Trizol method (Invitrogen, Carlsbad, CA, USA)

treatment_protocol: A: Ara-C; E: Etoposide; N: Novantrone; D: Daunorubicin; T: thioguanin; I: Idarubicin

tag: fab

tag: Sex

value: F

tag: cr (days)

value: A/E/N

tag: os (days)

tag: time of sampling

value: taken relapse after treatment


title: Patient 11 Rec

value: M

value: A/E/I


title: Sample 8_right_control

description: Sample 8

value: Scottish Mule Texel Cross Breed

value: male

value: right

value: left, right

value: GnRHa, none

value: reference


title: male 72.21902806y #20

value: blood


title: Sample 4_right_control

description: Sample 4

value: 50 weeks

value: amygdala

value: same twin pair as samples 15 and 16


title: Patient 9 Rec


title: female 60.77207392y #18

value: female


title: Patient 8 Rec

value: A/D/T


title: Sample 6_right_control

description: Sample 6

value: same twin pair as samples 17 and 18 (sample 18 was not used as RIN number was too low)

value: male, female


title: female 60.32306639y #16


title: male 58.63381246y #19


title: Patient 6 Rec

value: F

value: taken relapse after treatment


title: Sample 5_left_control

description: Sample 5

value: left


title: Patient 7 Rec

value: A/E/I


title: female 51.52361396y #17


title: Sample 1_left_control

description: Sample 1

value: Scottish Mule Texel Cross Breed

value: male

value: same twin pair as samples 13 and 14 (sample 13 was not used as RIN number was too low)


title: female 60.04380561y #15


title: Sample 2_right_control

description: Sample 2

value: right

value: left, right

value: GnRHa, none


title: male 53.43189596y #14

value: blood


title: male 61.21013005y #13


title: female 78.01232033y #12


title: mammary gland _PPARd+GW501516

first: Robert

middle: I

last: Glazer

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

description: Gene expression data from mammary gland in PPARd mice treated with GW501516

hyb_protocol: Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.

scan_protocol: The GeneChip® was scanned using an Agilent Gene Array scanner.

data_processing: Raw data generation was performed with the Affymetrix GeneChip® Operating software 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene. Genes with a signal <300 in all experimental groups were excluded from analysis.

source_name: MMTV-PPARd group treated with 0.005% GW501516

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

growth_protocol: Animal studies were conducted under GUACUC protocol 09-061. Female nulliparious MMTV-PPARd mice and age-matched FVB/wild-type littermates were used in this study.

extract_protocol: Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent). Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).

treatment_protocol: Mice were maintained on standard rodent chow or chow containing 0.005% GW501516 for 1 week

value: mammary gland

tag: genetic background

value: FVB

tag: genotype

value: MMTV-PPARd


title: Patient 5 Rec

value: A/D/T


title: mammary gland _WT+GW501516

description: Gene expression data from mammary gland in WT mice treated with GW501516

source_name: Wild-type group treated with 0.005% GW501516

tag: tissue

value: WT


title: Sample 3_left_control

description: Sample 3

value: 50 weeks

value: amygdala

value: same twin pair as samples 15 and 16

source_name: Pooled RNA from amygdala samples of all sexes and sides

value: male, female

value: reference


title: female 53.98494182y #11

extract_protocol: RNA was stabilized using PAXgene Tubes (Becton Dickinson) and RNA was isolated using the Qiagen PAXgene Blood RNA kit. Quality Control was performed with the Caliper Life Sciences LabChip GX system.

value: female


title: Patient 4 Rec

value: M

value: A/T

value: taken relapse after treatment


title: Patient 3 Rec

value: F

value: A/E/N


title: Patient 2 Rec


title: Patient 11 Diag

value: A/E/I

value: taken at diagnosis


title: Patient 1 Rec


title: mammary gland _PPARd

description: Gene expression data from mammary gland in PPARd mice

source_name: MMTV-PPARd group maintained on standard rodent chow

value: mammary gland

value: FVB


title: female 61.97399042y #9

value: blood


title: KG1_TatSF2 [array 2 of 2]

source_name: Tat ChIP DNA from KG-1 cells

tag: genotype/variation

value: Ad-TatSF2 (via infection with adenovirus construct)

tag: cell line

value: CD34+ myelomonocytic cell line KG-1

tag: growth protocol

value: KG-1 cells were differentiated into DCs

tag: chip antibody

value: FLAG (Sigma M2)

source_name: Input DNA from KG-1 cells

value: control (no infection)

value: none (input DNA)


title: KG1_TatSF2G48R57A [array 2 of 2]

value: Ad-TatSF2G48R57A, the mutant that does not go to the nucleus (via infection with adenovirus construct)


title: KG1_tTA [array 2 of 2]

value: Ad-tTA control (via infection with adenovirus construct)


title: Patient 9 Diag

tag: age

tag: treatment


title: Patient 10 Diag


title: female 60.62696783y #6

value: female


title: male 55.14579055y #10

value: male


title: male 72.06570842y #8


title: mammary gland _WT

description: Gene expression data from mammary gland in WT mice

source_name: Wild-type group maintained on standard rodent chow

value: WT


title: Patient 8 Diag

value: F

value: A/D/T


title: female 56.55030801y #4


title: HepG2 miR-497 24h Ago2-IP

description:
Ago2-IP RNA
miRNA expression after 24h of miR-497 overexpression in Hep G2 Ago2-IP fraction

source_name: Hep G2, miR-497, 24h, Ago2-IP

label_protocol: Cyanine-3 (Cy3) labeled cRNAs were prepared from 10 ng of Ago2-IP RNAs using the Agilent miRNA Complete Labeling and Hyb kit (Agilent according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Hep G2 were maintained in appropriate media, D-MEM medium supplemented with 10%fetal bovine serum.

extract_protocol: Ago2-IP RNA containing lysates from the immunopriticipation, RNA fractions were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. The protocol includes clean up step after DNaseI (TaKaRa, Shiga, Japan) digestion. RNAs were quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were transfected with or without 5 nM of miCENTURY OC miNatural mimicking miR-195 or miR-497(COSMO BIO, Tokyo, Japan) using Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA) . 24hours after transfection, Immunopriticipation with anti-human Argonute 2 was performed using microRNA Isolation Kit, Human Ago2 (Wako, Pure Chemical, Osaka, Japan) according to the manufacturer's instructions.

tag: antibody

tag: antibody manufacturer

value: Wako

value: miR-497 overexpression


title: female 74.03969884y #3

tag: gender

tag: age (y)


title: Patient 7 Diag

tag: fab

tag: Sex

value: A/E/I

value: taken at diagnosis


title: male 59.38945927y #5

value: blood


title: HepG2 miR-195 24h Ago2-IP

description:
Ago2-IP RNA
miRNA expression after 24h of miR-195 overexpression in Hep G2 Ago2-IP fraction

source_name: Hep G2, miR-195, 24h, Ago2-IP

value: miR-195 overexpression


title: female 46.64750171y #7


title: Patient 5 Diag

tag: cr (days)

tag: os (days)


title: Patient 6 Diag

tag: time of sampling


title: Patient 4 Diag

value: M

value: A/T


title: Ptbp2 KO cortex 2 [Matrix junction]

description: Ptbp2 KO cortex 2

scan_protocol: Affymetrix GeneChip Operating Software (GCOS) v1.4; GeneChip Scanner 3000 7G.

data_processing:
The average probe values were obtained using Aspire version 3 (PMID: 20601959).
mjay.r1.pgf

source_name: mouse Ptbp2 knockout cortex

value: cortex

tag: strain

value: CD1 and C57BL/6 mixed background

tag: developmental stage

value: embryonic day 18.5


title: female 57.3744011y #1

tag: tissue


title: Ptbp2 KO cortex 3 [Matrix junction]

description: Ptbp2 KO cortex 3


title: Patient 3 Diag

value: A/E/N


title: female 63.26625599y #2

value: female


title: Patient 2 Diag


title: Wild type cortex 2 [Matrix junction]

description: Wild type cortex 2

source_name: mouse wild type cortex


title: Patient 1 Diag


title: Wild type cortex 3 [Matrix junction]

description: Wild type cortex 3


title: HepG2 NT Ago2-IP

description:
Ago2-IP RNA
miRNA expression of non-treated Hep G2 Ago2-IP fraction

source_name: Hep G2, NT, 24h, Ago2-IP

tag: cell line

value: control


title: Wild type cortex 1 [Matrix junction]

description: Wild type cortex 1


title: Ptbp2 KO cortex 1 [Matrix junction]

description: Ptbp2 KO cortex 1


title: NPC_astro

status: Public on May 30 2013

city: Houston

first: Ying

last: Liu

address: 1825 Pressler

institute: UTHealth

description:
hESC derived cells
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalised using quantile normalisation with GenomeStudio software (Illumina, Inc.)
Background was subtracted and arrays were normalized using quantile. Gene expression levels were considered significant only when their detection p-value ≤0.01.

source_name: Cultured astrocytes derived from NPC

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

growth_protocol: Cultured human cells

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

tag: cell type

value: astrocyte

tag: differentiated from

value: Olig2 negative hESC-derived neural progenitor cells (NPC-Astro)


title: GSK-3 inhibitor 8hours-1

city: Chapel Hill

first: Albert

last: Baldwin

state: NC

address: 450 West Drive

department: LCCC

institute: UNC-Chapel Hill

description: DMSO (vehicle control) for 8hours

hyb_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent G2505C fluorescent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction (v10.5) software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken using Agilent Feature Extraction (v10.5) software.

source_name: Human Reference

tag: sample type

value: Stratagene Human reference RNA

source_name: Human pancreatic tumor explant in nude mice

label_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050)

extract_protocol: Qiagen Rneasy Kit

treatment_protocol: 8hr treatment with drug AR-A014418

value: Patient Primary Pancreatic Tumor explant in mice

value: drug AR-A014418

tag: time

value: 8 h


title: DMSO control 2

description: DMSO (vehicle control) for 8hours

label_protocol: As described in Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp labeling) v 5.7 [Manual G4140-90050]

treatment_protocol: DMSO (vehicle control) for 8hours

tag: treatment


title: GSK-3 inhibitor 2hours-3

description: DMSO (vehicle control) for 8hours

treatment_protocol: 2hr treatment with drug AR-A014418

value: 2 h


title: GSK-3 inhibitor 2hours-2

description: DMSO (vehicle control) for 8hours


title: DMSO control 1

description: DMSO (vehicle control) for 8hours


title: GSK-3 inhibitor 8hours-2

description: DMSO (vehicle control) for 8hours


title: Donor (Sample 20)

city: Townsville

first: Erik

last: Biros

address: James Cook Drive

country: Australia

institute: James Cook University

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using standard normalization procedures recommended for the GeneSpring GX version 11.5.1 software for Illumina single-color array. Probes were filtered based on their flag values using P (present) and M (marginal) flags using standard GeneSpring GX software settings for Illumina single color arrays.

source_name: full thickness aortic wall biopsy

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit (Cat. No. IL1791) for Illumina arrays.

tag: subjects

value: heart-beating, brain-dead donor

tag: tissue type

value: normal aortic tissue


title: Donor (Sample 15)


title: GSK-3 inhibitor 2hours-1

description: DMSO (vehicle control) for 8hours


title: Donor (Sample 21)


title: AAA neck (Sample 13)

value: patient with AAA undergoing open surgery to treat AAA

value: non-aneurysmal AAA neck tissue


title: AAA neck (Sample 10)


title: Donor (Sample 22)


title: AAA neck (Sample 7)


title: AAA neck (Sample 3)


title: AAA neck (Sample 12)


title: Donor (Sample 18)


title: Donor (Sample 16)


title: AAA neck (Sample 6)


title: Donor (Sample 17)


title: AAA neck (Sample 8)


title: AAA neck (Sample 14)


title: AAA neck (Sample 5)


title: AAA neck (Sample 11)


title: AAA neck (Sample 4)


title: Olig2PC_astro

description:
hESC derived cells
replicate 1

source_name: Cultured astrocytes derived from Olig2PC

value: hESC-derived Olig2+ progenitor cells (Olig2PC-Astro)


title: AAA neck (Sample 2)


title: AAA neck (Sample 9)


title: Donor (Sample 19)


title: AAA neck (Sample 1)


title: Scrambled 24 hours_3

first: Ian

last: Mills

address: Gaustadalleen 21

department: Centre for Molecular Medicine Norway

institute: University of Oslo

hyb_protocol: Hybridisation of cRNA onto the Illumina HumanHT-12 v.4 Expression BeadChips (Illumina Inc, California, USA) was carried out as per manufacturer's instructions

scan_protocol: After scanning, the iScan software extracts signal intensities and saves all files for each BeadChip. Raw data is imported to Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0. Here the quality of each array and scan is investigated, and text files with both non-normalized and quantile normalized data exported.

data_processing: Data extraction, quantile normalization and initial quality control of the bead summary raw data were performed using GenomeStudio v2011.1 from Illumina and the Gene Expression module v1.9.0. The data were annotated using the HumanHT-12_V4_0_R2_15002873_B.bgx annotation file from Illumina.

source_name: Scrambled 24 hours_3

label_protocol: Labelling was performed with Illumina® TotalPrep™-96 RNA Amplification Kit according to manufacturer's instructions

growth_protocol: LNCaP cells were maintained in RPMI media supplemented with 10% FBS.

extract_protocol: RNA was collected by illustraMiniSpin (GE Healthcare) according to manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were plated directly on siRNA or drug / vehicle

value: LNCaP


title: ST045849 24 hours_3


title: Vehicle 12 hours_3

source_name: Vehicle 12 hours_3


title: siOGT 24 hours_2

source_name: siOGT 24 hours_2


title: siOGT 12 hours_3

source_name: siOGT 12 hours_3


title: siOGT 12 hours_1

source_name: siOGT 12 hours_1


title: siOGT 12 hours_2

source_name: siOGT 12 hours_2


title: Scrambled 12 hours_3

source_name: Scrambled 12 hours_3


title: Vehicle 24 hours_1

source_name: Vehicle 24 hours_1


title: ST045849 12 hours_3


title: Vehicle 24 hours_2

source_name: Vehicle 24 hours_2


title: Scrambled 24 hours_1

source_name: Scrambled 24 hours_1


title: CRC108 liver metastatic variant, rep#2

city: Shanghai

first: Li

last: Qingquan

address: No.138，Yixueyuan Rd.

country: China

institute: fudan university

description: Gene expression in CRC108LM cells

hyb_protocol: Following Agilent instructions.

scan_protocol: Agilent DNA Microarray Scanner G2567AA.

data_processing: Feature Extraction Software Version A.7.5.1 (Agilent Technologies).

source_name: CRC108LM cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.

treatment_protocol: Cells were cultured in DMEM medium with 10% heat-inactivated fetal bovine serum.

value: colorectal cancer CRC108 liver metastasis cells

tag: subject


title: ST045849 24 hours_1


title: CRC108 pulmonary metastatic variant, rep#3

description: Gene expression in CRC108PM cells

source_name: CRC108PM cells

value: colorectal cancer CRC108 pulmonary metastasis cells


title: Scrambled 12 hours_1

source_name: Scrambled 12 hours_1


title: ST045849 12 hours_2


title: CRC108 liver metastatic variant, rep#3

description: Gene expression in CRC108LM cells


title: siOGT 24 hours_1

source_name: siOGT 24 hours_1


title: Scrambled 24 hours_2

source_name: Scrambled 24 hours_2


title: siOGT 24 hours_3

source_name: siOGT 24 hours_3


title: ST045849 12 hours_1


title: Vehicle 24 hours_3

source_name: Vehicle 24 hours_3


title: ST045849 24 hours_2


title: Vehicle 12 hours_2

source_name: Vehicle 12 hours_2


title: Vehicle 12 hours_1

source_name: Vehicle 12 hours_1


title: CRC108 pulmonary metastatic variant, rep#1

description: Gene expression in CRC108PM cells


title: CRC108 pulmonary metastatic variant, rep#2

description: Gene expression in CRC108PM cells


title: Scrambled 12 hours_2

source_name: Scrambled 12 hours_2


title: colorectal cancer CRC108 cells, rep#2

description: Gene expression in CRC108 cells

source_name: CRC108 cells

value: colorectal cancer CRC108 cells


title: CRC105 pulmonary metastatic variant, rep#2

description: Gene expression in CRC105PM cells

source_name: CRC105PM cells

value: colorectal cancer CRC105 pulmonary metastasis cells


title: colorectal cancer CRC105 cells, rep#2

description: Gene expression in CRC105 cells

source_name: CRC105 cells

value: colorectal cancer CRC105 cells


title: CRC105 liver metastatic variant, rep#2

description: Gene expression in CRC105LM cells

source_name: CRC105LM cells

value: colorectal cancer CRC105 liver metastasis cells


title: CRC108 liver metastatic variant, rep#1

description: Gene expression in CRC108LM cells


title: CRC102 pulmonary metastatic variant, rep#2

description: Gene expression in CRC102PM cells

source_name: CRC102PM cells

value: colorectal cancer CRC102 pulmonary metastasis cells


title: colorectal cancer CRC108 cells, rep#3

description: Gene expression in CRC108 cells


title: colorectal cancer CRC108 cells, rep#1

description: Gene expression in CRC108 cells


title: CRC105 pulmonary metastatic variant, rep#3

description: Gene expression in CRC105PM cells


title: CRC102 liver metastatic variant, rep#2

description: Gene expression in CRC102LM cells

source_name: CRC102LM cells

value: colorectal cancer CRC102 liver metastasis cells


title: colorectal cancer CRC102 cells, rep#2

description: Gene expression in CRC102 cells

source_name: CRC102 cells

value: colorectal cancer CRC102 cells


title: colorectal cancer CRC102 cells, rep#3

description: Gene expression in CRC102 cells


title: CRC105 liver metastatic variant, rep#1

description: Gene expression in CRC105LM cells


title: CRC102 liver metastatic variant, rep#3

description: Gene expression in CRC102LM cells


title: LT269763RL_ILD

city: Pittsburgh

first: John

last: Tedrow

state: PA

address: 3471 Fifth Avenue, Suite 1211

institute: University of Pittsburgh

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was hybridized to the specified arrays as per manufacturer instructions.  Hybridization was in a rotating oven at the specified temperature

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K arrays or 8x60K arrays as noted

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default perameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  The resulting array data was normalized using a cyclic loess approach in pairwise fashion.  Probes were then collapsed to one gene/one probe by highest signal intensity.

source_name: Flash frozen whole lung

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the QuickAmp kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: 30 mg of whole lung was homogenized with Trizol and then total RNA was extracted using the QiaCube system (Qiagen, Valencia CA).  RNA quality was determined by Agilent Bioanalyzer 2100 (Agilent Technologies Inc, Santa Clara, CA) with RIN > 7.0 being acceptable for microarray usage.

tag: disease state

value: Interstitial lung disease

tag: age

tag: gold stage

value: 0-At Risk

tag: smoker?

tag: %predicted fev1 (pre-bd)

tag: %predicted fvc (pre-bd)

tag: %predicted dlco

tag: ild subtype


title: CRC102 pulmonary metastatic variant, rep#3

description: Gene expression in CRC102PM cells


title: CRC105 liver metastatic variant, rep#3

description: Gene expression in CRC105LM cells


title: LT294945LU_COPD

value: Chronic Obstructive Lung Disease

tag: Sex

tag: pneumocystis colonization

value: Negative

tag: %emphysema (f-950)

value: 4-Very Severe COPD

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)


title: CRC105 pulmonary metastatic variant, rep#1

description: Gene expression in CRC105PM cells

tag: cell type


title: LT291673RM_COPD

value: 2-Moderate COPD


title: LT295167LU_COPD


title: LT290165RU_CTRL

value: Control


title: LT291578RU_COPD


title: colorectal cancer CRC105 cells, rep#1

description: Gene expression in CRC105 cells


title: CRC102 liver metastatic variant, rep#1

description: Gene expression in CRC102LM cells


title: CRC102 pulmonary metastatic variant, rep#1

description: Gene expression in CRC102PM cells


title: LT296771LL_ILD


title: colorectal cancer CRC102 cells, rep#1

description: Gene expression in CRC102 cells


title: LT284144LU_COPD


title: colorectal cancer CRC105 cells, rep#3

description: Gene expression in CRC105 cells


title: LT282467LL_COPD

value: Positive

value: 3-Severe COPD


title: LT275856LL_ILD


title: LT282562RM_CTRL


title: LT282031RU_COPD


title: LT277036RU_COPD


title: LT269381RU_ILD


title: LT277772LL_ILD


title: LT271851LU_COPD


title: LT265199LU_COPD


title: LT275526RU_ILD


title: LT271679LU_COPD


title: LT272570RL_CTRL


title: LT265662LU_CTRL


title: LT263234RL_ILD


title: LT274443LU_COPD


title: LT242420LU_COPD


title: LT250549RL_ILD


title: LT262496LU_COPD


title: LT230291LL_CTRL


title: LT230453LU_CTRL


title: LT230267RU_COPD


title: LT230745RM_CTRL


title: LT235584RU_COPD


title: LT230142RL_ILD


title: LT222702LL_ILD

value: 9-Hypersensitive Pneumonitis (HP)


title: LT219681RL_ILD


title: LT220547RL_CTRL


title: LT204017RL_COPD


title: LT206010LU_COPD


title: LT211728RU_COPD


title: LT211015LL_ILD


title: LT203446LL_ILD


title: LT217339RL_ILD


title: LT193936RU_COPD


title: LT191020LI_CTRL


title: LT200251RU_CTRL


title: LT211455LU_ILD


title: LT203431RL_ILD

value: 1-ILD of known cause, hypersensitivity or associated w/ CVD


title: LT218627LL_CTRL


title: LT185066RL_ILD


title: LT203006LL_ILD


title: LT184347RU_COPD


title: LT195192RL_ILD


title: LT174536LU_COPD


title: LT169564RU_COPD

value: 1-Mild COPD


title: LT163657RL_ILD


title: LT161707RU_COPD


title: LT185119LL_ILD


title: LT171905RL_ILD


title: LT166493RM_ILD


title: LT160089RU_COPD


title: LT188510RM_ILD


title: LT180758RM_ILD


title: LT168219RL_ILD


title: LT166565RU_COPD


title: LT152979LL_COPD


title: LT150340LU_COPD


title: LT159457LL_ILD


title: LT150981RU_COPD


title: LT154455RU_ILD


title: LT145086RU_COPD


title: LT145162RM_COPD


title: LT131887LL_ILD


title: LT139008LU_ILD


title: LT121841RU_COPD


title: LT132625RU_COPD


title: LT131432RU_COPD


title: LT142933RU_ILD


title: LT123457RU_COPD


title: LT121928RL_ILD


title: LT130350RU_COPD


title: LT144462RU_COPD


title: LT127070RL_COPD


title: LT125775RU_COPD


title: LT126571RU_COPD


title: LT123313RM_CTRL


title: LT147658RU_COPD


title: LT126293RU_COPD


title: LT133029RM_ILD


title: LT121014LL_ILD


title: LT128262RU_ILD


title: LT205707LL_ILD

value: 5-Respiratory bronchiolitis-interstitial lung disease (RB-ILD)


title: LT112339LI_COPD


title: LT118519RL_ILD

value: 4-Desquamative interstitial pneumonia (DIP)


title: LT106561LL_ILD


title: LT118098LU_ILD


title: LT109321RL_ILD


title: LT106997RU_CTRL


title: LT112491RM_ILD


title: LT111701RL_ILD


title: LT089958RL_ILD


title: LT178986RU_CTRL


title: LT105618RL_ILD


title: LT119300LU_ILD


title: LT113077LL_COPD


title: LT104717LL_ILD


title: LT084831RU_COPD


title: LT110408RU_COPD


title: LT106557LU_COPD


title: LT100654RL_ILD


title: LT107185RU_ILD

value: 7-Cryptogenic Organizing Pneumonia (COP)


title: LT086542RL_COPD


title: LT093665LI_ILD


title: LT081077RU_COPD


title: LT085240RU_COPD


title: LT100984RL_COPD


title: LT096554LU_COPD


title: LT090283LL_ILD


title: LT083491LU_ILD


title: LT073436LU_CTRL


title: LT075917RU_COPD


title: LT072789RU_ILD


title: LT070021RU_COPD


title: LT056024RL_ILD


title: LT059224RL_COPD


title: LT048637LL_ILD


title: LT079013RU_COPD


title: LT056627RU_COPD


title: LT051993RU_COPD


title: LT051568RU_COPD


title: LT060406RL_COPD


title: LT050246RU_COPD


title: LT049193LU_ILD


title: LT056301LL_ILD


title: LT066309LL_ILD


title: LT038591LU_COPD


title: LT042988LU_COPD


title: LT032411RU_COPD


title: LT059865RU_COPD


title: LT038075LL_COPD


title: LT024952RU_COPD


title: LT026458RL_COPD


title: LT046103LU_COPD


title: LT055841LL_ILD


title: LT047521RL_ILD


title: LT024857LU_ILD


title: LT009615LU_CTRL


title: LT046180RU_COPD


title: LT032775RU_COPD


title: LT045399RL_CTRL


title: LT009099RL_COPD


title: LT010491LL_COPD


title: LT001098RU_COPD


title: LT013743LL_ILD


title: LT007392RU_COPD


title: LT288719RL_ILD


title: LT295717RL_ILD


title: LT287196LL_ILD


title: LT286644RL_ILD


title: Control morpholino replicate 3

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

description: scrambled sequence of Ezh2 ATG MO

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented, combined with Agilent Hi-RPM Hybridization Buffer, and hybridized at 65C for 17 hours, then was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; room temperature) for 1 minute each, and finally dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing:
TIF files from microarray scanner processed using Agilent Feature Extraction software version 10.5.1.1.
Control features and non-uniform features were removed, and remaining values for each unique probe sequence were averaged, then log (base 2) transformed.
Log base 2 intensities were median centered between arrays.

organism: Xenopus laevis

source_name: Embryonic Xenopus control morpholino eyes

label_protocol: Agilent One-Color Quick Amp Labeling Protocol

extract_protocol: Total RNA extracted using Qiagen RNEasy mini kit

tag: tissue

value: embryonic eyes


title: LT291449RL_COPD


title: Control morpholino replicate 2

description: scrambled sequence of Ezh2 ATG MO


title: LT290677RU_CTRL


title: G05

city: aas

first: Fabian

last: Grammes

address: Arboretvn. 2

department: CIGENE

institute: Norwegian University of Life Sciences

hyb_protocol: Custom printed Agilent oligonucleotide microarrays in the 8x15 format were hybridized with Cy3 labled cRNA according to the manufacturer's protocol (One-color, Microarray-Based Gene Expression Analysis; version 6.5)

scan_protocol: Agilent scanner (G2565BA) with Agilent Feature Extraction Software (v.10.7.1.1) according to Agilents GE1_107_Sep09 protocol)

data_processing: Text files produced by Feature Extraction were analyzed using the statistical software R with Bioconductor package "limma". Control spots were removed and signal intensities (background corrected: gProcessed Signal) were quantile-normalized and log2 transformed.

organism: Salmo salar

source_name: Distal Intestine

label_protocol: The synthesis of cRNA was performed using the Low Input Quick Amp Labeling Kit, One color (Agilent p/n 5190-2305), according to manufacturer's protocol (One-color, Microarray-Based Gene Expression Analysis; version 6.5)

extract_protocol: Tissue samples were stored at -80. Total RNA was extracted by sample homogenization in QUIAzol followed by RNeasy column cleanup (Qiagen) according to the manufacturers protocols.

tag: diet = klyver

value: Lamina propria = 2

value: Epithelium = 1

value: Atrophy = 1

value: Oedema = 0


title: Ezh2 morpholino replicate 3

description: Ezh2 ATG MO siRNA

source_name: Embryonic Xenopus Ezh2 morpholino eyes


title: Control morpholino replicate 4

description: scrambled sequence of Ezh2 ATG MO


title: LT285906LL_COPD

value: Chronic Obstructive Lung Disease

value: Negative


title: Ezh2 morpholino replicate 4

description: Ezh2 ATG MO siRNA


title: LT297451LU_ILD

value: Interstitial lung disease

value: 0-At Risk


title: G09

value: Oedema = 1


title: G06

value: Lamina propria = 1


title: Ezh2 morpholino replicate 1

description: Ezh2 ATG MO siRNA


title: G08

value: Epithelium = 2

value: Atrophy = 2


title: G04


title: LT285031LU_CTRL

value: Control


title: LT282601LL_ILD


title: LT299181LU_ILD


title: G07

value: Lamina propria = 0.5


title: LT280282RL_ILD


title: LT280851LL_ILD


title: G10


title: Ezh2 morpholino replicate 2

description: Ezh2 ATG MO siRNA


title: LT285671LU_ILD

value: 3-Severe COPD

value: 1-ILD of known cause, hypersensitivity or associated w/ CVD


title: Control morpholino replicate 1

description: scrambled sequence of Ezh2 ATG MO

value: embryonic eyes


title: G03

value: Lamina propria = 2


title: LT277811RL_ILD


title: LT266817LL_ILD


title: F10

tag: diet = chlorella

value: Lamina propria = 0

value: Epithelium = 0

value: Atrophy = 0


title: F09

value: Oedema = 0


title: LT256920RU_CTRL

tag: disease state


title: LT259072LU_ILD

tag: age


title: F08


title: F05


title: F07


title: LT264283RL_ILD

tag: gold stage


title: F06


title: LT253677RL_ILD

tag: smoker?


title: G02

value: Atrophy = 1


title: G01

value: Epithelium = 1


title: LT270821RU_CTRL

value: 0-At Risk

tag: %predicted fev1 (pre-bd)


title: LT256221LL_CTRL

tag: %predicted fvc (pre-bd)


title: LT279828RU_ILD

value: Interstitial lung disease

tag: %predicted dlco


title: F03


title: LT253371RL_ILD

tag: ild subtype


title: F04

value: Epithelium = 0.5


title: LT251947LL_ILD

tag: Sex

value: 5-Respiratory bronchiolitis-interstitial lung disease (RB-ILD)


title: F02


title: LT253131RU_COPD

value: Chronic Obstructive Lung Disease

tag: pneumocystis colonization

value: Positive


title: LT251693LL_ILD

tag: %emphysema (f-950)

value: 9-Hypersensitive Pneumonitis (HP)


title: E09

tag: diet = b.yeast

value: Epithelium = 2

value: Atrophy = 2

value: Oedema = 2


title: F01


title: E08

value: Lamina propria = 2

value: Oedema = 1


title: LT249811RU_COPD

value: Negative

value: 2-Moderate COPD

tag: %predicted fev1 (post-bd)

tag: %predicted fvc (post-bd)


title: E10

value: Lamina propria = 1

value: Atrophy = 0

value: Oedema = 0


title: LT249481LU_ILD


title: LT247728RL_CTRL

value: Control

value: 0-At Risk


title: E06


title: E07


title: LT248906LL_ILD

value: Interstitial lung disease


title: E05


title: E03


title: E02


title: LT244824RU_ILD


title: E01

value: Lamina propria = 0.5

value: Epithelium = 1


title: LT245983LU_COPD

value: Chronic Obstructive Lung Disease

value: 4-Very Severe COPD


title: LT244399LU_COPD


title: E04

value: Epithelium = 2


title: LT246349LU_CTRL


title: D06

tag: diet = torula

value: Epithelium = 0


title: LT238765RL_COPD


title: D04

value: Atrophy = 2


title: D07

value: Lamina propria = 0


title: D09


title: LT236519LL_ILD

value: 9-Hypersensitive Pneumonitis (HP)


title: D02

value: Atrophy = 1

value: Oedema = 1


title: D03


title: LT246774RM_CTRL


title: D05


title: LT243794RL_ILD


title: LT236045LL_ILD


title: LT236557RL_CTRL


title: LT242161RL_ILD


title: LT235441RL_ILD


title: D08

value: Lamina propria = 1


title: B03

tag: diet = sbm

value: Lamina propria = 2

value: Oedema = 2


title: B02


title: D01


title: B07


title: LT234755LL_CTRL

value: Control


title: LT237439RU_COPD

value: Negative

value: 2-Moderate COPD


title: A10

tag: diet = fm

value: Atrophy = 0

value: Oedema = 0


title: A09


title: LT234774LU_COPD

tag: disease state

value: Chronic Obstructive Lung Disease


title: B01


title: D10


title: A07


title: A06


title: A08


title: B06


title: B04


title: LT228772LL_ILD

value: Interstitial lung disease

tag: age

value: 0-At Risk


title: LT228897LL_ILD


title: LT234205RL_ILD


title: LT221782LL_ILD


title: LT233821RL_COPD

value: Positive

tag: gold stage

value: 3-Severe COPD


title: LT221983RM_CTRL

tag: smoker?


title: LT232073LU_ILD

tag: %predicted fev1 (pre-bd)


title: LT232107RU_CTRL

tag: %predicted fvc (pre-bd)


title: LT229669RU_COPD

value: 4-Very Severe COPD

tag: %predicted dlco


title: B05

value: Epithelium = 2


title: LT221687RM_ILD

tag: ild subtype


title: LT241811LL_CTRL

tag: Sex


title: ExVivoRPTEC 2

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

description: miRNAs

hyb_protocol: 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: RPTEC

label_protocol: 600 ng of total RNA isolated from each cell lines were first dephosphorylated with a calf intestine alkaline phosphatase treatment for 30 minutes at 37°C before labeling. Samples were diluted with DMSO, denatured for 10 minutes at 100°C and labeled using pCp-Cy3 in T4 RNA ligation buffer. According to the Agilent kit guidelines, 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.

extract_protocol: Total RNA was extracted from a minimum of 10e6 cells/line using the miRNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.

tag: tissue

value: renal proximal tubular cells


title: A05

value: Lamina propria = 0

value: Epithelium = 0


title: A04


title: ExVivoMSC 3

description: miRNAs

source_name: MSC

value: mesenchymal stem cells


title: ExVivoRPTEC 1

description: miRNAs


title: LT213606RL_ILD


title: ExVivoRPTEC 3

description: miRNAs


title: LT223106RU_COPD

tag: pneumocystis colonization

tag: %emphysema (f-950)


title: ExVivoMSC 2

description: miRNAs


title: LT207073RU_ILD


title: ExVivogARPCs 10

description: miRNAs

source_name: SC GLOM

value: glomerular adult renal stem/progenitor cells


title: ExVivoMSC 1

description: miRNAs


title: LT220661RL_ILD


title: LT227135RL_ILD

tag: %predicted fev1 (post-bd)

value: 1-ILD of known cause, hypersensitivity or associated w/ CVD


title: LT206871LU_ILD


title: LT215341RU_COPD

value: Negative


title: LT201831RU_ILD

value: 5-Respiratory bronchiolitis-interstitial lung disease (RB-ILD)


title: A03

value: Atrophy = 0


title: LT204935LL_ILD


title: LT197821RL_CTRL

value: Control

tag: %predicted fvc (post-bd)


title: A02

value: Oedema = 0


title: LT221381RL_ILD

value: Interstitial lung disease


title: LT201348LL_ILD


title: A01


title: LT200930RL_COPD

value: Chronic Obstructive Lung Disease

value: 2-Moderate COPD


title: ExVivogARPCs 7

description: miRNAs


title: LT196677RU_COPD


title: LT197381LI_ILD

value: 0-At Risk


title: ExVivogARPCs 6

description: miRNAs


title: LT195522RU_ILD

value: 7-Cryptogenic Organizing Pneumonia (COP)


title: ExVivogARPCs 8

description: miRNAs


title: ExVivogARPCs 9

description: miRNAs


title: LT195207LL_ILD

value: 9-Hypersensitive Pneumonitis (HP)


title: ExVivotARPCs 5

description: miRNAs

source_name: tARPCs

value: tubular adult renal stem/progenitor cells


title: LT195011RL_ILD


title: LT196309RU_ILD


title: LT191675RL_ILD


title: LT195484RU_CTRL


title: LT180102RL_CTRL


title: LT184423LL_COPD


title: ExVivotARPCs 3

description: miRNAs


title: LT176510LU_COPD


title: LT185396RL_ILD


title: LT168902RM_ILD


title: ExVivotARPCs 4

description: miRNAs


title: LT191618LU_ILD


title: LT184901RL_COPD

value: 4-Very Severe COPD


title: LT173597LL_CTRL


title: LT190870RU_CTRL


title: LT175399RU_ILD


title: LT172093RL_COPD


title: LT173946RL_ILD


title: LT186388LL_ILD


title: LT168094RL_ILD


title: LT171097RL_CTRL


title: LT167906LL_ILD


title: LT167891LU_ILD


title: LT166111RU_ILD


title: LT166240RM_CTRL


title: LT165114RU_COPD

value: 3-Severe COPD


title: LT163384LL_ILD


title: LT157856LU_ILD


title: LT151370RL_ILD


title: LT134121RU_COPD


title: LT151513LL_ILD


title: LT145196LU_CTRL


title: LT162096RL_ILD


title: LT156171LL_CTRL


title: LT156481LL_CTRL


title: LT158795LL_ILD


title: LT123552RL_ILD


title: LT130603LL_ILD


title: LT116004RL_ILD


title: LT134776LL_ILD


title: LT126767LL_ILD

value: 8-Acute interstitial pneumonia (AIP)


title: LT144769RL_COPD


title: LT124161RL_ILD


title: LT142159RU_CTRL


title: LT143944LL_ILD


title: LT147610LL_ILD


title: LT139691RU_COPD


title: LT128191LL_ILD


title: LT139649RU_CTRL


title: LT159753LL_CTRL


title: LT123131RL_ILD


title: LT155318RL_ILD


title: LT118629RL_ILD

value: 4-Desquamative interstitial pneumonia (DIP)


title: LT135390LL_ILD


title: LT119682RL_CTRL


title: LT108067RU_COPD

value: Positive


title: LT102695LL_ILD


title: LT111916LL_ILD


title: LT102131RL_CTRL


title: LT093297LU_CTRL


title: LT099879RL_ILD


title: LT091552LL_ILD


title: LT100821RL_ILD


title: LT090666LI_ILD


title: LT077264RU_ILD


title: LT081282RM_CTRL


title: LT082461RL_ILD


title: LT058319LU_CTRL


title: LT080750LL_ILD


title: LT095342LU_COPD

value: Negative


title: LT078347LL_CTRL


title: LT084038RM_COPD


title: LT087826LL_ILD


title: LT060717LU_COPD


title: LT079487LL_CTRL


title: LT076421LL_ILD


title: LT062121LL_ILD

value: 1-ILD of known cause, hypersensitivity or associated w/ CVD


title: LT050079RL_ILD


title: LT053283RU_COPD


title: LT069585RL_ILD


title: LT059721LU_ILD


title: LT047152LL_ILD


title: LT083950RU_COPD


title: LT081498RL_COPD


title: LT067200LU_ILD


title: LT046539RL_ILD


title: LT041389RL_COPD


title: LT037710RU_COPD


title: LT030662LL_ILD


title: LT022271LU_CTRL


title: LT036383LL_ILD


title: LT024967LU_COPD


title: LT022562LL_ILD


title: LT021461RM_ILD


title: LT011501RL_ILD


title: LT019699RL_ILD


title: LT006946RM_ILD


title: LT026534RL_ILD


title: LT017495RL_ILD


title: LT021748RL_ILD


title: LT013011LU_CTRL


title: LT012933RL_ILD


title: LT017533RM_ILD


title: LT287158LU_ILD


title: LT298520RU_COPD

value: 1-Mild COPD


title: LT000379LU_ILD


title: LT030347RL_ILD


title: LT000216LL_ILD


title: LT002410RM_ILD


title: LT017811RM_CTRL

value: Control


title: LT286056RU_COPD


title: LT022251RL_ILD


title: LT270247RU_COPD


title: LT273284LL_COPD


title: LT005419RU_COPD


title: LT277002LL_ILD


title: LT271100LU_COPD


title: LT005256RL_ILD


title: LT268509LU_ILD


title: LT263636RU_COPD


title: LT261141RU_COPD


title: LT249917LL_COPD


title: LT239116RL_ILD


title: LT255244RU_COPD


title: LT245084RU_COPD


title: LT245840RL_COPD


title: LT255718RU_COPD


title: LT242119LU_COPD


title: LT266802RL_ILD


title: LT245031LL_COPD


title: LT230415RU_COPD


title: LT246702RU_COPD


title: LT233620RU_COPD


title: LT256532LL_ILD


title: LT244480LU_COPD


title: LT236710RL_ILD


title: LT238531RU_COPD


title: LT242530RU_COPD