title: Cells_MCF-7/Twist primary tumor_rep2

first: Venu

last: Raman

state: Maryland

address: 720 Rutland Ave, Traylor 338

department: Radiology

hyb_protocol: 16hrs at 45 C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with Partek GS 6.6.  RMA normalization created the quantile-normalized log2 transcript signal values used in subsequent ANOVA analyses.

source_name: MCF-7/Twist primary xenograft tumors

label_protocol: Affymetrix 3' IVT Express Kit per manufacturer's instructions.

growth_protocol: MCF-7 and MCF-7/Twist cell lines were grown in MEM media with 10 % FBS at 37C in a humidified cell culture incubator supplied with 5 % CO2.

extract_protocol: Total RNA was extracted using Rneasy columns (Qiagen) following the manufacturers protocol.

treatment_protocol: MCF-7/Twist primary xenograft tumors were reduced to single cells by DNAse and collagenase treatment, and grown in the same media in cell culture for 1-2 weeks to isolate tumor cultures free of fibroblast contamination.

tag: cell line background

value: MCF-7/Twist primary xenograft tumors

tag: tissue/cell type

value: primary tumor

tag: genotype/variation

value: overexpressing human Twist gene


title: Cells_MCF-7/Twist lung metastasis_10

status: Public on Jan 13 2017

type: RNA

city: Baltimore

country: USA

institute: Johns Hopkins University

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF-7/Twist lung metastasis

treatment_protocol: MCF-7/Twist lung metastases were reduced to single cells by DNAse and collagenase treatment, and grown in the same media in cell culture for 1-2 weeks to isolate tumor cultures free of fibroblast contamination.

value: MCF-7/Twist lung metastasis

value: lung metastasis


title: 7452

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: Array hybridization, washing and scanning were performed according to the manufacturer’s recommendations.

scan_protocol: Scanned images were subjected to visual inspection and a chip quality report was generated by the Affymetrix's GeneChip Operating System (GCOS) and Expression console (Affymetrix).

data_processing: The image data was processed using the Affymetrix GCOS algorithm utilizing quantile normalization or the Robust Multiarray method (RMA) to determine the specific hybridizing signal for each gene.

source_name: subcutaneous adipose tissue

label_protocol: All target labeling reagents were purchased from Affymetrix (Santa Clara, CA). Double-stranded cDNAs were synthesized from 1ug total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and double strand conversion using the cDNA Synthesis System. Biotin-labeled cRNA was generated from the cDNA and used to probe Affymetrix Mouse Genome HT_MG-430A arrays.

extract_protocol: Qiazol with homogenization followed by Rneasy spin columns with option Dnase per manufacturers protocol

tag: tissue

value: subcutaneous adipose tissue

tag: gender

value: male

tag: age

tag: bmi

tag: whr

tag: ffmass

tag: totfa

tag: matsuda

tag: gfr

tag: homair

tag: systbp

tag: diastbp


title: Cells_MCF-7/Twist lung metastasis2


title: 7466


title: 7450


title: Cells_MCF-7/Twist lung metastasis8_rep2


title: Cells_MCF-7/Twist lung metastasis1


title: 7427


title: 7436


title: 7431


title: 7367


title: 7352


title: Cells_MCF-7/Twist lung metastasis8_rep1


title: 7400


title: Cells_MCF-7 cell line_rep2

source_name: MCF-7 cell line

value: MCF-7 cell line

value: non-metastatic MCF-7 breast cancer cells


title: Cells_MCF-7/Twist primary tumor_rep1


title: Cells_MCF-7 cell line_rep1


title: Cells_MCF-7/Twist cell line_rep1

source_name: MCF-7/Twist cell line

treatment_protocol: MCF-7 breast cancer cell line stably transfected with human Twist gene

value: MCF-7/Twist cell line

value: estrogen-independent metastatic breast cancer cell line MCF-7/Twist


title: Cells_MCF-7/Twist cell line_rep2


title: 7343


title: 7315


title: 7384


title: 7370


title: 7286


title: 7381


title: MT1hypo.MT1sh51.d12

first: Stephen

middle: B

last: Baylin

state: MD

address: 1650 Orleans St. Suite 541

description: DNMT1 shRNA#51 knockdown in MT1hypo cells

hyb_protocol: standard as recommended by Agilent

scan_protocol: standard as recommended by Agilent

data_processing: Data were normalized using loess and aquantile methods as described in the Bioconductor limma package

label_protocol: standard as recommended by Agilent

growth_protocol: standard as recommended by ATCC

extract_protocol: Trizol method

tag: cell type

value: MT1hypo colorectal cancer cells

tag: treatment

value: MT1hypo, non-silencing control


title: 7421


title: HCT116.10nMDAC

description: HCT116 cells subject to 10nM decitabine treatment for 48h

value: HCT116 colorectal cancer cells

value: HCT116, untreated


title: 7295


title: HCT116.shUHRF1.d14(KD90)

description: UHRF1 shRNA knockdown in HCT116 cells (knockdown efficiency 90%)

source_name: HCT116.shUHRF1.d14 (KD90)

value: HCT116, non-silencing control


title: RKO.shUHRF1.d14

description: UHRF1 shRNA knockdown in RKO cells

value: RKO colorectal cancer cells

value: UHRF1 shRNA knockdown in RKO cells

source_name: RKO

value: RKO, non-silencing conrol


title: HCT116.10nMDAC.shUHRF1 (KD60)

description: HCT116 cells subject to 10nM decitabine treatment for 48h and UHRF1 shRNA knockdown (knockdown efficiency 60%)

source_name: HCT116.10nMDAC.shUHRF1 (KD60)


title: HCT116.10nMDAC.shUHRF1 (KD90)

description: HCT116 cells subject to 10nM decitabine treatment for 48h and UHRF1 shRNA knockdown (knockdown efficiency 90%)

source_name: HCT116.10nMDAC.shUHRF1(KD90 set)


title: MT1hypo

description: Genetic disruption of DNMT1 in HCT116 cells (MT1hypo)

value: HCT116, parental


title: 7222


title: 7200


title: 7186


title: Leishmania_HAT2-heterozygous knockout_rep2 [SAMPLE 3B]

city: New Delhi

first: Swati

last: Saha

state: Delhi

address: Benito Juarez Raod

department: Microbiology

country: India

institute: University of Delhi

description:
SAMPLE 3B; gProcessedSignal_3B
Gene expression in HAT2-heterozygous knockout cells-biological replicate 2.

hyb_protocol: Hybridization was done using Agilent's In situ Hybridization kit (5188-5242) according to manufacturer's instructions.

scan_protocol: The hybridized and washed microarray slides were scanned on a G2565C scanner (Agilent Technologies).

data_processing:
Raw data were analysed using GeneSpring GX 12.1 Software. Normalization of the data was done using the same software using the 75th percentile shift method (included in the sample table; gProcessedSignal columns in the Complete_data_with_fold-changes.xls as well).
Fold change with respect to control (Samples 1A and 1B) calculated are GeneSpring-normalized, in terms of log base 2 (provided in the 'Complete_data_with_fold-changes.xls').

organism: Leishmania donovani

source_name: Leishmania_HAT2-heterozygous knockout

label_protocol: Complementary RNA was labelled with Cy3 using Agilent's Quick-Amp labeling kit. Random hexamer method of labeling was done followed by T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis).

growth_protocol: Grown in M199 medium supplemented with 10% FBS, hemin (5µg/ml), 100µM adenine at 26°C.

extract_protocol: RNA was isolated using the PureLink RNA mini-kit (Invitrogen).

treatment_protocol: RNA isolated from logarithmically growing cells.

tag: strain

value: L. donovani 1S

value: HAT2-heterozygous knockout

value: promastigotes

tag: growth stage

value: logarithmically growing


title: HCT116.MT1sh51.d12

description: DNMT1 shRNA#51 knockdown in HCT116 cells


title: Leishmania_HAT2-heterozygous knockout_rep1 [SAMPLE 3A]

description:
SAMPLE 3A; gProcessedSignal_3A
Gene expression in HAT2-heterozygous knockout cells-biological replicate 1.

tag: genotype/variation


title: 7264

tag: tissue

value: subcutaneous adipose tissue

value: male


title: 7180

tag: gender


title: 7162

tag: age


title: 7126

tag: bmi


title: 7137

tag: whr


title: 7136

tag: ffmass


title: 7119

tag: totfa


title: 7099

tag: matsuda


title: 7174

tag: gfr


title: 7149

tag: homair


title: 7097

tag: systbp


title: 7096

tag: diastbp


title: 7091


title: 7080


title: 7048


title: 7687


title: 7052


title: 7038


title: 7020


title: 7007


title: 6982


title: 6950


title: 6959


title: 6886


title: 6875


title: 6969


title: 7092


title: 6872


title: 6930


title: 7033


title: 6880


title: 6974


title: 6978


title: 6860


title: 6849


title: 6823


title: 6807


title: 6868


title: 6922


title: 6835


title: 6801


title: 6851


title: 6725


title: 6781


title: 6715


title: 6737


title: 6675


title: 6608


title: 6775


title: 6648


title: 6800


title: 6628


title: 6632


title: 6639


title: 6611


title: 6684


title: 6778


title: 6589


title: 6671


title: 6631


title: 6561


title: 6689


title: 6557


title: 6605


title: 6680


title: 6572


title: 6666


title: 6548


title: 6537


title: 6564


title: 6515


title: 6525


title: 6469


title: 6380


title: 6517


title: 6419


title: 6376


title: 6318


title: 6433


title: 6484


title: 6201


title: 6331


title: 6183


title: 6200


title: 6203


title: 6311


title: 6135


title: 6178


title: 6305


title: 6194


title: 6220


title: 6287


title: 6260


title: 6089


title: 6083


title: 6106


title: 6266


title: 6101


title: 6761


title: 6041


title: 5972


title: 6028


title: 6063


title: 6051


title: 6016


title: 5954


title: 5880


title: 6058


title: 5962


title: 5919


title: 6040


title: 5949


title: 5859


title: 6006


title: 5849


title: 5833


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title: 5935


title: 5790


title: 6024


title: 5951


title: 5871


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title: 5845


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title: 5481


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title: 5510


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title: 5273


title: 5203


title: 5166


title: 5263


title: 5394


title: 5210


title: 5157


title: 5242


title: 5708


title: 4951


title: 4871


title: 4856


title: 5194


title: 5006


title: 5084


title: 5015


title: 5049


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title: 4644


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title: 4336


title: 4344


title: 4321


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title: 4377


title: 4604


title: 4372


title: 4370


title: 4380


title: 4311


title: 4347


title: 4295


title: 4257


title: 4148


title: 4241


title: 4219


title: 4154


title: 4184


title: 4244


title: 3000


title: 4137


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title: 4000


title: 3981


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title: 4008


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title: 2242


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title: 2226


title: 2278


title: 2262


title: 2230


title: 2415


title: 2200


title: 2165


title: 2198


title: 2161


title: 2129


title: 2131


title: 2176


title: 1994


title: 2057


title: 1984


title: 1964


title: 2220


title: 2048


title: 2126


title: 2055


title: 1999


title: 2064


title: 2143


title: 1944


title: 2091


title: 2033


title: 1932


title: 2113


title: 1924


title: 2114


title: 1974


title: 2109


title: 1961


title: 1947


title: 2006


title: 2019


title: 1987


title: 2050


title: 1892


title: 1875


title: 1871


title: 1915


title: 1911


title: 1855


title: 1848


title: 1867


title: 1869


title: 1921


title: 1896


title: 1841


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title: 1822


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title: 1834


title: 1792


title: 1820


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title: 1840


title: 1801


title: 1777


title: 2222


title: 1747


title: 1764


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title: 1773


title: 1722


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title: 1775


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title: 1678


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title: 1673


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title: 1578


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title: 1642


title: 1633


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title: 1568


title: 1580


title: 1520


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title: 1653


title: 1573


title: 1559


title: 1516


title: 1530


title: 1550


title: 1518


title: 1527


title: 1504


title: Hif-3 Replicate 1

city: Ann Arbor

first: Peng

last: Zhang

state: MI

address: 830 N. University Ave.

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description: Gene expression after 12hr Hif-3a mRNA injection

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

scan_protocol: Slides were scanned by the Agilent DNA Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default setting, Dye channel: Green, Scan resolution is 5um, PMT is set to 100%, 10%, 16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) was used to read the raw data.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US), followed the manufacturer's instructions.

organism: Danio rerio

source_name: Hif-3, 12hpf, pooled RNA

label_protocol: RNA was labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol. Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s recommendations. Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: Tuebingen

tag: developmental stage

value: whole embryo

value: 12hr Hif-3a mRNA injection


title: 1502


title: 1531


title: 1483


title: 1500


title: Control Replicate 2

description: Gene expression after 12hr GFP mRNA injection

source_name: GFP control, 12hpf, pooled RNA

tag: treatment

value: 12hr GFP mRNA injection


title: Hif-3 Replicate 2

tag: strain


title: Hif-1 Replicate 1

description: Gene expression after 12hr Hif-1a mRNA injection

source_name: Hif-1, 12hpf, pooled RNA

value: 12hr Hif-1a mRNA injection


title: Control Replicate 1


title: Hif-1 Replicate 2


title: 1462


title: Hif-1 Replicate 3


title: Hif-3 Replicate 3


title: 1455


title: 1454


title: 1449


title: 1469


title: 1436


title: Control Replicate 3


title: 1446


title: 1394


title: 1375


title: 1353


title: 1409


title: 1344


title: 1447


title: 1439


title: 1452


title: 1343


title: 1321


title: 1366


title: 1619


title: 1303


title: 1319


title: 1290


title: 1312


title: Zebrafish-embryo_8hpf_Nrf2a-overexpression_Experiment3-rep1

city: Nagoya

first: Shin'ichi

last: Akiyama

state: Aichi

address: 65 Tsurumaicho

department: Department of Nephrology

country: Japan

institute: Nagoya University Graduate School of Medicine

description: This data set is one of duplicates array analysis in bilogical experiment group #3.

hyb_protocol: The dual-color hybridization of the MZH chips was performed according to the manufacture’s instructions of AceGene DNA microarray (Hitachi-soft).

scan_protocol: After hybridization, MZH chips were scanned using Affimetrix 428 array scanner (Affimetrix).

data_processing: Microarray data were processed from raw data image files with Affymetrix Jaguar (Affimetrix) and normalized. Processed data were subsequently imported into Excel (Microsoft) to compare gene expression profiles of Nrf2 overexpressing samples to that of control samples.

source_name: Embryo Nrf2a mRNA injected

label_protocol: Amino-allyl-modified amplified RNA (aRNA) was synthesized in one amplification round from 1 μg of purified total RNA using the amino-allyl RNA amplification kit (Sigma-Aldrich). Subsequently, 5 μg of amino-allyl-modified aRNA was used for coupling of monoreactive Cy3 and Cy5dyes (GE Healthcare) and column purified.

growth_protocol: All embryo were incubated at 28°C.

extract_protocol: The collected zebrafish embryos were quickly homogenized with QIAzol reagent (Qiagen), and subsequently stored at -80°C. Total RNA was extracted according to the manufacturer’s instructions. Isolated total RNA was further purified using RNAeasy mini kit (Qiagen).

treatment_protocol: For the overexpression of zebrafish nrf2a, capped nrf2a mRNA was synthesized from pCS2nrf2 using an SP6 mMESSAGE mMACHINE in vitro transcription kit (Ambion). One hundred pg of mRNA was injected into 1-cell stage embryo by an IM300 microinjector (Narishige). At 8 hours after injection, the embryos were collected.

tag: biological experiment replicates

value: Group #3

tag: condition

value: Test

value: AB

value: Embryo

value: 8 hours post fertilization

value: Injected with Nrf2a mRNA into a 1-cell stage embryo

value: Whole body

source_name: Embryo Nrf2a mRNA uninjected

value: Control

value: Uninjected with any mRNA


title: Zebrafish-embryo_8hpf_Nrf2a-overexpression_Experiment3-rep2

tag: tissue


title: 1269

tag: gender


title: Zebrafish-embryo_8hpf_Nrf2a-overexpression_Experiment2-rep2

description: This data set is one of duplicates array analysis in bilogical experiment group #2.

value: Group #2

tag: age


title: 1280

value: subcutaneous adipose tissue

tag: bmi


title: 1264

value: male

tag: whr


title: 1211

tag: ffmass


title: 1167

tag: totfa


title: Zebrafish-embryo_8hpf_Nrf2a-overexpression_Experiment1-rep1

description: This data set is one of triplicates array analysis in bilogical experiment group #1.

value: Group #1


title: 1186

tag: matsuda


title: 1228

tag: gfr


title: 1247

tag: homair


title: 1288

tag: systbp


title: 1258

tag: diastbp


title: Zebrafish-embryo_8hpf_Nrf2a-overexpression_Experiment1-rep3

tag: developmental stage


title: 1165


title: Zebrafish-embryo_8hpf_Nrf2a-overexpression_Experiment2-rep1

tag: treatment


title: 1263


title: 1164


title: 1223


title: 1187


title: 1278


title: Zebrafish-embryo_8hpf_Nrf2a-overexpression_Experiment1-rep2

tag: strain


title: 1180


title: aged injured 1

city: Tokyo

first: Morito

last: Takano

address: 35 Shinanomachi, Shinjuku-ku

department: Orthopaedic Surgery

institute: Keio University

description:
Gene expression data from aged injured spinal cord
aged injured 1 Takano

hyb_protocol: Total RNA was , and hybridized to a GeneChip® Mouse Genome 430 2.0 Array (Affymetrix Inc., Santa Clara, CA, USA). The array was subsequently washed and stained in a Fluidics Station 450 according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G.

data_processing: The raw image files were converted to normalized signal intensity values using the MAS 5.0 algorithm. PCA was performed using the Gene Spring GX software (Agilent Technologies Inc.). For cluster analyses, the normalized data were narrowed down using cutoff values for each expression signal (>50) and fold changes (i.e., the difference between the signal from the young injured spinal cords and that of the aged injured spinal cords was greater than 2). The heat map was created with GeneSpring GX. GO term enrichment was performed for the genes that exceeded the above-described cut-off value.

organism: Mus musculus

source_name: aged injured spinal cord

label_protocol: For microarray analyses, RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA), and 100 ng of total RNA was reverse transcribed, biotin labeled.

extract_protocol: Injured and naive mice were anesthetized and transcardially perfused with heparinized saline (5 U/ml) 9 days after injury (n=3 each). Dissected segments of the spinal cord at the Th9 level were rapidly frozen and placed in TRIzol (Invitrogen). Total RNA was isolated using an RNeasy Mini Kit (Qiagen Inc., Hilgen, Germany), following the manufacturer’s instructions.

value: female

value: 15-18 month

value: injured spinal cord


title: aged injured 2

description:
Gene expression data from aged injured spinal cord
aged injured 2 Takano


title: 1154


title: 1111


title: 1162


title: 1160


title: aged normal 3

description:
Gene expression data from aged normal spinal cord
aged normal 3 Takano

source_name: aged normal spinal cord

value: normal spinal cord


title: 1105


title: 1149


title: young injured 3

description:
Gene expression data from young injured spinal cord
young injured 3 Takano

source_name: young injured spinal cord

value: 2-3 month


title: 1095


title: young normal 3

description:
Gene expression data from young normal spinal cord
young normal 3 Takano

source_name: young normal spinal cord


title: 1080

source_name: subcutaneous adipose tissue


title: aged normal 1

description:
Gene expression data from aged normal spinal cord
aged normal 1 Takano


title: 1082


title: 1086


title: aged normal 2

description:
Gene expression data from aged normal spinal cord
aged normal 2 Takano


title: 1147


title: aged injured 3

description:
Gene expression data from aged injured spinal cord
aged injured 3 Takano


title: 1092


title: 1077


title: young injured 1

description:
Gene expression data from young injured spinal cord
young injured 1 Takano


title: young injured 2

description:
Gene expression data from young injured spinal cord
young injured 2 Takano


title: 1106


title: 1079


title: 1063


title: 1058


title: young normal 1

description:
Gene expression data from young normal spinal cord
young normal 1 Takano


title: 1044


title: young normal 2

description:
Gene expression data from young normal spinal cord
young normal 2 Takano


title: 1054


title: 999


title: 1052


title: 977


title: 950


title: 987


title: 1018


title: 982


title: 951


title: 964


title: 942


title: 966


title: 888


title: 906


title: 904


title: 979


title: 908


title: 960


title: 971


title: 958


title: 875


title: 874


title: 845


title: 880


title: 998


title: 844


title: 864


title: 859


title: 854


title: 871


title: 840


title: 806


title: 833


title: 827


title: 801


title: 799


title: 803


title: 1049


title: 780


title: 787


title: 758


title: 828


title: 797


title: 1148


title: 785


title: 839


title: 747


title: 725


title: 783


title: 708


title: 794


title: 635


title: 634


title: 569


title: 718


title: 579


title: 602


title: 581


title: 598


title: 644


title: 618


title: 633


title: 623


title: 594


title: AML 4

city: stanford

first: chunjiang

last: he

address: 265 campus drive

institute: stanford university

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.
Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: AML

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

growth_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

extract_protocol: Total RNA from bone marrow mononuclear cells were extracted using TRIzol reagent following the manufacturer's instructions. ArrayStar lncRNA array V3 was performed to detect the differentially expressed lncRNAs and mRNAs.

treatment_protocol: Mononuclear cells were extracted from patient bone marrows using FICOLL solution.

value: bone marrow

tag: cell type

value: mononuclear

tag: disease state

value: AML


title: Non-leukemia control 1

description: Total RNA from bone marrow mononuclear cells were extracted using TRIzol reagent following the manufacturer's instructions

source_name: non-leukemia

tag: tissue

value: non-leukemia


title: RKO.MT1sh49

description: DNMT1 shRNA#49 knockdown in RKO cells

value: colorectal cancer cells

value: DNMT1 shRNA#49 knockdown

tag: cell line

value: RKO

value: non-silencing conrol


title: AML 1


title: RKO.MT1sh51

description: DNMT1 shRNA#51 knockdown in RKO cells

value: DNMT1 shRNA#51 knockdown


title: 575

value: subcutaneous adipose tissue

tag: gender

tag: age


title: AML 5


title: AML 2


title: AML 3


title: AML 6


title: Non-leukemia control 2


title: HCT116.shUHRF1.d14(KD60)

description: UHRF1 shRNA knockdown in HCT116 cells (knockdown efficiency 60%)

value: UHRF1 shRNA knockdown

value: HCT116 (knockdown efficiency 60%)

value: non-silencing control


title: HT29.MT1sh51

description: DNMT1 shRNA#51 knockdown in HT29 cells


title: HT29.MT1sh49

description: DNMT1 shRNA#49 knockdown in HT29 cells


title: 555

value: male

tag: bmi

tag: whr


title: 553

tag: ffmass

tag: totfa


title: 551

tag: matsuda

tag: gfr


title: 539

tag: homair

tag: systbp


title: 535

tag: diastbp


title: DLD1.MT1sh51

description: DNMT1 shRNA#51 knockdown in DLD1 cells

tag: treatment


title: DLD1.MT1sh49

description: DNMT1 shRNA#49 knockdown in DLD1 cells


title: 522


title: 521


title: 520


title: BEECH_cleanair_rep1

city: Munich

first: Sebastian

last: Oeder

address: Biedersteinerstr. 29

department: Center for Allergy and Environment (ZAUM)

country: Germany

institute: Technische Universität München

hyb_protocol: Purified labeled cRNA was fragmented and hybridized on Human Gene Expression Microarrays (Sure Print G3 Human Gene Expression Microarray  8x60 K, Agilent, Waldbronn, Germany) using ozone-barrier slide covers and hybridization gasket slides (Ozone-Barrier Slide Cover Kit, Hybridization Gasket Slide Kit and Gene Expression Hybridisation Kit, Agilent, Waldbronn, Germany) for 17h at 65°C in a hybridization oven.

scan_protocol: After washing (Gene Expression Wash Buffer Kit, Agilent, Waldbronn,  Germany) slides were scanned (Agilent C microarray scanner, Agilent,  Waldbronn, Germany).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1  (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid:  028004_D_F_20140813) to obtain background subtracted and spatially  detrended Processed Signal intensities.  Features flagged in Feature  Extraction as Feature Non-uniform outliers were excluded.

source_name: A549, beech clean air

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the  LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the  manufacturer's instructions, followed by RNeasy column purification  (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop  ND-1000 Spectrophotometer.

growth_protocol: Human lung epithelial cell line A549 (ATCC® CCL-185™) was cultured in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum (FBS), 100 U/ml penicillin, 100 mg/ml streptomycin (all from Life Technologies, Darmstadt).

extract_protocol: Total RNA was extracted using Rneasy Mini plus Kit (Qiagen) including  genomic DNA removal according to the manufacturer s protocol.

treatment_protocol: Confluent layers of A549 cells were exposed to the diluted log wood and pellet combustion aerosols for 4 h. At the same time clean air exposures of confluent layers of A549 cells were performed as reference under the same conditions.

tag: organ

value: lung

value: epithelium


title: BEECH_aerosol_rep3

source_name: A549, beech aerosol


title: 493


title: 495


title: BEECH_aerosol_rep1


title: 473


title: BEECH_ cleanair_rep2


title: 492


title: 400


title: PELLET_ cleanair_rep2

source_name: A549, pellet clean air


title: PELLET_cleanair_rep1


title: 490


title: 441


title: 449


title: BEECH_aerosol_rep2


title: 482


title: BEECH_ cleanair_rep3


title: 422


title: 429


title: PELLET_aerosol_rep1

source_name: A549, pellet aerosol


title: PELLET_aerosol_rep2


title: PELLET_aerosol_rep3


title: 379


title: PELLET_ cleanair_rep3


title: 388


title: 378


title: 420


title: 377


title: Slide 347282

status: Public on Jan 12 2017

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 2

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F532 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown in CDM with 0.5% Glucose and 0.5 % N-acetyleglucosamine (NAG), and harvested at respective mid-exponential phase.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from Two replicate cultures.

tag: protocol

value: N-acetyleglucosamine (NAG)

source_name: F635 Mean

value: Glucose


title: Slide 347280

description: Sample 1


title: LPS+LA1 rep3

city: Silver Spring

first: BIJU

last: ISSAC

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was preprocessed on GeneSpring GX 13.0 from Agilent. Raw data was quantile normalized and log2 transformed

source_name: monocyte derived macrophages

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

growth_protocol: Human macrophages (2 X 10^6 cells per well) were seeded into 6-well tissue culture dishes and cultured in RPMI1640 with GlutaMAX and autologous human serum (5%) at 37°C in a humidified atmosphere containing 5% CO2

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.

treatment_protocol: Cells were treated with vehicle DMSO (1% DMSO), LA1 (20 μM), LPS (100 ng/mL), or LPS (100ng/mL) and LA1 (20 μM) for 4h

value: LPS (100ng/mL) and LA1 (20 μM)


title: LPS+LA1 rep2

description: replicate 2


title: LA1 rep1

description: replicate 1


title: LPS+LA1 rep1

description: replicate 1


title: 369


title: LPS rep2

description: replicate 2

value: LPS (100 ng/mL)


title: LPS rep3

description: replicate 3


title: Control rep3

description: replicate 3

value: DMSO


title: Control rep1

description: replicate 1


title: LPS rep1

description: replicate 1


title: LA1 rep2

description: replicate 2


title: LA1 rep3

description: replicate 3


title: Control rep2

description: replicate 2


title: healthy_39

city: Krakow

first: Marek

last: Sierżęga

address: Kopernika 40

country: Poland

institute: Jagiellonian University Meical College

hyb_protocol: The labelled RNA samples were hybridized to the miRCURY LNA™ microRNA Array 7th Gen (Exiqon, Denmark) containing capture probes targeting all microRNAs of human origin registered in the miRBASE 19.0. The hybridization was performed using a Tecan HS4800™ hybridization station (Tecan, Austria) according to the manufacturer’s protocol.

scan_protocol: After hybridization, the microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, USA)

data_processing:
Microarrays were analysed with the ImaGene® 9 software (BioDiscovery, CA, USA). The obtained signals were background corrected and data normalization was performed with the Lowess (Locally Weighted Scatterplot Smoothing) algorithm. MicroRNAs with intensities above threshold in less than 20% of the samples were removed from the final dataset used for the expression analysis.
The average_FC_data.txt contains the following data columns;
logFC – log FoldChange of individual microRNAs of cancer vs healthy mucosa
AvgExpr – average expression for a given microRNA
AvgHy3 – average Hy3 signal well above background
P.Value – raw P value
adj.P.Val – adjusted P value

label: Cy3, Cy5

source_name: adjacent healthy gastric mucosa

label_protocol: Total RNA (750 ng) isolated from tumour and healthy mucosa samples was labelled with Hy3™ and Hy5™ fluorescent labels, respectively, using the miRCURY LNA™ microRNA Hi-Power Labelling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following manufacturer's instructions.

extract_protocol: Pairs of primary tumours and corresponding normal gastric mucosa were sampled from patients’ surgical specimens immediately after resection. The fresh specimens were collected into RNase free polypropylene tubes filled with RNAlater® stabilization solution (Qiagen, Valencia, CA, USA) and stored at −80 °C until RNA was extracted. Total tissue RNA was extracted using miRCURY RNA Isolation Kits (Exiqon, Denmark) according to the manufacturer’s instructions. RNA concentrations were measured with NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA) and overall sample quality was determined by RNA integrity number (RIN) using Agilent Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

tag: subject status

value: patients diagnosed with gastric cancer

tag: patient id number

tag: tissue type

value: healthy gastric mucosa


title: tumour_38

source_name: gastric tumour

value: primary tumor


title: healthy_38


title: Muscle_7-day old_rep2

city: Newark

first: Ruoxin

last: Wang

state: NJ

address: 185 south orange avenue

department: Department of Cell Biology and Molecular Medicine

institute: RUTGERS NEW JERSEY MEDICAL SCHOOL

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures using GeneChip® Scanner 3000

data_processing: Affymetrix® Microarray Suite Version 5.0

source_name: Cardiac muscle, 7-day old

label_protocol: standard Affymetrix procedures

extract_protocol: Total RNA was isolated from mouse heart.

tag: strain

tag: tissue

value: Heart, cardiac muscle

tag: developmental stage

value: 7-day old


title: Muscle_7-day old_rep3


title: BL21(DE3)_LB_OD1.54

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

hyb_protocol: The fragmented and labeled RNA was hybridized with the tiling array for 17 hours at 65 °C.

scan_protocol: After the hybridization and wash steps described in the array manufacturer’s instructions, arrays were scanned using an Agilent DNA microarray Scanner (Agilent Technologies).

data_processing: Signal intensity and local background were determined using Feature Extraction software (Agilent Technologies).

organism: Escherichia coli BL21(DE3)

source_name: LB medium, OD600=1.54

label_protocol: The resulting RNA was directly labeled with Cy3 using a Label IT µArray Labeling Kit (Mirus, Madison, WI, USA), per the manufacturer’s instruction.

growth_protocol: Growth curve experiments were conducted at 37°C in batch fermentations.

extract_protocol: Total RNA was prepared using a mirVana miRNA Isolation Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA), per the manufacturer’s instruction. Any contaminating DNA was digested with Turbo DNase (Applied Biosystems, Austin, TX, USA) for 30 minutes at 37 C and then removed using the filter cartridges supplied with the mirVana miRNA Isolation Kit.

treatment_protocol: Culture broth (4.0 x 108 cells) was immediately mixed with two volumes of RNAprotect Bacteria Reagent (Qiagen, Düsseldorf, Germany).

tag: culture medium

value: LB (complex medium)

tag: cell density in od600

tag: growth stage

value: exponential phase


title: Muscle_7-day old_rep1


title: Muscle_10-week old_rep3

source_name: Cardiac muscle, 10-week old

value: 10-week old


title: Muscle_24-hour old_rep2

source_name: Cardiac muscle, 24-hour old

value: 24-hour old


title: Muscle_24-hour old_rep1


title: healthy_37


title: tumour_37


title: Muscle_10-week old_rep2


title: tumour_39


title: tumour_32


title: healthy_32


title: Muscle_24-hour old_rep3


title: Muscle_10-week old_rep1


title: tumour_29


title: tumour_28


title: healthy_24


title: tumour_23


title: tumour_24


title: BL21(DE3)_LB_OD5

source_name: LB medium, OD600=5

value: stationary phase


title: healthy_29


title: healthy_28


title: healthy_21


title: healthy_23


title: healthy_20


title: tumour_20


title: tumour_19


title: tumour_21


title: tumour_18


title: healthy_17


title: healthy_19


title: healthy_18


title: tumour_14


title: tumour_17


title: BL21(DE3)_MR_OD14

source_name: MR medium, OD600=14

value: Modified R (minimal medium)


title: healthy_14


title: BL21(DE3)_LB_OD0.24

source_name: LB medium, OD600=0.24


title: tumour_13


title: healthy_13


title: tumour_12


title: wild type testis

city: tokyo

first: Takashi

last: Nakasuji

address: 1-5-45 yushima bunkyo

institute: Tokyo Medical and Dental University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Data were normalized by robust multichip analysis (RMA) procedure using Affymetrix Expression Console.

source_name: adult testis

label_protocol: Biotinylated cRNA were prepared  according to the manufacturer's instructions from 300ng total RNA (GeneChip® 3' IVT Express Kit, Affymetrix).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions.(ReliaPrep RNA Tissue Miniprep System, Promega)

value: testis

tag: genotype

value: wild type

tag: age

value: 4 month old


title: BL21(DE3)_MR_OD1.5

source_name: MR medium, OD600=1.5


title: tumour_11


title: healthy_12


title: healthy_11


title: tumour_10


title: lung_irradiated

city: Busan

first: Beomseok

last: Son

address: 322 Biology Building, 2 Busandaehakro 63beon-gil, Geumjeong-gu

institute: Pusan National University

description: Gene expression data from α-smooth muscle actin-overexpressing mice (which was confirmed by western blotting)

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: Mouse lungs, irradiated, 25 weeks

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: The mice were maintained in animal care facilities in a temperature-regulated room (23±1°C) with a 12 h light/dark cycle. All animals were fed water and standard mouse chow ad libitum.

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

treatment_protocol: A single dose of γ-rays using a Gamma Cell-40 Exactor (Nordion International, Inc., Kanata, Ontario, Canada) at a dose rate of 0.81 Gy/min.

value: lung

tag: gender

value: male


title: lung_nonirradiated

description: Gene expression data from negative control mice

source_name: Mouse lungs, nonirradiated, 25 weeks


title: healthy_10


title: patient G14T

city: Beijing

first: Hanjiang

last: Fu

address: 27 Taiping Road

department: Department of Biochemistry and Molecular Biology

country: China

institute: Beijing Institute of Radiation Medicine

description: human GC  tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Raw signal intensities were normalized in quantile method by GeneSpring GX v11.5.1, and low intensity LncRNAs was filtered.

source_name: human GC  tissue

label_protocol: 1ug of total RNA was reverse transcripted into cDNA with T7 Promoter Primer and MMLV-Rtase, and then was labled with T7 polymerase and Cyanine-3-CTP.

extract_protocol: GC and adjacent normal tissues were prefrozen with liquid nitrogen, then ground into powder with mortar, and extracted with TRIzol regeant according its protocal.

value: human GC tissue

tag: Sex

value: female


title: healthy_9

value: patients diagnosed with gastric cancer

value: healthy gastric mucosa


title: tumour_9

value: primary tumor


title: patient G14N

description: human GC adjacent normal tissue

source_name: human GC adjacent normal tissue

value: human GC adjacent normal tissue


title: Zfy1,2 double knockout testis

value: Zfy1,2 double knockout


title: patient G8T

description: human GC  tissue


title: healthy_7


title: 20mGyAA5/ reference male mouse7

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

molecule: genomic DNA

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

value: tail

source_name: reference male mouse7


title: patient G8N

description: human GC adjacent normal tissue


title: tumour_7


title: Control keratinocytes, Non-UV, healthy individual 2

city: Linköping

first: Charlotta

last: Enerbäck

address: Faculty of Medicine and Health Sciences

department: Ingrid Asp Psoriasis Research Center

institute: Linköping University

hyb_protocol: The Affymetrix HTA 2.0 microarrays were hybridized in a GeneChip® hybridization oven at 45°C, at 60 rpm, for 16 h. The washing and staining procedure was performed in an Affymetrix GeneChip® Fluidics Station 450.

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

data_processing: The data were analyzed with the GeneSpring GX software (version 13.0; Agilent Technologies), using Affymetrix default analysis settings and standard Robust Multi-array Average (RMA) normalization.

source_name: Control keratinocytes, Non-UV

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

growth_protocol: Tissue samples were obtained as 4 mm punch biopsies of the skin. After incubation with dispase (2 mg/ml) at 4°C for 18 h, the epidermal layer was separated from the dermal part of the skin and placed in 0.05% trypsin to receive a single cell suspension. The keratinocytes were cultured in Dulbecco’s modified Eagle’s medium (DMEM)-Ham’s F-12 (3:1) with 10% fetal bovine serum and supplemented with penicillin (50 U/ml), streptomycin (50 µg/ml) and fungizone (50 µg/ml), insulin (5 µg/ml), cholera toxin (0.1 nM), hydrocortisone (0.4 µg/ml), triiodothyronine (2 nM), transferrin (5 µg/ml) and adenine (0.18 mM), and epidermal growth factor (10 ng/ml).

extract_protocol: Extraction of total RNA was performed with Rneasy Plus mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The keratinocytes were irradiated in PBS with the UVB doses of 200 mJ/cm2 and collected 6 h post-irradiation. The UVB source comprised two Philips TL20W/12 tubes (Philips, Eindhoven, The Netherlands) emitting in the 280-370 nm range, with a main output of 305-320 nm. A Schott WG 305 cut-off filter (50% absorption below 305 nm, Mainz, Germany) was used. The non-irradiated control cells were handled identically but not irradiated.

tag: uv/non-uv

value: Non-UV exposed

tag: tissue origin

value: healthy control indivudual


title: reference male mouse7/ 20mGyAA2

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: Control keratinocytes, Non-UV, healthy individual 1


title: 20mGyAA4/ reference male mouse7


title: Control keratinocytes, UV irradiated, healthy individual 1

source_name: Control keratinocytes, UV irradiated

value: UV exposed


title: Control keratinocytes, UV irradiated, healthy individual 2


title: 20mGyAA2/ reference male mouse7


title: reference male mouse7/ 20mGyAAF


title: reference male mouse7/ 20mGyAA4


title: 20mGyAAM/ reference male mouse7


title: 20mGyAA1/ reference male mouse7


title: Psoriatic unvolved keratinocytes, UV irradiated, patient 2

value: psoriasis (uninvolved skin) patient


title: 20mGyAAF/ reference male mouse7


title: reference male mouse7/ 20mGyAA5


title: 20mGyZ3/ reference male mouse7


title: reference male mouse7/ 20mGyZ5


title: reference male mouse7/ 20mGyAA1


title: reference male mouse7/ 20mGyAAM


title: reference male mouse7/ 20mGyAA3


title: Psoriatic involved keratinocytes, Non-UV, patient 2

value: psoriasis (involved skin) patient


title: 20mGyAA3/ reference male mouse7


title: 20mGyZ5/ reference male mouse7


title: 20mGyZ1/ reference male mouse7


title: 20mGyZ2/ reference male mouse7


title: Psoriatic involved keratinocytes, UV irradiated, patient 2


title: Psoriatic unvolved keratinocytes, UV irradiated, patient 1


title: Slide US45102948_256525610006_S01.3

description: Sample 1

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test.. Further analysis was performed with a Cyber-T Student T-test for paired data.

source_name: F550 Mean

growth_protocol: Cells were grown in CDM + 0.5% N-acetylglucosamine (NAG) and harvested at respective mid-exponential phase of growth.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: genotype/variation

value: CcpA mutant

source_name: F650 Mean

value: Wild type


title: reference male mouse7/ 20mGyZ2


title: 20mGyZ4/ reference male mouse7


title: reference male mouse7/ 20mGyZ4


title: Psoriatic involved keratinocytes, UV irradiated, patient 1


title: 20mGyZM/ reference male mouse7


title: Digester_co_97D1

city: BEIJING

first: LINWEI

last: WU

address: NO.1 TSGINAHU UNIVERSITY

institute: TSINGHUA UNIVERSITY

description: co digestion with dairy manure and poultry wast, OLR=1.5

hyb_protocol: The DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. Then re-suspended in hybridization solution. GeoChip hybridization was carried out at 67 °C in an Agilent hybridization oven for 24 hrs.

scan_protocol: After slides washed, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only 9 out of 21 samples.

organism: sludge metagenome

source_name: sludge microbes_co digester_day 97_OLR=1.5

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-3 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: DNA was extracted from sludge samples using previously described protocols (Ma et al., 2015). Briefly, the sludge sample was resuspended in 630 µL DNA-extraction buffer, followed by treatment with 60 µL of a lysozyme mixture (37 °C, 60 min), 60 µL of a protease mixture (37 °C, 30 min), and 80 µL 20% sodium dodecyl sulfate (37 °C, 90 min). Treated sample suspension was subsequently extracted with the phenol–chloroform–isoamyl alcohol (25:24:1) at 65 °C for 20 min, and supernatant was extracted using the chloroform–isoamyl alcohol (24:1). DNA extract was then mixed with 0.6 volume of isopropanol and stored at 4 °C overnight. In addition, DNA was obtained by centrifuging the pellet, washing with 70% cold ethanol, drying and resuspension in nuclease-free water. DNA quality was evaluated with a NanoDrop spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA). Final DNA concentrations were quantified by PicoGreen, using a FLUO star Optima instrument (BMG Labtech, Jena, Germany). Purified DNA was stored at -80 °C.

tag: organism

value: sludge microbes from anaerobic digesters

tag: digester id

value: co digester 1

tag: organic loading rate

tag: time points

value: Day 97

tag: digester set


title: Psoriatic involved keratinocytes, Non-UV, patient 1


title: Digester_co_97D3

value: co digester 3

value: co digestion with dairy manure and poultry wast, OLR=1.5


title: Slide US45102948_256525610007_S01.8

description: Sample 2


title: 20mGyZF/ reference male mouse7

tag: strain

tag: tissue


title: reference male mouse7/ 20mGyZF


title: reference male mouse7/ 20mGyZ3


title: Digester_co_90D3

source_name: sludge microbes_co digester_day 90_OLR=1.5

value: Day 90


title: Psoriatic uninvolved keratinocytes, Non-UV, patient 1


title: reference male mouse7/ 20mGyZM


title: Psoriatic uninvolved keratinocytes, Non-UV, patient 2


title: Digester_co_90D1


title: reference male mouse7/ 20mGyZ1


title: Digester_co_87D1

source_name: sludge microbes_co digester_day 87_OLR=1.5

value: Day 87


title: 20mGyY6/ reference male mouse7


title: Digester_co_87D2

value: co digester 2


title: Digester_co_87D3


title: Digester_co_90D2


title: Digester_co_97D2


title: 20mGyY4/ reference male mouse7


title: reference male mouse7/ 20mGyY6


title: Digester_co_83D1

source_name: sludge microbes_co digester_day 83_OLR=1.5

value: Day 83


title: 20mGyY5/ reference male mouse7

value: tail


title: reference male mouse7/ 20mGyY5


title: Digester_co_69D2

description: co digestion with dairy manure and poultry wast, OLR=1.3

source_name: sludge microbes_co digester_day 69_OLR=1.3

value: Day 69


title: Digester_co_83D2


title: Digester_co_69D3

value: co digestion with dairy manure and poultry wast, OLR=1.3


title: 20mGyY2/ reference male mouse7


title: Digester_co_69D1


title: Digester_co_83D3


title: 20mGyY3/ reference male mouse7


title: Digester_co_66D3

source_name: sludge microbes_co digester_day 66_OLR=1.3

value: Day 66


title: Digester_co_66D1


title: reference male mouse7/ 20mGyY3


title: 20mGyY1/ reference male mouse7


title: reference male mouse7/ 20mGyY2


title: reference male mouse7/ 20mGyY4


title: Digester_co_62D2

source_name: sludge microbes_co digester_day 62_OLR=1.3

value: Day 62


title: 20mGyYF/ reference male mouse7


title: reference male mouse7/ 20mGyYF


title: Digester_co_62D3


title: reference male mouse7/ 20mGyY1


title: reference male mouse7/ 20mGyYM


title: 20mGyX6/ reference male mouse7


title: Digester_mono_97C1

description: mono digestion with dairy manure, OLR=1

source_name: sludge microbes_mono digester_day 97_OLR=1

value: mono digester 1

value: mono digestion with dairy manure, OLR=1


title: 20mGyX7/ reference male mouse7


title: Digester_co_66D2


title: 20mGyYM/ reference male mouse7


title: reference male mouse7/ 20mGyX7


title: Digester_mono_90C3

description: mono digestion with dairy manure, OLR=1

source_name: sludge microbes_mono digester_day 90_OLR=1

value: mono digester 3


title: 20mGyX5/ reference male mouse7


title: 20mGyX4/ reference male mouse7


title: reference male mouse7/ 20mGyX6


title: reference male mouse7/ 20mGyX5


title: Digester_mono_97C2

description: mono digestion with dairy manure, OLR=1

value: sludge microbes from anaerobic digesters

value: mono digester 2


title: Digester_mono_97C3

description: mono digestion with dairy manure, OLR=1

value: Day 97


title: Digester_co_62D1

value: co digester 1


title: Digester_mono_90C1

description: mono digestion with dairy manure, OLR=1


title: Digester_mono_87C3

description: mono digestion with dairy manure, OLR=1

source_name: sludge microbes_mono digester_day 87_OLR=1


title: reference male mouse7/ 20mGyX2


title: reference male mouse7/ 20mGyX3


title: Digester_mono_87C2

description: mono digestion with dairy manure, OLR=1


title: Digester_mono_83C3

description: mono digestion with dairy manure, OLR=1

source_name: sludge microbes_mono digester_day 83_OLR=1


title: Digester_mono_83C1

description: mono digestion with dairy manure, OLR=1


title: Digester_mono_83C2

description: mono digestion with dairy manure, OLR=1


title: 20mGyX3/ reference male mouse7


title: Digester_mono_69C3

description: mono digestion with dairy manure, OLR=1

source_name: sludge microbes_mono digester_day 69_OLR=1


title: Digester_mono_90C2

description: mono digestion with dairy manure, OLR=1


title: Digester_mono_69C2

description: mono digestion with dairy manure, OLR=1


title: Digester_mono_69C1

description: mono digestion with dairy manure, OLR=1


title: Digester_mono_87C1

description: mono digestion with dairy manure, OLR=1


title: Digester_mono_66C3

description: mono digestion with dairy manure, OLR=1

source_name: sludge microbes_mono digester_day 66_OLR=1


title: Digester_mono_66C2

description: mono digestion with dairy manure, OLR=1


title: Digester_mono_66C1

description: mono digestion with dairy manure, OLR=1


title: SBC3_siYAP1

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

description: 48 h after siYAP transfection

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software  (Affymetrix, Inc).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3'IVT PLUS Reagent Kit User Manual).

growth_protocol: SBC3 and SBC5 cells were cultured with DMEM + 10% FBS.

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

treatment_protocol: SBC3 and SBC5 cells were transfected with 20 nM siRNA using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions.

tag: cell line

value: SCLC cell line

tag: transfection

value: 48 h after siYAP transfection


title: SBC3_siNC

description: 48 h after siNC transfection

value: 48 h after siNC transfection


title: SBC5_siYAP1

description: 48 h after siYAP transfection


title: Digester_mono_62C2

description: mono digestion with dairy manure, OLR=1

source_name: sludge microbes_mono digester_day 62_OLR=1


title: 20mGyXF/ reference male mouse7

source_name: reference male mouse7


title: reference male mouse7/ 20mGyX1


title: reference male mouse7/ 20mGyXM


title: SBC5_siNC

description: 48 h after siNC transfection


title: Digester_mono_62C1

description: mono digestion with dairy manure, OLR=1


title: 20mGyW2/ reference male mouse6

source_name: reference male mouse6


title: reference male mouse6/ 20mGyW2


title: reference male mouse6/ 20mGyW5


title: 20mGyW4/ reference male mouse6


title: AISx112x4

status: Public on Jan 11 2017

city: Philadelphia

first: Annamarie

middle: D

last: Horan

state: PA

address: 3737 Market Street, 6th Floor

institute: University of Pennsylvania

description:
5200_57416_AISx112x4
Acutely injured subject #112 Day 4

hyb_protocol: Labeled RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 4.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: GeneChip 3000 7G scanner with software version AGCC.

data_processing: Partek Genomics Suite, version 6.6 or lower was used to import data using Quartile Normalization, Median Polish summarization. ANOVA with multiple test correction (with a stepped up p value of 0.05 to 0.1 and fold change ± 1.5) was used for discovery rather than statistical purposes, with repeated measures of Acutely Injured Subjects (AIS) included in the analysis to identify potential miRNAs that were differentially expressed between AIS and healthy volunteers. We then validated performance on RT-qPCR.

label: Biotin

source_name: Whole blood, AIS, day 4

label_protocol: Affymetrix FlashTag™ Biotin RNA Labeling Kit.

growth_protocol: Not applicable.

extract_protocol: PaxGene microRNA Isolation kit.

treatment_protocol: Not applicable for healthy volunteers. Standard care surgery for Acutely Injured and Nonunion patients.

value: Whole blood

value: Male

value: 38 yr

tag: race

value: Black

tag: disease state

value: Fracture

tag: time

value: Day 4

tag: group

value: Acutely injured

tag: subject id


title: AISx119x2

description:
5203_57470_AISx119x2
Acutely injured subject #119 Day 2

source_name: Whole blood, AIS, day 2

tag: Sex

value: Female

tag: age

value: 76 yr

value: White

value: Day 2


title: reference male mouse7/ 20mGyXF

value: tail


title: reference male mouse6/ 20mGyW6


title: 20mGyX1/ reference male mouse7


title: AISx086x3

description:
5200_57413_AISx086x3
Acutely injured subject #086 Day 3

source_name: Whole blood, AIS, day 3

value: 55 yr

value: Day 3


title: AISx086x1

description:
5200_57411_AISx086x1
Acutely injured subject #086 Day 1

source_name: Whole blood, AIS, day 1

value: Day 1


title: 20mGyW6/ reference male mouse6


title: AISx112x2

description:
5200_57415_AISx112x2
Acutely injured subject #112 Day 2


title: Digester_mono_62C3

description: mono digestion with dairy manure, OLR=1

value: sludge microbes from anaerobic digesters

value: mono digester 3

value: Day 62

value: mono digestion with dairy manure, OLR=1


title: 20mGyW3/ reference male mouse6


title: 20mGyXM/ reference male mouse7


title: AISx084x4

description:
5200_57410_AISx084x4
Acutely injured subject #084 Day 4

value: Whole blood

value: Male

value: 27 yr


title: AISx112x1

description:
5200_57414_AISx112x1
Acutely injured subject #112 Day 1

value: 38 yr

value: Black

value: Fracture


title: AISx119x3

description:
5203_57471_AISx119x3
Acutely injured subject #119 Day 3

value: Female

value: 76 yr

value: Acutely injured


title: reference male mouse6/ 20mGyW4

value: tail


title: 20mGyW5/ reference male mouse6


title: reference male mouse6/ 20mGyWF


title: 20mGyW1/ reference male mouse6


title: reference male mouse6/ 20mGyWM


title: Bone-Frozen Left Humerus

description:
4068_3981_20
Acute fracture remnant bone

hyb_protocol: Labeled RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 2.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

source_name: Remnant bone

value: Remnant bone (Frozen Left Humerus)

value: 50 yr

value: Unknown


title: Bone-Frozen Left Femur

description:
4068_3981_18
Acute fracture remnant bone

value: Remnant bone (Frozen Left Femur)

value: 47 yr

value: White


title: Bone-Heat Stbl Left Humerus

description:
4068_3981_19
Acute fracture remnant bone

value: Remnant bone (Heat Stbl Left Humerus)


title: Bone-Frozen Jaw

description:
4068_3981_16
Acute fracture remnant bone

value: Remnant bone (Frozen Jaw)

value: 34 yr


title: AISx056x2

description:
5200_57402_AISx056x2
Acutely injured subject #056 Day 2

value: Whole blood

value: Male

value: 39 yr

value: Day 2


title: 20mGyWF/ reference male mouse6


title: Bone-Heat Stbl Jaw

description:
4068_3981_15
Acute fracture remnant bone

value: Remnant bone (Heat Stbl Jaw)

value: Female

value: Fracture


title: AISx084x2

description:
5200_57408_AISx084x2
Acutely injured subject #084 Day 2

value: 27 yr

value: Acutely injured


title: AISx056x1

description:
5200_57401_AISx056x1
Acutely injured subject #056 Day 1

value: Black

value: Day 1


title: AISx078x4

description:
5200_57406_AISx078x4
Acutely injured subject #078 Day 4

value: 25 yr

value: Day 4


title: AISx078x1

description:
5200_57404_AISx078x1
Acutely injured subject #078 Day 1


title: AISx078x2

description:
5200_57405_AISx078x2
Acutely injured subject #078 Day 2


title: AISx084x3

description:
5200_57409_AISx084x3
Acutely injured subject #084 Day 3

value: White

value: Day 3


title: AISx084x1

description:
5200_57407_AISx084x1
Acutely injured subject #084 Day 1


title: AISx056x4

description:
5200_57403_AISx056x4
Acutely injured subject #056 Day 4


title: reference male mouse7/ 20mGyX4

value: tail


title: AISx051x4

description:
5200_57400_AISx051x4
Acutely injured subject #051 Day 4

value: 51 yr


title: 20mGyX2/ reference male mouse7


title: Bone-Frozen Unspecified

description:
4068_3981_14
Acute fracture remnant bone

value: Remnant bone (Frozen Unspecified)

value: 18 yr


title: AISx051x3

description:
5200_57399_AISx051x3
Acutely injured subject #051 Day 3

value: Whole blood

value: Male


title: AISx119x1

description:
5203_57469_AISx119x1
Acutely injured subject #119 Day 1

value: 76 yr


title: Bone-Heat Stbl Humerus

description:
4068_3981_11
Acute fracture remnant bone

value: Remnant bone (Heat Stbl Humerus)

value: Female

value: 52 yr


title: Bone-Heat Stbl Unspecified

description:
4068_3981_13
Acute fracture remnant bone

value: Remnant bone (Heat Stbl Unspecified)

value: Fracture


title: Bone-Frozen Humerus

description:
4068_3981_12
Acute fracture remnant bone

value: Remnant bone (Frozen Humerus)


title: AISx051x2

description:
5200_57398_AISx051x2
Acutely injured subject #051 Day 2

value: Day 2

value: Acutely injured


title: AISx097x2

description:
5200_57395_AISx097x2
Acutely injured subject #097 Day 2

value: 57 yr

value: White


title: Bone-Heat Stbl Left Femur

description:
4068_3981_17
Acute fracture remnant bone

value: Remnant bone (Heat Stbl Left Femur)

value: 47 yr


title: AISx097x3

description:
5200_57396_AISx097x3
Acutely injured subject #097 Day 3

value: Day 3


title: AISx097x1

description:
5200_57394_AISx097x1
Acutely injured subject #097 Day 1

value: Day 1


title: AISx083x4

description:
5200_57393_AISx083x4
Acutely injured subject #083 Day 4

value: Whole blood

value: 63 yr

value: Day 4


title: HV-033-0

description:
4068_33219_65
Healthy volunteer day#0

source_name: Whole venous blood, HV

value: Whole venous blood

value: Healthy


title: HV-035-0

description:
4068_33220_66
Healthy volunteer day#0

value: Male

value: 38 yr


title: HV-037-0

description:
4068_33221_67
Healthy volunteer day#0

value: Female

value: 58 yr


title: AISx083x1

description:
5200_57391_AISx083x1
Acutely injured subject #083 Day 1

value: Fracture


title: HV-038-0

description:
4068_33222_68
Healthy volunteer day#0

value: 43 yr

value: Black


title: AIS-010(nonunion)-185

description:
4068_33216_62
Nonunion subject day#185

source_name: Whole venous blood, NU

value: 31 yr

value: White

value: Nonunion


title: AISx055x1

description:
5200_57389_AISx055x1
Acutely injured subject #055 Day 1

value: 70 yr

value: Acutely injured


title: AIS-010(nonunion)-326

description:
4068_33217_63
Nonunion subject day#326


title: HV-032-0

description:
4068_33218_64
Healthy volunteer day#0

value: 20 yr


title: AISx055x2

description:
5200_57390_AISx055x2
Acutely injured subject #055 Day 2

value: Whole blood

value: Day 2


title: AISx083x2

description:
5200_57392_AISx083x2
Acutely injured subject #083 Day 2

value: 63 yr


title: AIS-004-89

description:
4068_33215_61
Acutely injured subject day#89

source_name: Whole venous blood, AIS

value: Whole venous blood

value: 60 yr


title: AIS-018-12

description:
4068_33214_60
Acutely injured subject day#12

value: 56 yr


title: reference male mouse6/ 20mGyW3

value: tail


title: AISx040x2

description:
5200_57388_AISx040x2
Acutely injured subject #040 Day 2

value: Male

value: 24 yr


title: reference male mouse6/ 20mGyW1


title: AISx040x1

description:
5200_57387_AISx040x1
Acutely injured subject #040 Day 1

value: Fracture

value: Day 1


title: AISx051x1

description:
5200_57397_AISx051x1
Acutely injured subject #051 Day 1

value: 51 yr


title: AISx119x3

description:
5202_57468_AISx119x3
Acutely injured subject #119 Day 3

hyb_protocol: Labeled RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Gene 2.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

source_name: Whole blood, AIS, Day 3

label_protocol: NuGen Pico v2.

value: Female

value: 76 yr

value: White

value: Day 3


title: Bone-Frozen Left elbow

description:
4068_3981_10
Acute fracture remnant bone

value: Remnant bone (Frozen Left elbow)


title: AISx112x4

description:
5201_57465_AISx112x4
Acutely injured subject #112 Day 4

source_name: Whole blood, AIS, Day 4

value: Whole blood

value: 38 yr

value: Black

value: Day 4

value: Acutely injured


title: AISx119x1

description:
5202_57466_AISx119x1
Acutely injured subject #119 Day 1

source_name: Whole blood, AIS, Day 1


title: AISx119x2

description:
5202_57467_AISx119x2
Acutely injured subject #119 Day 2

source_name: Whole blood, AIS, Day 2

value: Day 2


title: AIS-018-11

description:
4068_33213_59
Acutely injured subject day#11

value: Whole venous blood

value: 56 yr


title: AISx035x1

description:
5200_57386_AISx035x1
Acutely injured subject #035 Day 1

value: Male

value: 34 yr


title: AISx086x3

description:
5201_57462_AISx086x3
Acutely injured subject #086 Day 3

value: 55 yr

value: Fracture


title: AISx020x1

description:
5200_57384_AISx020x1
Acutely injured subject #020 Day 1

value: 42 yr

value: Day 1


title: AISx086x1

description:
5201_57460_AISx086x1
Acutely injured subject #086 Day 1

value: White


title: AISx112x1

description:
5201_57463_AISx112x1
Acutely injured subject #112 Day 1


title: AISx032x1

description:
5200_57385_AISx032x1
Acutely injured subject #032 Day 1

value: 30 yr


title: AISx084x3

description:
5201_57458_AISx084x3
Acutely injured subject #084 Day 3

value: 27 yr

value: Day 3


title: AISx084x2

description:
5201_57457_AISx084x2
Acutely injured subject #084 Day 2

value: Whole blood


title: AISx103x3

description:
5200_57383_AISx103x3
Acutely injured subject #103 Day 3

value: 69 yr


title: AISx103x2

description:
5200_57382_AISx103x2
Acutely injured subject #103 Day 2


title: AISx084x4

description:
5201_57459_AISx084x4
Acutely injured subject #084 Day 4

value: Day 4


title: AISx068x2

description:
5200_57380_AISx068x2
Acutely injured subject #068 Day 2

value: Female

value: 24 yr

value: Acutely injured


title: AISx103x1

description:
5200_57381_AISx103x1
Acutely injured subject #103 Day 1


title: AISx084x1

description:
5201_57456_AISx084x1
Acutely injured subject #084 Day 1


title: AISx056x1

description:
5201_57450_AISx056x1
Acutely injured subject #056 Day 1

value: 39 yr

value: Black


title: AISx078x1

description:
5201_57453_AISx078x1
Acutely injured subject #078 Day 1

value: 25 yr


title: AISx056x2

description:
5201_57451_AISx056x2
Acutely injured subject #056 Day 2

value: Male

value: Day 2


title: AISx078x4

description:
5201_57455_AISx078x4
Acutely injured subject #078 Day 4

value: Fracture


title: AISx078x2

description:
5201_57454_AISx078x2
Acutely injured subject #078 Day 2


title: AISx051x4

description:
5201_57449_AISx051x4
Acutely injured subject #051 Day 4

value: 51 yr


title: AISx065x3

description:
5200_57378_AISx065x3
Acutely injured subject #065 Day 3

value: 23 yr

value: White


title: AISx068x1

description:
5200_57379_AISx068x1
Acutely injured subject #068 Day 1

value: Day 1


title: 20mGyWM/ reference male mouse6

value: tail


title: AISx065x2

description:
5200_57377_AISx065x2
Acutely injured subject #065 Day 2

value: Whole blood


title: AISx051x3

description:
5201_57448_AISx051x3
Acutely injured subject #051 Day 3

value: Day 3


title: AISx051x2

description:
5201_57447_AISx051x2
Acutely injured subject #051 Day 2


title: AISx097x3

description:
5201_57445_AISx097x3
Acutely injured subject #097 Day 3

value: 57 yr


title: AISx065x1

description:
5200_57376_AISx065x1
Acutely injured subject #065 Day 1


title: AISx051x1

description:
5201_57446_AISx051x1
Acutely injured subject #051 Day 1


title: AISx056x4

description:
5201_57452_AISx056x4
Acutely injured subject #056 Day 4

value: Day 4


title: AISx060x3

description:
5200_57374_AISx060x3
Acutely injured subject #060 Day 3

value: 42 yr


title: AISx060x4

description:
5200_57375_AISx060x4
Acutely injured subject #060 Day 4

value: Acutely injured


title: AISx083x4

description:
5201_57442_AISx083x4
Acutely injured subject #083 Day 4

value: Female

value: 63 yr


title: ZJ_LCLs_Male_rep1

first: Rui

last: Zhang

address: 52 Fucheng Road

institute: Peking University Cancer Hospital & Institute

description:
LCLs sample
ZJ-LCL-1.AVG_Beta

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

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

data_processing: GenomeStudio and Minfi R package

source_name: LCLs

label_protocol: Standard Illumina Protocol

growth_protocol: Mononuclear cells were isolated by density gradient centrifugation in Ficoll-Hypaque. B-cells were isolated by positive selection using CD19 Dynabeads PanB magnetic beads (Invitrogen).

extract_protocol: genomic DNA was extracted and purified from B cells and LCLs samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: We cultured the cell lines for 4-6 weeks until the cultures contained 20 million cells.

tag: gender


title: AISx112x2

description:
5201_57464_AISx112x2
Acutely injured subject #112 Day 2

value: 38 yr

value: Black


title: AISx083x2

description:
5201_57441_AISx083x2
Acutely injured subject #083 Day 2

value: Day 2


title: AISx083x1

description:
5201_57440_AISx083x1
Acutely injured subject #083 Day 1

value: Fracture


title: cells at day 50, biological rep3

city: Albuquerque

first: Jason

last: Weick

state: New Mexico

address: 915 Camino de Salud NE

department: Neurosciences

institute: University of New Mexico Health Sciences Center

description:
Gene expression data from human pluripotent stem cell-derived neurons after 50 days of differentiation.
HPSNs_Day50-3

hyb_protocol: Two hundred microliters (containing 10 micrograms of fragmented cRNA) of each cocktail was separately hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array for 16h at 45 degree Celsius in the Hybridization Oven 640.

scan_protocol: Arrays were washed on Affymetrix’s GeneChip Fluidics Station 450 using a primary streptavidin phycoerythrin (SAPE) stain, subsequent biotinylated antibody stain, and secondary SAPE stain. Arrays were scanned on Affymetrix’s GeneChip Scanner 3000 7G with AutoLoader. Scanned images obtained by the Affymetrix GeneChip Operating Software (GCOS) v1.2 were used to extract raw signal intensity values per probe set on the array.

data_processing: The data were analyzed with Robust Multi-array Average (RMA) algorithm implemented in R/Bioconductor package affy. The raw intensity values were background corrected, log2 transformed and then quantile normalized. Next, a linear model was fit to the normalized data to obtain an expression measure for each probe set on each array. These procedures were done by reading the raw .CEL files of arrays to an Affybatch object and then running the function rma with the Affybatch object to generate an ExpressionSet object. From the ExpressionSet object we retrieved expression data which are represented in the Sample Data tables. We did not use any custom CDF. The affy package automatically downloaded the appropriate CDF environment for processing the data.

source_name: derivative of WA09

label_protocol: Isolated total RNA was double round amplified, cleaned, and biotin-labeled using Affymetrix’s GeneChip Two-Cycle Target Labeling kit (Santa Clara, CA) with a T7 promoter and Ambion’s MEGAscript T7 High Yield Transcription kit (Austin, TX) as per manufacturer’s protocol. Amplified and labeled cRNA was quantified on a spectrophotometer and run on a 1% TAE gel to check for an evenly distributed range of transcript sizes. Twenty micrograms of cRNA was fragmented to approximately 35-200bp by alkaline treatment (200 mM Tris-acetate, pH 8.2, 500 mM KOAc, 150 mM MgOAc) and run on a 1% TAE gell to verify fragmentation. Separate hybridization cocktails were made using 15 micrograms of fragmented cRNA from each sample as per Affymetrix’s protocol.

growth_protocol: WA09 hESCs were maintained on MEF layers according to previously published protocol (Zhang et al., 2001).

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

treatment_protocol: hESCs were detached from feeder layers and grown in suspension in hESC medium for 4 days and subsequently transitioned to neurosphere medium for 2 more days containing DMEM/F-12 (Invitrogen, San Diego, CA) supplemented with N2 (1:100; Invitrogen), MEM nonessential amino acids (1:100; Invitrogen), heparin (2  g/ml; Sigma, St. Louis, MO). hES aggregates (embryoid bodies) were plated onto tissue culture wells and after 7 days of rosette formation were enzymatically lifted with dispase (1 mg/mL; Roche Diagnostics, Indianapolis, IN) and suspended in neurosphere medium for another 7 days. Aggregates were then plated onto polyornithine-laminin-coated glass coverslips in a neuronal differentiation medium containing Neurobasal medium (Invitrogen), N2 (Invitrogen), supplemented with BDNF (10 ng/ml; PeptroTech, Rocky Hill, NJ), GDNF (10 ng/mL; R & D Systems), cAMP (1 µM; Sigma), ascorbic acid (200 µM; Sigma), and laminin (20 µg/ml; Sigma). Cells remained in this medium throughout differentiation and media was changed every other day.

tag: culture protocol

value: cultured cells (plated)

tag: genotype

value: no known mutations

value: female (XX)

value: day 50

tag: cell type

value: pluripotent stem cell-derived neurons


title: AISx060x1

description:
5200_57372_AISx060x1
Acutely injured subject #060 Day 1

value: Whole blood

value: Male

value: White

value: Day 1


title: AISx097x2

description:
5201_57444_AISx097x2
Acutely injured subject #097 Day 2

value: 57 yr


title: AISx060x2

description:
5200_57373_AISx060x2
Acutely injured subject #060 Day 2

value: 42 yr

value: Acutely injured


title: Bone-HST Femur, rep2 [mRNA]

description:
3808a_24889_8
Acute fracture remnant bone

hyb_protocol: Labeled RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Human Gene 1.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 640. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

source_name: Remnant bone, femur, HST

label_protocol: WT Ambion.

treatment_protocol: Bone fragments were captured at room temperature in the OR and transported on ice to the lab where they were cut into two pieces of approximately equal size. One piece was immediately dropped into liquid nitrogen. The other was placed onto a Mantainor(R) tissue card (Denator, Uppsala Science Park, Sweden) and heat stabilized using the Denator Stabilizer (TM). Prior to RNA extraction, each bone fragment was crushed with the Covaris CryoPrep dry tissue Pulverizer Impactor system.

value: Remnant bone (HST Femur)

value: 97 yr

value: fracture


title: YSLi_LCLs_Female_rep1

description:
LCLs sample
YSLi-LCL.AVG_Beta

value: Female


title: AISx097x1

description:
5201_57443_AISx097x1
Acutely injured subject #097 Day 1

value: Fracture


title: AISx055x1

description:
5201_57438_AISx055x1
Acutely injured subject #055 Day 1

value: 70 yr

value: Black


title: XYL_LCLs_Female_rep1

description:
LCLs sample
XYL-LCL-1.AVG_Beta


title: ZJFeng_LCLs_Male_rep1

description:
LCLs sample
ZJFeng-LCL.AVG_Beta


title: AISx054x4

description:
5200_57371_AISx054x4
Acutely injured subject #054 Day 4

value: 32 yr

value: Day 4


title: AISx054x3

description:
5200_57370_AISx054x3
Acutely injured subject #054 Day 3

value: Day 3


title: cells at day 50, biological rep1

description:
Gene expression data from human pluripotent stem cell-derived neurons after 50 days of differentiation.
HPSNs_Day50-1

value: cultured cells (plated)

value: no known mutations

value: female (XX)

value: day 50

value: pluripotent stem cell-derived neurons


title: Bone-Frozen Elbow [mRNA]

description:
3808a_24887_6
Acute fracture remnant bone

source_name: Remnant bone, elbow, frozen

value: Remnant bone (Frozen Elbow)

value: Male

value: 51 yr

value: White


title: AISx055x2

description:
5201_57439_AISx055x2
Acutely injured subject #055 Day 2

value: Whole blood

value: Day 2

value: Acutely injured


title: SSLing_LCLs_Female_rep1

description:
LCLs sample
SSLing-LCL.AVG_Beta

value: Female


title: LYL_LCLs_Female_rep1

description:
LCLs sample
LYL-LCL-2.AVG_Beta


title: Myong_LCLs_Female_rep1

description:
LCLs sample
MYong-LCL.AVG_Beta


title: Bone-HST Elbow [mRNA]

description:
3808a_24886_5
Acute fracture remnant bone

source_name: Remnant bone, elbow, HST

value: Remnant bone (HST Elbow)

value: fracture


title: AISx040x1

description:
5201_57436_AISx040x1
Acutely injured subject #040 Day 1

value: 24 yr

value: Black

value: Fracture

value: Day 1


title: AISx040x2

description:
5201_57437_AISx040x2
Acutely injured subject #040 Day 2


title: cells at day 30, biological rep3

description:
Gene expression data from immature human pluripotent stem cell-derived neurons after 30 days of differentiation.
HPSNs_Day30-3

value: cultured cells (plated)

value: no known mutations

value: female (XX)

value: day 30

value: immature pluripotent stem cell-derived neurons


title: Lyu_LCLs_Female_rep1

description:
LCLs sample
LYu-LCL.AVG_Beta


title: AISx054x1

description:
5200_57368_AISx054x1
Acutely injured subject #054 Day 1

value: Male

value: 32 yr


title: Bone-Frozen Femur, rep2 [mRNA]

description:
3808a_24888_7
Acute fracture remnant bone

source_name: Remnant bone, femur, frozen

value: Remnant bone (Frozen Femur)

value: 97 yr


title: SSLing_B cells_Female_rep1

description:
normal B cells sample
SSLing-blood.AVG_Beta

source_name: B cells


title: AISx035x1

description:
5201_57435_AISx035x1
Acutely injured subject #035 Day 1

value: Whole blood

value: 34 yr

value: White

value: Acutely injured


title: Bone-HST Mandible [mRNA]

description:
3808a_24884_3
Acute fracture remnant bone

source_name: Remnant bone, mandible, HST

value: Remnant bone (HST Mandible)

value: 39 yr

value: fracture


title: cells at day 30, biological rep1

description:
Gene expression data from immature human pluripotent stem cell-derived neurons after 30 days of differentiation.
HPSNs_Day30-1


title: Bone-Frozen Mandible [mRNA]

description:
3808a_24885_4
Acute fracture remnant bone

source_name: Remnant bone, mandible, frozen

value: Remnant bone (Frozen Mandible)

value: Black


title: postreatment epithelium (tumor) 1457 2013

city: L'HOSPITALET DE LLOBREGAT

first: DAVID

middle: G

last: MOLLEVI

state: Barcelona

address: Gran Via 197-203

department: PROCURE

country: Spain

institute: ICO

description: Laser Capture Microdissection

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: none provided by submitter

source_name: postreatment epithelium (tumor)

label_protocol: standard Affymetrix protocol

extract_protocol: Arcturus Histogene LCM Frozen Section kit

tag: mandard's class

tag: rna extraction mehod

tag: amplification protocol


title: AISx032x1

description:
5201_57434_AISx032x1
Acutely injured subject #032 Day 1

tag: tissue

value: 30 yr

value: Fracture

value: Day 1


title: cells at day 17, biological rep3

description:
Gene expression data from human pluripotent stem cells after 17 days of differentiation.
Day17-3

value: cultured cells (suspension)

value: no known mutations

value: female (XX)

value: day 17

value: pluripotent stem cells


title: cells at day 50, biological rep2

description:
Gene expression data from human pluripotent stem cell-derived neurons after 50 days of differentiation.
HPSNs_Day50-2

value: cultured cells (plated)

value: day 50

value: pluripotent stem cell-derived neurons


title: Bone-HST Femur, rep1 [mRNA]

description:
3808a_24883_2
Acute fracture remnant bone

value: Remnant bone (HST Femur)

value: Female

value: 49 yr

value: White


title: YSLi_B cells_Female_rep1

description:
normal B cells sample
YSLi-blood.AVG_Beta


title: postreatment epithelium (tumor) 1456 2013

description: Laser Capture Microdissection

value: Arcturus Histogene LCM Frozen Section kit


title: AISx020x1

description:
5201_57433_AISx020x1
Acutely injured subject #020 Day 1

value: Whole blood

value: Male

value: 42 yr

value: Acutely injured


title: cells at day 17, biological rep2

description:
Gene expression data from human pluripotent stem cells after 17 days of differentiation.
Day17-2

value: cultured cells (suspension)


title: cells at day 30, biological rep2

description:
Gene expression data from immature human pluripotent stem cell-derived neurons after 30 days of differentiation.
HPSNs_Day30-2

value: no known mutations

value: day 30

value: immature pluripotent stem cell-derived neurons


title: LY_B cells_Female_rep1

description:
normal B cells sample
LY-Blood-2.AVG_Beta


title: Bone-Frozen Femur, rep1 [mRNA]

description:
3808a_24882_1
Acute fracture remnant bone

value: Remnant bone (Frozen Femur)

value: fracture


title: postreatment epithelium (tumor) 1455 2013

description: Laser Capture Microdissection


title: Zjan_B cells_Male_rep1

description:
normal B cells sample
ZJian-blood.AVG_Beta


title: cells at day 17, biological rep1

description:
Gene expression data from human pluripotent stem cells after 17 days of differentiation.
Day17-1

value: female (XX)

value: day 17

value: pluripotent stem cells


title: XYL_B cells_Female_rep1

description:
normal B cells sample
XYL-Blood-2.AVG_Beta

value: Female


title: AISx103x3

description:
5201_57432_AISx103x3
Acutely injured subject #103 Day 3

value: 69 yr

value: Fracture

value: Day 3


title: AISx054x2

description:
5200_57369_AISx054x2
Acutely injured subject #054 Day 2

source_name: Whole blood, AIS, day 2

value: Whole blood

value: 32 yr

value: White

value: Day 2


title: LYL_B cells_Female_rep1

description:
normal B cells sample
LYL-Blood.AVG_Beta


title: AISx103x2

description:
5201_57431_AISx103x2
Acutely injured subject #103 Day 2

value: Male

value: Acutely injured


title: AISx103x1

description:
5201_57430_AISx103x1
Acutely injured subject #103 Day 1

value: Day 1


title: postreatment epithelium (tumor) 1454 2013

description: Laser Capture Microdissection

value: Arcturus Histogene LCM Frozen Section kit


title: AISx068x1

description:
5201_57428_AISx068x1
Acutely injured subject #068 Day 1

value: 24 yr


title: TF1 with human PRL3_5

city: Singapore

first: Chong-Lei

last: Bi

address: #12-02, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

description: gene expression data of TF-1 transfected with (human) PRL-3 gene

hyb_protocol: Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip HG1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000 7G

data_processing: The data were analyzed with Genespring GX 11(Agilent Technologies)

source_name: TF1 hPRL3

label_protocol: Biotinylated cDNA were prepared using Nugen Applause WT kit and Encore biotin module (Nugen, USA) according to the manufecturer's instructions from 100ng total RNA.

growth_protocol: 90% RPMI + 10% FBS + 5 ng/ml human IL-3

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

tag: cell line

value: acute myeloid leukemia (AML) cell line TF-1


title: cells at day 10, biological rep1

description:
Gene expression data from human pluripotent stem cells after 10 days of differentiation.
Day10-1

value: cultured cells (suspension)

value: no known mutations

value: female (XX)

value: day 10


title: ZJFeng_B cells_Male_rep1

description:
normal B cells sample
ZJF-Blood.AVG_Beta


title: cells at day 10, biological rep3

description:
Gene expression data from human pluripotent stem cells after 10 days of differentiation.
Day10-3

value: pluripotent stem cells


title: postreatment epithelium (tumor) 1451 2013

description: Laser Capture Microdissection


title: MY_B cells_Female_rep1

description:
normal B cells sample
MY-Blood-2.AVG_Beta

value: Female


title: cells at day 6, biological rep3

description:
Gene expression data from human pluripotent stem cells after 6 days of differentiation.
Day6-3

value: day 6


title: AISx065x3

description:
5201_57427_AISx065x3
Acutely injured subject #065 Day 3

value: Whole blood

value: 23 yr

value: Fracture

value: Day 3


title: postreatment epithelium (tumor) 1450 2013

description: Laser Capture Microdissection


title: TF1 with human PRL3_4

tag: transfection


title: TF1 with human PRL3_6


title: postreatment epithelium (tumor) 1449 2013

description: Laser Capture Microdissection


title: AISx068x2

description:
5201_57429_AISx068x2
Acutely injured subject #068 Day 2

tag: race

value: White

value: Day 2


title: TF1 with control vector_3

description: gene expression data of TF-1 transfected with control vector

source_name: TF1 pEGFP

value: control


title: postreatment epithelium (tumor) 1453 2013

description: Laser Capture Microdissection

value: Arcturus Histogene LCM Frozen Section kit


title: cells at day 10, biological rep2

description:
Gene expression data from human pluripotent stem cells after 10 days of differentiation.
Day10-2


title: TF1 with control vector_2


title: TF1 with control vector_1


title: AISx065x2

description:
5201_57426_AISx065x2
Acutely injured subject #065 Day 2

value: Male

tag: disease state

value: Acutely injured


title: postreatment epithelium (tumor) 1452 2013

description: Laser Capture Microdissection


title: cells at day 6, biological rep2

description:
Gene expression data from human pluripotent stem cells after 6 days of differentiation.
Day6-2

value: cultured cells (suspension)

tag: time


title: pretreatment epithelium (tumor) 1448 2013

description: Laser Capture Microdissection

source_name: pretreatment epithelium (tumor)


title: Bone-Frozen Femur, rep2 [miRNA]

description:
3808_24888_7
Acute fracture remnant bone

hyb_protocol: Labeled RNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 48ºC to MicroRNA 1.0 GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

value: Remnant bone (Frozen Femur)

value: 97 yr

value: Black

value: fracture


title: AISx065x1

description:
5201_57425_AISx065x1
Acutely injured subject #065 Day 1

value: Day 1

tag: group


title: Bone-Frozen Elbow [miRNA]

description:
3808_24887_6
Acute fracture remnant bone

value: Remnant bone (Frozen Elbow)

value: 51 yr


title: AISx060x4

description:
5201_57424_AISx060x4
Acutely injured subject #060 Day 4

source_name: Whole blood, AIS, Day 4

value: Whole blood

value: 42 yr

value: Day 4

tag: subject id


title: pretreatment epithelium (tumor) 1446 2013

description: Laser Capture Microdissection


title: cells at day 6, biological rep1

description:
Gene expression data from human pluripotent stem cells after 6 days of differentiation.
Day6-1

value: no known mutations

value: female (XX)

value: day 6

value: pluripotent stem cells


title: cells at day 0, biological rep3

description:
Gene expression data from human pluripotent stem cells in culture before differentiation
Day0-3

source_name: Cell line WA09, NIH registry # 0062

value: cultured cells (monolayer)

value: isolated from blastocyst

value: day 0

value: pluripotent stem cells in culture


title: Bone-Frozen Mandible [miRNA]

description:
3808_24885_4
Acute fracture remnant bone

value: Remnant bone (Frozen Mandible)

tag: Sex

value: Male

value: 39 yr


title: pretreatment epithelium (tumor) 1445 2013

description: Laser Capture Microdissection

value: Arcturus Histogene LCM Frozen Section kit


title: cells at day 0, biological rep1

description:
Gene expression data from human pluripotent stem cells in culture before differentiation
Day0-1

tag: age


title: cells at day 0, biological rep2

description:
Gene expression data from human pluripotent stem cells in culture before differentiation
Day0-2

tag: gender


title: AISx060x2

description:
5201_57422_AISx060x2
Acutely injured subject #060 Day 2

source_name: Whole blood, AIS, Day 2

value: White

value: Fracture

value: Day 2

value: Acutely injured


title: pretreatment epithelium (tumor) 1444 2013

description: Laser Capture Microdissection


title: pretreatment epithelium (tumor) 1443 2013

description: Laser Capture Microdissection


title: Bone-HST Mandible [miRNA]

description:
3808_24884_3
Acute fracture remnant bone

value: Remnant bone (HST Mandible)

value: Black

value: fracture


title: Bone-Frozen Femur, rep1 [miRNA]

description:
3808_24882_1
Acute fracture remnant bone

value: Remnant bone (Frozen Femur)

value: Female

value: 49 yr


title: Bone-HST Femur, rep1 [miRNA]

description:
3808_24883_2
Acute fracture remnant bone

value: Remnant bone (HST Femur)


title: AISx060x1

description:
5201_57421_AISx060x1
Acutely injured subject #060 Day 1

source_name: Whole blood, AIS, Day 1

value: Whole blood

value: 42 yr

value: Day 1


title: AISx054x4

description:
5201_57420_AISx054x4
Acutely injured subject #054 Day 4

value: Male

value: 32 yr

value: Day 4


title: AISx054x3

description:
5201_57419_AISx054x3
Acutely injured subject #054 Day 3

source_name: Whole blood, AIS, Day 3

value: White

value: Day 3


title: pretreatment epithelium (tumor) 1442 2013

description: Laser Capture Microdissection

value: Arcturus Histogene LCM Frozen Section kit


title: AISx054x2

description:
5201_57418_AISx054x2
Acutely injured subject #054 Day 2

value: Fracture

value: Day 2

value: Acutely injured


title: AISx060x3

description:
5201_57423_AISx060x3
Acutely injured subject #060 Day 3


title: Bone-HST Elbow [miRNA]

description:
3808_24886_5
Acute fracture remnant bone

value: Remnant bone (HST Elbow)

value: 51 yr

value: fracture


title: pretreatment epithelium (tumor) 1439 2013

description: Laser Capture Microdissection


title: pretreatment epithelium (tumor) 1441 2013

description: Laser Capture Microdissection


title: pretreatment epithelium (tumor) 1440 2013

description: Laser Capture Microdissection


title: AISx054x1

description:
5201_57417_AISx054x1
Acutely injured subject #054 Day 1


title: pretreatment epithelium (tumor) 1438 2013

description: Laser Capture Microdissection