title: Recurence2

description: FFPE NSLC


title: NonRecurence85

status: Public on Feb 13 2018

type: RNA

city: WARREN

first: nien

last: wei

state: NJ

address: 9 northridge way

country: USA

institute: Auspex Diagnostics

description: FFPE NSLC

hyb_protocol: The hybridization cocktails contains 3.75 ug of the fragmented, end-labeled cDNA were applied to the Affy Human Gene 2.0 ST arrays. Hybridization was performaed for 17 hours, and the arrays were washed and stained with GeneChip Fluidicd Station 450.

scan_protocol: Arrays were scanned using Affymetrix  GCS 3000 7G and GeneChip Operating sofware v. 1.4 to produce Cel intensity files.

data_processing: Affymetrix Expression Console is used to extract data

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: surgical tumor tissue

label_protocol: Samples were fragmented and labeled using NuGen Encore Biotin kit

extract_protocol: Total RNA from patient samples were extracted on the Qiasymphony using Qiasymphony RNA kit

tag: group

value: No Recurrence during follow-up


title: NonRecurence82

description: FFPE NSLC


title: NonRecurence84

description: FFPE NSLC


title: NonRecurence81

description: FFPE NSLC


title: NonRecurence75

description: FFPE NSLC


title: NonRecurence76

description: FFPE NSLC


title: NonRecurence88

description: FFPE NSLC


title: NonRecurence83

description: FFPE NSLC


title: NonRecurence80

description: FFPE NSLC


title: NonRecurence77

description: FFPE NSLC


title: NonRecurence72

description: FFPE NSLC


title: NonRecurence70

description: FFPE NSLC


title: NonRecurence69

description: FFPE NSLC


title: NonRecurence66

description: FFPE NSLC


title: NonRecurence71

description: FFPE NSLC


title: NonRecurence74

description: FFPE NSLC


title: NonRecurence73

description: FFPE NSLC


title: NonRecurence68

description: FFPE NSLC


title: NonRecurence65

description: FFPE NSLC


title: NonRecurence61

description: FFPE NSLC


title: NonRecurence64

description: FFPE NSLC


title: NonRecurence62

description: FFPE NSLC


title: NonRecurence56

description: FFPE NSLC


title: NonRecurence59

description: FFPE NSLC


title: NonRecurence49

description: FFPE NSLC


title: NonRecurence60

description: FFPE NSLC


title: NonRecurence53

description: FFPE NSLC


title: NonRecurence57

description: FFPE NSLC


title: NonRecurence54

description: FFPE NSLC


title: NonRecurence67

description: FFPE NSLC


title: NonRecurence50

description: FFPE NSLC


title: NonRecurence63

description: FFPE NSLC


title: NonRecurence58

description: FFPE NSLC


title: NonRecurence47

description: FFPE NSLC


title: NonRecurence51

description: FFPE NSLC


title: NonRecurence44

description: FFPE NSLC


title: NonRecurence55

description: FFPE NSLC


title: NonRecurence48

description: FFPE NSLC


title: NonRecurence52

description: FFPE NSLC


title: NonRecurence46

description: FFPE NSLC


title: NonRecurence41

description: FFPE NSLC


title: NonRecurence45

description: FFPE NSLC


title: exosomes_2mM sodium oxalate_48h_rep3

city: Nanning

first: Xiaofeng

last: Guan

state: Guangxi

address: No 6 SHUANGYONG ROAD

country: China

institute: First Affiliated Hospital of Guangxi Medical University

description: sample name: 32

hyb_protocol: The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min.Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon).

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change.

source_name: exosomes

label_protocol: 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of  fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C.Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: The HK-2 cells in the experimental groups were exposed to 1, 2 mM sodium oxalate for 48 h, and the HK-2 cells with PBS was used as control. 200 ml supernatants were centrifuged (Beckman Coulter, USA) at 300×g at 4℃ for 10 min to remove sodium oxalate and detached cells, followed by 2,000×g for 15 min and 10,000×g for 40 min to deplete residual cellar debrisr, and then the supernatant was filtered through a 0.22 µm filter (MerckMillipore, Germany). The filtered supernatant was centrifuged at 110,000×g for 75 min twice by ultracentrifuge (Beckman Coulter, USA). After isolation, exosomes were resuspended in PBS and Stored at -80℃.

tag: cell line

tag: cell compartment

value: exosomes


title: exosomes_1mM sodium oxalate_48h_rep3

description: sample name: 31


title: NonRecurence39

description: FFPE NSLC


title: NonRecurence38

description: FFPE NSLC


title: exosomes_2mM sodium oxalate_48h_rep2

description: sample name: 22


title: exosomes_0mM sodium oxalate_48h_rep3

description: sample name: 30


title: NonRecurence42

description: FFPE NSLC


title: NonRecurence43

description: FFPE NSLC


title: NonRecurence40

description: FFPE NSLC


title: NonRecurence36

description: FFPE NSLC


title: exosomes_1mM sodium oxalate_48h_rep1

description: sample name: 11


title: NonRecurence37

description: FFPE NSLC


title: NonRecurence34

description: FFPE NSLC


title: exosomes_2mM sodium oxalate_48h_rep1

description: sample name: 12


title: exosomes_0mM sodium oxalate_48h_rep2

description: sample name: 10+20


title: exosomes_0mM sodium oxalate_48h_rep1

description: sample name: 0


title: exosomes_1mM sodium oxalate_48h_rep2

description: sample name: 21


title: NonRecurence78

description: FFPE NSLC


title: NonRecurence30

description: FFPE NSLC


title: NonRecurence31

description: FFPE NSLC


title: NonRecurence28

description: FFPE NSLC


title: NonRecurence27

description: FFPE NSLC


title: NonRecurence32

description: FFPE NSLC


title: NonRecurence26

description: FFPE NSLC


title: NonRecurence29

description: FFPE NSLC


title: NonRecurence33

description: FFPE NSLC


title: NonRecurence35

description: FFPE NSLC


title: NonRecurence24

description: FFPE NSLC


title: NonRecurence20

description: FFPE NSLC


title: NonRecurence22

description: FFPE NSLC


title: Macrophages infected with virulent strain_6h_rep3

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

description: mRNA profile expression of macrophages infected with Leptospira spp, at 6h.

hyb_protocol: Hybridization of samples to the strips was carried out at 48ºC for 20h in a GeneAtlas™ Hybridization Oven, according to the instructions of the GeneAtlas® Hybridization, Wash, and Stain Kit for mRNA Array Strips.

scan_protocol: Following hybridization, wash and stain of strips were performed using the GeneAtlas® Hybridization, Wash, and Stain Kit for mRNA Array Strips in the GeneAtlas Robotic Wash Station. Following, strips were and scanned using the GeneAtlas® Imaging System (Affymetrix).

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Expression Console (Affymetrix) using the Robust Multi-array Average (RMA) algorithm.

organism: Mus musculus

source_name: J774A.1 macrophages in vitro, infected with L. interrogans serovar Copenhageni L1-130

label_protocol: mRNA profiles were obtained from 250 ng/sample of total RNA (RIN 10) using WT PLUS Amplification and Labeling Process. First setp is first strand cDNA synthesis; second strand cDNA synthesis; cRNA amplification; 2nd-cycle ss-cDNA synthesis; template RNA removal; ss-cDNA purification and qualification; fragmentation; terminal labeling and hybridization process in Mouse Gene 2.1 ST Array Strips.

growth_protocol: Murine macrophage cell line J774A.1, provided by the Paul Ehrlich cell bank, Rio de Janeiro, Brazil, was maintained in RPMI-1640 media (Sigma®, USA) supplemented with 10% heat-inactivated fetal bovine serum (Gibco, USA), 100ug/mL streptomycin (Sigma Chemical Co St.Louis, MO), 0.03% L-glutamine solution (Sigma) and 100 UI/mL of penicillin. Cells were incubated at 37º C, 5% CO2 until formation of a confluent monolayer in 6-well plates (3cm wells).

extract_protocol: Total RNA was extracted from macrophages with RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s instructions.  RNA samples were immediately stored at -80ºC. Quantification was performed using NanoDrop (ND-2000 spectrophotometer, Thermo Scientific, Wilmington, DE, USA) and quality of samples was assessed using capillary electrophoresis (Bioanalyzer 2100 Agilent, Santa Clara, CA, USA).

treatment_protocol: Cultured cells were washed tree times with sterile phosphate buffer solution (pH 7,2) for removal of antibiotics and non-adherent cells. L. interrogans and L. biflexa were harvested by centrifugation and the pellet was resuspended in RPMI-1640 media (Sigma®, USA), and 100:1 bacteria:cell were added to macrophages at >90% confluency. Treatments, performed in triplicates, were carried as follows: infection of macrophages with a virulent strain (L. interrogans), infection with attenuated strain (L. interrogans), saprophyte strain (L. biflexa) and non-infected macrophages (controls). All treatments were incubated in fresh RPMI medium, without antibiotics, for 6h at 37º C, 5% C02. Following this period, RNA extraction was immediately performed as described below.

value: J774A.1 murine macrophages

tag: leptospira strain

value: L. interrogans serovar Copenhageni (FIOCRUZ L1-130)


title: NonRecurence21

description: FFPE NSLC


title: NonRecurence25

description: FFPE NSLC


title: Macrophages infected with virulent strain_6h_rep1


title: NonRecurence16

description: FFPE NSLC


title: NonRecurence23

description: FFPE NSLC


title: NonRecurence18

description: FFPE NSLC


title: Macrophages infected with attenuated strain_6h_rep1

source_name: J774A.1 macrophages in vitro, infected with L. interrogans serovar Copenhageni M20

value: L. interrogans serovar Copenhageni M20


title: Macrophages infected with attenuated strain_6h_rep3

value: L. interrogans serovar Copenhageni M22


title: NonRecurence19

description: FFPE NSLC


title: Macrophages infected with virulent strain_6h_rep2


title: NonRecurence17

description: FFPE NSLC


title: Macrophages infected with saprophyte strain_6h_rep3

source_name: J774A.1 macrophages in vitro, infected with L. biflexa serovar Patoc

value: L.biflexa serovar Patoc (FIOCRUZ -Patoc I)


title: Macrophages infected with attenuated strain_6h_rep2

value: L. interrogans serovar Copenhageni M21


title: Macrophages infected with saprophyte strain_6h_rep1


title: Macrophages infected with saprophyte strain_6h_rep2


title: NonRecurence13

description: FFPE NSLC


title: Macrophages_non-infected_6h_rep2

description: mRNA profile expression of macrophages non-infected, at 6h

source_name: J774A.1 macrophages in vitro, non-infected


title: NonRecurence14

description: FFPE NSLC


title: NonRecurence12

description: FFPE NSLC


title: NonRecurence15

description: FFPE NSLC


title: Macrophages_non-infected_6h_rep3


title: NonRecurence11

description: FFPE NSLC


title: Macrophages_non-infected_6h_rep1


title: Mock IP ChIP-exo replicate 3

type: SRA

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description: Replicate 3

library_source: genomic

data_processing:
Library strategy: ChIP-exo
For human ChIP-exo assay, Basecalls were performed using Bcl2fastq version 2.16.
For yeast ChIP-exo assay, Basecalls were performed using Bcl2fastq version 2.20.
For human ChIP-exo, reads were aligned to hg19 genome assembly using bwa mem version 0.7.12 for paired reads.
For yeast ChIP-exo, reads were aligned to sacCer3 genome assembly using bwa mem version 0.7.12 for paired reads. The yeast data are just control experiments that are used in simulations in the manuscript.
ChExMix peak caller; https://github.com/seqcode/chexmix
Genome_build: hg19, sacCer3
Supplementary_files_format_and_content: bed, binding events

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast Mock IP ChIP-exo

growth_protocol: Cells were cultured using YPD media at 25°C to an O.D600 of 0.8-1.0.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols with a minor modification; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

tag: chip antibody

value: Non-specific antibody (Sigma, i5006)

tag: strain

tag: cell type

value: yeast


title: Mock IP ChIP-exo replicate 1

description: Replicate 1


title: Mock IP ChIP-exo replicate 2

description: Replicate 2


title: NonRecurence10

description: FFPE NSLC


title: NonRecurence9

description: FFPE NSLC


title: NonRecurence7

description: FFPE NSLC


title: NonRecurence8

description: FFPE NSLC


title: NonRecurence5

description: FFPE NSLC


title: NonRecurence6

description: FFPE NSLC


title: NonRecurence2

description: FFPE NSLC


title: NonRecurence3

description: FFPE NSLC


title: NonRecurence1

description: FFPE NSLC


title: NonRecurence4

description: FFPE NSLC


title: 5500014072141081110329_H05

city: Hanover

first: Viktor

last: Martyanov

state: NH

address: 7400 Remsen

department: Genetics

institute: Geisel School of Medicine at Dartmouth

hyb_protocol: 2.5 µg of labeled cDNA was hybridized on GeneChip HT HG-U133A Array Plate (Affymetrix) at 48 °C for 17 hours.

scan_protocol: Hybridized array plate was washed and stained on GeneTitan MC Instrument (Affymetrix) and scanned by GeneChip HT Array Plate Scanner (Affymetrix), both operated by Affymetrix GeneChip Command Console Software, version 2.0.

data_processing: Scanned images were subjected to visual inspection and a chip quality report was generated by Affymetrix Expression Console Software. The image data were processed using Robust Multichip Average (RMA) to determine the specific hybridizing signal for each gene. CEL files with the gene expression data were pre-processed via RMA.

source_name: Sample: Human Tissue Biopsy

label_protocol: RNA samples were arrayed into 96-Well Microtiter Microplates (Thermo Fisher Scientific) with randomized design for target labeling process. 50 ng of total skin RNA was amplified and labeled with WT-Ovation Pico System and Encore Biotin Module (NuGEN Technologies) by GeneChip Array Station (Affymetrix).

extract_protocol: RNA was isolated from skin biopsies by RNeasy Fibrous Tissue Mini Kit (Qiagen), with on-column DNase digestion. RNA quality was monitored by Agilent 2100 Bioanalyzer (Agilent Technologies). RNA quantity was measured with NanoDrop  (Thermo Fisher Scientific).

tag: agent


title: MDS1291

city: Taipei City

first: Chi-Yuan

last: Yao

address: No.7, Chung Shan S. Rd.

country: Taiwan

institute: National Taiwan University Hospital

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 24

hyb_protocol: cDNA was hybridized to Affymetrix GeneChip Human Transcriptome Array 2.0 according to the manufacturer’s instructions.

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

data_processing: Expression values were processed with Signal Space Transformation (SST) and Robust Multichip Average method, which included log2 transformation and quantile normalization.

source_name: Bone marrow

label_protocol: RNA was amplified (in vitro transcription) and generate biotin labeled Single-stranded cDNA according to manufacturer's instructions.

extract_protocol: RNA was extracted by TriZol reagent according to manufacturer's instructions. One microgram of RNA from each sample was processed with the QIAGEN miRNeasy mini kit (QIAGEN, Hilden, Germany).

tag: cohort

value: validation

tag: disease state

value: MDS

tag: tissue

value: Bone marrow

tag: condition

value: Pre-treatment

tag: age

tag: gender

value: Male


title: MDS1300

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 28


title: 5500014072141081110329_G05

value: dasatinib


title: MDS1284

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 20


title: 5500014072141081110329_G07


title: MDS1292

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 25

value: Female


title: MDS1281

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 19


title: 5500014072141081110329_E09


title: MDS1288

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 23


title: 5500014072141081110329_F07


title: 5500014072141081110329_H07


title: 5500014072141081110329_E05


title: MDS1301

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 29


title: MDS1269

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 13


title: 5500014072141081110329_F09


title: 5500014072141081110329_E07


title: MDS1278

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 17


title: MDS1293

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 26


title: 5500014072141081110329_F05


title: MDS1271

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 15


title: MDS1286

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 22


title: MDS1302

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 30


title: MDS1285

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 21


title: MDS1280

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 18


title: MDS1277

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 16


title: MDS1270

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 14


title: MDS1294

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 27


title: 5500014072141081110329_D09


title: 5500014072141081110329_D07


title: 5500014072141081110329_C09


title: 5500014072141081110329_C07


title: MDS1263

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 9


title: 5500014072141081110329_D05


title: MDS1265

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 10


title: MDS1266

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 11


title: MDS1261

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 8


title: 5500014072141081110329_B09


title: 5500014072141081110329_A09


title: 5500014072141081110327_H07


title: 5500014072141081110329_A07


title: MDS1257

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 6


title: MDS1259

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 7


title: 5500014072141081110329_C05


title: 5500014072141081110327_H09


title: 5500014072141081110327_H05


title: MDS1267

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 12


title: 5500014072141081110329_A05


title: MDS1246

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 3


title: MDS1243

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 2


title: MDS1254

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 5


title: MDS1240

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 1


title: 5500014072141081110329_B05


title: MDS1163

description:
lncRNA expression data from BM mononuclear cells
TRAINING 175

value: training


title: MDS1166

description:
lncRNA expression data from BM mononuclear cells
TRAINING 176


title: MDS1087

description:
lncRNA expression data from BM mononuclear cells
TRAINING 173


title: MDS1248

description:
lncRNA expression data from BM mononuclear cells
VALIDATION 4


title: 5500014072141081110327_F09


title: 5500014072141081110327_G07


title: MDS1079

description:
lncRNA expression data from BM mononuclear cells
TRAINING 171


title: 5500014072141081110327_G09


title: 5500014072141081110327_D07


title: 5500014072141081110327_F07


title: 5500014072141081110327_E09


title: 5500014072141081110327_G05


title: 5500014072141081110327_F05


title: 5500014072141081110327_D05


title: 5500014072141081110327_C09


title: MDS1161

description:
lncRNA expression data from BM mononuclear cells
TRAINING 174


title: MDS1075

description:
lncRNA expression data from BM mononuclear cells
TRAINING 170


title: MDS1056

description:
lncRNA expression data from BM mononuclear cells
TRAINING 164


title: MDS1070

description:
lncRNA expression data from BM mononuclear cells
TRAINING 168


title: MDS1059

description:
lncRNA expression data from BM mononuclear cells
TRAINING 166


title: 5500014072141081110327_D09


title: MDS1073

description:
lncRNA expression data from BM mononuclear cells
TRAINING 169


title: MDS1063

description:
lncRNA expression data from BM mononuclear cells
TRAINING 167


title: MDS1053

description:
lncRNA expression data from BM mononuclear cells
TRAINING 163


title: MDS1057

description:
lncRNA expression data from BM mononuclear cells
TRAINING 165


title: 5500014072141081110327_E07


title: 5500014072141081110327_C07


title: 5500014072141081110327_C05


title: 5500014072141081110327_E05


title: MDS1052

description:
lncRNA expression data from BM mononuclear cells
TRAINING 162


title: MDS1049

description:
lncRNA expression data from BM mononuclear cells
TRAINING 161


title: 5500014072141081110327_B07


title: MDS1047

description:
lncRNA expression data from BM mononuclear cells
TRAINING 159


title: 5500014072141081110327_B05


title: MDS1048

description:
lncRNA expression data from BM mononuclear cells
TRAINING 160


title: 5500014072141081110327_B09


title: MDS1046

description:
lncRNA expression data from BM mononuclear cells
TRAINING 158


title: 5500014072141081110327_A07


title: 5500014072141081110327_A09


title: 5500014072141081110327_A05


title: MDS1039

description:
lncRNA expression data from BM mononuclear cells
TRAINING 154


title: MDS1040

description:
lncRNA expression data from BM mononuclear cells
TRAINING 155


title: MDS1045

description:
lncRNA expression data from BM mononuclear cells
TRAINING 157


title: MDS1035

description:
lncRNA expression data from BM mononuclear cells
TRAINING 152


title: MDS1036

description:
lncRNA expression data from BM mononuclear cells
TRAINING 153


title: MDS1044

description:
lncRNA expression data from BM mononuclear cells
TRAINING 156


title: MDS1029

description:
lncRNA expression data from BM mononuclear cells
TRAINING 151


title: cMCL P194

city: Barcelona

first: Guillem

last: Clot

address: Rosselló, 153

country: Spain

institute: IDIBAPS

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

scan_protocol: The data were analyzed with the Expression Console applilcation from Affymetrix. We performed RMA to summarize the data.

data_processing: Signal obtained with RMA

source_name: B cell lymphocytes from cMCL patient

label_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HU133plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

extract_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using the 3' IVT Express kit from Affymetrix

treatment_protocol: Total RNA was extracted from peripheral blood samples and spleen preparations using TRIZOL. RNA quality and quantity was assessed using the bionalyzer 2100 and nanodrop spectrophotometer

value: Pheripheral blood


title: FL P199

source_name: B cell lymphocytes from FL patient


title: MDS1025

description:
lncRNA expression data from BM mononuclear cells
TRAINING 148


title: MDS1027

description:
lncRNA expression data from BM mononuclear cells
TRAINING 150


title: MDS1021

description:
lncRNA expression data from BM mononuclear cells
TRAINING 147


title: MDS1020

description:
lncRNA expression data from BM mononuclear cells
TRAINING 146


title: cMCL P195


title: cMCL P189


title: cMCL P193


title: MDS1026

description:
lncRNA expression data from BM mononuclear cells
TRAINING 149


title: nnMCL P191

source_name: B cell lymphocytes from nnMCL patient


title: cMCL P190


title: cMCL P188


title: SDRPL P200

source_name: B cell lymphocytes from SDRPL patient


title: cMCL P192


title: MDS1083

description:
lncRNA expression data from BM mononuclear cells
TRAINING 172


title: MDS1017

description:
lncRNA expression data from BM mononuclear cells
TRAINING 144


title: FL P198


title: MDS1016

description:
lncRNA expression data from BM mononuclear cells
TRAINING 143


title: MDS1018

description:
lncRNA expression data from BM mononuclear cells
TRAINING 145


title: MDS1014

description:
lncRNA expression data from BM mononuclear cells
TRAINING 142


title: SDRPL P197


title: MDS1008

description:
lncRNA expression data from BM mononuclear cells
TRAINING 141


title: cMCL P186


title: cMCL P185


title: MDS1005

description:
lncRNA expression data from BM mononuclear cells
TRAINING 139


title: MDS1007

description:
lncRNA expression data from BM mononuclear cells
TRAINING 140


title: MDS1000

description:
lncRNA expression data from BM mononuclear cells
TRAINING 136


title: cMCL P183


title: cMCL P187


title: nnMCL P184


title: cMCL P182


title: MDS1001

description:
lncRNA expression data from BM mononuclear cells
TRAINING 137


title: MDS1002

description:
lncRNA expression data from BM mononuclear cells
TRAINING 138


title: cMCL P179


title: B-CLPD NOS P176

source_name: B cell lymphocytes from B-CLPD NOS patient


title: cMCL P180


title: B-CLPD NOS P174


title: MDS0993

description:
lncRNA expression data from BM mononuclear cells
TRAINING 135


title: MDS0969

description:
lncRNA expression data from BM mononuclear cells
TRAINING 128


title: MDS0985

description:
lncRNA expression data from BM mononuclear cells
TRAINING 134


title: MDS0981

description:
lncRNA expression data from BM mononuclear cells
TRAINING 133


title: MDS0971

description:
lncRNA expression data from BM mononuclear cells
TRAINING 129


title: MDS0980

description:
lncRNA expression data from BM mononuclear cells
TRAINING 132


title: HCLv P177

source_name: B cell lymphocytes from HCL-v patient


title: SMZL P178

source_name: B cell lymphocytes from SMZL patient


title: LPL  P175

source_name: B cell lymphocytes from LPL patient


title: B-CLPD NOS P170


title: MDS0967

description:
lncRNA expression data from BM mononuclear cells
TRAINING 127


title: SMZL P171


title: MDS0979

description:
lncRNA expression data from BM mononuclear cells
TRAINING 131


title: MDS0962

description:
lncRNA expression data from BM mononuclear cells
TRAINING 126


title: MDS0976

description:
lncRNA expression data from BM mononuclear cells
TRAINING 130


title: B-CLPD NOS P173


title: B-CLPD NOS P165


title: SMZL P168


title: B-CLPD NOS P166


title: MDS0961

description:
lncRNA expression data from BM mononuclear cells
TRAINING 125


title: MDS0954

description:
lncRNA expression data from BM mononuclear cells
TRAINING 121


title: MDS0957

description:
lncRNA expression data from BM mononuclear cells
TRAINING 123


title: MDS0959

description:
lncRNA expression data from BM mononuclear cells
TRAINING 124


title: MDS0955

description:
lncRNA expression data from BM mononuclear cells
TRAINING 122


title: SMZL P167


title: HCLv P162


title: B-CLPD NOS P163


title: B-CLPD NOS P164


title: MDS0949

description:
lncRNA expression data from BM mononuclear cells
TRAINING 118


title: B-CLPD NOS P159


title: B-CLPD NOS P161


title: MDS0952

description:
lncRNA expression data from BM mononuclear cells
TRAINING 119


title: MDS0953

description:
lncRNA expression data from BM mononuclear cells
TRAINING 120


title: B-CLPD NOS P160


title: MDS0945

description:
lncRNA expression data from BM mononuclear cells
TRAINING 117


title: MDS0941

description:
lncRNA expression data from BM mononuclear cells
TRAINING 115


title: MDS0926

description:
lncRNA expression data from BM mononuclear cells
TRAINING 114


title: MDS0911

description:
lncRNA expression data from BM mononuclear cells
TRAINING 110


title: MDS0921

description:
lncRNA expression data from BM mononuclear cells
TRAINING 112


title: B-CLPD NOS P155


title: SMZL P157


title: MDS0944

description:
lncRNA expression data from BM mononuclear cells
TRAINING 116


title: B-CLPD NOS P158


title: SMZL P156


title: MDS0920

description:
lncRNA expression data from BM mononuclear cells
TRAINING 111


title: HCLv P153


title: MDS0924

description:
lncRNA expression data from BM mononuclear cells
TRAINING 113


title: B-CLPD NOS P152


title: MDS0882

description:
lncRNA expression data from BM mononuclear cells
TRAINING 107


title: MDS0903

description:
lncRNA expression data from BM mononuclear cells
TRAINING 109


title: MDS0873

description:
lncRNA expression data from BM mononuclear cells
TRAINING 104


title: LPL P148


title: MDS0884

description:
lncRNA expression data from BM mononuclear cells
TRAINING 108


title: B-CLPD NOS P146


title: B-CLPD NOS P144


title: HCLv P143


title: MDS0879

description:
lncRNA expression data from BM mononuclear cells
TRAINING 106


title: MDS0868

description:
lncRNA expression data from BM mononuclear cells
TRAINING 102


title: CLL P142

source_name: B cell lymphocytes from CLL patient


title: MDS0870

description:
lncRNA expression data from BM mononuclear cells
TRAINING 103


title: FL P141


title: MDS0875

description:
lncRNA expression data from BM mononuclear cells
TRAINING 105


title: nnMCL P181


title: SMZL P145


title: MDS0866

description:
lncRNA expression data from BM mononuclear cells
TRAINING 101


title: SMZL P150


title: MDS0860

description:
lncRNA expression data from BM mononuclear cells
TRAINING 99


title: MDS0849

description:
lncRNA expression data from BM mononuclear cells
TRAINING 97


title: cMCL P135


title: cMCL P137


title: MDS0864

description:
lncRNA expression data from BM mononuclear cells
TRAINING 100


title: cMCL P140


title: nnMCL P133


title: nnMCL P139


title: cMCL P134


title: cMCL P131


title: cMCL P138


title: B-CLPD NOS P136


title: MDS0844

description:
lncRNA expression data from BM mononuclear cells
TRAINING 95


title: MDS0823

description:
lncRNA expression data from BM mononuclear cells
TRAINING 89


title: cMCL P132


title: MDS0826

description:
lncRNA expression data from BM mononuclear cells
TRAINING 91


title: nnMCL P130


title: MDS0836

description:
lncRNA expression data from BM mononuclear cells
TRAINING 94


title: MDS0824

description:
lncRNA expression data from BM mononuclear cells
TRAINING 90


title: MDS0846

description:
lncRNA expression data from BM mononuclear cells
TRAINING 96


title: MDS0829

description:
lncRNA expression data from BM mononuclear cells
TRAINING 92


title: MDS0833

description:
lncRNA expression data from BM mononuclear cells
TRAINING 93


title: cMCL P128


title: MDS0821

description:
lncRNA expression data from BM mononuclear cells
TRAINING 88


title: nnMCL P127


title: nnMCL P125


title: cMCL P129


title: nnMCL P126


title: MDS0817

description:
lncRNA expression data from BM mononuclear cells
TRAINING 87


title: MDS0810

description:
lncRNA expression data from BM mononuclear cells
TRAINING 86


title: MDS0801

description:
lncRNA expression data from BM mononuclear cells
TRAINING 85


title: nnMCL P120


title: MDS0788

description:
lncRNA expression data from BM mononuclear cells
TRAINING 82


title: nnMCL P118


title: MDS0787

description:
lncRNA expression data from BM mononuclear cells
TRAINING 81


title: nnMCL P122


title: MDS0795

description:
lncRNA expression data from BM mononuclear cells
TRAINING 84


title: MDS0786

description:
lncRNA expression data from BM mononuclear cells
TRAINING 80


title: nnMCL P121


title: nnMCL P119


title: cMCL P123


title: MDS0792

description:
lncRNA expression data from BM mononuclear cells
TRAINING 83


title: MDS0782

description:
lncRNA expression data from BM mononuclear cells
TRAINING 78


title: cMCL P116


title: MDS0781

description:
lncRNA expression data from BM mononuclear cells
TRAINING 77


title: nnMCL P113


title: cMCL P112


title: MDS0784

description:
lncRNA expression data from BM mononuclear cells
TRAINING 79


title: nnMCL P114


title: cMCL P117


title: MDS0770

description:
lncRNA expression data from BM mononuclear cells
TRAINING 74


title: MDS0777

description:
lncRNA expression data from BM mononuclear cells
TRAINING 76


title: cMCL P115


title: nnMCL P109


title: nnMCL P110


title: nnMCL P108


title: nnMCL P111


title: nnMCL P105


title: nnMCL P106


title: MDS0771

description:
lncRNA expression data from BM mononuclear cells
TRAINING 75


title: MDS0764

description:
lncRNA expression data from BM mononuclear cells
TRAINING 71


title: MDS0766

description:
lncRNA expression data from BM mononuclear cells
TRAINING 73


title: MDS0740

description:
lncRNA expression data from BM mononuclear cells
TRAINING 67


title: MDS0759

description:
lncRNA expression data from BM mononuclear cells
TRAINING 70


title: MDS0765

description:
lncRNA expression data from BM mononuclear cells
TRAINING 72


title: MDS0742

description:
lncRNA expression data from BM mononuclear cells
TRAINING 68


title: MDS0724

description:
lncRNA expression data from BM mononuclear cells
TRAINING 66


title: nnMCL P107


title: MDS0757

description:
lncRNA expression data from BM mononuclear cells
TRAINING 69


title: cMCL P103


title: MDS0711

description:
lncRNA expression data from BM mononuclear cells
TRAINING 64


title: MDS0699

description:
lncRNA expression data from BM mononuclear cells
TRAINING 62


title: MDS0693

description:
lncRNA expression data from BM mononuclear cells
TRAINING 61


title: MDS0708

description:
lncRNA expression data from BM mononuclear cells
TRAINING 63


title: MDS0719

description:
lncRNA expression data from BM mononuclear cells
TRAINING 65


title: nnMCL P104


title: SMZL P100


title: MDS0858

description:
lncRNA expression data from BM mononuclear cells
TRAINING 98


title: MDS0686

description:
lncRNA expression data from BM mononuclear cells
TRAINING 60


title: B-CLPD NOS P101


title: MDS0672

description:
lncRNA expression data from BM mononuclear cells
TRAINING 57


title: MDS0665

description:
lncRNA expression data from BM mononuclear cells
TRAINING 56


title: MDS0683

description:
lncRNA expression data from BM mononuclear cells
TRAINING 59


title: cMCL P102


title: MDS0674

description:
lncRNA expression data from BM mononuclear cells
TRAINING 58


title: MDS0662

description:
lncRNA expression data from BM mononuclear cells
TRAINING 55


title: SMZL P097


title: MDS0661

description:
lncRNA expression data from BM mononuclear cells
TRAINING 54


title: SMZL P099


title: SMZL P091


title: MDS0653

description:
lncRNA expression data from BM mononuclear cells
TRAINING 53


title: SMZL P092


title: SMZL P098


title: SMZL P095


title: SMZL P096


title: SMZL P090


title: SDRPL P094


title: B-CLPD NOS P093


title: SMZL P088


title: MDS0650

description:
lncRNA expression data from BM mononuclear cells
TRAINING 52


title: MDS0625

description:
lncRNA expression data from BM mononuclear cells
TRAINING 49


title: LPL P085


title: MDS0624

description:
lncRNA expression data from BM mononuclear cells
TRAINING 48


title: MDS0626

description:
lncRNA expression data from BM mononuclear cells
TRAINING 50


title: MDS0637

description:
lncRNA expression data from BM mononuclear cells
TRAINING 51


title: SMZL P087


title: B-CLPD NOS P082


title: MDS0612

description:
lncRNA expression data from BM mononuclear cells
TRAINING 47


title: LPL P084


title: B-CLPD NOS P083


title: CLL P081


title: B-CLPD NOS P080


title: MDS0600

description:
lncRNA expression data from BM mononuclear cells
TRAINING 46


title: MDS0592

description:
lncRNA expression data from BM mononuclear cells
TRAINING 45


title: SMZL P086


title: B-CLPD NOS P079


title: MDS0570

description:
lncRNA expression data from BM mononuclear cells
TRAINING 43


title: B-CLPD NOS P078


title: MDS0565

description:
lncRNA expression data from BM mononuclear cells
TRAINING 42


title: MDS0560

description:
lncRNA expression data from BM mononuclear cells
TRAINING 41


title: MDS0549

description:
lncRNA expression data from BM mononuclear cells
TRAINING 39


title: B-CLPD NOS P076


title: MDS0557

description:
lncRNA expression data from BM mononuclear cells
TRAINING 40


title: MDS0589

description:
lncRNA expression data from BM mononuclear cells
TRAINING 44


title: MDS0540

description:
lncRNA expression data from BM mononuclear cells
TRAINING 38


title: CLL P077


title: MDS0539

description:
lncRNA expression data from BM mononuclear cells
TRAINING 37


title: CLL P074


title: B-CLPD NOS P075


title: B-CLPD NOS P073


title: MDS0530

description:
lncRNA expression data from BM mononuclear cells
TRAINING 35


title: CLL P072


title: MDS0537

description:
lncRNA expression data from BM mononuclear cells
TRAINING 36


title: CLL P070


title: MDS0527

description:
lncRNA expression data from BM mononuclear cells
TRAINING 34


title: MDS0525

description:
lncRNA expression data from BM mononuclear cells
TRAINING 33


title: METASTASIS_Metastasis_patient30

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description:
1025
Tumor metastasis of patient 30.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were log(2) transformed and robust spline normalized using the lumi package in R.

source_name: Clinical breast cancer specimen, metastasis

label_protocol: Biotinylated cRNA were prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays.

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

value: female

value: breast cancer

tag: tumor class

value: metastasis

tag: tumor type

tag: patient


title: LRC_Recurrence_patient38

description:
1017
Local recurrence of patient 38.

source_name: Clinical breast cancer specimen, LRC

value: local recurrence cancer

value: recurrence


title: MDS0520

description:
lncRNA expression data from BM mononuclear cells
TRAINING 31


title: MBC_Controlateral_patient20

description:
1002
Second tumor of patient 20 with metachronous bilateral cancer.

source_name: Clinical breast cancer specimen, MBC

value: metachronous bilateral cancer

value: controlateral


title: MDS0523

description:
lncRNA expression data from BM mononuclear cells
TRAINING 32


title: LRC_Recurrence_patient35

description:
1014
Local recurrence of patient 35.


title: METASTASIS_Primary_patient30

description:
646
Primary tumor of patient 30 with metastasis.

value: primary


title: LRC_Primary_patient38

description:
582
Primary tumor of patient 38 with local recurrence.


title: CLL P071


title: MDS0515

description:
lncRNA expression data from BM mononuclear cells
TRAINING 29


title: CLL P069


title: CLL P067


title: MDS0514

description:
lncRNA expression data from BM mononuclear cells
TRAINING 28


title: MBC_Primary_patient20

description:
518
Primary tumor of patient 20 with metachronous bilateral cancer.


title: MDS0519

description:
lncRNA expression data from BM mononuclear cells
TRAINING 30


title: CLL P065


title: CLL P066


title: MBC_Primary_patient29

description:
555
Primary tumor of patient 29 with metachronous bilateral cancer.


title: CLL P063


title: CLL P064


title: MBC_Controlateral_patient29

description:
1011
Second tumor of patient 29 with metachronous bilateral cancer.


title: LRC_Primary_patient35

description:
569
Primary tumor of patient 35 with local recurrence.


title: MBC_Primary_patient28

description:
547
Primary tumor of patient 28 with metachronous bilateral cancer.


title: CLL P062


title: MBC_Controlateral_patient25

description:
1007
Second tumor of patient 25 with metachronous bilateral cancer.


title: MDS0512

description:
lncRNA expression data from BM mononuclear cells
TRAINING 27


title: LRC_Recurrence_patient42

description:
1022
Local recurrence of patient 42.


title: MBC_Primary_patient25

description:
531
Primary tumor of patient 25 with metachronous bilateral cancer.


title: MDS0504

description:
lncRNA expression data from BM mononuclear cells
TRAINING 26


title: CLL P060


title: LRC_Primary_patient42

description:
603
Primary tumor of patient 42 with local recurrence.


title: CLL P061


title: MDS0395

description:
lncRNA expression data from BM mononuclear cells
TRAINING 25


title: MDS0394

description:
lncRNA expression data from BM mononuclear cells
TRAINING 24


title: CLL P059


title: MDS0389

description:
lncRNA expression data from BM mononuclear cells
TRAINING 22


title: CLL P057


title: MDS0391

description:
lncRNA expression data from BM mononuclear cells
TRAINING 23


title: CLL P058


title: CLL P056


title: MDS0388

description:
lncRNA expression data from BM mononuclear cells
TRAINING 21


title: MBC_Controlateral_patient28

description:
1010
Second tumor of patient 28 with metachronous bilateral cancer.


title: CLL P055


title: MBC_Primary_patient23

description:
526
Primary tumor of patient 23 with metachronous bilateral cancer.


title: MDS0381

description:
lncRNA expression data from BM mononuclear cells
TRAINING 20


title: CLL P052


title: MBC_Controlateral_patient23

description:
1005
Second tumor of patient 23 with metachronous bilateral cancer.


title: LRC_Primary_patient39

description:
590
Primary tumor of patient 39 with local recurrence.


title: CLL P054


title: MDS0380

description:
lncRNA expression data from BM mononuclear cells
TRAINING 19


title: SBC_B_patient4

description:
10021
Primary tumor of patient 4 with synchronous bilateral cancer. Sample B.

source_name: Clinical breast cancer specimen, SBC

value: synchronous bilateral cancer

value: B


title: MDS0373

description:
lncRNA expression data from BM mononuclear cells
TRAINING 17

value: MDS

value: Bone marrow


title: SBC_B_patient12

description:
10040
Primary tumor of patient 12 with synchronous bilateral cancer. Sample B.


title: MDS0365

description:
lncRNA expression data from BM mononuclear cells
TRAINING 16

value: Pre-treatment

value: Male


title: MDS0353

description:
lncRNA expression data from BM mononuclear cells
TRAINING 15

value: Female


title: CLL P051


title: SBC_A_patient12

description:
10039
Primary tumor of patient 12 with synchronous bilateral cancer. Sample A.

value: A


title: LRC_Primary_patient32

description:
558
Primary tumor of patient 32 with local recurrence.


title: CLL P050

value: Pheripheral blood


title: CLL P047


title: CLL P048


title: MDS0307

description:
lncRNA expression data from BM mononuclear cells
TRAINING 13

value: training


title: CLL P049


title: MDS0376

description:
lncRNA expression data from BM mononuclear cells
TRAINING 18


title: MBC_Controlateral_patient26

description:
1008
Second tumor of patient 26 with metachronous bilateral cancer.

value: female

value: breast cancer


title: MBC_Primary_patient26

description:
540
Primary tumor of patient 26 with metachronous bilateral cancer.


title: CLL P044


title: MDS0303

description:
lncRNA expression data from BM mononuclear cells
TRAINING 11


title: CLL P045


title: MBC_Controlateral_patient19

description:
1001
Second tumor of patient 19 with metachronous bilateral cancer.


title: MDS0298

description:
lncRNA expression data from BM mononuclear cells
TRAINING 10


title: KL KO repl 3

city: Durham

first: LUIGI

last: RACIOPPI

state: North Carolina

address: La Salle, GSRB1 2006

department: Medicine

institute: Duke University

description:
Gene expression from KL isolated from Camkk2-/- mice
BM-KL7

hyb_protocol: Hybridizations were performed at Sequencing and Genome Technologies Shared Resource (Duke University) according to standard operative procedures.

scan_protocol: Scans were performed at Sequencing and Genome Technologies Shared Resource (Duke University) according to standard operative procedures.

data_processing: Partek Genomics Suite 6.6 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on the entire data set. Multi-way ANOVA and fold change were performed to select target genes that were differentially expressed between ___ and ___. Top differentially expressed genes were selected with p value cutoff of ___ based on ANOVA test and fold change cutoff of __. Hierarchical Clustering was performed on differentially expressed genes based on Average Linkage with Pearson's Dissimilarity.

label: Biotin

source_name: KL KO

label_protocol: Labellings were performed at Sequencing and Genome Technologies Shared Resource (Duke University) according to standard operative procedures.

extract_protocol: Eukaryote Total RNA Pico

tag: genotype/variation

value: Bone Marrow

value: KL cells


title: CLL P046


title: CLL P043


title: KL KO repl 4

description:
Gene expression from KL isolated from Camkk2-/- mice
BM-KL8


title: KL KO repl 2

description:
Gene expression from KL isolated from Camkk2-/- mice
BM-KL6


title: MBC_Primary_patient19

description:
508
Primary tumor of patient 19 with metachronous bilateral cancer.

value: metachronous bilateral cancer


title: MDS0273

description:
lncRNA expression data from BM mononuclear cells
TRAINING 9


title: MDS0312

description:
lncRNA expression data from BM mononuclear cells
TRAINING 14


title: MDS0305

description:
lncRNA expression data from BM mononuclear cells
TRAINING 12


title: KL KO repl 1

description:
Gene expression from KL isolated from Camkk2-/- mice
BM-KL5


title: MDS0267

description:
lncRNA expression data from BM mononuclear cells
TRAINING 8


title: CLL P042


title: KL WT repl 3

description:
Gene expression from KL isolated from WT mice
BM-KL3

source_name: KL WT

value: WT


title: KL WT repl 4

description:
Gene expression from KL isolated from WT mice
BM-KL4


title: MDS0203

description:
lncRNA expression data from BM mononuclear cells
TRAINING 6


title: KL WT repl 2

description:
Gene expression from KL isolated from WT mice
BM-KL2


title: CLL P040


title: MDS0152

description:
lncRNA expression data from BM mononuclear cells
TRAINING 4


title: MDS0129

description:
lncRNA expression data from BM mononuclear cells
TRAINING 3


title: KL WT repl 1

description:
Gene expression from KL isolated from WT mice
BM-KL1


title: CLL P041


title: CLL P038


title: MDS0213

description:
lncRNA expression data from BM mononuclear cells
TRAINING 7


title: LRC_Recurrence_patient39

description:
1019
Local recurrence of patient 39.

value: local recurrence cancer

value: recurrence


title: SBC_B_patient14

description:
10046
Primary tumor of patient 14 with synchronous bilateral cancer. Sample B.

value: synchronous bilateral cancer

value: B


title: MDS0154

description:
lncRNA expression data from BM mononuclear cells
TRAINING 5

value: MDS

value: Bone marrow


title: CLL P037


title: MBC_Primary_patient22

description:
520
Primary tumor of patient 22 with metachronous bilateral cancer.

value: primary


title: LRC_Primary_patient37

description:
581
Primary tumor of patient 37 with local recurrence.


title: SBC_A_patient14

description:
10045
Primary tumor of patient 14 with synchronous bilateral cancer. Sample A.


title: SBC_B_patient5

description:
10023
Primary tumor of patient 5 with synchronous bilateral cancer. Sample B.


title: NoAb ChIP-exo replicate 1

description: Replicate 1

source_name: MCF-7 cell ChIP-exo

growth_protocol: Cells were cultured using DMEM with 10% heat inactivated FBS at 37°C with 5% CO2 in air.

treatment_protocol:
Cells were incubated in phenol red-free, charcoal stripped FBS for 48 hours and then treated for 1 hour with 17 β-estradiol (E2, Sigma) at 100 μM.
Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

tag: cell line

value: epithelial


title: MDS0114

description:
lncRNA expression data from BM mononuclear cells
TRAINING 2

source_name: Bone marrow

value: Pre-treatment

value: Male


title: KSL KO repl 4

description:
Gene expression from KSL isolated from Camkk2-/- mice
BM-KSL16

source_name: KSL KO

value: KSL cells


title: LRC_Recurrence_patient37

description:
1016
Local recurrence of patient 37.

value: female


title: CLL P036

value: Pheripheral blood


title: FoxA1 ChIP-exo replicate 2

description:
Replicate 2
FoxA1_MCF7_ChIP-exo_ChExMixPeaks.bed

value: FoxA1 (Santa Cruz, sc-514695 X, Lot I2116)


title: FoxA1 ChIP-exo replicate 1

description:
Replicate 1
FoxA1_MCF7_ChIP-exo_ChExMixPeaks.bed


title: CTCF ChIP-exo replicate 1

description:
Replicate 1
CTCF_MCF7_ChIP-exo_ChExMixPeaks.bed


title: MDS0060

description:
lncRNA expression data from BM mononuclear cells
TRAINING 1

value: training


title: KSL KO repl 1

description:
Gene expression from KSL isolated from Camkk2-/- mice
BM-KSL13

value: Bone Marrow


title: LRC_Recurrence_patient32

description:
1012
Local recurrence of patient 32.

value: breast cancer


title: ERalpha ChIP-exo replicate 2

description:
Replicate 2
Era_MCF7_ChIP-exo_ChExMixPeaks.bed

value: ERalpha (Santa Cruz, sc-8002 X, Lot B0416)


title: KSL WT repl 4

description:
Gene expression from KSL isolated from WT mice
BM-KSL12

source_name: KSL WT

value: WT


title: CLL P039


title: CLL P034


title: SBC_A_patient5

description:
10022
Primary tumor of patient 5 with synchronous bilateral cancer. Sample A.

value: synchronous bilateral cancer

value: A


title: CLL P032


title: KSL KO repl 2

description:
Gene expression from KSL isolated from Camkk2-/- mice
BM-KSL14


title: SBC_B_patient13

description:
10044
Primary tumor of patient 13 with synchronous bilateral cancer. Sample B.

value: B


title: SBC_A_patient13

description:
10043
Primary tumor of patient 13 with synchronous bilateral cancer. Sample A.


title: KSL WT repl 2

description:
Gene expression from KSL isolated from WT mice
BM-KSL10


title: KSL WT repl 3

description:
Gene expression from KSL isolated from WT mice
BM-KSL11


title: CLL P035


title: ERalpha ChIP-exo replicate 1

description:
Replicate 1
Era_MCF7_ChIP-exo_ChExMixPeaks.bed

value: ERalpha (Abcam, ab108398, Lot GR2992441)


title: LRC_Primary_patient33

description:
608
Primary tumor of patient 33 with local recurrence.

value: local recurrence cancer

value: primary


title: LRC_Recurrence_patient33

description:
1023
Local recurrence of patient 33.

value: recurrence


title: CLL P031


title: KSL KO repl 3

description:
Gene expression from KSL isolated from Camkk2-/- mice
BM-KSL15


title: MBC_Controlateral_patient22

description:
1004
Second tumor of patient 22 with metachronous bilateral cancer.

value: metachronous bilateral cancer

value: controlateral


title: SBC_A_patient4

description:
10020
Primary tumor of patient 4 with synchronous bilateral cancer. Sample A.

value: female


title: CLL P033

value: Pheripheral blood


title: CLL P030


title: LRC_Recurrence_patient40

description:
1020
Local recurrence of patient 40.


title: LRC_Primary_patient40

description:
599
Primary tumor of patient 40 with local recurrence.


title: KSL WT repl 1

description:
Gene expression from KSL isolated from WT mice
BM-KSL9

value: KSL cells


title: CLL P029


title: CLL P028


title: MBC_Primary_patient24

description:
527
Primary tumor of patient 24 with metachronous bilateral cancer.


title: CLL P026


title: CLL P025


title: SBC_A_patient11

description:
10037
Primary tumor of patient 11 with synchronous bilateral cancer. Sample A.


title: CLL P024


title: SBC_B_patient11

description:
10038
Primary tumor of patient 11 with synchronous bilateral cancer. Sample B.


title: MBC_Primary_patient27

description:
542
Primary tumor of patient 27 with metachronous bilateral cancer.


title: SMZL P019


title: HCL P017

source_name: B cell lymphocytes from HCL patient


title: CLL P022


title: CLL P027


title: SDRPL P020

source_name: B cell lymphocytes from SDRPL patient


title: MBC_Controlateral_patient27

description:
1009
Second tumor of patient 27 with metachronous bilateral cancer.


title: SBC_B_patient9

description:
10034
Primary tumor of patient 9 with synchronous bilateral cancer. Sample B.


title: LRC_Primary_patient36

description:
579
Primary tumor of patient 36 with local recurrence.


title: LRC_Recurrence_patient36

description:
1015
Local recurrence of patient 36.


title: CLL P021


title: CLL P023


title: SMZL P018


title: SBC_A_patient9

description:
10033
Primary tumor of patient 9 with synchronous bilateral cancer. Sample A.


title: B-CLPD NOS P016

source_name: B cell lymphocytes from B-CLPD NOS patient


title: SBC_A_patient10

description:
10035
Primary tumor of patient 10 with synchronous bilateral cancer. Sample A.


title: SBC_B_patient1

description:
10002
Primary tumor of patient 1 with synchronous bilateral cancer. Sample B.


title: SBC_B_patient10

description:
10036
Primary tumor of patient 10 with synchronous bilateral cancer. Sample B.


title: CaTLO4 no H2O2 (Cy3) v.s. CaTLO4 +5 mM H2O2  (Cy5) 3

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

hyb_protocol: Hybridization and washing of the arrays was carried out using the Agilent Gene Expression Hybridization Kit and Gene Expression Wash Pack according the manufacturer’s instructions.

scan_protocol: Slides were scanned using the GenePix personal 4100A scanner (Axon) and data was extracted with GenePix Pro 6.1 (Axon).

data_processing: Spots were flagged absent if the signal was less than background +1 standard deviation in both fluorescent channels. Raw data was exported to GeneSpring GX10 and signals for each replicate spot were background corrected and normalized using Loess normalization. Log2 fluorescence ratios were generated for each replicate spot and averaged. Oligonucleotides were excluded from analysis if >50% of replicates in each condition were flagged absent.

organism: Candida dubliniensis

source_name: ∆∆tlo::TLO4 - untreated

label_protocol: Total RNA was labelled with Cy5 or Cy3 using the Agilent Two-Color Low RNA input Linear Amplification Kit PLUS

growth_protocol: Strains ∆∆tlo::TLO1 and ∆∆tlo::TLO4 were grown to exponential phase (OD600 of 0.8 nm) at 37 °C in 100 ml YEPD with shaking at 200 rpm. Each culture was then divided into two 50 ml cultures, with one treated with 5 mM H2O2 and both cultures were incubated for a further 30 min at 37 °C.

extract_protocol: Total RNA was extracted using Tri-reagent (Sigma) using a microdismembrator (Braun, Melsungen,Germany).

treatment_protocol: Cells were spun down at 2,500 x g for 5 min and flash frozen in liquid N2

tag: genotype

tag: treatment

source_name: Strains ∆∆tlo::TLO4 - with H2O2

value: YEPD broth containing 5 mM H2O2


title: CaTLO4 no H2O2 (Cy5) v.s. CaTLO4 +5 mM H2O2  (Cy3) 2


title: CaTLO4 no H2O2 (Cy3) v.s. CaTLO4 +5 mM H2O2  (Cy5) 1


title: CaTLO4 no H2O2 (Cy3) v.s. CaTLO4 +5 mM H2O2  (Cy5) 4


title: CaTLO1 no H2O2 (Cy5) v.s. CaTLO1 +5 mM H2O2  (Cy3) 2

source_name: ∆∆tlo::TLO1 - untreated

source_name: Strains ∆∆tlo::TLO1 - with H2O2


title: SBC_B_patient15

description:
10048
Primary tumor of patient 15 with synchronous bilateral cancer. Sample B.


title: CaTLO1 no H2O2 (Cy3) v.s. CaTLO1 +5 mM H2O2  (Cy5) 3


title: CaTLO1 no H2O2 (Cy3) v.s. CaTLO1 +5 mM H2O2  (Cy5) 1


title: B-CLPD NOS P015


title: SBC_B_patient7

description:
10029
Primary tumor of patient 7 with synchronous bilateral cancer. Sample B.


title: SBC_A_patient1

description:
10001
Primary tumor of patient 1 with synchronous bilateral cancer. Sample A.


title: SBC_A_patient7

description:
10028
Primary tumor of patient 7 with synchronous bilateral cancer. Sample A.


title: HCL P014


title: HCL P013


title: B-CLPD NOS P012


title: SBC_A_patient15

description:
10047
Primary tumor of patient 15 with synchronous bilateral cancer. Sample A.


title: SBC_B_patient2

description:
10008
Primary tumor of patient 2 with synchronous bilateral cancer. Sample B.


title: SMZL P010

source_name: B cell lymphocytes from SMZL patient


title: SBC_A_patient2

description:
10007
Primary tumor of patient 2 with synchronous bilateral cancer. Sample A.


title: FL P007

source_name: B cell lymphocytes from FL patient


title: HCL P011


title: SBC_A_patient6

description:
10024
Primary tumor of patient 6 with synchronous bilateral cancer. Sample A.


title: CaTLO1 no H2O2 (Cy3) v.s. CaTLO1 +5 mM H2O2  (Cy5) 4


title: SBC_B_patient17

description:
10055
Primary tumor of patient 17 with synchronous bilateral cancer. Sample B.


title: Cx E2 1908

city: Beaverton

first: Ov

middle: D

last: Slayden

state: OR

address: 505 NW 185th Ave

department: Division of Reproductive Sciences

institute: Oregon National Primate Research Center; Oregon Health & Science University

description:
gene expression data from the cervix in the follicular phase
623OS

hyb_protocol: Amplified and labeled cDNA target samples were each hybridized to a Rhesus Gene 1.0 ST array at 45 degrees celcius for 18hrs at a rotation speed of 60rpm.

scan_protocol: Image processing was performed using Affymetrix GeneChip Command Consol (AGCC) v.3.1.1 software.

data_processing: Expression analysis was performed using Affymetrix Expression Console build 1.4.1.46.

organism: Macaca mulatta

source_name: cervix after 14 days of estrogen only exposure

label_protocol: Labeled target cDNA was prepared from the total RNA samples. Samples were amplified and labeled using the NuGEN Pico WTA system v.2 w/ Encore labeling.

growth_protocol: Twenty five rhesus macaques were ovariectomized and assigned into five hormone profile groups (E2 only, E+1P, E+3P, E+7P, and E+14P). Macaques were artificially cycled with subcutaneous estrogen (E2) and progesterone (P) implants. All twenty five subjects had an estrogen implant placed in their scapular region. P implants were also placed in four of the groups for either one, three, seven, or fourteen days.

extract_protocol: Tissue was homogenized in trizol according to the manufacturer's instructions. Extraction of total RNA was performed using the Qiagen RNeasy® Mini Kit.

treatment_protocol: All five groups were necropsied at their respective hormonal time point in the artifical cycle. Tissue was collected, dissected fresh, and frozen in -80 degrees celcius prior to RNA extraction.

value: cervix


title: FL P008


title: Cx E2 1907


title: FL P009


title: FL P004


title: SBC_B_patient18

description:
10058
Primary tumor of patient 18 with synchronous bilateral cancer. Sample B.

source_name: Clinical breast cancer specimen, SBC

value: breast cancer


title: FL P006


title: FL P003


title: FL P005


title: Nuclear RNA-seq XRN2-AID minus auxin rep 2

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

country: United Kingdom

institute: University of Exeter

library_source: transcriptomic

data_processing:
Adapters removed from sequencing reads using Trim Galore v0.4.4 (wrapper tool for Cutadapt v1.9.1).
Alignment with Hisat2 v2.0.5 to ensembl GRCh38. mNET-seq files used the paired-end parmameter '--fr' to select concordatly mapped pairs.
Extraction of properly mapped single end reads using samtools v1.4.1.
mNET-seq profiles were generated with the 3' most nucleotide of fragments (reverse complement of the 5' most nucleotide of the second read displayed with the strandedness of the first read) for concordantly mapped reads with the samflag pairs 99/147 and 83/163.
Bigwig files were generated from BAM files using the bamCoverage of Deeptools v2.5.3-2-503c71b.
Genome_build: GRCh38
Supplementary_files_format_and_content: Bigwig files represent read coverage (RPKM) over 50bp windows across the genome.

molecule: nuclear RNA

source_name: HCT116 Nuclear RNA-seq XRN2-AID Sleeping Beauty(TIR1) minus auxin

growth_protocol: HCT116 cell lines were maintianed in DMEM with 10% fetal bovine serum, pen/strep at 37 °C and 5% CO2.

extract_protocol:
Nuclear RNA was extracted from isolated nuclei using Trizol reagent.
Nuclear RNA was depleted of ribosomal RNA using Illumina Ribo-Zero Gold (Illumina #MRZE706). Library was constructed using Illumina TruSeq® Stranded Total RNA (Illumina #20020596)

treatment_protocol: Control: Treated for 1 hour with ethanol.

value: Control:auxin untreated Nuclear RNA

tag: molecule subtype

value: Nucleoplasmic RNA


title: Cx E2 1897


title: SBC_A_patient17

description:
10054
Primary tumor of patient 17 with synchronous bilateral cancer. Sample A.

value: synchronous bilateral cancer


title: Nuclear RNA-seq Unmodified at XRN2 rep 2

source_name: HCT116 Nuclear RNA-seq unmodified at XRN2 Sleeping Beauty(TIR1)


title: Nuclear RNA-seq XRN2-AID plus auxin rep 2

source_name: HCT116 Nuclear RNA-seq XRN2-AID Sleeping Beauty(TIR1) plus auxin

treatment_protocol: Auxin was added to cell media at a final concentration of 500 µM  1 h  prior to collection.

value: auxin treated Nuclear RNA


title: SBC_A_patient18

description:
10057
Primary tumor of patient 18 with synchronous bilateral cancer. Sample A.

value: A


title: SBC_A_patient8

description:
10031
Primary tumor of patient 8 with synchronous bilateral cancer. Sample A.


title: SBC_B_patient6

description:
10025
Primary tumor of patient 6 with synchronous bilateral cancer. Sample B.

value: B


title: SBC_B_patient8

description:
10032
Primary tumor of patient 8 with synchronous bilateral cancer. Sample B.


title: Cx E2 1919


title: Cx E+14P 1703

description:
gene expression data from the cervix in the late luteal phase
623OS

source_name: cervix after 14 days of progesterone exposure


title: Cx E+14P 1798


title: Cx E2 1874


title: Nuclear RNA-seq Unmodified at XRN2 rep 1


title: SBC_B_patient3

description:
10015
Primary tumor of patient 3 with synchronous bilateral cancer. Sample B.


title: Nuclear RNA-seq XRN2-AID minus auxin rep 1


title: FL P002


title: FL P001


title: Total mNET-seq XRN2-AID plus auxin rep2

description: library strategy: mNET-seq

source_name: HCT116 Total mNET-seq XRN2-AID Sleeping Beauty(TIR1) plus auxin

extract_protocol:
Pol II associated RNAs were selected by IP of all forms of RNA Pol II CTD in solubilised chromatin (CMA601, MBL Technologies). A detailed description of the mNET-seq protocol can be found by Nojima, T., Gomes, T., Carmo-Fonseca, M., and Proudfoot, N.J. (2016). Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide. Nature Protocols 11, 413-428.
NEBNEXT Small RNA Library Prep Set for Illumina (NEB #E7330S)

treatment_protocol: Auxin was added to cell media at a final concentration of 500 µM  2 h  prior to collection.

value: auxin treated Total CTD

value: RNA Polymerase II bound RNA


title: Cx E+14P 1263


title: SBC_A_patient3

description:
10014
Primary tumor of patient 3 with synchronous bilateral cancer. Sample A.


title: Nuclear RNA-seq XRN2-AID plus auxin rep 1


title: MBC_Controlateral_patient24

description:
1006
Second tumor of patient 24 with metachronous bilateral cancer.

source_name: Clinical breast cancer specimen, MBC


title: Cx E+14P 1564


title: Total mNET-seq XRN2-AID minus auxin rep2

description: library strategy: mNET-seq

source_name: HCT116 Total mNET-seq XRN2-AID Sleeping Beauty(TIR1) minus auxin

treatment_protocol: Control: Treated for 2 h with ethanol.

value: Control:auxin untreated Total CTD


title: MBC_Controlateral_patient21

description:
1003
Second tumor of patient 21 with metachronous bilateral cancer.

value: metachronous bilateral cancer


title: Total mNET-seq XRN2-AID plus auxin rep1

description: library strategy: mNET-seq


title: Cx E+14P 1567


title: MBC_Primary_patient21

description:
519
Primary tumor of patient 21 with metachronous bilateral cancer.

value: primary


title: Total mNET-seq XRN2-AID minus auxin rep1

description: library strategy: mNET-seq


title: METASTASIS_Primary_patient31

description:
675
Primary tumor of patient 31 with metastasis.

source_name: Clinical breast cancer specimen, metastasis

value: female

value: metastasis


title: Cx E+7P 1861

description:
gene expression data from the cervix in the mid-late luteal phase
623OS

source_name: cervix after 7 days of progesterone exposure


title: Cx E+7P 1928


title: Cx E+7P 1568


title: METASTASIS_Metastasis_patient31

description:
1026
Tumor metastasis of patient 31.


title: LRC_Recurrence_patient41

description:
1021
Local recurrence of patient 41.

source_name: Clinical breast cancer specimen, LRC

value: local recurrence cancer

value: recurrence


title: LRC_Primary_patient41

description:
600
Primary tumor of patient 41 with local recurrence.


title: SBC_B_patient16

description:
10052
Primary tumor of patient 16 with synchronous bilateral cancer. Sample B.


title: Cx E+3P 1878

description:
gene expression data from the cervix in the early-mid luteal phase
623OS

source_name: cervix after 3 days of progesterone exposure

value: cervix


title: Cx E+3P 1876


title: Cx E+3P 1880


title: Cx E+1P 1911

description:
gene expression data from the cervix in the early luteal phase
623OS

source_name: cervix after 1 day of progesterone exposure


title: Cx E+7P 1882


title: NMuMG 3D spheroid; 250 ng/mL GDF11 for 4 hr, replicate #4

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

description: Sample name: NMuMG_GDF11_4

hyb_protocol: Complementary RNA was hybridized to a MouseRef-8 v2.0 Expression BeadChip (Illumina) according to the manufacturer's recommendation.

scan_protocol: BeadChip was scanned using an iScan (Illumina) according to the manufacturer's recommendations.

data_processing: The data were processed as variance-stabilized (approximately log2) transformed values with the Bioconductor package lumi (Bioinformatics 24:1547-8 [2008]).

source_name: NMuMG 3D spheroids

label_protocol: Biotin-labeled complementary RNA was synthesized with the T7-based TotalPrep-96 RNA Amplification kit (Illumina) according to the manufacturer's recommendation.

growth_protocol: NMuMG cells were grown according to ATCC recommendations, plated in on top Matrigel at 5,000 cells/wells in an 8 well chamber slide (Methods 30:256-68 [2003] and Nat Cell Biol 16: 345-56 [2014]) for six days in the ATCC recommended growth media.  Cultures were refed with the ATCC recommended growth media at day four of culture.

extract_protocol: RNA was isolated by lysing individual wells in 500 uL RNA Stat-60.  200 uL aqueous phase after chloroform extraction was mixed with 700 uL Buffer RLT from the Qiagen MinElute Cleanup Kit and purified based on manufacturers recommendation.  Two wells were pooled into one common biological replicate and ethanol precipitated before complementary RNA synthesis.

treatment_protocol: Cells were stimulated with serum free medium (notx), 250 ng/mL GDF11, or 50 ng/mL TGFB1

value: NMuMG 3D spheroids

tag: cell seeding

value: 5,000 cells / well in 8-well chamber slide, cultured for 6 days before stimulation

tag: stimulation

value: 250 ng/mL GDF11 for 4 hr


title: Cx E+3P 1875


title: Cx E+1P 1914


title: NMuMG 3D spheroid; 50 ng/mL TGFB1 for 4 hr, replicate #3

description: Sample name: NMuMG_TGFB1_3

tag: cell type

value: 50 ng/mL TGFB1 for 4 hr


title: Cx E+3P 1881


title: NMuMG 3D spheroid; serum-free media for 4 hr, replicate #4

description: Sample name: NMuMG_notx_4

value: serum-free media


title: NMuMG 3D spheroid; 50 ng/mL TGFB1 for 4 hr, replicate #4

description: Sample name: NMuMG_TGFB1_4


title: NMuMG 3D spheroid; 50 ng/mL TGFB1 for 4 hr, replicate #2

description: Sample name: NMuMG_TGFB1_2


title: NMuMG 3D spheroid; 250 ng/mL GDF11 for 4 hr, replicate #1

description: Sample name: NMuMG_GDF11_1


title: Cx E+1P 1902


title: NMuMG 3D spheroid; 50 ng/mL TGFB1 for 4 hr, replicate #1

description: Sample name: NMuMG_TGFB1_1


title: HUVECs infected by CA07-24h-2

city: Beijing

first: Wu

last: Ying

address: No. 11, Bei San Huan Dong Lu, Chaoyang District

department: Department of Microbiology and Immunology

institute: Beijing University of Chinese Medicine

description: HUVECs infected by CA07-24h-2

hyb_protocol: Briefly, the process begins with a brief poly(A) tailing reaction followed by ligation of the biotinylated signal molecule to the target RNA sample. The labeled miRNA was hybridized to Affymetrix® GeneChip® miRNA (Affymetrix miRNA 4.0) according to the manufacturer’s protocols.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner (GCS) 3000 7G.

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

source_name: HUVECs infected with influenza A virus CA07

label_protocol: RNA quantification was performed according to the Affymetrix recommended protocols. Total RNA was labeled using the FlashTag™ Biotin RNA Labeling Kit

growth_protocol: Type Culture Collection (ATCC) and maintained in Endothelial Cell Medium (ECM, Sciencecell) supplemented with 1% Endothelial Cell Growth supplements (ECGS), 5% fetal calf serum serum (FCS, Sigma), 1% penicillin and 1% streptomycin. Madin Darby canine kidney (MDCK) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, GIBCO) supplemented with 10% fetal bovine serum (FBS, Sigma), 1% penicillin and 1% streptomycin. The cells were cultured in a humidified atmosphere of 5% CO2 at 37℃.

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

treatment_protocol: When grown to 90% confluency, HUVECs were removed from the culture medium and washed twice with PBS. Cells were infected with inﬂuenza A virus in serum-free media at a multiplicity of infection (MOI) of 20~40 and harvested at the indicated time points. The non-infected cells were used as normal control.Total RNA was extracted from uninfected and infected HUVECs using Trizol reagent (Invitrogen) following the manufacturer’s protocol. RNA pellets were resuspended in RNase-free water. RNA quantification was performed according to the Affymetrix recommended protocols.

value: human umbilical vein endothelial cells (HUVECs)

tag: infected with

value: influenza A virus CA07

tag: time point


title: NMuMG 3D spheroid; 250 ng/mL GDF11 for 4 hr, replicate #3

description: Sample name: NMuMG_GDF11_3


title: Cx E+1P 1915

tag: tissue


title: NMuMG 3D spheroid; serum-free media for 4 hr, replicate #3

description: Sample name: NMuMG_notx_3


title: Cx E+1P 1918


title: SBC_A_patient16

description:
10051
Primary tumor of patient 16 with synchronous bilateral cancer. Sample A.

value: breast cancer

value: synchronous bilateral cancer

value: A


title: NMuMG 3D spheroid; serum-free media for 4 hr, replicate #2

description: Sample name: NMuMG_notx_2


title: NMuMG 3D spheroid; 250 ng/mL GDF11 for 4 hr, replicate #2

description: Sample name: NMuMG_GDF11_2


title: NMuMG 3D spheroid; serum-free media for 4 hr, replicate #1

description: Sample name: NMuMG_notx_1


title: HUVECs infected by CA07-24h-1

description: HUVECs infected by CA07-24h-1


title: HUVECs  infected by CA07-12h-3

description: HUVECs  infected by CA07-12h-3


title: Dnmt1 KO Jejunum [miRNA]

city: Reno

first: Seungil

last: Ro

state: NV

address: 1664 North Virginia St

department: Physiology and Cell Biology

institute: University of Nevada School of Medicine

description:
smMHCCre-eGFP/+;Dnmt1-/-
small RNA

data_processing:
The 3' adaptor was trimmed from raw reads and reads with the length less tha 10 were excluded to constitute the mappable reads.
The mappable reads were alinged to the mouse genome and miRbase using Bowtie.
Genome_build: UCSC mm10; miRbase v21

extract_protocol:
mirVana miRNA Isolation Kit
Illumina TruSeq Small RNA Sample Preparation

value: Dnmt1 KO

tag: background strain

tag: strain

value: Jejunum smooth muscle

value: 15 days


title: Dnmt1 WT Jejunum [miRNA]

description:
smMHCCre-eGFP/+;Dnmt1-/-
small RNA

value: Dnmt1 WT

tag: age


title: HUVECs  infected by CA07-12h-2

description: HUVECs  infected by CA07-12h-2


title: Dnmt1 KO Jejunum [mRNA]

data_processing:
Illumina basecalling
Reads were aligned against mouse genome (mm10) for junction identification using Tophat v1.4.1.
Abundance estimation and differential expression analysis are done using Cufflinks v2.0.2.
Genome_build: UCSC mm10

extract_protocol:
mirVana miRNA Isolation Kit
TruSeq RNA Sample Preparation


title: Dnmt1 WT Jejunum [mRNA]


title: HUVECs  infected by PR8-24h-3

description: HUVECs  infected by PR8-24h-3

source_name: HUVECs infected with influenza A virus  PR8

value: influenza A virus PR8


title: HUVECs  infected by PR8-24h-1

description: HUVECs  infected by PR8-24h-1


title: HUVECs  infected by PR8-24h-2

description: HUVECs  infected by PR8-24h-2


title: HUVECs  infected by PR8-12h-3

description: HUVECs  infected by PR8-12h-3


title: HUVECs  non-infected-24h-3

description: HUVECs  non-infected-24h-3

source_name: HUVECs non-infected with influenza A virus

value: none (uninfected)


title: HUVECs  non-infected-24h-1

description: HUVECs  non-infected-24h-1


title: HUVECs  non-infected-24h-2

description: HUVECs  non-infected-24h-2


title: HUVECs  infected by CA07-12h-1

description: HUVECs  infected by CA07-12h-1


title: HUVECs non-infected-12h-1

description: HUVECs non-infected-12h-1


title: HUVECs  infected by PR8-12h-1

description: HUVECs  infected by PR8-12h-1


title: HUVECs non-infected-12h-2

description: HUVECs non-infected-12h-2


title: HUVECs  infected by PR8-12h-2

description: HUVECs  infected by PR8-12h-2


title: HUVECs non-infected-12h-3

description: HUVECs non-infected-12h-3


title: WT_B334_36h_4

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.

source_name: Nasal Epithelial Cells

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Human nasal epithelial cells (hNECs) were obtained from non-diseased hosts during endoscopic sinus surgery for non-infection related conditions and grown in culture at the air-liquid interface (ALI) as previously described (Lane et al., 2004; Ramanathan and Lane, 2007; Ramanathan et al., 2007). Tissue processing, differentiation medium, and culture conditions have been previously described in detail (Fischer et al., 2015).  Seasonal influenza A virus A/Victoria/361/2011 (H3N2) and an antigenically-matched live attenuated influenza vaccine virus (LAIV; WT HA and NA, all other proteins from A/Ann Arbor/6/1960) were utilized in this study.  Viral seed stocks were obtained from Medimmune.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Differentiated hNECs where infected at a multiplicity of infection (MOI) of 5 50% tissue culture infectious dose per cell.  All incubations were performed at 32oC in a humidified environment with 5% CO2.  Prior to infection, cells were apically washed with 200 μl DMEM (supplemented with 0.3% BSA, 2mM Glutamax, 100 U/ml Penicillin, and 100 µg/ml Streptomycin) and the basolateral media was refreshed with 500 μl of fresh LHC Basal Medium:DMEM-H.  The virus inoculum was added to the apical compartment in a volume of 100 μl and incubated for 2 hours, after which the inoculum was aspirated and the apical chamber was washed three times with 200 μl phosphate buffered saline containing calcium and magnesium (PBS+).  The plates were then returned to the incubator. Both apical washes and basolateral medium were collected and stored at -70oC. Virus production each time point was quantified by limited dilution infection of MDCKs using apical wash samples.  The TCID50 for each sample was calculated using the Reed-Muench algorithm (Reed, 1938).  RNA was isolated from Trizol homogenates from samples harvested at 24hpi and 36hpi.

value: Nasal Epithelial Cells

tag: infection

value: WT

tag: sampleID

tag: timepoint


title: WT_B334_36h_2


title: WT_B334_36h_1


title: WT_B334_36h_3


title: Cx E+7P 1927

value: cervix


title: HUVECs infected by CA07-24h-3

description: HUVECs infected by CA07-24h-3


title: WT_B330_36h_2


title: WT_B321_36h_3


title: WT_B330_36h_4


title: WT_B321_36h_4


title: WT_B321_36h_2


title: WT_B330_36h_1


title: WT_B330_36h_3


title: WT_B321_36h_1


title: WT_B314_36h_4


title: WT_B314_36h_3


title: WT_B314_36h_2


title: WT_B314_36h_1


title: WT_746_36h_3


title: WT_746_36h_4


title: WT_746_36h_2


title: NA19239_methylation

type: genomic

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description:
iPSC
Bisulfite Converted DNA

hyb_protocol: The samples were bisulphite-converted and hybridized to the Infinium HumanMethylation450 BeadChip at the University of Chicago Functional Genomics facility.

scan_protocol: scan protocol not provided

data_processing:
To ensure high data quality, probes were mapped to a bisulfite converted genome and only uniquely mapped probes were retained. Additionally, probes with low detection (P > 0.01) in more than 25% of samples were discarded. Samples were than normalized using the SWAN method to control for different probe types. Finally, red and green color channels were independently quantile normalized.
We transformed methylation levels to a standard normal within each individual and five principal components were removed to account for unknown variation

source_name: iPSC

label_protocol: Standard illumina protocols

extract_protocol: DNA was extracted from samples using Zymo dual extraction kits (Zymo Research)

value: iPSC

tag: gender

value: Male


title: NA19257_methylation

description:
iPSC
Bisulfite Converted DNA

value: Female


title: NA19206_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19207_methylation

description:
iPSC
Bisulfite Converted DNA


title: WT_746_36h_1


title: NA19225_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18489_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18501_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19160_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19192_methylation

description:
iPSC
Bisulfite Converted DNA


title: WT_745_36h_4


title: NA19204_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19193_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19210_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19152_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19209_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19238_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19190_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19153_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19144_methylation

description:
iPSC
Bisulfite Converted DNA


title: WT_735_36h_2


title: NA19127_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19159_methylation

description:
iPSC
Bisulfite Converted DNA


title: WT_745_36h_1


title: WT_745_36h_2


title: WT_745_36h_3


title: Mock_B330_36h_4

value: Mock


title: Mock_B334_36h_1


title: NA19140_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19119_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19128_methylation

description:
iPSC
Bisulfite Converted DNA


title: Mock_B330_36h_2


title: WT_735_36h_1


title: Mock_B330_36h_1


title: Mock_B321_36h_2


title: Mock_B330_36h_3


title: NA19116_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19143_methylation

description:
iPSC
Bisulfite Converted DNA


title: Mock_B321_36h_3


title: Mock_B334_36h_2


title: NA19138_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19108_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19130_methylation

description:
iPSC
Bisulfite Converted DNA


title: Mock_B321_36h_1


title: Mock_B314_36h_4


title: Mock_B314_36h_3


title: NA19101_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19102_methylation

description:
iPSC
Bisulfite Converted DNA


title: Mock_B314_36h_2


title: Mock_746_36h_4


title: Mock_746_36h_2


title: Mock_746_36h_3


title: Mock_B321_36h_4


title: Mock_B314_36h_1


title: NA18912_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19099_methylation

description:
iPSC
Bisulfite Converted DNA


title: Mock_746_36h_1


title: NA19098_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18862_methylation

description:
iPSC
Bisulfite Converted DNA


title: Mock_745_36h_1


title: Mock_745_36h_4


title: Mock_745_36h_2


title: Mock_735_36h_2


title: NA19093_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA19092_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18870_methylation

description:
iPSC
Bisulfite Converted DNA


title: Mock_745_36h_3


title: NA18858_methylation

description:
iPSC
Bisulfite Converted DNA


title: S. aureus, treated, 6.25 µM C162, biological replicate2

city: UKM Bangi

first: Cin

last: Kong

state: Selangor

address: Faculty of Science and Technology

department: School of Bioscience and Biotechnology

country: Malaysia

institute: Universiti Kebangsaan Malaysia

description: Gene expression data of S. aureus in the presence of 6.25 µM C162.

hyb_protocol: Following fragmentation, the cDNA were hybridized for 16 hour at 45°C with rotation at 60 rpm to Affymetrix GeneChip S. aureus Genome Array. GeneChips were washed and stained using the FS450_0005 fluidics protocol on fluidics station.

scan_protocol: GeneChips were scanned using an Affymetric 3000 7G scanner.

data_processing: To perform data quality control (QC), feature intensity (CEL) files generated from GeneChip® Command Console® Software (AGCC) were imported into Affymetrix Expression Console (EC) 1.4 software. MAS5 algorithm were used for normalizing probe-level intensity. Gene expression analysis was performed using three independent mRNA samples for each group. To perform statistical analysis and obtain a list of differentially expressed genes, the resultant data (CHP files) were subjected to Affymetrix® Transcriptome Analysis Console (TAC) software for Gene Level Differential Expression Analysis.

organism: Staphylococcus aureus

source_name: C162-treated, S. aureus

label_protocol: 50 ng of total RNA was processed using SensationPlusTM FFPE Amplification and 3' IVT Labeling Kit (Affymetrix) according to manufacturer's protocol to produce biotinylated cDNA.

growth_protocol: S. aureus was cultured for 16 - 18 hours in the presence and absence of benzimidazole compound C162 (6.25 µM) at 37°C with agitation 250 rpm.

extract_protocol: Total bacterial RNA was extracted using Epicentre MasterPureTM Complete DNA and RNA purification kit, followed by Qiagen's RNeasy Mini Kit and DNase treatment using Qiagen's RNase-Free DNase Set according to the manufacturers' instructions.

treatment_protocol: The samples were treated with 2.5 mg/mL lysozyme (Sigma-Aldrich) for 30 minutes at 37°C and proteinase K for 15 minutes at 65°C.

tag: growth phase

value: overnight culture (16-18 hours, lag phase)


title: NA18852_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18855_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18907_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18859_methylation

description:
iPSC
Bisulfite Converted DNA


title: S. aureus, treated, 6.25 µM C162, biological replicate3


title: Mock_735_36h_1


title: LAIV_B334_36h_4

value: LAIV


title: S. aureus, treated, 6.25 µM C162, biological replicate1


title: NA18913_methylation

description:
iPSC
Bisulfite Converted DNA


title: LAIV_B334_36h_3


title: S. aureus, control, 0 µM C162, biological replicate2

description: Gene expression data of S. aureus in the absence of C162.

source_name: Untreated, S. aureus

value: control


title: LAIV_B334_36h_2


title: LAIV_B330_36h_4


title: LAIV_B334_36h_1


title: S. aureus, control, 0 µM C162, biological replicate1


title: S. aureus, control, 0 µM C162, biological replicate3


title: NA18522_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18510_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18856_methylation

description:
iPSC
Bisulfite Converted DNA


title: Dnmt1 WT Jejunum

data_processing:
Raw data files had their adapters removed using trim_galore, quality trimming was also done, reads shorter than 20 bp were discarded
Pre-processed fastq files were aligned to human hg19 using bismark
Methylation calling was done on the bamfiles to create browser tracks for CpG, CHG, and CHH sites for each sample, these are in bigbed format
Genome_build: mm10
Supplementary_files_format_and_content: bigbed, browser tracks that contain methylation count and total count of reads per site

source_name: Jejunum

extract_protocol:
AllPrep DNA Spin Column
Methyl-MidiSeq® libraries were prepared from 300 ng of genomic DNA digested with 40 units of BfaI, 40 units of MseI, and 80 units of MspI and the fragments produced were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine. Adapter-ligated fragments were filled in and 3’-terminal-A extended, then purified using the Zymo Research (ZR) DNA Clean & ConcentratorTM – 5 kit (Cat#: D4003). Bisulfite treatment of the fragments was done using the EZ DNA Methylation – Lightning kit (ZR, Cat#: D5030). PCR was performed and the size and concentration of the fragments were confirmed on the Agilent 2200 TapeStation, then sequenced on the Illumina Hiseq with 50 bp PE parameters.

tag: sample

tag: genotype/variation


title: Dnmt1 KO Jejunum


title: LAIV_B330_36h_1


title: LAIV_B330_36h_2


title: Silenced replicate 2 vs Control replicate 2

city: Santa Fe

first: Elina

last: WELCHEN

state: Santa Fe

address: Colectora Ruta Nac. Nº168 km. 0

country: Argentina

institute: Instituto de Agrobiotecnologia del Litoral

description:
amiCOX19#17 2 vs WT2
Biological replicate 2-2

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned on an Agilent G2505B-C scanner using Agilent Feature Extraction Software (10.7.31)

data_processing: Median intensity signals were processed in the R statistical programming environment using the limma package. Probes were filtered to exclude those with log2-background intensities above 7.2. Intensities were then background corrected employing the ‘normexp’ method with an offset of 16. Next, arrays were normalized using the locally weighted scatter plot smoothing (LOESS) procedure.

organism: Arabidopsis thaliana

source_name: WT 2

label_protocol: 200 ng total RNA per sample were used to generate cRNA with labelling protocol version GE2 v6.5 for CY3 and CY5

growth_protocol: Arabidopsis seeds from control and silenced plants were grown on MS for 10 days under long day (16-h/8-h dark) at 23°C and 100 µM.m-1.s-1 of light intensity.

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

treatment_protocol: Plants grown on 0.5x MS for 10 days

tag: ecotype

value: wild type

value: shoot (leaves)

value: 10 days

value: reduced expression of AtCOX19-1 and AtCOX19-2


title: LAIV_B321_36h_4


title: NA18517_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18520_methylation

description:
iPSC
Bisulfite Converted DNA


title: LAIV_B321_36h_2


title: NA18861_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18853_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18519_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18502_methylation

description:
iPSC
Bisulfite Converted DNA


title: LAIV_B321_36h_3


title: LAIV_B314_36h_3


title: NA18507_methylation

description:
iPSC
Bisulfite Converted DNA


title: LAIV_B314_36h_1


title: Silenced replicate 1 vs Control replicate 1

description:
amiCOX19#17 1 vs WT1
Biological replicate 1-2

source_name: amiCOX19#17 1


title: LAIV_746_36h_4


title: LAIV_745_36h_3


title: LAIV_746_36h_2


title: LAIV_735_36h_3


title: LAIV_B314_36h_4


title: LAIV_745_36h_2


title: NA18511_methylation

description:
iPSC
Bisulfite Converted DNA


title: WT_B299_24h_2


title: LAIV_B330_36h_3


title: LAIV_735_36h_2


title: LAIV_745_36h_1


title: LAIV_745_36h_4


title: WT_B299_24h_11


title: WT_B298_24h_3


title: WT_B298_24h_1


title: WT_B298_24h_2


title: LAIV_746_36h_3


title: Mock_B298_24h_1


title: NA18498_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18508_methylation

description:
iPSC
Bisulfite Converted DNA


title: Mock_B298_24h_2


title: Mock_B299_24h_1


title: LAIV_B299_24h_2


title: LAIV_B299_24h_31


title: Mock_B298_24h_3


title: Mock_B299_24h_2


title: LAIV_B299_24h_1


title: LAIV_B298_24h_3


title: NA18486_methylation

description:
iPSC
Bisulfite Converted DNA


title: NA18505_methylation

description:
iPSC
Bisulfite Converted DNA


title: LAIV_B298_24h_2


title: WT_B276_24h_2


title: LAIV_B298_24h_1


title: WT_B272_24h_3


title: WT_B272_24h_2


title: LAIV_B321_36h_1


title: WT_B276_24h_11


title: WT_B272_24h_1


title: WT_B276_24h_1


title: Mock_B276_24h_1


title: Mock_B276_24h_2


title: Mock_B272_24h_1


title: LAIV_B276_24h_1


title: LAIV_B276_24h_3


title: WT_B284_24h_3


title: Mock_B272_24h_2


title: Mock_B276_24h_3


title: Mock_B272_24h_3


title: LAIV_B272_24h_3


title: LAIV_B272_24h_2


title: LAIV_B276_24h_2


title: LAIV_B272_24h_1


title: WT_B299_24h_3


title: Mock_B284_24h_1


title: LAIV_B284_24h_3


title: LAIV_746_36h_1


title: WT_B284_24h_1


title: LAIV_B284_24h_1


title: HepG2 cells TCF19 siRNA treated,  maintained in high glucose biological replicate_2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: Array hybridization were performed per recommended specifications (Asuragen, Austin, TX).

scan_protocol: Scanning were performed per recommended specifications (Asuragen, Austin, TX).

data_processing: Genechip PrimeView Human Arrays were utilized (Affymetrix, Santa Clara, CA). CEL files were analyzed utilizing R/Bioconductor package, oneChannelGUI. Briefly, normalization of expression values was performed utilizing the “Expresso” option, selecting “RMA” as the background correction, “quantiles” as normalization, “pmonly” as the PM correction, and “MAS” as the expression. Probes were filtered with IQR settings of 0.25. P values were calculated using a two-tailed Student’s t-test.

source_name: Human(Male) hepatocellular carcinoma cells, TCF19 siRNA treated, maintained in 40mM glucose for 48 hours

label_protocol: Per Affymetrix Protocol

growth_protocol: DMEM+ 10%FBS+1% antibiotic + 40mM glucose at 37⁰C at 5% CO2

extract_protocol: RNA was isolated from control and treated cells utilizing the TRIzol (Thermo Fischer) extraction per manufacturer’s instructions.

treatment_protocol: Control sets were seeded in DMEM low glucose medium overnight, and henceforth maintained in 40mM glucose for 48 hours,having treated with non-targeting control siRNA after the first 24 hours. Tretaed sets were maintained in 24 hours with 40mM glucose, then treated with  TCF19 siRNA, and further maintained in same glucose conc. for 24 hours.

tag: cell line

value: Liver


title: HepG2 cells, non-targeting control siRNA treated,  maintained in high glucose biological replicate_1

source_name: Human(Male) hepatocellular carcinoma cells, non-targeting siRNA treated, grown in 40mM glucose for 48 hours


title: Mock_B284_24h_2


title: HepG2 cells TCF19 siRNA treated,  maintained in high glucose biological replicate_1


title: Patient Derived Xenograft LTL-467R

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour and 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 10.10 to produce spatially detrended and background subtracted gProcessedSignal intensities. Data were quantile normalized in GeneSpring 12.0.

source_name: Prostate Tumor

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

extract_protocol: RNA were extracted by using the mirVana RNA Isolation Kit (Ambion, Burlington, Canada).  The quality and quantity of RNA were assessed with an Agilent 2100 Bioanalyzer (Caliper Technologies Corp., Canada)

value: prostate cancer tumor

tag: tumor foci

value: Patient Derived Xenograft


title: Patient Derived Xenograft LTL-484R


title: Patient Derived Xenograft LTL-313HR


title: Patient Derived Xenograft LTL-418R


title: HepG2 cells, non-targeting control siRNA treated,  maintained in high glucose biological replicate_2


title: H827_rep3

city: New Taipei City

first: Sheng-Ming

last: Wu

address: No.291, Zhongzheng Rd., Zhonghe District

institute: Taipei Medical University Shuang-Ho Hospital

description: 18880_H827-2.txt:gProcessedSignal(normalized)

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.  Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature (quantile normalization and log2 transformation).

source_name: H827 cell without MDM

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent  Technologies, USA) during the in vitro transcription process.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen).

treatment_protocol: Human peripheral monoctyte cells (PBMCs) from lung cancer patients were collected. PBMCs were treated with GM-CSF and differentiated to MDM. MDM cells were cocultured with or without lung cancer cells for 24h. Total RNAs were extracted from H827 cancer cells.

tag: cell type

value: lung cancer cells

tag: cocultured with


title: Patient Derived Xenograft LTL-311R


title: H827_rep1

description: 18872_H827.txt:gProcessedSignal(normalized)


title: H827 w/ MDM_rep1

description: 18874_H827M.txt:gProcessedSignal(normalized)

source_name: H827 cell with MDM

value: monocyte-derived macrophages (MDM) for 24hrs

tag: mdm source

value: differentiated from peripheral monoctyte cells (PBMCs) from lung cancer patients


title: H827 w/ MDM_rep2

description: 18878_H827M-1.txt:gProcessedSignal(normalized)


title: LAIV_B284_24h_2

tag: tissue

value: Nasal Epithelial Cells


title: H827 w/ MDM_rep3

description: 18882_H827M-2.txt:gProcessedSignal(normalized)