title: U937_COM

city: Ningbo

first: Kongfei

last: Li

state: Zhejiang

address: Baizhang East Road 251#

department: the Department of Hematology

institute: Ningbo Yinzhou Hospital

description: Gene expression after U937_COM

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

source_name: U937 cells,COM

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: we treated U937 cells. U937 cells were treated with DAC 0.2μM for 3 days, IDA  20nM for 1 day, DAC 0.2μM for 2 days followed by  IDA 20nM for 1 day.

value: decitabine + idarubicin

tag: cell line


title: AML3 no IL-3 16h

status: Public on Feb 13 2014

type: RNA

city: Adelaide

first: Chung

middle: H

last: Kok

state: South Australia

address: North Terrace

country: Australia

institute: South Australia Health and Medical Research Institute

hyb_protocol: Genechips  were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

scan_protocol: Genechips were scanned using the Affymetrix GSC3000 scanner.

data_processing: Raw CEL files were normalised with RMA method using aroma.affymetrix.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary AML MNCs

label_protocol: Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.

growth_protocol: Mononuclear AML cells were thawed and recovered overnight in IMDM with 20% FBS and DNase (50U/mL). Non-viable cells were subsequently removed using Lymphoprep (Axis-Shield PLC). AML cells were then cultured in IMDM with 10% FBS and stimulated with IL-3 as described below.

extract_protocol: Total RNA was purified using the miRNeasy protocol (Qiagen)

treatment_protocol: Mononuclear AML cells thawed overnight and cultured in IMDM with 10% FBS were treated +/- 15ng/mL hIL-3 for 6 or 16h.

tag: cell type

value: Primary AML MNCs

tag: treatment

value: no IL-3 16h

tag: disease

value: Acute myeloid leukaemia

tag: cytogenetics

value: normal


title: SKR6-Vector cells, biological replicate 1

city: Boston

first: Shannon

middle: Terrell

last: Bailey

state: MA

address: 450 Brookline Avenue, D728

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: Gene expression data of SKR6-Vector cells, which are SKR6 cells that were retrovirally transduced with the pQCXIP empty retroviral vector and selected with puromycin

hyb_protocol: The biotinylated complementary RNA (cRNA) was purified from the IVT reaction mixture using magnetic particles, and it was quantified spectrophotometrically. The purity of the cRNA was also assessed by spectrophometric measurements.  The purified cRNA was first fragmented to facilitate hybridization, and the fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control) and hybridized to a microarray chip overnight at 45Â°C after which the hybridization solution was removed. The chips were transferred to a fluidics instrument that washed away and cRNA that did not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluorophores were then added using a biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The expression data were normalized using the robust multichip average (RMA) method and processed using linear models for microarray data (Limma) using R.

label: biotin

source_name: SKR6-Vector cells

label_protocol: RNA was converted into cDNA using a T7 promoter-tailed oligo-dT primer to synthesize the first cDNA strand and a second strand cDNA synthesis was then performed.  The double-stranded cDNA was used as a template for an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.

growth_protocol: The SKR6, SKR6-Vector, SKR6CA, and SKR6LR cells were seeded in RPMI 1640 medium supplemented with 10% fetal bovine serum and grown for 48 hours prior to total RNA extraction. The SKLR cells were maintained in the presence of 0.2 uM lapatinib.

extract_protocol: A hybrid Trizol/Qiagen Rneasy protocol was used to isolate total RNA

tag: parental cell line


title: High-grade serous ovarian carcinomas [OV 2]

city: Oslo

first: Bente

middle: Vilming

last: Elgaaen

address: Ullernchausseen 70

department: Department of Gynecological Oncology

country: Norway

institute: Oslo University Hospital

description: OV 2

hyb_protocol: Labeled RNAs was hybridized to the GeneChip miRNA 2.0 Array (Affymetrix, Santa Clara, CA) as recommended by the vendor. The arrays were washed and stained using FS-450 fluidics station (Affymetrix).

scan_protocol: Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA). The scanned images were processed using the AGCC (Affymetrix GeneChip Command Console) software.

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc. MO, USA). The Robust Multichip Analysis (RMA) algorithm was applied for generation of signal values and normalization.For expression comparisons of different groups, profiles  were compared using a 1-way ANOVA model. The results were expressed as FC (fold change) with p-values and calculation of FDR (false discovery rate).

source_name: High-grade serous ovarian carcinoma

label_protocol: 400 ng of total RNA was used for labeling of microRNA by the Genisphere FlashTag HSR kit following the manufacturer's recommendations (Genisphere, Hatfield, PA).

extract_protocol: Frozen tissue specimens of less than 50 mg were homogenized directly for 3 minutes in 700 µl QIAzol using a TissueLyzer (Qiagen.com). Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden Germany) and Phase Lock Gel™ Heavy (5 PRIME GmbH, Hamburg, Germany). RNA was quantified with a NanoDrop® ND-1000 Spectrophotometer (Saveen Werner, Malmö, Sweden), and quality assessed on an Agilent 2100 Bioanalyzer RNA 6000 Nano Kits (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Cancer tissue samples and OSE scrapings from normal ovaries were immediately harvested from removed ovaries at surgery and snap-frozen in liquid nitrogen or transferred to TRIzol solution (Invitrogen.com), respectively. The samples were stored at -80⁰C until processed.

tag: tissue

value: ovary

tag: disease status

value: High-grade serous ovarian carcinoma

tag: progression (0=no, 1=yes)

tag: time (months) until progression or last follow-up

tag: death (0=no, 1=yes)

tag: time (months) until death or last follow-up


title: U937_DAC_72h

country: China

description: Gene expression after U937_DAC_72h

source_name: U937 cells,DAC

value: decitabine


title: SKR6 cells, biological replicate 3

description: Gene expression data of SKR6 cells, which represent an SKBR-3 cell population with elevated HER2 expression

source_name: SKR6 cells


title: U937_IDA_24h

description: Gene expression after U937_IDA_24h

source_name: U937 cells,IDA

value: idarubicin


title: SKR6CA cells, biological replicate 1

description: Gene expression data of SKR6CA cells, which are SKR6 cells that were retrovirally transduced with constitutively active NF-κB relA/p65 (CAp65) and selected with puromycin

source_name: SKR6CA cells


title: AML2 + IL-3 16h


title: MCF7_Hypoxia_32h_rep1 [mRNA]

city: Oxford

first: Carme

last: Camps

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics/ U. of Oxford

description:
Hypoxia_32h_R1
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalised (quantile normalisation) using preprocessCore package from Bioconductor

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit.

growth_protocol: MCF-7 cells were grown in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 2mmol/L of L-glutamine.

extract_protocol: RNA was extracted from cells using the miRVana miRNA isolation kit (Ambion) in accordance with the prescribed protocol provided with the kit. RNA quality was assessed after extraction using Agilent bioanalyser.

treatment_protocol: Exposure of cell cultures to hypoxia (1% oxygen) was undertaken in an In vivo2 Hypoxia Work Station (Ruskin Technologies) in parallel with cells maintained in normoxic conditions (21% oxygen). Cells were recovered after 16h, 32h and 48h of exposure to hypoxia.

tag: oxygen

tag: time of exposure


title: MCF7_Normoxia_rep3 [mRNA]

description:
Normoxia_R3
replicate 3


title: AML1 no IL-3 6h

value: no IL-3 6h


title: MCF7_Hypoxia_16h_rep2 [mRNA]

description:
Hypoxia_16h_R2
replicate 2


title: SKR6-Vector cells, biological replicate 3

value: SKR6-Vector cells, which are SKR6 cells that were retrovirally transduced with the pQCXIP empty retroviral vector and selected with puromycin


title: AML1 + IL-3 16h


title: U937_PBS_control

description: Gene expression after U937_PBS_control

source_name: U937 cells,PBS

value: PBS


title: dendritic cell_sulforaphane treated_replicate2

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix MoGene 2.1 ST Array Plates. Hybridization, washing, staining and scanning was performed fully automated on a Gene Titan instrument using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: see hyb protocol

data_processing: The data were analysed using Bioconductor package 'oligo' 1.20.4 under R-2.15.1. Background correction, normalization and probe summarization was performed with RMA.

organism: Mus musculus

source_name: mouse dendritic cells, Solforaphane treated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA using the GeneChip® WT PLUS Reagent Kit (Affymetrix).

growth_protocol: Bone marrow-derived DC from C57BL/6 mice were isolated and cultivated as described in Lutz MB et al., J Immunol Methods 1999;223:77-92.

extract_protocol: DC were lysed and total RNA was isolated using the peqGOLD Total RNA Kit (peqlab) following the manufacturer's protocols.

treatment_protocol: DC were harvested on day 7, incubated with 0.3 µM sulforaphane (Sigma-Aldrich) in DMSO or DMSO alone as control for 2 hours and then activated with 100 ng/ml LPS from E. coli O111:B4 (Sigma-Aldrich) for 1 hour.

tag: strain

value: Sulforaphane

value: dendritic cells


title: MCF7_Hypoxia_16h_rep1 [mRNA]

description:
Hypoxia_16h_R1
replicate 1


title: MCF7_Normoxia_rep2 [mRNA]

description:
Normoxia_R2
replicate 2


title: dendritic cell_sulforaphane treated_replicate1


title: dendritic cell_control treated_replicate1

source_name: mouse dendritic cells, DMSO treated

value: DMSO


title: MCF7_Normoxia_rep1 [mRNA]

description:
Normoxia_R1
replicate 1


title: SKR6 cells, biological replicate 1

value: SKBR-3 cell population with elevated HER2 expression


title: dendritic cell_control treated_replicate2


title: SKR6 cells, biological replicate 2


title: Primary human hepatocytes donor 5737 HCV infected 1dpi rep3

status: Public on Feb 12 2014

city: Chapel Hill

first: Timothy

middle: P

last: Sheahan

state: North Carolina

address: 3113 MHRC 135 Dauer Drive, Campus Box 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

hyb_protocol: As per Nugen's suggestion, each sample was hybridized to Illumina, HumanHT-12 V4 0 R2 at 48˚C. Other than this deviation, the samples were hybridized according to standard Illumina protocol.

scan_protocol: Arrays were scanned according to Illumina protocol.

data_processing:
The array text files for each experiment were uploaded in the Genespring GX 11.0.2 using the advanced analysis setting. Present cutoff 0.8, Absent cutoff 0.6 (stock options). Threshold raw to 1.0. Quantile normalization. Baseline to median. Statistical significance was determined by ANOVA with a Benjamin Hochberg multiple testing correction and a false discovery rate of 5% comparing HCV infected or adjacent to a time matched mock. Only genes with a fold change greater than two fold over mock were considered for analysis.
The matrix non-normalized data represents the raw array data for each probe prior to Genespring analysis. The matrix normalized data represents the quantile normalized data prior to processing via ANOVA.

source_name: HCV infected 1 day post infection

label_protocol: Amplified transcriptomes were biotin labeled using Nugen Encore Biotin IL according to protocol.

growth_protocol: Primary fetal hepatocytes were maintained in serum free medium according to standard protocol. Cells were obtained from several donors and treated similarly.

extract_protocol: For each population of interest, 30 cells isolated by laser capture microdissection were directly lysed and their transcriptomes were amplified using Nugen OneDirect according to protocol.

treatment_protocol: Cells were infected with hepatitis C virus at a similar multiplicity of infection (MOI) or mock infected for 6hrs afterwhich cells were extensively rinsed. At various times post infection, cultures were rinsed, fixed in 100% ethanol and immediately used for laser capture microdissection.

tag: cell population

value: HCV Infected

tag: days post infection

tag: donor id

tag: ifnl3 rs12979860 genotype

value: C/T


title: Primary human hepatocytes donor 5737 adjacent 1dpi rep4

source_name: Adjacent 1 day post infection

value: cells adjacent to infected cells


title: Primary human hepatocytes donor 5737 HCV infected 1dpi rep4


title: Primary human hepatocytes donor 5737 HCV infected 1dpi rep2


title: Primary human hepatocytes donor 5737 mock infected 1dpi rep2

source_name: Mock Infected 1 day post infection

value: Mock Infected


title: Primary human hepatocytes donor 5737 adjacent 1dpi rep2


title: Primary human hepatocytes donor 5763 adjacent 1dpi rep2

value: C/C


title: Primary human hepatocytes donor 5737 HCV infected 1dpi rep1


title: Primary human hepatocytes donor 5763 adjacent 1dpi rep4


title: Primary human hepatocytes donor 5763 HCV infected 1dpi rep3


title: Primary human hepatocytes donor 5763 adjacent 1dpi rep1


title: Primary human hepatocytes donor 5763 HCV infected 1dpi rep2


title: Primary human hepatocytes donor 5737 mock infected 1dpi rep4


title: Primary human hepatocytes donor 5763 adjacent 1dpi rep3


title: Primary human hepatocytes donor 5737 adjacent 1dpi rep1


title: Primary human hepatocytes donor 5763 mock infected 1dpi rep2


title: Primary human hepatocytes donor 5763 HCV infected 1dpi rep1


title: Primary human hepatocytes donor 5763 mock infected 1dpi rep3


title: Primary human hepatocytes donor 5737 mock infected 1dpi rep1


title: Primary human hepatocytes donor 5763 HCV infected 1dpi rep4


title: Primary human hepatocytes donor 5763 mock infected 1dpi rep1


title: Primary human hepatocytes donor 5763 mock infected 1dpi rep4


title: Primary human hepatocytes donor 4728 adjacent 1dpi rep1


title: Primary human hepatocytes donor 4728 adjacent 1dpi rep4


title: Primary human hepatocytes donor 4728 HCV infected 1dpi rep4


title: Primary human hepatocytes donor 4728 adjacent 1dpi rep2


title: High-grade serous ovarian carcinomas [OV 3]

description: OV 3


title: Primary human hepatocytes donor 4728 adjacent 1dpi rep3


title: Primary human hepatocytes donor 4728 mock infected 1dpi rep4


title: Primary human hepatocytes donor 4728 HCV infected 1dpi rep1


title: Primary human hepatocytes donor 4728 HCV infected 1dpi rep3


title: Primary human hepatocytes donor 5780 adjacent 1dpi rep3


title: Primary human hepatocytes donor 5780 adjacent 1dpi rep4


title: Primary human hepatocytes donor 4728 mock infected 1dpi rep3


title: Primary human hepatocytes donor 4728 mock infected 1dpi rep2


title: Primary human hepatocytes donor 5780 adjacent 1dpi rep1


title: Primary human hepatocytes donor 4728 mock infected 1dpi rep1


title: Primary human hepatocytes donor 5780 HCV infected 1dpi rep2


title: Primary human hepatocytes donor 5780 HCV infected 1dpi rep1


title: Primary human hepatocytes donor 4728 HCV infected 1dpi rep2


title: Primary human hepatocytes donor 5780 HCV infected 1dpi rep4


title: Primary human hepatocytes donor 5123 adjacent 7dpi rep3

source_name: Adjacent 7 day post infection


title: Primary human hepatocytes donor 5780 mock infected 1dpi rep2


title: Primary human hepatocytes donor 5780 adjacent 1dpi rep2


title: Primary human hepatocytes donor 5780 mock infected 1dpi rep1


title: Primary human hepatocytes donor 5780 mock infected 1dpi rep4


title: Primary human hepatocytes donor 5780 HCV infected 1dpi rep3


title: Primary human hepatocytes donor 5780 mock infected 1dpi rep3


title: Primary human hepatocytes donor 5123 adjacent 7dpi rep4


title: Primary human hepatocytes donor 5123 adjacent 7dpi rep2


title: Primary human hepatocytes donor 5737 mock infected 1dpi rep3


title: Primary human hepatocytes donor 5123 mock infected 7dpi rep3

source_name: Mock Infected 7 day post infection


title: Primary human hepatocytes donor 5123 HCV infected 7dpi rep1

source_name: HCV infected 7 day post infection


title: Primary human hepatocytes donor 3868 adjacent 7dpi rep5

value: T/T


title: Primary human hepatocytes donor 3868 adjacent 7dpi rep4


title: Primary human hepatocytes donor 5123 adjacent 7dpi rep1


title: Primary human hepatocytes donor 5123 HCV infected 7dpi rep2


title: Primary human hepatocytes donor 3868 adjacent 7dpi rep3


title: Primary human hepatocytes donor 3868 mock infected 7dpi rep3


title: Primary human hepatocytes donor 5123 adjacent 3dpi rep2

source_name: Adjacent 3 day post infection


title: Primary human hepatocytes donor 5123 HCV infected 3dpi rep3

source_name: HCV infected 3 day post infection


title: Primary human hepatocytes donor 3868 HCV infected 7dpi rep2


title: Primary human hepatocytes donor 3868 HCV infected 7dpi rep5


title: Primary human hepatocytes donor 3868 HCV infected 7dpi rep4


title: Primary human hepatocytes donor 5123 mock infected 7dpi rep4


title: Primary human hepatocytes donor 5123 mock infected 7dpi rep1


title: Primary human hepatocytes donor 3868 HCV infected 7dpi rep3


title: Primary human hepatocytes donor 3868 mock infected 7dpi rep4


title: Primary human hepatocytes donor 5123 mock infected 7dpi rep2


title: Primary human hepatocytes donor 3868 HCV infected 7dpi rep1


title: Primary human hepatocytes donor 5123 HCV infected 3dpi rep4


title: Primary human hepatocytes donor 3868 mock infected 7dpi rep1


title: Primary human hepatocytes donor 3868 mock infected 7dpi rep2


title: Primary human hepatocytes donor 3868 adjacent 7dpi rep1


title: Primary human hepatocytes donor 5123 adjacent 3dpi rep1


title: Primary human hepatocytes donor 5123 adjacent 3dpi rep4


title: Primary human hepatocytes donor 5123 adjacent 3dpi rep3


title: Primary human hepatocytes donor 5123 HCV infected 3dpi rep2


title: Primary human hepatocytes donor 5737 adjacent 1dpi rep3


title: Primary human hepatocytes donor 5123 mock infected 3dpi rep3

source_name: Mock Infected 3 day post infection


title: Primary human hepatocytes donor 3868 mock infected 3dpi rep4


title: Primary human hepatocytes donor 5123 mock infected 3dpi rep2


title: Primary human hepatocytes donor 5123 HCV infected 1dpi rep3


title: Primary human hepatocytes donor 5123 mock infected 3dpi rep4


title: Primary human hepatocytes donor 5123 adjacent 1dpi rep1


title: Primary human hepatocytes donor 3868 mock infected 3dpi rep2


title: Primary human hepatocytes donor 3868 adjacent 1dpi rep2


title: Primary human hepatocytes donor 5123 HCV infected 1dpi rep1


title: Primary human hepatocytes donor 5123 HCV infected 1dpi rep4


title: Primary human hepatocytes donor 3868 mock infected 3dpi rep3


title: Primary human hepatocytes donor 5123 mock infected 1dpi rep4


title: Primary human hepatocytes donor 5123 mock infected 1dpi rep2


title: Primary human hepatocytes donor 5123 mock infected 1dpi rep1


title: Primary human hepatocytes donor 5123 adjacent 1dpi rep3


title: Primary human hepatocytes donor 5123 mock infected 3dpi rep1


title: Primary human hepatocytes donor 3868 HCV infected 1dpi rep4


title: Primary human hepatocytes donor 3868 HCV infected 1dpi rep2


title: Primary human hepatocytes donor 3868 adjacent 1dpi rep1


title: Primary human hepatocytes donor 3868 adjacent 1dpi rep4


title: Primary human hepatocytes donor 3868 HCV infected 1dpi rep3


title: Primary human hepatocytes donor 3868 adjacent 1dpi rep3


title: Primary human hepatocytes donor 5123 HCV infected 3dpi rep1


title: Primary human hepatocytes donor 5123 HCV infected 1dpi rep2


title: Primary human hepatocytes donor 5123 adjacent 1dpi rep4


title: Primary human hepatocytes donor 5123 mock infected 1dpi rep3


title: Primary human hepatocytes donor 3868 mock infected 3dpi rep1


title: Primary human hepatocytes donor 5123 adjacent 1dpi rep2


title: Primary human hepatocytes donor 3868 mock infected 1dpi rep2


title: Primary human hepatocytes donor 7185 HCV infected 7dpi rep2


title: Primary human hepatocytes donor 7185 adjacent 7dpi rep4


title: Primary human hepatocytes donor 7185 adjacent 7dpi rep3


title: Primary human hepatocytes donor 7185 mock infected 7dpi rep7


title: Primary human hepatocytes donor 3868 mock infected 1dpi rep4


title: Primary human hepatocytes donor 7185 mock infected 7dpi rep6


title: Primary human hepatocytes donor 7185 HCV infected 7dpi rep3


title: Primary human hepatocytes donor 3868 mock infected 1dpi rep3


title: Primary human hepatocytes donor 7185 mock infected 7dpi rep5


title: Primary human hepatocytes donor 7185 adjacent 3dpi rep3


title: Primary human hepatocytes donor 7185 mock infected 7dpi rep3


title: Primary human hepatocytes donor 3868 HCV infected 1dpi rep1


title: Primary human hepatocytes donor 7185 adjacent 7dpi rep1


title: Primary human hepatocytes donor 3868 mock infected 1dpi rep1


title: Primary human hepatocytes donor 7185 mock infected 7dpi rep1


title: Primary human hepatocytes donor 7185 adjacent 7dpi rep2


title: Primary human hepatocytes donor 7185 HCV infected 7dpi rep4


title: Primary human hepatocytes donor 7185 adjacent 3dpi rep1


title: Primary human hepatocytes donor 7185 adjacent 3dpi rep4


title: Primary human hepatocytes donor 7185 mock infected 7dpi rep2


title: Primary human hepatocytes donor 7185 HCV infected 7dpi rep1


title: Primary human hepatocytes donor 7185 HCV infected 3dpi rep2


title: Primary human hepatocytes donor 7185 HCV infected 3dpi rep1


title: Primary human hepatocytes donor 7185 HCV infected 3dpi rep4


title: Primary human hepatocytes donor 7185 mock infected 7dpi rep4


title: Primary human hepatocytes donor 7185 HCV infected 3dpi rep3


title: Primary human hepatocytes donor 7185 adjacent 3dpi rep2


title: Primary human hepatocytes donor 3868 adjacent 7dpi rep2


title: Primary human hepatocytes donor 7185 mock infected 3dpi rep4


title: Primary human hepatocytes donor 7185 adjacent 1dpi rep3


title: Primary human hepatocytes donor 7185 HCV infected 1dpi rep3


title: Primary human hepatocytes donor 7185 mock infected 1dpi rep3


title: Primary human hepatocytes donor HFTR adjacent 7dpi rep3

value: HFTR


title: Primary human hepatocytes donor 7185 mock infected 3dpi rep1


title: Primary human hepatocytes donor 7185 adjacent 1dpi rep4


title: Primary human hepatocytes donor 7185 HCV infected 1dpi rep1


title: Primary human hepatocytes donor HFTR mock infected 7dpi rep3


title: Primary human hepatocytes donor 7185 adjacent 1dpi rep1


title: Primary human hepatocytes donor 7185 HCV infected 1dpi rep4


title: Primary human hepatocytes donor HFTR adjacent 7dpi rep4


title: Primary human hepatocytes donor HFTR adjacent 3dpi rep3


title: Primary human hepatocytes donor 7185 mock infected 1dpi rep2


title: Primary human hepatocytes donor HFTR adjacent 3dpi rep4


title: Primary human hepatocytes donor 7185 adjacent 1dpi rep2


title: Primary human hepatocytes donor 7185 mock infected 1dpi rep1


title: Primary human hepatocytes donor HFTR mock infected 7dpi rep2


title: Primary human hepatocytes donor 7185 mock infected 1dpi rep4


title: Primary human hepatocytes donor HFTR adjacent 7dpi rep1


title: Primary human hepatocytes donor HFTR HCV infected 7dpi rep4


title: Primary human hepatocytes donor HFTR HCV infected 7dpi rep3


title: Primary human hepatocytes donor 7185 mock infected 3dpi rep2


title: Primary human hepatocytes donor HFTR HCV infected 7dpi rep2


title: Primary human hepatocytes donor HFTR mock infected 7dpi rep1


title: Primary human hepatocytes donor 7185 HCV infected 1dpi rep2


title: Primary human hepatocytes donor HFTR adjacent 7dpi rep2


title: Primary human hepatocytes donor HFTR mock infected 7dpi rep4


title: Primary human hepatocytes donor 7185 mock infected 3dpi rep3


title: Primary human hepatocytes donor HFTR HCV infected 7dpi rep1


title: Primary human hepatocytes donor HFTR adjacent 3dpi rep2


title: Primary human hepatocytes donor HFTR HCV infected 3dpi rep3


title: Primary human hepatocytes donor HFTR mock infected 3dpi rep4


title: Primary human hepatocytes donor HFTR mock infected 3dpi rep2


title: Primary human hepatocytes donor HFTR HCV infected 3dpi rep4


title: Primary human hepatocytes donor HFTR adjacent 1dpi rep2


title: Primary human hepatocytes donor HFTR adjacent 3dpi rep1


title: Primary human hepatocytes donor HFTR HCV infected 1dpi rep4


title: Primary human hepatocytes donor HFTR HCV infected 3dpi rep1


title: Primary human hepatocytes donor HFTR adjacent 1dpi rep3


title: Primary human hepatocytes donor HFTR mock infected 1dpi rep2


title: Primary human hepatocytes donor HFTR HCV infected 3dpi rep2


title: Primary human hepatocytes donor HFTR adjacent 1dpi rep1


title: Primary human hepatocytes donor HFTR HCV infected 1dpi rep1


title: Primary human hepatocytes donor HFTR mock infected 1dpi rep3


title: Wt-dmso-sample 1

city: Hanover

first: George

middle: E

last: Schaller

state: NE

address: 339 Life Sciences Center, HB 6044

department: Biological Sciences

institute: Dartmouth College

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix gene-chip data files were imported into GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA), and the data normalized per chip to the 50th percentile and per gene to the median following the recommended procedure. Fold change mode was used for normalization.

organism: Arabidopsis thaliana

label_protocol: standard Affymetrix protocol

growth_protocol: Arabidopsis seeds were surface-sterilized and cold-treated for 3 d in the dark at 4C, before being moved into the light. Seedlings were grown for 14 days on filter paper on media containing 0.8% (w/v) phytoagar (Research products international corp., Mt. Prospect, IL) 1 X Murashige and Skoog (MS) salts containing Gamborgs vitamins (Phytotechnology Laboratories, Shawnee Mission, KS), 1% (w/v) sucrose, 0.05% (w/v) MES (pH 5.7). Seeds were grown under continuous white light (25 µE/m2/s) at 22C, with white light being generated by standard fluorescent bulbs augmented with 18,000 K fluorescent bulbs (Aqua-Glo, Rolf C. Hagen Corp., Mansfield, MA). Layers of black nylon mesh were used to reduce light levels as needed.

extract_protocol: Total RNA was isolated by using the RNeasy plant kit according to the manufacturer (QIAGEN, Valencia, CA). The nucleic acid integrity was assessed by agarose gel electrophoresis for detection of ribosomal RNA bands, and its quality by 260/280 and 260/230 ratios. If necessary, the RNA was cleaned further by phenol/chloroform/iso-amyl alcohol (25:24:1) extraction, followed by precipitation with 0.15 M sodium acetate, 50% (v/v) isopropanol.

treatment_protocol: Seedlings on filter paper were transferred to liquid MS media containing either 10 µM BA or a DMSO vehicle control for 1 hr. The roots were removed and discarded, and the shoots frozen at -80?C until RNA was extracted.

tag: genotype/variation

value: Wild Type

tag: age

value: 14 days

value: seedling

tag: treated with

value: DMSO (control) for 1hr


title: Primary human hepatocytes donor HFTR mock infected 1dpi rep4


title: Primary human hepatocytes donor HFTR HCV infected 1dpi rep3


title: Primary human hepatocytes donor HFTR mock infected 3dpi rep3


title: arr-BA-sample 1

source_name: arr1,10,12 mutant_BA

value: arr1,10,12 mutant

value: 10 µM benzyladenine (BA) for 1hr


title: arr-dmso-sample 1

source_name: arr1,10,12 mutant_DMSO


title: Wt-BA-sample 2


title: arr-dmso-sample 2


title: arr-BA-sample 2


title: Mouse 3, SP

city: New York

first: Gerold

last: Bongers

state: NY

address: 1425 Madison Ave, 12-26A

department: Immunology Institute

institute: Icahn School of Medicine at Mount Sinai

description:
790
7991003006_G

data_processing: Raw data files were converted using GenomeStudio and further processed using using lumi v2.10.0 Bioconductor/R and limma v3.14.4 Bioconductor/R.

source_name: Cecal CD45+ cells

label_protocol: Biotinylated cRNA was prepared from 500 ng total RNA with the Illumina® TotalPrepTM RNA Amplification Kit according to manufactures protocol (AMIL1791) and loaded on  MouseRef-8 BeadChip Kit430 2.0 Expression BeadChip arrays.

extract_protocol: Intestines were cut into 2 cm pieces and washed in ice-cold PBS. To release the intestinal epithelial cells, the pieces were incubated in PBS containing 1.3 mM EDTA for 30 min at 4°C. After vigorous shaking, intestinal epithelial cells were collected in the supernatant and used to prepare RNA extracts using the RNeasy Mini Kit (QIAGEN). The remaining tissue was digested in DMEM containing 1 mg/ml dispase II (Roche) for 20 min at 37oC, incubated with CD45 microbeads (Miltenyi Biotec) and purified using MACS columns (Miltenyi Biotec) according to manufacture’s protocol. RNA was extracted from the CD45 enriched purified cells using the RNeasy Mini Kit (QIAGEN) including a DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

value: HBUS

value: Serrated polyp


title: Wt-BA-sample 1


title: Primary human hepatocytes donor HFTR mock infected 3dpi rep1


title: Primary human hepatocytes donor HFTR HCV infected 1dpi rep2


title: Primary human hepatocytes donor HFTR mock infected 1dpi rep1


title: Wt-dmso-sample 2


title: Mouse 3, Surrounding

description:
791
7991003006_H

value: Normal surrounding (distal) cecum


title: logarithmic WT, biological rep2

city: Warsaw

first: Aneta

middle: Agnieszka

last: Bartosik

address: Pawinskiego 5A

department: Institute of Biochemistry and Biophysics

country: Poland

institute: Polish Academy of Sciences

description:
PAO1161 Log WT2
Gene expression data from logarithmic phase of growth of control strain.

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45 degrees Cent. on GeneChip P. aeruginosa Genome Array in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 beta software (Partek Inc., Louis, MO). Raw data (.CEL files) were imported and processed, using GeneChip Robust Multiarray Averaging (GC RMA) background correction, quantile normalization, log2 transformation and median polish summarization.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa control strain in logarithmic phase of growth

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, (Affymetrix).

growth_protocol: Cells of P. aeruginosa PAO1161 derivative strains were taken from a deep-frozen stock, spread on L-agar plates and grown overnight at 37 degrees Cent. Bacteria from single colonies were then used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures and grown overnight with shaking at 37 degrees Cent. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth and grown with shaking at 37oC. Samples from the cultures were taken at regular intervals to measure the optical density at 600 nm (OD600) (UV-1800 Shimadzu Spectrophotometer) and to determine the c.f.u. ml-1. Aliquots of 2 ml from exponential phase cultures (OD600 0.5; c.f.u. ml-1 1 x 10^9 cells) were subjected to RNA extraction.

extract_protocol: Three independent biological replicates of total RNA were isolated from each strain using a RNeasy mini-kit with on-column DNase digestion (Qiagen) according to the manufacturer's instructions followed by DNase digestion using TURBO DNase kit (Ambion) to eliminate DNA contamination.

tag: strain/background

tag: genotype

value: wild-type

tag: growth phase

value: logarithmic


title: KO+1

first: Stacey

middle: J

last: Baker

address: One Gustave L. Levy Place, Box 1130

department: Oncological Sciences

description: total RNA

scan_protocol: Standard Illumina scan protocol

data_processing: The data were normalized using quantile normalization

source_name: mouse bone marrow-derived LSK+ cells

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

extract_protocol: RNA was extracted using the Arctucus Picopure RNA isolation kit followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided by the manufacturer (Life Technologies). Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Mice were treated with pIpC 1 week prior to harvesting total bone marrow from control and B-myb floxed-MxCre mice. LKS+ cells were obtained via FACS.

value: B-myb floxed-MxCre

value: 12-16 weeks

tag: cell type

value: bone marrow-derived LSK+ cells


title: logarithmic WT, biological rep3

description:
PAO1161 Log WT3
Gene expression data from logarithmic phase of growth of control strain.


title: Mouse 1, SP

description:
784
7991003006_A

tag: tissue


title: KO+3

description: total RNA


title: Mouse 1, Surrounding

description:
785
7991003006_B


title: logarithmic B, biological rep3

description:
PAO1161 Log B3
Gene expression data from logarithmic phase of growth of parB mutant.

source_name: Pseudomonas aeruginosa parB mutant in logarithmic phase of growth

value: parB disruption mutant


title: CON+2

description: total RNA

value: control


title: logarithmic WT, biological rep1

description:
PAO1161 Log WT1
Gene expression data from logarithmic phase of growth of control strain.


title: logarithmic B, biological rep2

description:
PAO1161 Log B2
Gene expression data from logarithmic phase of growth of parB mutant.


title: logarithmic B, biological rep1

description:
PAO1161 Log B1
Gene expression data from logarithmic phase of growth of parB mutant.


title: Mouse 2, Surrounding

description:
787
7991003006_D


title: CON+1

description: total RNA


title: logarithmic A, biological rep3

description:
PAO1161 Log A3
Gene expression data from logarithmic phase of growth of parA mutant.

source_name: Pseudomonas aeruginosa parA mutant in logarithmic phase of growth

value: parA disruption mutant


title: logarithmic A, biological rep2

description:
PAO1161 Log A2
Gene expression data from logarithmic phase of growth of parA mutant.


title: logarithmic A, biological rep1

description:
PAO1161 Log A1
Gene expression data from logarithmic phase of growth of parA mutant.


title: Retina from Nxnl1+/+, 5000 lux, biological rep 2

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

description: mice retina nxnl1++ exposed 5000 lux light

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

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

data_processing: Normalization: gcRMA, data analysis: R/Bioconductor

source_name: Retina RNA from BALB/c Nxnl1+/+ mice, 5000 lux

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix)

growth_protocol: Animals, males and females in equal proportion, were raised under a 12 h, 50 lux / 12 h, dark cycle and given ad-libitum access to food and water. Mice used were 11-16 weeks of age.

extract_protocol: Animals were sacrificed by cervical dislocation and enucleated 24 h after light exposure. The neural retina was dissected free of RPE and RNAs were purified using cesium chloride gradient ultracentrifugation

treatment_protocol: Mice were first dark adapted 16 h prior to light exposure. They were exposed to a light source, monitored in lx, generated by a diffuse, cool, white fluorescent lamps to animals placed in aluminum foil-wrapped polycarbonate cages (one mouse per cage) for 1 hr. The mice then recovered for 24 hr in the dark

value: BALB/c

value: retina

tag: dose


title: Mouse 2, SP

description:
786
7991003006_C


title: ctl_S51 vs. 3D_S51

city: Seoul

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

country: South Korea

institute: NAR Center, Inc. & Genoplan, Inc.

description: S51 non-inoculated susceptible leaves vs. S51 inoculated susceptible leaves in the soybean leaves(3D)

hyb_protocol: After checking labeling efficiency, each 750 ng of cyanine 3-labeled and cyanine 5-labeled cRNA targets were mixed and the fragmentation of cRNA was performed by adding 10x blocking agent and 25x fragmentation buffer and incubating at 60 °C for 30 min. The fragmented cRNA was resuspended with 2x hybridization buffer and directly pipetted onto soybean microarray placed in Hybridization Chamber (Agilent Technologies). The arrays hybridized at 65 °C for 16 h using Agilent Hybridization Oven. The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology).

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray scanner and the data quantification was performed using Agilent Feature Extraction software.

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring GX 7.3 (Agilent Technology). Genes were filtered with removing flag-out genes in each experiment. Intensity-dependent normalization (LOWESS) was performed, where the ratio was reduced to the residual of the Lowess fit of the intensity vs. ratio curve.

organism: Glycine max

source_name: S51 non-inoculated susceptible leaves

label_protocol: For non-inoculated (Cy3) and inoculated (resistant or susceptible) (Cy5) soybean RNAs, the synthesis of target cRNA and hybridization were performed using Agilent’s Low RNA Input Linear Amplification Kit PLUS (Agilent Technology) according to the manufacturer’s instructions.

growth_protocol: We developed two sets of near-isogenic line (NIL) by selecting heterozygous F5 plants among pedigree breeding lines from the cross Saturn x SS97225 (Lee x Seunheuk). F5 pedigree lines were grown in 2006 and inoculated with Xag strain 8ra. Seed from F5 plants that were heterozygous for the disease resistance was harvested and F5:6 pedigree lines were grown in 2007. About 40 F6 plants from each segregating F5:6 lines were inoculated with the strain 8ra. F6 lines that were homozygous for the disease resistance were selected and harvested as F6:7 pedigree lines. About 40 F7 plant from each F6:7 lines were inoculated with the strain 8ra and homozygous for the disease resistance. Thus a NIL set consisted of F5 derived families homozygous phenotype for the disease resistance.

extract_protocol: Ten leaves, non-inoculated (control sample) and inoculated resistant or susceptible leaves at two time points, 3-hour, 12-hour, and  3-day (test groups, 2-condition x 3-time), for total RNA isolation were homogenized using liquid nitrogen with a mortar and pestle. Total RNA and genomic DNA from homogenized sample were extracted using TRIZOL reagent (GibcoBRL, Rockville, MD, USA) according to the protocol of the manufacturer. Total RNA was treated with the RNase-free DNase I (Promega, Madison, WI, USA) to reduce DNA contamination. Total RNA concentration and purity were determined spectrophotometrically by the absorbance ratio at 260:280 nm 1.8 or more. The integrity of total RNA samples was also ascertained by appearance of distinct 28S and 18S bands of ribosomal RNA using Bioanalyzer 2100 system (Agilent Technology, Santa Clara, CA, USA).

treatment_protocol: In the green house experiment, individual plant was inoculated with the strain 8ra Xag. The inoculum was prepared by culturing in PDA (potato dextrose agar) medium. Bacterial cells on the culture plates were sterile distilled water and adjusted to optical density 0.3~0.5 (108 colony forming units (cfu) per milliliter) at 600 nm in UV/Visible spectrophotometer. Inoculations were conducted on recently expanded second trifoliate leaves of 20- to 25-day-old plants. Surface of the leaves were sprayed with inoculum suspensions until water-soaking appearance. For better development of disease symptoms after inoculation, green house condition was held at 28 °C and 100% relative humidity by spraying water and by covering another polypropylene vinyl to protect infected soybean plants from direct sunlight.

value: non-inoculated susceptible leaves

source_name: S51 inoculated susceptible leaves

value: inoculated susceptible leaves


title: ctl_R46 vs. 3D_R46

description: R46 non-inoculated resistant leaves vs. R46 inoculated resistant leaves in the soybean leaves(3D)

source_name: R46 non-inoculated resistant leaves

value: non-inoculated resistant leaves

source_name: R46 inoculated resistant leaves

value: inoculated resistant leaves


title: ctl_R49 vs. 3D_R49

description: R49 non-inoculated resistant leaves vs. R49 inoculated resistant leaves in the soybean leaves(3D)

source_name: R49 non-inoculated resistant leaves

source_name: R49 inoculated resistant leaves


title: Retina from Nxnl1-/-, 2500 lux, biological rep 2

description: mice retina nxnl1 mutant exposed to 2500 lux light

source_name: Retina RNA from BALB/c Nxnl1-/- mice, 2500 lux


title: ctl_S52 vs. 3D_S52

description: S52 non-inoculated susceptible leaves vs. S52 inoculated susceptible leaves in the soybean leaves(3D)

source_name: S52 non-inoculated susceptible leaves

source_name: S52 inoculated susceptible leaves


title: ctl_R47 vs. 3D_R47

description: R47 non-inoculated resistant leaves vs. R47 inoculated resistant leaves in the soybean leaves(3D)

source_name: R47 non-inoculated resistant leaves

source_name: R47 inoculated resistant leaves


title: Retina from Nxnl1-/-, 2500 lux, biological rep 1


title: Retina from Nxnl1-/-, 5000 lux, biological rep 2

description: mice retina nxnl1 mutant exposed to 5000 lux light

source_name: Retina RNA from BALB/c Nxnl1-/- mice, 5000 lux


title: Retina from Nxnl1+/+, 5000 lux, biological rep 3


title: ctl_S50 vs. 3D_S50

description: S50 non-inoculated susceptible leaves vs. S50 inoculated susceptible leaves in the soybean leaves(3D)

source_name: S50 non-inoculated susceptible leaves

source_name: S50 inoculated susceptible leaves


title: Retina from Nxnl1-/-, 2500 lux, biological rep 3


title: Retina from Nxnl1+/+, 2500 lux, biological rep 3

description: mice retina nxnl1++ exposed to 2500 lux light

source_name: Retina RNA from BALB/c Nxnl1+/+ mice, 2500 lux


title: Retina from Nxnl1+/+, 2500 lux, biological rep 2


title: Retina from Nxnl1+/+, 5000 lux, biological rep 1


title: ctl_S50 vs. 12h_S50

description: S50 non-inoculated susceptible leaves vs. S50 inoculated susceptible leaves in the soybean leaves(12h)


title: ctl_S52 vs. 12h_S52

description: S52 non-inoculated susceptible leaves vs. S52 inoculated susceptible leaves in the soybean leaves(12h)


title: ctl_S51 vs. 12h_S51

description: S51 non-inoculated susceptible leaves vs. S51 inoculated susceptible leaves in the soybean leaves(12h)


title: Retina from Nxnl1+/+, 2500 lux, biological rep 1


title: ctl_R49 vs. 3h_R49

description: R49 non-inoculated resistant leaves vs. R49 inoculated resistant leaves in the soybean leaves(3h)


title: ctl_R49 vs. 12h_R49

description: R49 non-inoculated resistant leaves vs. R49 inoculated resistant leaves in the soybean leaves(12h)


title: ctl_S51 vs. 3h_S51

description: S51 non-inoculated susceptible leaves vs. S51 inoculated susceptible leaves in the soybean leaves(3h)


title: ctl_R47 vs. 12h_R47

description: R47 non-inoculated resistant leaves vs. R47 inoculated resistant leaves in the soybean leaves(12h)


title: Retina from Nxnl1-/-, 50 lux, biological rep 1

description: mice retina nxnl1 mutant exposed to 50 lux light

source_name: Retina RNA from BALB/c Nxnl1-/- mice, 50 lux

value: 50 lux


title: Retina from Nxnl1+/+, 50 lux, biological rep 1

description: mice retina nxnl1++ exposed to 50 lux light

source_name: Retina RNA from BALB/c Nxnl1+/+ mice, 50 lux


title: Retina from Nxnl1-/-, 5000 lux, biological rep 1


title: ctl_R46 vs. 12h_R46

description: R46 non-inoculated resistant leaves vs. R46 inoculated resistant leaves in the soybean leaves(12h)


title: Retina from Nxnl1-/-, 50 lux, biological rep 3


title: KYSE170-luc_SOX17_overexpression_12hr_rep1

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

description:
mRNA expression data from cancer cell line transfect SOX17 vector
11S133P009.CEL

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip® Operating Software v1.4 (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Transfection SOX17 in Esophageal sequamous tumor cell-KYSE170 luc cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA. (All protocol followed GeneChip Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix)

growth_protocol: KYSE170-luc cells were grown in RPMI-1640 with 10% FBS and 1% pen/strep

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

treatment_protocol: Cells were cultured in 10 cm plates and transfect with empty vector and SOX17 for 12 hours.

tag: cell line

value: esophageal cancer cell (ESCC) line KYSE170-luc

tag: transfection


title: PfHda2 knockdown 90 hours post invasion

status: Public on Feb 11 2014

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex, Pollock Rd

department: Biochemistry and Molecular Biology

institute: Penn State University

description: 3D7 gene PfHda2 with C-terminal destabilizatin domain. Not stabilized (no Shld1).

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2505B Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction.

organism: Plasmodium falciparum 3D7

source_name: PfHda2-DD -Shld1 RNA

growth_protocol: P. faciparum 3D7 with PfHda2 C-terminal destabilization domain: highly synchronized parasites treated ± Shld1 were grown under shaking conditions.

extract_protocol: Starting at 44 hours post Shld1 removal, samples were harvested in Trizol for total RNA extraction every 6 hours for 66 hours.

value: PfHda2-DD -Shld1 RNA

tag: hours post invasion

source_name: 3D7 Mixed Stage Reference Pool

tag: reference

value: Mixed Stage Reference Pool


title: PfHda2 knockdown 78 hours post invasion

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).


title: PfHda2 knockdown 84 hours post invasion


title: KYSE170-luc_EV_overexpression_12hr_rep1

description:
mRNA expression data from cancer cell line transfect Empty vector
11S133P008.CEL

source_name: Transfection EV in Esophageal sequamous tumor cell-KYSE170 luc cell

value: empty vector


title: PfHda2 knockdown 96 hours post invasion


title: ctl_R46 vs. 3h_R46

description: R46 non-inoculated resistant leaves vs. R46 inoculated resistant leaves in the soybean leaves(3h)

source_name: R46 non-inoculated resistant leaves

source_name: R46 inoculated resistant leaves


title: ctl_S50 vs. 3h_S50

description: S50 non-inoculated susceptible leaves vs. S50 inoculated susceptible leaves in the soybean leaves(3h)


title: Retina from Nxnl1-/-, 50 lux, biological rep 2

tag: strain


title: ctl_R47 vs. 3h_R47

description: R47 non-inoculated resistant leaves vs. R47 inoculated resistant leaves in the soybean leaves(3h)


title: Retina from Nxnl1+/+, 50 lux, biological rep 2


title: PfHda2 knockdown 102 hours post invasion


title: PfHda2 knockdown 72 hours post invasion


title: Wildtype 84 hours post invasion

description: 3D7 gene PfHda2 with C-terminal destabilizatin domain. Stabilized by Shld1.

source_name: PfHda2-DD +Shld1 RNA

value: PfHda2-DD +Shld1 RNA


title: Wildtype 96 hours post invasion


title: Wildtype 90 hours post invasion


title: PfHda2 knockdown 50 hours post invasion


title: Wildtype 78 hours post invasion


title: D-tumor-lymph node

city: shanghai

first: lei

last: guo

address: changhai road 225

institute: EHBH

description: LncRNA expression of  metastasis-related lymph node in gastric cancer patients D

hyb_protocol: Agilent Gene Expression Hybridization Kit  (Agilent p/n 5188-5242):

scan_protocol: Agilent Microarray Scanner (Agilent p/n G2565BA)was used to analyze acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 7 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering and differentially expressed LncRNAs and mRNAs were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.
Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering and differentially expressed LncRNAs and mRNAs were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.

label_protocol: For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: lymph node

tag: tumor size

tag: tnm stage

value: Ⅳ

tag: gender

value: Male


title: Wildtype 102 hours post invasion

tag: genotype/variation


title: PfHda2 knockdown 44 hours post invasion


title: Wildtype 66 hours post invasion


title: M+T/M+M(d5)

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridization, and washing steps were carried out according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7 except that 300 ng of each labeled cRNA sample were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2505C (pixel resolution 5 µm, extended dynamic range mode).

data_processing: Data extraction and normalization were performed with the Feature Extraction Software V9.5.3.1 (or V10.7.3.1) by using the recommended default extraction protocol file: GE2-v5_95_Feb07.xml (or GE2_107_Sep09.xml). To correct for systematic bias at the high end of the fluorescence intensity measurements, the highest ranking 2% of Processed Signals in the green channel (gPS) were further normalized according to an intensity-dependent, non-linear strategy, to optimize fitting to their respective counterparts in the red channel.

label: Alexa Fluor 647

source_name: Monocytes 50h Medium

label_protocol: Total RNA was used to prepare AlexaFluor555- or AlexaFluor647-labeled cRNA (Amino Allyl MessageAmp™ II Kit; Ambion) according to the manufacturer’s instructions

growth_protocol: Blood samples from healthy donors were kindly provided by the Institute for Transfusion Medicine, Medical School Hannover. Informed patient consent was obtained and the experiments were approved by the ethics committee of the Hannover Medical School in accordance to the Declaration of Helsinki. Monocytes were isolated by Biocoll (Biochrom) density gradient centrifugation using LeucoSep®tubes (Greiner Bio-One) followed by negative selection with magnetic anti-biotin microbeads (Monocyte Isolation Kit II, Miltenyi Biotec) according to manufacturer’s instructions. Purified cells were cultured in 12 well plates (Thermo Scientific) at a density of 4x106 cells in a final volume of 2 ml RPMI 1640 supplemented with 7% fetal calf serum (FCS), 100 U/ml penicillin, 100 μg/ml streptomycin (all Biochrom), 1,8% OPI Media Supplement (Sigma-Aldrich) and 0,8% Gibco® MEM Non-Essential Amino Acids Solution (Invitrogen) or in 24 well plates (Thermo Scientific) at a density of 2x106 cells in 1 ml culture medium. For further purification cells were washed three times after an adherence step. All cell culture media and reagents were routinely tested for endotoxin content using the Limulus Amoebocyte Lysate (LAL) assay (Lonza) (<10 pg endotoxin / ml).

extract_protocol: Cultured cells were lysed and total RNA was isolated using the RNeasy Mini Kit or Micro Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Unless indicated otherwise, cells were pretreated with 40 or 400 U TNF/ml (Sigma-Aldrich) for 48 h followed by short exposure with 400 U TNF/ml for 2 h for RNA experiments.

tag: donor#

value: Primary human monocytes

tag: pre-incubated with

value: Medium for 48hr

value: Medium for 2hr

label: Alexa Fluor 555

source_name: Monocytes 48h Medium 2h TNF(400U)

value: TNF(400U) for 2hr


title: Wildtype 72 hours post invasion


title: A-tumor-lymph node

description: LncRNA expression of  metastasis-related lymph node in gastric cancer patients A

tag: age


title: M+T/M+M(d3)

tag: treated with


title: Wildtype 60 hours post invasion


title: 40+T/40+M(d4)

source_name: Monocytes 48h TNF(40U) 2h Medium

value: TNF(40U) for 48hr

source_name: Monocytes 48h TNF(40U) 2h TNF(400U)


title: normal tissue

description: LncRNA expression of  Normal gastirc tissue

source_name: primary normal gastric tissue

value: mixed normal gastric tissue

value: mixed


title: E-tumor tissue

description: LncRNA expression of  gastric cancer tissue from patients E

source_name: primary gastric cancer tissue from patients E

value: tumor gastric tissue

value: Female


title: D-tumor tissue

description: LncRNA expression of  gastric cancer tissue from patients D

source_name: primary gastric cancer tissue from patients D


title: Wildtype 56 hours post invasion


title: A-tumor tissue

description: LncRNA expression of  gastric cancer tissue from patients A

source_name: primary gastric cancer tissue from patients A


title: E-tumor-lymph node

description: LncRNA expression of  metastasis-related lymph node in gastric cancer patients E


title: Wildtype 44 hours post invasion


title: 40+T/40+M(d5)


title: Wildtype 50 hours post invasion


title: M+T/M+M(d4)


title: M+T/M+M(d1)


title: 400+T/400+M(d1)

source_name: Monocytes 48h TNF(400U) 2h Medium

value: TNF(400U) for 48hr

source_name: Monocytes 48h TNF(400U) 2h TNF(400U)


title: M+T/M+M(d2)


title: 400+T/400+M(d3)


title: PfHda2 knockdown 66 hours post invasion

value: PfHda2-DD -Shld1 RNA


title: PfHda2 knockdown 56 hours post invasion

value: Mixed Stage Reference Pool


title: PfHda2 knockdown 60 hours post invasion


title: XYB_24

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

hyb_protocol: Affymetrix GeneChip Mouse Exon 1.0 ST microarrays were hybridized with 4.7 µg of labelled DNA

scan_protocol: Washes, staining and scan of microarrays were conducted using an Affymetrix GCS3000 platform

data_processing:
Microarrays were analyzed using RMA (Robust Multi-array Analysis) as available in the bioconductor affy package (http://www.bioconductor.org), normalized using subset normalisation, in which we only considered genes on Autosomes, and annotated using the xmapcore database for Ensembl mouse version 62 (http://annmap.picr.man.ac.uk/download/). For each gene the expression is calculated by averaging over probesets that detect the maximum number of transcripts per gene.
Probes are assigned to probe sets using the cdf mouseexonpmcdf (this is the standard cdf in xmapcore), and one can get it at the xmapcore website: http://annmap.picr.man.ac.uk/downloads/index
Attached supplementary file (GPL16682_table_map_probeset_ensg.txt) is used to assign the probes that map to consensus exons, i.e. exons that are contained in the majority of transcripts. This file was generated using xmapcore.

source_name: XY mESCs 24 hours after differentiation start

label_protocol: Affymetrix mouse Exon 1.0 ST arrays were hybridised according to Affymetrix's recommendations using the Ambion WT protocol (Life technologies) and Affymetrix labelling and hybridization kits. 100ng of total RNA (RIN=10) were processed and amplified in parallel with an external Universal Mouse Reference RNA (Agielent, #740100) to control robustness of the data. The mean yield of labelled DNA was   7.2 µg (min: 6.4µg; max: 7.7µg).

growth_protocol: Pgk12.1 and E14 ES cells were adapted, during passages 21-26, to 2i culture conditions, consisting of N2B27 medium (50% DMEM/F12 (Invitrogen), 50% Neurobasal medium (Invitrogen), NDiff supplement (Millipore), B27 supplement (Invitrogen), 2mM Glutamine, 100 µM β-Mercaptoethanol), supplemented with 3 µM Gsk3 inhibitor CT-99021, 1 µM Mek1 inhibitor PD-0325901 and 100U/ml LIF (Millipore).

extract_protocol: 200 µl of Chloroform was added and after 15 min centrifugation (12000xg, 4°C) the aqueous phase was mixed with 700 µl 70% ethanol and applied to a Silica column (Qiagen RNAeasy Mini kit). RNA was then purified according to the instruction of the manufacturer, including on-column DNAse digestion.

treatment_protocol: For EpiSC differentiation9 8*10^5 cells per well were seeded in a Fibronectin coated (10 µg/ml, Millipore) 6-well plate in differentiation medium (N2B27 medium, 20ng/ml Activin A, 12 ng/ml Fgf-basic, R&D), subsequently the medium was changed daily. At the time of differentiation indicated in the sample name, cells were lysed by direct addition of 1 ml Trizol to the wells

tag: sex chromosome complement

value: XY

tag: time


title: ctl_S52 vs. 3h_S52

description: S52 non-inoculated susceptible leaves vs. S52 inoculated susceptible leaves in the soybean leaves(3h)

source_name: S52 non-inoculated susceptible leaves

tag: tissue

value: non-inoculated susceptible leaves

source_name: S52 inoculated susceptible leaves

value: inoculated susceptible leaves


title: XYB_84

source_name: XY mESCs 84 hours after differentiation start

tag: cell type


title: 400+T/400+M(d1replicate)


title: XYB_32

source_name: XY mESCs 32 hours after differentiation start


title: XXX_00

description: mESCs 84 hours after differentiation start

source_name: Universal Mouse Reference RNA (Agilent, #740100)

value: Reference


title: XYB_48

source_name: XY mESCs 48 hours after differentiation start


title: XYB_72

source_name: XY mESCs 72 hours after differentiation start


title: M+T/M+M(d1replicate)

source_name: Monocytes 50h Medium

source_name: Monocytes 48h Medium 2h TNF(400U)


title: XYA_00

description: undifferentiated mESCs

source_name: undifferentiated XY mESCs


title: XYB_16

source_name: XY mESCs 16 hours after differentiation start


title: Deer_Peak lactation_subject 3

first: Magdalena

last: Łój

address: Nowoursynowska 166

department: Department of Physiological Sciences

institute: Warsaw University of Life Sciences

hyb_protocol: according to the manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Cervus elaphus

source_name: peripheral blood nuclear cells

extract_protocol: Total RNA extracted using Rneasy Protect Animal Blood Kit following manufacturer's instructions (Qiagen, USA)

treatment_protocol: Blood collection into Rneasy Protect Animal Blood Tubes  (Qiagen, USA)

tag: breed

value: Deer

tag: physiological state

value: peak lactation

source_name: peripheral blood nuclear cells - common reference

tag: sample type

value: peripheral blood nuclear cells from 20 bovine which were not included in the research groups


title: Deer_Dry period_subject 3

label_protocol: according to the manufacturer's protocol

value: dry period


title: XYB_60

source_name: XY mESCs 60 hours after differentiation start


title: 400+T/400+M(d2)

source_name: Monocytes 48h TNF(400U) 2h Medium

value: Primary human monocytes

value: Medium for 2hr

value: TNF(400U) for 2hr


title: XOB_84

source_name: XO mESCs 84 hours after differentiation start

value: XO


title: Deer_Peak lactation_subject 2


title: Deer_Peak lactation_subject 4


title: Deer_Peak lactation_subject 1


title: XYB_08

source_name: XY mESCs 8 hours after differentiation start


title: Deer_Dry period_subject 1


title: Deer_Dry period_subject 4


title: Deer_Dry period_subject 2


title: XOB_72

source_name: XO mESCs 72 hours after differentiation start


title: XYB_00

description: undifferentiated mESCs


title: Polish Red_Peak lactation_subject 4

organism: Bos taurus

value: Polish Red


title: Polish Red_Peak lactation_subject 3


title: Polish Red_Peak lactation_subject 1


title: Polish Red_Peak lactation_subject 2


title: XOB_66

source_name: XO mESCs 66 hours after differentiation start


title: Polish Red_Dry period_subject 4


title: VDL902_Cy5

type: genomic

city: Ames

first: Zuo-Wei

last: Wu

state: IA

address: 1113 Veterinary Medicine Bldg

institute: Iowa state university

description: VDL902-replicate 2

hyb_protocol: The hybrization and wash were perfomed following (http://www.mycroarray.com/) standard protocol

scan_protocol: Arrays were scanned at 532-nm (Cy3) and 635-nm (Cy5) wavelengths using GenePix 4100A (Molecular Devices, Sunnyvale, CA) following the manufacturer's protocol

data_processing: Fluorescence intensities of each spot were extracted using GenepixPro 7.0.(Molecular Devices). Because the probes of the whole array were disigned for mutiple C. jejuni strains (IA3902, RM1221, 81-176, 269.97, NCTC11168, CG8421, plasmid pCJ1170) and used as pan-array,  in this study only the probes targeted at IA3902 CDS were retained for following analysis. (i) After local background correction, the fluorescence intensity in each wavelength was log2 transformed and normalized using locally weighted linear regression (LOWESS) in statistical software R (http://www.r-project.org); (ii) Genes with the signal intensity ratio (Test/Reference) less than 0.6 in both replicate slides were considered divergent between the test genome and the reference genome

molecule: genomic DNA

organism: Campylobacter jejuni

source_name: reference: IA3902

label_protocol: The genomic DNA was labeled following Mycroarry (http://www.mycroarray.com/) standard protocol

growth_protocol: C. jejuni cells were incubated for 20hrs on Mueller-Hinton (MH) agar

extract_protocol: Total DNA was extracted using the Wizard® Genomic DNA Purification Kit  from Promega following the manufacturer's instruction

tag: isolate

tag: note

value: causing sheep abortion


title: Polish Red_Dry period_subject 3


title: VDL1957_Cy3

description: VDL1957-replicate 1


title: XOB_56

source_name: XO mESCs 56 hours after differentiation start


title: Holstein Friesian_Peak lactation_sucject 4

value: Holstein-Fresian


title: Polish Red_Dry period_subject 1


title: XOB_60

source_name: XO mESCs 60 hours after differentiation start


title: Holstein Friesian_Peak lactation_subject 3


title: XOB_44

source_name: XO mESCs 44 hours after differentiation start


title: VDL213-Cy5

description: VDL213-replicate 2


title: Polish Red_Dry period_subject 2


title: VDL902_Cy3

description: VDL902-replicate 1


title: VDL213_Cy3

description: VDL213-replicate 1


title: UK18-Cy5

description: Uk18-replicate 2


title: XOB_52

source_name: XO mESCs 52 hours after differentiation start


title: Uk18_Cy3

description: Uk18-replicate 1


title: XOB_40

source_name: XO mESCs 40 hours after differentiation start


title: Holstein Friesian_Peak lactation_subject 2


title: XOB_48

source_name: XO mESCs 48 hours after differentiation start


title: Holstein Friesian_Dry period_subject 4


title: ND9-Cy5

description: ND9-replicate 2


title: Holstein Friesian_Dry period_subject 3


title: ND9-Cy3

description: ND9-replicate 1


title: CA3e_Cy3

description: CA3e-replicate 1


title: Holstein Friesian_Peak lactation_subject 1


title: XOB_36

source_name: XO mESCs 36 hours after differentiation start


title: XOB_28

source_name: XO mESCs 28 hours after differentiation start


title: VDL2945_cy5

description: VDL2945-replicate 2

hyb_protocol: The hybrization and wash were perfomed following JCVI standard protocol

scan_protocol: Arrays were scanned at 532-nm (Cy3) and 635-nm (Cy5) wavelengths using a ScanArray3000 scanner (PerkinElmer, Waltham, MA) or GenePix 4100A (Molecular Devices, Sunnyvale, CA) following the manufacturer's protocol

data_processing: Fluorescence intensities of each spot were extracted using the Imagene 8.0 software (Axon Instruments, Foster City, California) or GenepixPro 7.0.(Molecular Devices) Because the probes of the whole array were disigned for mutiple C. jejuni strains (IA3902, RM1221, 81-176, 269.97, NCTC11168, CG8421, plasmid pCJ1170) and used as pan-array,  in this study only the probes targeted at IA3902 CDS were retained for following analysis. (i) After local background correction, the fluorescence intensity in each wavelength was log2 transformed and normalized using locally weighted linear regression (LOWESS) in statistical software R (http://www.r-project.org); (ii) Genes with the signal intensity ratio (Test/Reference) less than 0.6 in both replicate slides were considered divergent between the test genome and the reference genome

label_protocol: The genomic DNA was labeled following JCVI standard protocol


title: XOB_12

source_name: XO mESCs 12 hours after differentiation start


title: VDL3080_cy5

description: VDL3080-replicate 2


title: VDL2945_cy3

description: VDL2945replicate 1


title: XOB_18

source_name: XO mESCs 18 hours after differentiation start


title: Holstein Friesian_Dry period_subject 2

source_name: peripheral blood nuclear cells

source_name: peripheral blood nuclear cells - common reference


title: Holstein Friesian_Dry period_subject 1


title: XOB_06

source_name: XO mESCs 6 hours after differentiation start


title: VDL3080_cy3

description: VDL3080-replicate 1


title: VDL1957-cy5

description: VDL1957-replicate 2


title: VDL705_cy3

description: VDL705-replicate 1


title: VDL705_cy5

description: VDL705-replicate 2


title: UK33_cy5

description: UK33-replicate 2


title: VDL35_cy3

description: VDL35-replicate 1


title: UK33_cy3

description: UK33-replicate 1


title: XOA_00

description: undifferentiated mESCs

source_name: undifferentiated XO mESCs


title: VDL35_cy5

description: VDL35-replicate 2


title: XOA_36

description: mESCs 36 hours after differentiation start


title: UK29_cy3

description: UK29-replicate 1


title: ID15_cy3

description: ID15-replicate 1


title: UK29_cy5

description: UK29-replicate 2


title: ID8_cy5

description: ID8-replicate 2


title: UK24_cy3

description: UK24-replicate 1


title: XXB_84

source_name: XX mESCs 84 hours after differentiation start

value: XX


title: XXB_52

source_name: XX mESCs 52 hours after differentiation start


title: XOB_24

source_name: XO mESCs 24 hours after differentiation start


title: XXB_56

source_name: XX mESCs 56 hours after differentiation start


title: XOB_00

description: undifferentiated mESCs


title: XXB_60

source_name: XX mESCs 60 hours after differentiation start


title: XXB_72

source_name: XX mESCs 72 hours after differentiation start


title: UK24_cy5

description: UK24-replicate 2

source_name: reference: IA3902


title: ID15_cy5

description: ID15-replicate 2


title: XXB_48

source_name: XX mESCs 48 hours after differentiation start


title: XXB_36

source_name: XX mESCs 36 hours after differentiation start


title: CA6e-cy5

description: CA6e-replicate 2


title: XXB_44

source_name: XX mESCs 44 hours after differentiation start


title: XXB_66

source_name: XX mESCs 66 hours after differentiation start


title: E2B2a_cy5

description: E2B2a-replicate 2


title: XXB_40

source_name: XX mESCs 40 hours after differentiation start


title: XXB_24

source_name: XX mESCs 24 hours after differentiation start


title: XXB_32

source_name: XX mESCs 32 hours after differentiation start


title: ID8_cy3

description: ID8-replicate 1


title: XXB_12

source_name: XX mESCs 12 hours after differentiation start


title: hEpSC-1

city: Philadelphia

first: Xiaowei

last: Xu

state: PA

address: 3400 Spruce st

institute: University of Pennsylvania

description:
Keratinocyte-1
K.1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with lumi in R.

source_name: human epithelial stem cells

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

growth_protocol: Human iPSCs and EpSCs were cultured before they reached 70% confluency.

extract_protocol: Cells were washed again with HBSS and lysed directly in TRI Reagent® RNA Isolation Reagent (Sigma) and stored at -20°C.

value: epithelial stem cells

tag: tissue origin

value: fetal scalp tissues


title: XXB_18

source_name: XX mESCs 18 hours after differentiation start


title: CA6e-cy3

description: CA6e-replicate 1


title: XXA_36


title: hiPSC-EpSC-2

description:
iPS-keratinocyte-2
iPS.K.2

source_name: human iPSC-derived epithelial stem cells

value: iPSC-derived epithelial stem cells

value: normal skin


title: hEpSC-2

description:
Keratinocyte-2
K.2


title: hiPSC-1

description:
iPS-1
iPS.1

source_name: human induced pluripotent stem cells (iPSCs)

value: induced pluripotent stem cells (iPSCs)


title: hiPSC-EpSC-3

description:
iPS-keratinocyte-3
iPS.K.3


title: PHIL_FFPE28_post

status: Public on Feb 10 2014

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

institute: Md Anderson Cancer center

description: pretreatment sample record; GSM1174013

hyb_protocol: Standard Illumina whole genome DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization in the R language environment was used to normalize the data

label: whole genome DASL

source_name: Bladder tumor

label_protocol: Standard Illuminal whole genome DASL method

extract_protocol: Total RNA from FFPE was extracted by High Pure miRNA Isolation Kit (Roche). Quality control was performed by NanoDrop ND-1000.

tag: cstage

tag: sample procured

value: Cystectomy (post treatment)

tag: treatment

value: dose-dense (dd) MVAC


title: XXB_00

description: undifferentiated mESCs

source_name: undifferentiated XX mESCs


title: CA3e-cy5

description: CA3e-replicate 2


title: hiPSC-2

description:
iPS-2
iPS.2


title: E2B2a_cy3

description: E2B2a-replicate 1


title: XXB_06

source_name: XX mESCs 6 hours after differentiation start


title: PHIL_FFPE26_post

description: pretreatment sample record; GSM1174011


title: XXA_00

description: undifferentiated mESCs


title: XOB_32

source_name: XO mESCs 32 hours after differentiation start


title: hiPSC-EpSC-1

description:
iPS-keratinocyte-1
iPS.K.1


title: liver-control-haras-rep2

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

country: Switzerland

institute: Novartis

hyb_protocol: Arrays were hybridized according to the Agilent miRNA microarray method ‘miRNA Microarray System with miRNA Complete Labeling and Hyb Kit’ (G4170-90011).

scan_protocol: Following hybridization and washing, the arrays were scanned on an Agilent Microarray Scanner (#G2505B) according to the manufacturer’s protocol. Images from the scanner were processed using Agilent Feature Extraction Software v9.5.1.

data_processing: The raw microarray data was normalized using the AFE-TGS method implemented in the package AgiMicroRna for R (v.2.14.1)/Bioconductor (v.2.9). Quantile normalization was applied to correct for experimental variation between arrays. The normalized total gene signals (TGS) were log2-transformed and probesets which were not expressed in any of the analyzed experimental conditions were removed.

source_name: Non-mutated liver control (non-tumor) tissue

label_protocol: 25ng total RNA was end-labeled using the miRNA complete labeling and hybridization kit (Agilent# 5190-0456).

growth_protocol: 29–32 days old male C3H/HeJ mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups (n = 10).

extract_protocol: Total RNA including miRNA was isolated using the miRNeasy Mini Kit (QIAGEN, Hilden, Germany). RNA integrity was checked with an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behavior and sacrificed on the last day of dosing (day 28).

tag: strain

value: liver

value: Control

value: diet

value: oral

value: ad libitum

value: 27 weeks


title: liver-tumor-ras-rep3

source_name: Ha-ras-mutated liver tumor tissue


title: PHIL_FFPE42_post

description: pretreatment sample record; GSM1174027


title: PHIL_FFPE34_post

description: pretreatment sample record; GSM1174019


title: PHIL_FFPE40_post

description: pretreatment sample record; GSM1174025


title: PHIL_FFPE11_post

description: pretreatment sample record; GSM1173996


title: liver-control-ctnnb1-rep5

value: Phenobarbital


title: PHIL_FFPE12_post

description: pretreatment sample record; GSM1173997


title: liver-tumor-ctnnb1-rep7

source_name: Ctnn1b-mutated liver tumor tissue


title: PHIL_FFPE39_post

description: pretreatment sample record; GSM1174024


title: liver-tumor-ras-rep2


title: PHIL_FFPE23_post

description: pretreatment sample record; GSM1174008


title: PHIL_FFPE35_post

description: pretreatment sample record; GSM1174020


title: liver-tumor-ctnnb1-rep6


title: PHIL_FFPE19_post

description: pretreatment sample record; GSM1174004


title: liver-control-haras-rep1


title: PHIL_FFPE4_post

description: pretreatment sample record; GSM1173989


title: liver-tumor-ras-rep1


title: PHIL_FFPE37_post

description: pretreatment sample record; GSM1174022


title: liver-control-ctnnb1-rep6


title: PHIL_FFPE21_post

description: pretreatment sample record; GSM1174006


title: liver-control-haras-rep3


title: PHIL_FFPE31_post

description: pretreatment sample record; GSM1174016


title: liver-control-ctnnb1-rep4


title: PHIL_FFPE6_post

description: pretreatment sample record; GSM1173991


title: PHIL_FFPE5_post

description: pretreatment sample record; GSM1173990


title: PHIL_FFPE20_post

description: pretreatment sample record; GSM1174005


title: liver-tumor-ctnnb1-rep3


title: liver-tumor-ctnnb1-rep4


title: liver-tumor-ctnnb1-rep2


title: liver-tumor-ctnnb1-rep5


title: PHIL_FFPE33_post

description: pretreatment sample record; GSM1174018


title: MDA_MVAC21

tag: tissue type

value: muscle-invasive bladder cancer (MIBC)

tag: response to mvac (downstaged to p0 or t1 w/ nac)

value: no

tag: subset type

value: basal

tag: pstage


title: PHIL_FFPE10_post

description: pretreatment sample record; GSM1173995


title: liver-tumor-ctnnb1-rep1


title: liver-tumor-ras-rep1

type: protein

hyb_protocol: Detection of proteins and protein modifications was performed using a direct two-step immunoassay using specific primary antibodies; details on the assay procedure are found in Pirnia et al., 2009 (PMID: 19609961).

scan_protocol: Images of the microarrays were taken using the ZeptoREADER microarray imager (Zeptosens), and image analysis was performed using the ZeptoVIEW Pro 3.1 software package (Zeptosens). Signal intensity for each spot was determined as background-corrected mean intensity with the local background subtracted from the spot intensity; the determined values were referenced against adjacent reference spots as implemented in the software package giving referenced fluorescence intensity.

data_processing:
The blank-corrected normalized relative fluorescence intensities (RFI) were for each analyte centered to the median signal level observed for the corresponding control samples and then log2-transformed.  Measurements for which the background noise (i.e., signal of secondary antibody) was higher than the combined foreground and background signal (i.e., signal of primary and secondary antibody) were treated as missing values (<1%) and imputed using the k-Nearest-Neighbor (kNN) algorithm.
Please note that csv files contain data  obtained from the corresponding feature extraction software ZeptoVIEW Pro 3.1. However, these data could not be automatically generated using the software, since manual interactions are required to perform some of the preprocessing steps. Furthermore, the raw data matrix obtained from the software was split, such that one raw data file can be provided for each sample.

molecule: protein

label_protocol: Fluorescence signal was generated using Alexa647-/Cy5-labeled anti-species secondary antibodies (Invitrogen, Darmstadt, Germany); details on the assay procedure are found in Pirnia et al., 2009 (PMID: 19609961).

extract_protocol: Frozen liver tissue was grinded using a ball mill (Mikro-Dismembrator U; Sartorius, Goettingen, Germany). Tissue lysates were generated under denaturing conditions by adding a 8-fold excess (vol/wt) of CeLyA Lysis Buffer CLB1 (Zeptosens).


title: p34

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: The profiles were dewaved (van de wiel et al, Bioinformatics. 2009, median normalized and corrected for tumor cell percentage by using the R package CGHcall (van de Wiel et al, Bioinformatics. 2007)

source_name: Colorectal cancer

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al, J Pathol. 2010

value: Colorectal cancer tissue sample (FFPE)

tag: patient

tag: type

value: primarytumor

tag: site

value: Colorectum

source_name: normal colorectum mucosa

value: normal colorectum mucosa


title: p29

tag: tissue


title: p27


title: p37


title: p40


title: p47


title: p52


title: liver-tumor-ras-rep2


title: liver-tumor-ras-rep3


title: p21


title: liver-control-haras-rep3


title: liver-control-haras-rep2


title: liver-control-haras-rep1


title: p22


title: p33


title: p44


title: liver-control-ctnnb1-rep5


title: liver-control-ctnnb1-rep4


title: p20


title: p16


title: liver-control-ctnnb1-rep6


title: p9


title: 4 weeks MPTP-treated mouse retina 1

first: Sabina

last: Lim

address: #1 Hoegi-dong Dongdaemoon-gu

institute: East-West Medical Research Institute, Kyung Hee University

description: Gene expression data from MPTP-treated retina for 4 weeks

hyb_protocol: Following labeling, each cDNA was hybridized for 16 hr at 45℃ at 60 rpm on Affymetrix MouseGene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0007.

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

data_processing: The quality control was estimated by confirming the order of the signal intensities of the Poly-A controls and Hybridization controls using Expression Console Software (Affymetrix, USA). The microarray data was analyzed using a GenPlex V3.0 (ISTECH, Korea). The data were analyzed with Robust Multichip Analysis (RMA) quantification method as a probe set summarization algorithm for log transformation with base 2 (log2) and Quantile normalization method as a normalization method in the Preprocessing module of GenPlex V3.0. The mean signal intensities of all genes (35,557 probes (28,853 genes) in a platform) were obtained from 2 chips of each experimental group.

source_name: C57BL/6 mouse retina treated with MPTP for 4 weeks

label_protocol: Fragmented and biotinylated cDNA were prepared according to the SPIA cDNA with Biotin labeling kit from 100 ng total RNA (NuGen, USA).

growth_protocol: Six-week old male inbred C57BL/6 mice (20-22 g) were grown up.

extract_protocol: The total RNA in the retinal tissues of each group was extracted using RNeasy Plus Mini kit (QIAGEN, USA) according to the manufacturer’s instruction.

tag: gender

value: Male

value: Retinal tissue

tag: developmental stage

value: Adult


title: 4 weeks saline-treated mouse retina 2

description: Gene expression data from normal retina for 4 weeks

source_name: C57BL/6 mouse retina treated with saline for 4 weeks


title: p15


title: 4 weeks MPTP-treated mouse retina 2


title: p14


title: p3


title: p6


title: p18


title: p11


title: 4 weeks saline-treated mouse retina 1


title: p12


title: p19


title: p17


title: p5


title: p2


title: p10


title: m63_LymphNode

description: Normal colon mucosa from the same patient as the tumor was used as reference in the oaCGH experiments

source_name: Lymph node metastasis

value: Lymph node metastasis (FFPE)

value: metastasis

value: Lymph node

value: normal colon mucosa obtained from the same patient as ch1


title: p1


title: p4


title: p8


title: p7


title: liver-tumor-ctnnb1-rep7

value: liver

value: diet

value: oral

value: ad libitum


title: liver-tumor-ctnnb1-rep6

value: Phenobarbital

value: 27 weeks


title: m63_Ovarian

source_name: Ovarian metastasis

value: Ovarian metastasis (FFPE)

value: Ovary


title: liver-tumor-ctnnb1-rep2


title: liver-tumor-ctnnb1-rep4


title: liver-tumor-ctnnb1-rep5


title: liver-tumor-ctnnb1-rep3


title: 1 week MPTP-treated mouse retina 2

description: Gene expression data from MPTP-treated retina for 1 week

source_name: C57BL/6 mouse retina treated with MPTP for 1 week


title: liver-tumor-ctnnb1-rep1


title: 1 week saline-treated mouse retina 2

description: Gene expression data from normal retina for 1 week

source_name: C57BL/6 mouse retina treated with saline for 1 week


title: m62_Liver

source_name: Liver metastasis

value: Liver metastasis (FFPE)

value: Liver


title: 1 week saline-treated mouse retina 1

value: Male


title: 1 week MPTP-treated mouse retina 1

value: Retinal tissue


title: m60_LymphNode


title: p63

value: Colorectal cancer (FFPE)

value: primarytumor

value: Colorectum


title: m61_Liver

value: metastasis


title: m62_Lung

source_name: Lung metastasis

value: Lung metastasis (FFPE)

value: Lung

value: normal colon mucosa obtained from the same patient as ch1


title: ST-362 24hr_rep2

city: Washington

first: Ronit

middle: Iris

last: Yarden

state: DC

address: 3900 Reservoir Rd., NW

department: Human Science

institute: Georgetown University

description:
SAMPLE 10
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).

hyb_protocol: Hybridization and washing of HumanHT-12_v4_BeadChip was performed according to the Whole-Genome Gene Expression Direct Hybridization Assay Guide (Illumina, Catalog # BD-901-1002, Part # 11322355 Rev. A).

scan_protocol: Twelve samples were run on one BeadChip and Illumina iScan Control Software was used for scanning.

data_processing: Data were extracted using GenomeStudio software. Background was subtracted and the data were normalized using quantile function.

source_name: ST-362 24hr, U2OS cells

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep-96 RNA Amplification Kit (By Ambion, Inc.) starting with 200ng total RNA- according to the manufacturer’s directions.

extract_protocol: Total RNA was prepared from cells with Trizol reagent according to manufacturer instructions.

treatment_protocol: Cells were treated with 5 ppm of either ST362 or MEB55 (both analogues of strigolactones) dissolved in acetone for either 6 hr or 24 hr. control cells were treated with vehicle alone with the amount corresponding to treatment groups.

tag: cell line

tag: agent

tag: time


title: MEB55 24hr_rep1

description:
SAMPLE 11
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).

source_name: MEB55 24hr, U2OS cells


title: p61


title: p58


title: MEB55 24hr_rep2

description:
SAMPLE 12
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).


title: ST-362 24hr_rep1

description:
SAMPLE 9
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).


title: Control 24hr_rep1

description:
SAMPLE 7
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).

source_name: Control 24hr, U2OS cells

value: Control


title: p60


title: m58_LymphNode

value: Lymph node metastasis (FFPE)

value: Lymph node


title: p62


title: ST-362 6hr_rep1

description:
SAMPLE 3
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).

source_name: ST-362 6hr, U2OS cells


title: MEB55 6hr_rep1

description:
SAMPLE 5
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).

source_name: MEB55 6hr, U2OS cells


title: p57


title: Control 24hr_rep2

description:
SAMPLE 8
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).


title: Control 6hr_rep2

description:
SAMPLE 2
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).

source_name: Control 6hr, U2OS cells


title: MEB55 6hr_rep2

description:
SAMPLE 6
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).


title: m59_Ovarian


title: ST-362 6hr_rep2

description:
SAMPLE 4
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).


title: m57_LymphNode


title: Control 6hr_rep1

description:
SAMPLE 1
U2OS cells are osteosarcoma cell line originated from a bone tissue and available from ATCC (originated from 15 yrs old caucasian female).


title: p59


title: m56_Omental

source_name: Omental metastasis

value: Omental metastasis (FFPE)

value: Omentum


title: m55_Omental


title: Ma.Mel71

city: Bonn

first: Michael

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

institute: University Hospital Bonn

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Variance stabilization and normalisation using vsn package from bioconductor in R without background correction

source_name: melanoma culture_untreated

label_protocol: 100ng RNA was converted to biotinylated cRNA using one round of amplification with Illumina Labelling Kit and one round of T7 polymerase

growth_protocol: Human melanoma cell lines were cultured in RPMI/10% FCS

extract_protocol: Total RNA was isolated using RLT buffer (Quiagen) and purified using spin columns. RNA quality was assayed using Agilent Bioanalyzer

treatment_protocol: Melanoma cell cultures were stimulated with 1000U/ml TNF-alpha for 72 hours or left untreated.

tag: cell type

value: human melanoma cells

tag: stimulated with

value: none (untreated control)

tag: braf

value: wild-type

tag: nras

tag: hras


title: Ma.Mel48

value: mutated


title: Ma.Mel19_TNF

source_name: melanoma culture_TNFalpha stimulated

value: 1000U/ml TNF-alpha for 72 hrs


title: m52_Lung

source_name: normal colorectum mucosa


title: Ma.Mel37


title: p54

source_name: Colorectal cancer

value: Colorectal cancer (FFPE)


title: Ma.Mel85_TNF


title: Ma.Mel85


title: m48_Lung


title: m51_Omental


title: m50_Ovarian

value: Ovarian metastasis (FFPE)

value: Ovary


title: m53_Lung

value: metastasis


title: p55

value: primarytumor

value: Colorectum


title: p56

value: normal colon mucosa obtained from the same patient as ch1


title: p50


title: Ma.Mel71_TNF


title: p53


title: m49_Liver

value: Liver metastasis (FFPE)

value: Liver


title: Ma.Mel36_TNF


title: Ma.Mel37_TNF


title: m54_Omental


title: Ma.Mel102_TNF


title: MZ7_TNF


title: Ma.Mel54a_TNF


title: Ma.Mel103b


title: p49


title: p48


title: p46


title: m47_Liver


title: m46_Liver


title: Ma.Mel48_TNF


title: p51


title: Ma.Mel36


title: Ma.Mel103b_TNF


title: Ma.Mel04


title: m45_LymphNode

source_name: Lymph node metastasis

value: Lymph node metastasis (FFPE)

value: Lymph node


title: MZ7


title: Ma.Mel65


title: m43_Omental

value: Omental metastasis (FFPE)

value: Omentum


title: p45


title: m44_Liver


title: Ma.Mel102

value: human melanoma cells

value: none (untreated control)


title: m42_LymphNode


title: p43


title: Ma.Mel54a

value: mutated

value: wild-type


title: m41_Liver


title: Ma.Mel04_TNF

value: 1000U/ml TNF-alpha for 72 hrs


title: Ma.Mel19


title: p42

value: Colorectal cancer (FFPE)


title: Ma.Mel65_TNF


title: m40_Lung

value: Lung metastasis (FFPE)

value: Lung


title: Ma.Mel67_TNF


title: Ma.Mel15_TNF


title: Ma.Mel79


title: SK-Mel28


title: p41

value: primarytumor


title: m39_Ovarian

source_name: Ovarian metastasis

value: Ovarian metastasis (FFPE)

value: metastasis

value: Ovary


title: Ma.Mel67


title: SK-Mel28_TNF


title: Ma.Mel15


title: p39

value: Colorectum

value: normal colon mucosa obtained from the same patient as ch1


title: Ma.Mel27


title: m37_Ovarian


title: m38_Lung


title: m40_Liver

value: Liver metastasis (FFPE)

value: Liver


title: p38


title: human neural progenitor cell line_mir137_mimic_replicate1

city: Cardiff

first: Matthew

middle: James

last: Hill

address: Maindy Road

institute: Cardiff University

scan_protocol: Standard Illumina scan protocol

data_processing: Sample probe profile were exported from GenomeStudio. Data were then imported into lumi (bioconductor) and Variance Stabilizing transformation applied, Robust Spline Normalized and log2 transformed.

label_protocol: Biotinylated cDNA were prepared using the Custom Illumina® TotalPrep™-96 Kit (Ambion)

growth_protocol: Cells were maintained as described by Pollock K et al, Exp Neurol. 2006 May;199(1):143-55.

extract_protocol: Standard Trizol extraction, RNA dissolved in water.

treatment_protocol: Transfection of either control, mirVanaTM miRNA inhibitor (MH10513; Life Technologies) or a mirVanaTM miRNA mimic of the miR-137 precursor (MC10513; Life Technologies). Cells were harvested using acutase 3 days after transfection.

value: CTXOE03 cell line

value: Male

value: Neural progenitor

tag: brain region of origin

value: Fetal cortical neuroepithelium


title: p36


title: human neural progenitor cell line_mir137_inhibitor_replicate4


title: p35


title: m35_LymphNode

value: Lymph node metastasis (FFPE)

value: Lymph node


title: human neural progenitor cell line_mir137_inhibitor_replicate3


title: m34_Liver


title: Ma.Mel27_TNF

value: human melanoma cells

value: 1000U/ml TNF-alpha for 72 hrs

value: wild-type

value: mutated


title: human neural progenitor cell line_mir137_mimic_replicate3


title: human neural progenitor cell line_mir137_mimic_replicate4


title: p32

value: Colorectal cancer (FFPE)

value: primarytumor


title: human neural progenitor cell line_mir137_inhibitor_replicate1


title: human neural progenitor cell line_mir137_mimic_replicate2


title: m32_Liver

value: metastasis


title: m36_Omental

value: Omental metastasis (FFPE)

value: Omentum


title: human neural progenitor cell line_Control_replicate1

source_name: control


title: human neural progenitor cell line_mir137_inhibitor_replicate2


title: p30

value: Colorectum

value: normal colon mucosa obtained from the same patient as ch1


title: m33_LymphNode


title: p31


title: m31_Lung

value: Lung metastasis (FFPE)

value: Lung


title: m30_Liver

value: Liver metastasis (FFPE)

value: Liver


title: human neural progenitor cell line_Control_replicate3

value: CTXOE03 cell line

value: Male

value: Neural progenitor

value: Fetal cortical neuroepithelium


title: human neural progenitor cell line_Control_replicate4


title: m28_Liver


title: m29_LymphNode

value: Lymph node metastasis (FFPE)

value: Lymph node


title: p25

value: Colorectal cancer (FFPE)


title: p28

value: primarytumor


title: m26_Liver

value: metastasis


title: p26


title: m24_Ovarian

value: Ovarian metastasis (FFPE)

value: Ovary


title: p24

value: Colorectum


title: human neural progenitor cell line_Control_replicate2


title: m22_Liver

value: normal colon mucosa obtained from the same patient as ch1


title: m21_Liver


title: m27_Liver


title: m19_Liver


title: m19_Lung

value: Lung metastasis (FFPE)


title: m23_Lung

value: Lung


title: m20_Ovarian


title: m15_Liver

value: Liver metastasis (FFPE)


title: m25_Lung