title: t53107

status: Public on Dec 31 2016

type: RNA

city: London

first: YF

last: Lee

address: 15 Cotswold Rd

country: United Kingdom

institute: Institute of Cancer Research

description: control RNA from cell lines (HTB-175, HTB-115, CCL-121, CCL-224, T91-95)

hyb_protocol: The microarray slide was submerged in 70% (v/v) deionised formamide, 2 x SSC pH7.0 at 65oC for 1 min (denaturation). Slides were then rinsed twice with 70% ethanol, then with 80% and 100% (v/v) ethanol, blown dry with canned air (RS Components) and pre-warmed to 37oC in a hybridisation chamber (BDH Precision Engineers, Cambridge) for 30 to 60 min. The labelled samples (from 4 ug each of total RNA from tumour and control pool) were made up to 50 ul in hybridisation mix (6x SSPE pH 7.4, 12.5 mM EDTA pH 8, 0.1% (v/v) Tween 20, 50% (v/v) deionised formamide). This mixture was heated to 99oC for 2 min and then 37oC for 10 min, pipetted onto a microarray slide and covered with a Hybrislip (22mmx60mm, Sigma). 150 ul of 6x SSPE was pipetted underneath the slide, the hybridisation chamber sealed and incubated at 65oC for 1.5 hr and then 42 oC for 2 days. The slide was then soaked briefly in 50 ml 4x SSPE, 10 mM EDTA at 42oC and transferred to a second wash of 50 ml 4x SSPE, 10 mM EDTA at 42oC and rocked gently until the coverslip fell off. The slide was then washed with 4x SSPE, 10 mM EDTA for 1 min at 42oC; then 50% formamide, 6x SSPE at 42oC for 15 sec with gentle rocking; then 2x SSPE, 10mM EDTA for 30 sec at room temperature; and 0.1x SSPE for 30 sec at room temperature. The slide was then rinsed briefly with HPLC grade water and dried with canned air.

scan_protocol: Hybridised microarray slides were scanned in a GenePix 4000B scanner (Axon Instruments, Foster City, CA). Slides were scanned at PMT (photomultiplier tube) voltage levels that provided a Cy5:Cy3 hybridisation ratio across the slide of roughly 1.

data_processing: Data processing and analyses were performed with the GenePix Pro 4.0 software (Axon Instruments, Foster City, CA) and the GeneSpring software (Silicon Genetics, Redwood City, CA) as in Lee YF, John M, Falconer A, Edwards S, Clark J, Flohr P, et al. A gene expression signature associated with metastatic outcome in human leiomyosarcomas. Cancer Res 2004;64:7201-4.

molecule: total RNA

organism: Homo sapiens

source_name: leiomyosarcoma

label_protocol: RNA labelling was performed as in Lee et al. (2003), except that after the final wash with 400 ul l 0.5x SSPE, the sample was reduced to a volume of 4 ul

growth_protocol: The tumour samples were snap-frozen in liquid nitrogen and stored at –80ºC until RNA extraction.

extract_protocol: Total RNA was extracted from the tumours and cell lines by the TRIZOL method (GibcoBRL) according to manufacturer's instructions.

tag: location

value: non-extremity

source_name: control RNA from cell lines

tag: sample type

value: reference


title: t4380


title: t704

value: extremity


title: t3232

value: not known


title: t2868


title: t1928


title: t9995


title: t278


title: t9689


title: t7008


title: t2592


title: t6858


title: t3779


title: t9652


title: t8749


title: t1643


title: t158


title: t9118


title: t16


title: t33107


title: blastocyst, vitrified, rep1

city: Beijing

first: xueming

last: zhao

address: No.2 Yuanmingyuanwestern road

country: China

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

description: V1; Test

data_processing:
For the normalization it uses the endogenous gene:U6.
Target gene signals normalized to the endogenous gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_U6)]
sample data table reports normalized signal (against endogenous gene).
Fold_Change.txt reports test/control (vitrified blastocyst/fresh blastocyst) ratios.

label: FAM

organism: Mus musculus

source_name: vitrified blastocyst

label_protocol: Reverse transcription of 30 ng of total RNA from fresh and vitrified blastocysts was carried out using a TaqMan® MicroRNA Reverse Transcription Kit. TaqMan® PreAmp Master Mix was used to pre-amplify small amounts of cDNA without introducing amplification bias to the sample. MiRNAs were measured in triplicate using the TaqMan® Array Rodent MicroRNA A+B Cards Set v3.0 with an Applied Biosystems 7900 HT Fast Real-time PCR system.  Quantitative real-time PCR were performed with 40 cycles at 97 °C for 30 seconds and 59.7 °C for 60 seconds.

growth_protocol: The embryos were cultured in CZB medium.

extract_protocol: Total RNA was extracted from vitrified/fresh blastocysts using an RNeasy Mini Kit (Qiagen, CA, USA) followed by DNase treatment

treatment_protocol: Vitrification group: The embryos were equilibrated in pretreatment solution (10%EG + 10%DMSO) for 30 seconds, loaded into an OPS with EDFS30 for 25 seconds, and plunged into liquid nitrogen (LN2).The blastocysts were thawed by rinsing in 0.5 M sucrose under mineral oil for 5 minutes and washed three times in CZB.

tag: strain

value: Kunming mouse of China

tag: cell type

value: blastocyst

tag: treatment

value: vitrification


title: blastocyst, vitrified, rep2

description: V2; Test


title: blastocyst, vitrified, rep3

description: V3; Test


title: blastocyst, fresh, rep1

description: F1; Control

source_name: fresh blastocyst

value: control


title: blastocyst, fresh, rep2

description: F2; Control


title: blastocyst, fresh, rep3

description: F3; Control


title: Hanatee, untreated plant, rep3

city: Yokohama

first: Tetsuya

last: Sakurai

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

description: Gene expression data from untreated Hanatee plant

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacture's instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent microarray (GPL14139) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with GeneSpring GX (Agilent). Quantile normalization was performed for each chip.

organism: Manihot esculenta

source_name: Hanatee control

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

growth_protocol: The cassava plants used in this study were grown under natural light and temperature conditions in a greenhouse of Mahidol University in Thailand for about 8 weeks after cutting.

extract_protocol: The total RNA was extracted from the plants before or after drought treatment using RNeasy Plant Mini kit (QIAGEN) according to manufacture’s instruction.

treatment_protocol: The spore suspensions of C. gloeosporioides f. sp. manihotis was measured at 3.5x106 spores/ml. Two month-old of both cassava varieties, HB60 and HN, were inoculated at the inter-nodal regions by stem puncture. Total of 4 inter-nodal regions were inoculated 5 times per one region of each plant. Control plants received sterile distilled water. All plants were continuously watered to maintain a high relative humidity around the inoculated plants. The third fully expanded cassava leaves were collected at time points of 24 and 72 hour post inoculation (hpi) and kept at -80°C until used.

tag: tissue

value: Leaves

tag: age

value: 8 weeks plant after cutting

tag: cultivar

value: Hanatee

value: untreated


title: Hanatee, CAD-Infected plant at 72h after infection, rep2

description: Gene expression data from Hanatee plant at 72h after CAD infection

source_name: Hanatee Infected 72h

value: 72h after CAD infection


title: Hanatee, CAD-Infected plant at 72h after infection, rep3


title: Hanatee, untreated plant, rep2


title: Hanatee, CAD-Infected plant at 72h after infection, rep1


title: patient 40 CHC-001

city: Kamakura

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

description:
chronic hepatitis C (CHC)
HCV-CHC018-1

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: exosome

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

extract_protocol: RNA samples were extracted from serum using 3D-Gene RNA extraction reagent from liquid sampld (Toray Industries Inc., Tokyo, Japan)..

tag: individual

value: patient 40

tag: disease state

value: CHC

tag: treatment status of liver disease

value: before IFN treatment

value: exosome


title: patient 40 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC018-2

value: after IFN treatment


title: patient 40 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC018-3


title: patient 42 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC020-1

value: patient 42


title: patient 41 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC019-1

value: patient 41


title: patient 41 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC019-2


title: patient 41 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC019-3


title: patient 42 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC020-3


title: patient 42 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC020-2


title: Hanatee, CAD-Infected plant at 24h after infection, rep3

description: Gene expression data from Hanatee plant at 24h after CAD infection

source_name: Hanatee Infected 24h

value: 24h after CAD infection


title: Hanatee, CAD-Infected plant at 24h after infection, rep1


title: Huay Bong 60, CAD-Infected plant at 72h after infection, rep2

description: Gene expression data from Huay Bong 60 plant at 72h after CAD infection

source_name: Huay Bong 60 Infected 72h

value: Huay Bong 60


title: Huay Bong 60, untreated plant, rep3

description: Gene expression data from untreated Huay Bong 60 plant

source_name: Huay Bong 60 control


title: patient 39 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC017-3

value: patient 39


title: patient 39 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC017-1


title: patient 39 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC017-2


title: Huay Bong 60, untreated plant, rep1


title: Huay Bong 60, CAD-Infected plant at 24h after infection, rep2

description: Gene expression data from Huay Bong 60 plant at 24h after CAD infection

source_name: Huay Bong 60 Infected 24h


title: Huay Bong 60, CAD-Infected plant at 72h after infection, rep3


title: patient 38 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC016-3

value: patient 38


title: Huay Bong 60, CAD-Infected plant at 72h after infection, rep1


title: patient 38 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC016-2


title: Hanatee, CAD-Infected plant at 24h after infection, rep2


title: patient 37 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC015-2

value: patient 37


title: patient 37 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC015-3


title: Huay Bong 60, untreated plant, rep2

value: Leaves


title: Hanatee, untreated plant, rep1

value: 8 weeks plant after cutting


title: patient 38 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC016-1


title: patient 37 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC015-1


title: patient 35 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC013-1

value: patient 35


title: patient 35 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC013-2


title: patient 36 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC014-3

value: patient 36


title: patient 35 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC013-3


title: patient 36 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC014-1


title: patient 36 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC014-2


title: Huay Bong 60, CAD-Infected plant at 24h after infection, rep3


title: Huay Bong 60, CAD-Infected plant at 24h after infection, rep1


title: patient 34 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC012-2

value: patient 34


title: patient 34 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC012-3


title: patient 33 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC011-2

value: patient 33


title: patient 34 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC012-1

value: CHC


title: patient 32 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC010-3

value: patient 32


title: patient 33 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC011-1

value: before IFN treatment

value: exosome


title: patient 32 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC010-2

value: after IFN treatment


title: patient 32 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC010-1


title: patient 33 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC011-3


title: patient 30 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC008-2

value: patient 30


title: patient 31 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC009-2

value: patient 31


title: patient 31 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC009-1


title: patient 30 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC008-3


title: patient 31 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC009-3


title: patient 28 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC006-2

value: patient 28


title: patient 28 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC006-3


title: patient 29 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC007-3

value: patient 29


title: patient 29 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC007-1


title: patient 30 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC008-1


title: patient 28 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC006-1


title: patient 27 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC005-3

value: patient 27


title: patient 27 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC005-2


title: patient 25 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC003-2

value: patient 25


title: patient 29 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC007-2


title: patient 24 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC002-3

value: patient 24


title: patient 25 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC003-3


title: patient 27 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC005-1


title: patient 26 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC004-1

value: patient 26


title: patient 26 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC004-3


title: patient 26 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC004-2


title: patient 25 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC003-1


title: patient 24 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC002-2


title: patient 23 CHC-003

description:
chronic hepatitis C (CHC)
HCV-CHC001-3

value: patient 23


title: patient 24 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC002-1


title: patient 6 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC006-3

value: patient 6

value: HCC


title: patient 23 CHC-001

description:
chronic hepatitis C (CHC)
HCV-CHC001-1


title: patient 23 CHC-002

description:
chronic hepatitis C (CHC)
HCV-CHC001-2


title: patient 9 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC009-3

value: patient 9


title: patient 10 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC010-1

value: patient 10


title: patient 8 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC008-3

value: patient 8


title: patient 10 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC010-2


title: patient 9 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC009-2


title: patient 7 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC007-2

value: patient 7


title: patient 7 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC007-1

value: before IFN treatment

value: exosome


title: patient 7 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC007-3


title: patient 8 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC008-2

value: after IFN treatment


title: patient 8 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC008-1


title: patient 9 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC009-1


title: patient 10 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC010-3


title: patient 6 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC006-2


title: patient 4 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC004-3

value: patient 4


title: patient 5 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC005-2

value: patient 5


title: patient 5 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC005-1


title: patient 6 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC006-1


title: patient 5 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC005-3


title: patient 2 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC002-2

value: patient 2


title: patient 2 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC002-3


title: patient 4 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC004-2


title: patient 2 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC002-1


title: patient 4 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC004-1


title: patient 3 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC003-3

value: patient 3


title: patient 3 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC003-2


title: patient 3 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC003-1


title: patient 1 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC001-2

value: patient 1


title: patient 20 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 020-2

value: patient 20


title: patient 1 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC001-1


title: patient 20 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 020-3


title: patient 19 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 019-3

value: patient 19


title: patient 21 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 021-2

value: patient 21


title: patient 21 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 021-1


title: patient 21 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 021-3


title: patient 22 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 022-3

value: patient 22


title: patient 11 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 011-1

value: patient 11

value: HCC


title: patient 22 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 022-1


title: patient 11 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 011-2


title: patient 14 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 014-1

value: patient 14


title: patient 13 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 013-3

value: patient 13


title: patient 14 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 014-2


title: patient 22 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 022-2


title: patient 12 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 012-2

value: patient 12


title: patient 12 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 012-1

value: before IFN treatment


title: patient 12 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 012-3

value: exosome


title: patient 13 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 013-2

value: after IFN treatment


title: patient 13 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 013-1


title: patient 17 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 017-1

value: patient 17


title: patient 15 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 015-1

value: patient 15


title: patient 16 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 016-2

value: patient 16


title: patient 16 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 016-1


title: patient 16 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 016-3


title: patient 11 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 011-3


title: patient 15 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 015-3


title: patient 14 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 014-3


title: patient 17 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 017-2


title: patient 17 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 017-3


title: patient 18 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 018-1

value: patient 18


title: patient 18 HCC-003

description:
hepatocellular carcicoma (HCC)
SVR-HCC 018-3


title: patient 15 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 015-2


title: patient 20 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 020-1


title: patient 18 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 018-2


title: patient 19 HCC-002

description:
hepatocellular carcicoma (HCC)
SVR-HCC 019-2


title: patient 19 HCC-001

description:
hepatocellular carcicoma (HCC)
SVR-HCC 019-1


title: 079VB

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description: total RNA isolated from serum

data_processing:
Matrix non-normalized contains raw Cq-values, derived from second derivative maximum method
Matrix normalized contains delta Cq values: Normalization was performed through imputation of empty values and subsequently by global mean centering according to the spike-in data  Where a higher value indicates that a determined miRNA is more abundant in the analyzed sample.
For the fold change data, delta Cq values were averaged for each group and delta-delta Ct values were calculated, which correspond to the log2-transformed fold change. Log2 fold changes were calculated for the comparison of fracture vs control and diabetes-fracture vs diabetes

label: SYBR Green

source_name: Serum, Diabetes_Fracture_R18

label_protocol: From isolated total RNA, cDNA was synthesized using the Universal cDNA Kit II (Ex-iqon, Denmark). Reverse transcription reactions were performed in 50 µl reactions with 10 µl total RNA input, and each 2.5 µl of two synthetic RNA controls (cel-miR-39-3p, 0.002 fmole/µl; UniSp6, 0.15 fmole/µl) according to the recommendations of the manufacturer. For qPCR analysis, cDNA samples were diluted 1:50. For each sample, qPCR reactions were per-formed in 10 µl reactions in custom-designed 384-well plates, which contained 375 mi-croRNA specific primers, 5 spike-in primers (UniSp2,4,5,6, and cel-miR-39-3p), 3 distinct PCR control wells with pre-coated DNA template and primers referred to as “interplate-control 3 (IPC3)” and one negative control well (full list see Supplemental Data 1). For PCR the Exilent SYBR Green mastermix was used (Exiqon, Denmark) and plates were prepared using an Eppendorf epMotion liquid handling robot. PCR amplification was conducted in a Roche LC480 II instrument (Roche, Germany) with the following settings: 95°C for 10 minutes, 45 cycles of 95°C/10s and 60°C/60s, followed by melting curve analysis. Cycle crossing points (Cp) values were calculated using the second derivative maximum method provided with the LC480 II software.

extract_protocol: Serum samples were collected by centrifugation at room temperature at 2000xg for 15 minutes after incubation at room temperature for 30 minutes, and frozen at -80°C for long term storage. Serum samples were thawed at room temperature, centrifuged at 12 000 x g for 5 minutes. 200 µl serum were used for sample lysis by mixing with 1000 µl Qiazol, to which 1 µl of a synthetic RNA mixture of three different synthetic control RNAs (UniSp2, 2 fmole/µl; UniSp4, 0.02 fmole/µl; UniSp5, 0.0002 fmole/µl) had been added (Exiqon, Denmark). RNA extraction was performed using 200 µl chloroform and phase separation was achieved by centrifugation for 15 min at 12,000 x g at 4 °C. In case of two samples (one Co subject, and one DM subject) RNA isolation failed due to abundant precipitate formation after sample lysis. In all other samples, exactly 650 µl of the upper, aqueous phase was extracted which had been further precipitated and purified on a QIACube liquid handling robot using the miRNeasy isolation kit (Qiagen, Germany) with the following modifications: glycogen (Ambion, TX) was added to the aqueous phase to a final concentration of 50 µg/ml and precipitated with 750 µl 100% Ethanol. Columns were washed two times with RPE buffer and circulating RNA was eluted in a single round in 30 µl nuclease-free water and stored at -80°C.

tag: gender

value: Female

tag: batch day

tag: ethnicity

value: Black

tag: fracture

value: Yes

tag: type-2 diabetes


title: 074RR

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R13

value: White


title: 073WW

description: total RNA isolated from serum

source_name: Serum, Fracture_R19

value: No


title: 080RD

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R19

value: Asian


title: 076RB

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R15


title: 077TB

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R16


title: 078EW

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R17


title: 075KR

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R14


title: 065PT

description: total RNA isolated from serum

source_name: Serum, Fracture_R17


title: 070DW

description: total RNA isolated from serum

source_name: Serum, Fracture_R18


title: 071SC

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R11


title: 069SW

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R10


title: 067BH

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R8


title: 072PS

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R12


title: 066MK

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R7


title: 060LS

description: total RNA isolated from serum

source_name: Serum, Fracture_R15


title: 062LY

description: total RNA isolated from serum

source_name: Serum, Diabetes_R18


title: 064RT

description: total RNA isolated from serum

source_name: Serum, Diabetes_R19


title: 063AT

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R6


title: 061AD

description: total RNA isolated from serum

source_name: Serum, Fracture_R16


title: 059SB

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R5


title: 056BD

description: total RNA isolated from serum

source_name: Serum, Fracture_R13


title: 057LH

description: total RNA isolated from serum

source_name: Serum, Fracture_R14


title: 055NH

description: total RNA isolated from serum

source_name: Serum, Fracture_R12


title: 054JY

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R4

value: native Hawaiian or Pacific Islander


title: 052JS

description: total RNA isolated from serum

source_name: Serum, Fracture_R10


title: 053MT

description: total RNA isolated from serum

source_name: Serum, Fracture_R11


title: 051LA

description: total RNA isolated from serum

source_name: Serum, Control_R17


title: 050SF

description: total RNA isolated from serum

source_name: Serum, Diabetes_R17


title: 049MK

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R3


title: 043EH

description: total RNA isolated from serum

source_name: Serum, Control_R14


title: 044CR

description: total RNA isolated from serum

source_name: Serum, Control_R15


title: 041MA

description: total RNA isolated from serum

source_name: Serum, Fracture_R7


title: 030NS

description: total RNA isolated from serum

source_name: Serum, Fracture_R2


title: 032BL

description: total RNA isolated from serum

source_name: Serum, Fracture_R3


title: 039MB

description: total RNA isolated from serum

source_name: Serum, Fracture_R6


title: 046CN

description: total RNA isolated from serum

source_name: Serum, Fracture_R9


title: 031JW

description: total RNA isolated from serum

source_name: Serum, Control_R10


title: 045EV

description: total RNA isolated from serum

source_name: Serum, Fracture_R8


title: 042NW

description: total RNA isolated from serum

source_name: Serum, Control_R13


title: 068CM

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R9


title: 028LS

description: total RNA isolated from serum

source_name: Serum, Control_R9


title: 038RA

description: total RNA isolated from serum

source_name: Serum, Fracture_R5


title: 048WS

description: total RNA isolated from serum

source_name: Serum, Control_R16


title: 035PC

description: total RNA isolated from serum

source_name: Serum, Fracture_R4


title: 037AB

description: total RNA isolated from serum

source_name: Serum, Control_R12


title: 024KW

description: total RNA isolated from serum

source_name: Serum, Control_R8


title: 047SS

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R2


title: 025TP

description: total RNA isolated from serum

source_name: Serum, Diabetes_R13


title: 026MH

description: total RNA isolated from serum

source_name: Serum, Diabetes_R14


title: 036SJ

description: total RNA isolated from serum

source_name: Serum, Control_R11


title: 027CG

description: total RNA isolated from serum

source_name: Serum, Diabetes_R15


title: 021CF

description: total RNA isolated from serum

source_name: Serum, Fracture_R1


title: 022AA

description: total RNA isolated from serum

source_name: Serum, Control_R6


title: 023CG

description: total RNA isolated from serum

source_name: Serum, Control_R7


title: 017CH

description: total RNA isolated from serum

source_name: Serum, Diabetes_R11


title: 019FM

description: total RNA isolated from serum

source_name: Serum, Diabetes_R12


title: 018KS

description: total RNA isolated from serum

source_name: Serum, Control_R5


title: 015VW

description: total RNA isolated from serum

source_name: Serum, Diabetes_R9


title: 016EV

description: total RNA isolated from serum

source_name: Serum, Diabetes_R10


title: 013IJ

description: total RNA isolated from serum

source_name: Serum, Control_R4


title: 011JO

description: total RNA isolated from serum

source_name: Serum, Diabetes_R6


title: 014SB

description: total RNA isolated from serum

source_name: Serum, Diabetes_R8


title: 002JR

description: total RNA isolated from serum

source_name: Serum, Control_R2


title: 004JF

description: total RNA isolated from serum

source_name: Serum, Diabetes_R2


title: 010CL

description: total RNA isolated from serum

source_name: Serum, Diabetes_R5


title: 005DD

description: total RNA isolated from serum

source_name: Serum, Control_R3


title: 009KA

description: total RNA isolated from serum

source_name: Serum, Diabetes_R4


title: 007SB

description: total RNA isolated from serum

source_name: Serum, Diabetes_R3


title: 001JR

description: total RNA isolated from serum

source_name: Serum, Control_R1


title: 012AM

description: total RNA isolated from serum

source_name: Serum, Diabetes_R7


title: 003NC

description: total RNA isolated from serum

source_name: Serum, Diabetes_R1


title: Hemocytes of infected larvae of B. mori 2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Hemocytes of infected larvae of B. mori

hyb_protocol: 1650ng of labeled cRNA were hybridized on the array (AMADID: 66047) using the Agilent Gene Expression Hybridization kit (Part Number 5190-0404) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent).

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software ( Agilent).

organism: Bombyx mori

source_name: Hemocytes of infected larvae of B. mori

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0424). 500ng of total RNA was reverse transcribed using oligo dT based method. mRNA was primed with oligo dT primer tagged to T7 promoter sequence and converted into double stranded cDNA using MMLV-RT reverse transcriptase. Further, in the same reaction cDNA was in-vitro transcribed to cRNA using T7 RNA polymerase enzyme. During cRNA synthesis, Cy3 labeled Cytosine nucleotide was incorporated into the newly synthesized strands. Labeled cRNA thus obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop.

growth_protocol: B. mori larvae were infested with E. bombycis on day 1 fifth instar.

extract_protocol: RNA isolation was done by using QIAGEN RNeasy mini kit (Cat#74106)  as per the manufacturer’s instructions.

treatment_protocol: Haemolymph was collected at 6h after invasion of E. bombycis maggot, and hemocytes were pelleted by centrifugation and used for RNA extraction

value: Hemocyte

value: Infested


title: 012-005

description:
hepatocacellular carcinoma (HCC)
81

source_name: serum

value: patient 012

value: HCC

value: HCC operation

tag: order in which blood was collected during treatment

tag: sample

value: serum


title: 057-004

description:
hepatocacellular carcinoma (HCC)
421

value: patient 057


title: 045-001

description:
hepatocacellular carcinoma (HCC)
563

value: patient 045


title: 013-003

description:
hepatocacellular carcinoma (HCC)
554

value: patient 013


title: 022-002

description:
hepatocacellular carcinoma (HCC)
581

value: patient 022


title: Hemocytes of control larvae of B. mori 1

description: Hemocytes of control larvae of B. mori

source_name: Hemocytes of control larvae of B. mori

tag: sample type

value: Control


title: 025-002

description:
hepatocacellular carcinoma (HCC)
549

value: patient 025


title: 073-004

description:
hepatocacellular carcinoma (HCC)
158

value: patient 073


title: Hemocytes of infected larvae of B. mori 1

description: Hemocytes of infected larvae of B. mori


title: 025-001

description:
hepatocacellular carcinoma (HCC)
547


title: 071-002

description:
hepatocacellular carcinoma (HCC)
556

value: patient 071


title: 068-004

description:
hepatocacellular carcinoma (HCC)
263

value: patient 068


title: 034TZ

description: total RNA isolated from serum

source_name: Serum, Diabetes_R16

value: Female

value: Asian

value: No

value: Yes


title: Hemocytes of control larvae of B. mori 2

description: Hemocytes of control larvae of B. mori

value: Hemocyte


title: 044-002

description:
hepatocacellular carcinoma (HCC)
578

value: patient 044

value: HCC


title: 028-004

description:
hepatocacellular carcinoma (HCC)
72

value: patient 028

value: HCC operation

value: serum


title: 093-003

description:
hepatocacellular carcinoma (HCC)
533

value: patient 093


title: 067-002

description:
hepatocacellular carcinoma (HCC)
542

value: patient 067


title: 067-001

description:
hepatocacellular carcinoma (HCC)
540


title: 015-004

description:
hepatocacellular carcinoma (HCC)
562

value: patient 015


title: 054-001

description:
hepatocacellular carcinoma (HCC)
564

value: patient 054


title: 048-004

description:
hepatocacellular carcinoma (HCC)
558

value: patient 048


title: 013-002

description:
hepatocacellular carcinoma (HCC)
548

value: patient 013


title: 013-001

description:
hepatocacellular carcinoma (HCC)
546


title: 065-002

description:
hepatocacellular carcinoma (HCC)
535

value: patient 065


title: 077-002

description:
hepatocacellular carcinoma (HCC)
529

value: patient 077


title: 043-003

description:
hepatocacellular carcinoma (HCC)
527

value: patient 043


title: 040-002

description:
hepatocacellular carcinoma (HCC)
531

value: patient 040


title: 065-001

description:
hepatocacellular carcinoma (HCC)
530


title: 088-001

description:
hepatocacellular carcinoma (HCC)
524

value: patient 088


title: 071-001

description:
hepatocacellular carcinoma (HCC)
513

value: patient 071


title: 015-003

description:
hepatocacellular carcinoma (HCC)
501


title: 077-001

description:
hepatocacellular carcinoma (HCC)
526


title: 043-001

description:
hepatocacellular carcinoma (HCC)
521


title: 011-004

description:
hepatocacellular carcinoma (HCC)
491

value: patient 011


title: 074-002

description:
hepatocacellular carcinoma (HCC)
493

value: patient 074

value: HCC


title: 088-002

description:
hepatocacellular carcinoma (HCC)
525

value: HCC operation


title: 020-002

description:
hepatocacellular carcinoma (HCC)
506

value: patient 020

value: serum


title: 043-002

description:
hepatocacellular carcinoma (HCC)
523


title: 020-001

description:
hepatocacellular carcinoma (HCC)
484


title: 027-002

description:
hepatocacellular carcinoma (HCC)
478

value: patient 027


title: 027-001

description:
hepatocacellular carcinoma (HCC)
474


title: 056-002

description:
hepatocacellular carcinoma (HCC)
483

value: patient 056


title: 091-003

description:
hepatocacellular carcinoma (HCC)
520

value: patient 091


title: 062-002

description:
hepatocacellular carcinoma (HCC)
522

value: patient 062


title: 053-002

description:
hepatocacellular carcinoma (HCC)
511

value: patient 053


title: 053-001

description:
hepatocacellular carcinoma (HCC)
507


title: 037-002

description:
hepatocacellular carcinoma (HCC)
469

value: patient 037


title: 023-001

description:
hepatocacellular carcinoma (HCC)
465

value: patient 023


title: 040-001

description:
hepatocacellular carcinoma (HCC)
512


title: 079-001

description:
hepatocacellular carcinoma (HCC)
495

value: patient 079


title: 055-003

description:
hepatocacellular carcinoma (HCC)
473

value: patient 055


title: 079-002

description:
hepatocacellular carcinoma (HCC)
499


title: 052-002

description:
hepatocacellular carcinoma (HCC)
470

value: patient 052


title: 052-001

description:
hepatocacellular carcinoma (HCC)
466


title: 074-001

description:
hepatocacellular carcinoma (HCC)
489


title: 056-003

description:
hepatocacellular carcinoma (HCC)
487


title: 056-001

description:
hepatocacellular carcinoma (HCC)
464


title: 037-001

description:
hepatocacellular carcinoma (HCC)
463


title: 023-002

description:
hepatocacellular carcinoma (HCC)
468


title: 055-002

description:
hepatocacellular carcinoma (HCC)
459


title: 062-001

description:
hepatocacellular carcinoma (HCC)
457


title: 081-002

description:
hepatocacellular carcinoma (HCC)
454

value: patient 081


title: 055-001

description:
hepatocacellular carcinoma (HCC)
455


title: 026-001

description:
hepatocacellular carcinoma (HCC)
453

value: patient 026


title: 059-003

description:
hepatocacellular carcinoma (HCC)
442

value: patient 059


title: 081-001

description:
hepatocacellular carcinoma (HCC)
452

value: HCC


title: 066-002

description:
hepatocacellular carcinoma (HCC)
444

value: patient 066

value: HCC operation


title: 092-001

description:
hepatocacellular carcinoma (HCC)
447

value: patient 092

value: serum


title: 092-002

description:
hepatocacellular carcinoma (HCC)
448


title: 094-003

description:
hepatocacellular carcinoma (HCC)
439

value: patient 094


title: 064-002

description:
hepatocacellular carcinoma (HCC)
438

value: patient 064


title: 066-001

description:
hepatocacellular carcinoma (HCC)
440


title: 058-001

description:
hepatocacellular carcinoma (HCC)
408

value: patient 058


title: 058-002

description:
hepatocacellular carcinoma (HCC)
411


title: 094-002

description:
hepatocacellular carcinoma (HCC)
432


title: 059-001

description:
hepatocacellular carcinoma (HCC)
430


title: 064-001

description:
hepatocacellular carcinoma (HCC)
429


title: 085-002

description:
hepatocacellular carcinoma (HCC)
428

value: patient 085


title: 094-001

description:
hepatocacellular carcinoma (HCC)
425


title: 085-001

description:
hepatocacellular carcinoma (HCC)
426


title: 026-003

description:
hepatocacellular carcinoma (HCC)
462


title: 012-004

description:
hepatocacellular carcinoma (HCC)
406

value: patient 012


title: 059-002

description:
hepatocacellular carcinoma (HCC)
433


title: 041-002

description:
hepatocacellular carcinoma (HCC)
402

value: patient 041


title: 064-003

description:
hepatocacellular carcinoma (HCC)
441


title: 026-002

description:
hepatocacellular carcinoma (HCC)
456


title: 041-001

description:
hepatocacellular carcinoma (HCC)
397


title: 082-002

description:
hepatocacellular carcinoma (HCC)
391

value: patient 082


title: 082-003

description:
hepatocacellular carcinoma (HCC)
396


title: 050-003

description:
hepatocacellular carcinoma (HCC)
389

value: patient 050


title: 050-002

description:
hepatocacellular carcinoma (HCC)
387


title: 030-004

description:
hepatocacellular carcinoma (HCC)
383

value: patient 030


title: 082-001

description:
hepatocacellular carcinoma (HCC)
388


title: 050-001

description:
hepatocacellular carcinoma (HCC)
385


title: 033JF

description: total RNA isolated from serum

source_name: Serum, Diabetes_Fracture_R1

value: Female

value: Black

value: Yes


title: 113-003

description:
hepatocacellular carcinoma (HCC)
370

value: patient 113

value: HCC


title: 033-002

description:
hepatocacellular carcinoma (HCC)
369

value: patient 033

value: HCC operation


title: 091-002

description:
hepatocacellular carcinoma (HCC)
363

value: patient 091

value: serum


title: 080-003

description:
hepatocacellular carcinoma (HCC)
364

value: patient 080


title: 105-003

description:
hepatocacellular carcinoma (HCC)
382

value: patient 105


title: 105-002

description:
hepatocacellular carcinoma (HCC)
377


title: 033-004

description:
hepatocacellular carcinoma (HCC)
376


title: 105-001

description:
hepatocacellular carcinoma (HCC)
374


title: 033-001

description:
hepatocacellular carcinoma (HCC)
366


title: 033-003

description:
hepatocacellular carcinoma (HCC)
373


title: 068-003

description:
hepatocacellular carcinoma (HCC)
367

value: patient 068


title: 110-002

description:
hepatocacellular carcinoma (HCC)
358

value: patient 110


title: 019-002

description:
hepatocacellular carcinoma (HCC)
359

value: patient 019


title: 049-002

description:
hepatocacellular carcinoma (HCC)
332

value: patient 049


title: 087-002

description:
hepatocacellular carcinoma (HCC)
337

value: patient 087


title: 091-001

description:
hepatocacellular carcinoma (HCC)
357


title: 087-001

description:
hepatocacellular carcinoma (HCC)
333


title: 034-003

description:
hepatocacellular carcinoma (HCC)
330

value: patient 034


title: 109-003

description:
hepatocacellular carcinoma (HCC)
331

value: patient 109


title: 018-003

description:
hepatocacellular carcinoma (HCC)
341

value: patient 018


title: 110-001

description:
hepatocacellular carcinoma (HCC)
350


title: 069-004

description:
hepatocacellular carcinoma (HCC)
348

value: patient 069


title: 019-001

description:
hepatocacellular carcinoma (HCC)
353


title: 087-003

description:
hepatocacellular carcinoma (HCC)
345


title: 103-002

description:
hepatocacellular carcinoma (HCC)
325

value: patient 103


title: 034-001

description:
hepatocacellular carcinoma (HCC)
322

value: HCC


title: 034-002

description:
hepatocacellular carcinoma (HCC)
324


title: 060-003

description:
hepatocacellular carcinoma (HCC)
320

value: patient 060


title: 038-003

description:
hepatocacellular carcinoma (HCC)
326

value: patient 038

value: HCC operation


title: 046-003

description:
hepatocacellular carcinoma (HCC)
327

value: patient 046

value: serum


title: 103-001

description:
hepatocacellular carcinoma (HCC)
321


title: 061-002

description:
hepatocacellular carcinoma (HCC)
307

value: patient 061


title: 047-004

description:
hepatocacellular carcinoma (HCC)
312

value: patient 047


title: 060-002

description:
hepatocacellular carcinoma (HCC)
306


title: 060-001

description:
hepatocacellular carcinoma (HCC)
297


title: 047-003

description:
hepatocacellular carcinoma (HCC)
277


title: 036-004

description:
hepatocacellular carcinoma (HCC)
276

value: patient 036


title: 029-003

description:
hepatocacellular carcinoma (HCC)
275

value: patient 029


title: 017-003

description:
hepatocacellular carcinoma (HCC)
266

value: patient 017


title: 047-002

description:
hepatocacellular carcinoma (HCC)
274


title: 047-001

description:
hepatocacellular carcinoma (HCC)
273


title: 030-002

description:
hepatocacellular carcinoma (HCC)
265

value: patient 030


title: 030-003

description:
hepatocacellular carcinoma (HCC)
271


title: 069-003

description:
hepatocacellular carcinoma (HCC)
260


title: 076-002

description:
hepatocacellular carcinoma (HCC)
272

value: patient 076


title: 076-001

description:
hepatocacellular carcinoma (HCC)
269


title: 049-001

description:
hepatocacellular carcinoma (HCC)
252

value: patient 049


title: 068-002

description:
hepatocacellular carcinoma (HCC)
254

value: patient 068


title: 017-002

description:
hepatocacellular carcinoma (HCC)
251


title: 068-001

description:
hepatocacellular carcinoma (HCC)
250


title: 030-001

description:
hepatocacellular carcinoma (HCC)
255


title: 114-004

description:
hepatocacellular carcinoma (HCC)
249

value: patient 114


title: 031-003

description:
hepatocacellular carcinoma (HCC)
302

value: patient 031


title: 109-001

description:
hepatocacellular carcinoma (HCC)
299

value: patient 109

value: HCC


title: 109-002

description:
hepatocacellular carcinoma (HCC)
304


title: 069-001

description:
hepatocacellular carcinoma (HCC)
246

value: patient 069


title: 017-001

description:
hepatocacellular carcinoma (HCC)
234

value: HCC operation


title: 113-002

description:
hepatocacellular carcinoma (HCC)
242

value: patient 113


title: 039-003

description:
hepatocacellular carcinoma (HCC)
231

value: patient 039

value: serum


title: 113-001

description:
hepatocacellular carcinoma (HCC)
240


title: 069-002

description:
hepatocacellular carcinoma (HCC)
256


title: 104-003

description:
hepatocacellular carcinoma (HCC)
228

value: patient 104


title: 104-002

description:
hepatocacellular carcinoma (HCC)
238


title: 018-002

description:
hepatocacellular carcinoma (HCC)
223

value: patient 018


title: 089-002

description:
hepatocacellular carcinoma (HCC)
235

value: patient 089


title: 090-004

description:
hepatocacellular carcinoma (HCC)
227

value: patient 090


title: 108-001

description:
hepatocacellular carcinoma (HCC)
209

value: patient 108


title: 080-002

description:
hepatocacellular carcinoma (HCC)
221

value: patient 080


title: 046-002

description:
hepatocacellular carcinoma (HCC)
236

value: patient 046


title: 108-002

description:
hepatocacellular carcinoma (HCC)
222


title: 089-001

description:
hepatocacellular carcinoma (HCC)
217


title: 089-003

description:
hepatocacellular carcinoma (HCC)
230


title: 046-001

description:
hepatocacellular carcinoma (HCC)
214


title: 080-001

description:
hepatocacellular carcinoma (HCC)
216


title: 104-001

description:
hepatocacellular carcinoma (HCC)
219


title: 078-002

description:
hepatocacellular carcinoma (HCC)
215

value: patient 078


title: 016-002

description:
hepatocacellular carcinoma (HCC)
186

value: patient 016


title: 083-004

description:
hepatocacellular carcinoma (HCC)
192

value: patient 083


title: 111-002

description:
hepatocacellular carcinoma (HCC)
187

value: patient 111


title: 014-004

description:
hepatocacellular carcinoma (HCC)
207

value: patient 014

value: HCC


title: 084-003

description:
hepatocacellular carcinoma (HCC)
204

value: patient 084

value: HCC operation


title: 111-001

description:
hepatocacellular carcinoma (HCC)
184


title: 038-001

description:
hepatocacellular carcinoma (HCC)
189

value: patient 038


title: 038-002

description:
hepatocacellular carcinoma (HCC)
202

value: serum


title: 061-001

description:
hepatocacellular carcinoma (HCC)
201

value: patient 061


title: 111-003

description:
hepatocacellular carcinoma (HCC)
194


title: 078-001

description:
hepatocacellular carcinoma (HCC)
200


title: 018-001

description:
hepatocacellular carcinoma (HCC)
203

value: patient 018


title: 093-002

description:
hepatocacellular carcinoma (HCC)
183

value: patient 093


title: 015-002

description:
hepatocacellular carcinoma (HCC)
182

value: patient 015


title: 021-004

description:
hepatocacellular carcinoma (HCC)
176

value: patient 021


title: 036-003

description:
hepatocacellular carcinoma (HCC)
175

value: patient 036


title: 016-001

description:
hepatocacellular carcinoma (HCC)
174


title: 015-001

description:
hepatocacellular carcinoma (HCC)
173


title: 093-001

description:
hepatocacellular carcinoma (HCC)
171


title: 072-004

description:
hepatocacellular carcinoma (HCC)
167

value: patient 072


title: 036-001

description:
hepatocacellular carcinoma (HCC)
160


title: 039-002

description:
hepatocacellular carcinoma (HCC)
162

value: patient 039


title: 031-002

description:
hepatocacellular carcinoma (HCC)
159

value: patient 031


title: 036-002

description:
hepatocacellular carcinoma (HCC)
166


title: 051-003

description:
hepatocacellular carcinoma (HCC)
164

value: patient 051


title: 048-003

description:
hepatocacellular carcinoma (HCC)
163

value: patient 048


title: 057-003

description:
hepatocacellular carcinoma (HCC)
156

value: patient 057


title: 086-003

description:
hepatocacellular carcinoma (HCC)
161

value: patient 086

value: HCC


title: 114-003

description:
hepatocacellular carcinoma (HCC)
148

value: patient 114

value: HCC operation


title: 107-003

description:
hepatocacellular carcinoma (HCC)
157

value: patient 107

value: serum


title: 048-001

description:
hepatocacellular carcinoma (HCC)
146


title: 063-004

description:
hepatocacellular carcinoma (HCC)
155

value: patient 063


title: 106-003

description:
hepatocacellular carcinoma (HCC)
150

value: patient 106


title: 031-001

description:
hepatocacellular carcinoma (HCC)
154


title: 048-002

description:
hepatocacellular carcinoma (HCC)
152


title: 051-002

description:
hepatocacellular carcinoma (HCC)
143


title: 042-002

description:
hepatocacellular carcinoma (HCC)
142

value: patient 042


title: 107-002

description:
hepatocacellular carcinoma (HCC)
153


title: 070-003

description:
hepatocacellular carcinoma (HCC)
144

value: patient 070


title: 070-002

description:
hepatocacellular carcinoma (HCC)
140


title: 090-003

description:
hepatocacellular carcinoma (HCC)
145

value: patient 090


title: 057-002

description:
hepatocacellular carcinoma (HCC)
139


title: 028-003

description:
hepatocacellular carcinoma (HCC)
147

value: patient 028


title: 011-003

description:
hepatocacellular carcinoma (HCC)
134

value: patient 011


title: 101-004

description:
hepatocacellular carcinoma (HCC)
135

value: patient 101


title: 057-001

description:
hepatocacellular carcinoma (HCC)
129


title: 070-001

description:
hepatocacellular carcinoma (HCC)
128


title: 039-001

description:
hepatocacellular carcinoma (HCC)
127

value: patient 039


title: 011-002

description:
hepatocacellular carcinoma (HCC)
125


title: 014-003

description:
hepatocacellular carcinoma (HCC)
121

value: patient 014


title: 029-002

description:
hepatocacellular carcinoma (HCC)
122

value: patient 029


title: 084-002

description:
hepatocacellular carcinoma (HCC)
117

value: patient 084


title: 112-003

description:
hepatocacellular carcinoma (HCC)
68

value: patient 112

value: HCC


title: 021-001

description:
hepatocacellular carcinoma (HCC)
74

value: patient 021

value: HCC operation


title: 075-003

description:
hepatocacellular carcinoma (HCC)
78

value: patient 075

value: serum


title: 021-003

description:
hepatocacellular carcinoma (HCC)
79


title: 012-003

description:
hepatocacellular carcinoma (HCC)
82

value: patient 012


title: 112-001

description:
hepatocacellular carcinoma (HCC)
46


title: 012-002

description:
hepatocacellular carcinoma (HCC)
63


title: 028-001

description:
hepatocacellular carcinoma (HCC)
57


title: 072-003

description:
hepatocacellular carcinoma (HCC)
66

value: patient 072


title: 072-002

description:
hepatocacellular carcinoma (HCC)
45


title: 063-001

description:
hepatocacellular carcinoma (HCC)
47

value: patient 063


title: 073-002

description:
hepatocacellular carcinoma (HCC)
36

value: patient 073


title: 063-003

description:
hepatocacellular carcinoma (HCC)
58


title: 102-002

description:
hepatocacellular carcinoma (HCC)
8

value: patient 102


title: 073-003

description:
hepatocacellular carcinoma (HCC)
53


title: 035-004

description:
hepatocacellular carcinoma (HCC)
37

value: patient 035


title: 072-001

description:
hepatocacellular carcinoma (HCC)
27


title: 073-001

description:
hepatocacellular carcinoma (HCC)
28


title: 035-002

description:
hepatocacellular carcinoma (HCC)
11


title: 011-001

description:
hepatocacellular carcinoma (HCC)
119

value: patient 011


title: 101-003

description:
hepatocacellular carcinoma (HCC)
65

value: patient 101


title: 035-001

description:
hepatocacellular carcinoma (HCC)
7


title: 101-001

description:
hepatocacellular carcinoma (HCC)
56


title: 075-002

description:
hepatocacellular carcinoma (HCC)
6


title: 102-001

description:
hepatocacellular carcinoma (HCC)
5


title: 075-001

description:
hepatocacellular carcinoma (HCC)
3


title: 090-002

description:
hepatocacellular carcinoma (HCC)
116

value: patient 090


title: 083-003

description:
hepatocacellular carcinoma (HCC)
115

value: patient 083


title: 042-001

description:
hepatocacellular carcinoma (HCC)
2

value: patient 042


title: 029-001

description:
hepatocacellular carcinoma (HCC)
106

value: patient 029


title: 114-001

description:
hepatocacellular carcinoma (HCC)
110

value: patient 114

value: HCC


title: 051-001

description:
hepatocacellular carcinoma (HCC)
112

value: patient 051

value: HCC operation


title: 014-002

description:
hepatocacellular carcinoma (HCC)
108

value: patient 014

value: serum


title: 114-002

description:
hepatocacellular carcinoma (HCC)
114


title: 090-001

description:
hepatocacellular carcinoma (HCC)
111


title: 083-002

description:
hepatocacellular carcinoma (HCC)
101


title: 112-002

description:
hepatocacellular carcinoma (HCC)
102

value: patient 112


title: 084-001

description:
hepatocacellular carcinoma (HCC)
104

value: patient 084


title: 083-001

description:
hepatocacellular carcinoma (HCC)
86


title: 107-001

description:
hepatocacellular carcinoma (HCC)
87

value: patient 107


title: 086-001

description:
hepatocacellular carcinoma (HCC)
85

value: patient 086


title: 106-001

description:
hepatocacellular carcinoma (HCC)
84

value: patient 106


title: 028-002

description:
hepatocacellular carcinoma (HCC)
105

value: patient 028


title: 024-002

description:
hepatocacellular carcinoma (HCC)
589

value: patient 024


title: 035-003

description:
hepatocacellular carcinoma (HCC)
103

value: patient 035


title: 101-002

description:
hepatocacellular carcinoma (HCC)
89

value: patient 101


title: 024-001

description:
hepatocacellular carcinoma (HCC)
587


title: 022-003

description:
hepatocacellular carcinoma (HCC)
586

value: patient 022


title: 022-001

description:
hepatocacellular carcinoma (HCC)
582


title: 021-002

description:
hepatocacellular carcinoma (HCC)
98

value: patient 021


title: 102-003

description:
hepatocacellular carcinoma (HCC)
95

value: patient 102


title: 063-002

description:
hepatocacellular carcinoma (HCC)
93

value: patient 063

value: HCC


title: 106-002

description:
hepatocacellular carcinoma (HCC)
91

value: HCC operation


title: 014-001

description:
hepatocacellular carcinoma (HCC)
94

value: patient 014


title: 086-002

description:
hepatocacellular carcinoma (HCC)
92

value: serum


title: 032-002

description:
hepatocacellular carcinoma (HCC)
577

value: patient 032


title: 054-003

description:
hepatocacellular carcinoma (HCC)
574

value: patient 054


title: KO_3

type: SRA

city: Basel

first: Sean

middle: M

last: O'Toole

state: Basel-Stadt

address: Maulbeerstrasse 66

department: Neuroscience

country: Switzerland

institute: FMI

library_source: transcriptomic

data_processing:
trimming 3' adaptor with cutadapt (-a AGATCGGAAGAGC)
mapping on mm10 abundant sequences with bowtie2 to filter reads mapped on abundant sequences
mapping to transcriptome (UCSC mm10) and quantification by rsem-1.2.7
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated TPM values

source_name: parvalbumin positive neurons from lumbar 4 dorsal root ganglion

extract_protocol:
RNA extraction using the PicoPure kit
After extraction, RNA was processed into cDNA and amplified using the Ovation rna-seq system (Nugen). cDNA was sonicated to an average of 200 base pairs using the Covaris S220 system. Subsequently, the fragmented DNA repaired and ligated to adapters using the Ovation Rapid DR Multiplex System (Nugen). Finally, libraries were quantified with the KAPA qPCR system.

tag: genotype/variation

value: pvalb driven dicer knockout

tag: strain


title: WT_3

value: wild-type


title: KO_2


title: 032-001

description:
hepatocacellular carcinoma (HCC)
572

tag: treatment


title: 054-002

description:
hepatocacellular carcinoma (HCC)
569


title: WT_2


title: 045-002

description:
hepatocacellular carcinoma (HCC)
567

value: patient 045


title: WT_1


title: 38A_3T3

city: Lausanne

first: Jonathan

middle: Aryeh

last: Sobel

state: Vaud

address: EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15

department: School of Life Sciences

institute: EPFL

data_processing:
RNA-seq mapping was performed with the STAR mapping protocol (Dobin et al. Bioinformatics 2013)
bam2wig.py at http://rseqc.sourceforge.net/
wigToBigWig
To assess gene expression in NIH3T3 fibroblasts along the circadian cycle, we performed an RNA Seq experiment in synchronized cells, extracting RNA in duplicates every 4h for 48h (16h after Dex - 64h after Dex, 26 samples in total). We assessed quality and quantity of the samples using a NanoDrop (Thermo Fisher) and reverse transcribed 1  g of each RNA sample into cDNA (SuperScript II, Life Technologies) to perform qPCR on known rhythmic genes (Dbp, Bmal1) in order to check for phase and amplitude of circadian rhythms (see supplementary figure 1B). Values were determined as fold change compared to Gapdh housekeeping control and the mean of each cycle was set to 1. Samples were then submitted to the Lausanne Genomics Facility (University of Lausanne) for whole RNA single read Truseq Stranded RNA sequencing. Fastq sequence reads were mapped against the mm9 mouse genome using RNA-Star (Dobin et al., 2013) with default parameters. Reads per kilo base per million (RPKM) were computed using custom perl. For each gene (Ensembl annotation, (Curwen et al., 2004)), all reads overlapping an exon of the different transcripts of the gene are counted, but each read is only counted once. Selection is based upon unique mapping and strand selectivity (reads need to map to the same strand as the gene). The length of the gene is computed as the mean length of the different transcripts
Mouse liver RNA-seq data was generated from RNA samples provided by Fr  d  ric Gachon (University of Lausanne) from previously published work (Jouffe et al, 2013). The RNA was isolated through hybridization of poly(A) regions on magnetic beads. Isolated RNA was fragmented and cDNA was synthesized with random primers. Sequencing of these non-strand-specific 100-bp paired-end reads was performed with an Illumina HiSeq 2500 machine at the Lausanne Genomic Technologies Facility for two replicates. RNA-seq mapping was performed with the STAR mapping protocol using default options for the mm9 (NCBI37) genome. Quality control of the samples was performed and validated with Bioanalyzer assays and the FastQC read quality analysis package.
Genome_build: mm9
Supplementary_files_format_and_content: WIG and BigWig standard

source_name: NIH3T3 cells

growth_protocol:
NIH3T3 fibroblasts and undifferentiated 3T3-L1 cells were kept in DMEM high glucose medium (Life Technologies) supplemented with 1%  Penicilling/Streptomycin/Glutamate (PGS; Sigma Aldrich) solution and 10% fetal calf serum (FCS, Sigma Aldrich). They were split using trypsin (Tryple Express, Life Technologies) as detaching and dissociation agent as necessary depending on experimental conditions or when reaching confluency. For transient tranfection, cells were transfected with 2µg of DNA per 35mm dish using Fugene HD (Promega) or Lipfectamine 2000 (Life Technologies) reagent following supplier's instructions. For synchronization with dexamethasone (Dex; Sigma Aldrich), cells were incubated for 30 minutes with 100 nM Dex solution (stock 100µM in ethanol), then washed once with PBS and supplied with fresh medium. Stable Zeb1 knockdown cells were obtained by lentiviral transduction using MISSION shRNAs (Sigma Aldrich) TRCN0000235850,
All animal studies were conducted in accordance with our regional committee for ethics in animal experimentation and the regulations of the veterinary office of the Canton of Vaud. C57Bl/6J mice were purchased from Janvier (Le Genest) or Charles River Laboratory. In all experiments, male mice between 10 and 12 wk of age are used. Unless noted otherwise, mice were maintained under standard animal housing conditions, with free access to food and water and in 12-h light/12-h dark cycles. However, for all experiments, animals were fed only at night during 4 d before the experiment to reduce effects of feeding rhythm.

extract_protocol:
RNA preparation using the Ambion PureLink RNA Mini Kit (Life Technologies)
Briefly, fractions were precipitated by the addition of three volumes of ethanol and kept overnight at 280uC. After 30 min of centrifugation at 5,200 g, RNAs were extracted from the non- soluble fraction by classical protocol. Liver RNAs were extracted and analysed by real-time quantitative RT-PCR, mostly as previously described(Jouffe et al 2013). Briefly, 0.5 mg of liver RNA was reverse transcribed using random hexamers and SuperScript II reverse transcriptase (Life Technol- ogies). The cDNAs equivalent to 20 ng of RNA were PCR amplified in triplicate in an ABI PRISM 7700 Sequence Detection System (Applied Biosystem) using the TaqMan or the SYBR Green technologies
Illumina TruSeq RNA
Libraries for ultra-high throughput sequencing were prepared with the RNA-seq sample kit (Illumina) as recommended by the manufacturer.

treatment_protocol:
Dexamethasone synchronization for 3T3 Cells
Livers were homogenized in lysis buffer containing 20 mM HEPES (pH 7.6), 250 mM NaCl, 10 mM MgCl2, 10 mM DTT, 20 mg/ml cycloheximid, 10 U/ml RNase inhibitor, and a protease inhibitor cocktail containing 0.5 mM PMSF, 10 mg/ml Aprotinin, 0.7 mg/ml Pepstatin A, and 0.7 mg/ml Leupeptin.

tag: cell line

value: dexamethasone synchronized


title: 38B_3T3


title: 34C_3T3


title: 34A_3T3


title: 34B_3T3


title: 30C_3T3


title: 26C_3T3


title: 30B_3T3


title: 22B_3T3


title: 22C_3T3


title: 18C_3T3


title: 22A_3T3


title: 044-001

description:
hepatocacellular carcinoma (HCC)
576

value: patient 044


title: 18B_3T3


title: 18A_3T3


title: BreastSys_RPPA_pSRC_Y416

type: protein

city: Heidelberg

first: Ulrike

last: Korf

address: Im Neuenheimer Feld 580

department: Molecular Genome Analysis

country: Germany

institute: German Cancer Research Center

description:
Anti-rabbit IgG
Corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 1

hyb_protocol: Slides were blocked with 50% blocking buffer for fluorescent applications (Rockland) in TBS containing 5 mM NaF and 1 mM Na3VO4 for 2h at RT, prior to incubation with target specific primary antibodies at 4°C over night. Detection of the primary antibodies was done with Alexa Fluor® 680 F(ab')2 fragments of goat anti-mouse IgG or anti-rabbit IgG in 1:8000 dilution (Life Technologies).

scan_protocol: Images of all slides were obtained at an excitation wavelength of 685 nm and a resolution of 21 µm using the Odyssey Scanner (LI-COR). These 16-bit TIFF-files were then used to quantify the signal intensities for each individual spot with the software GenePix Pro 5.0 (Molecular Devices).

data_processing: A representative slide was stained for total protein quantification using the protein dye Fast Green FCF. To account for variation in total protein amount, a normalization factor for each spot was calculated using information obtained form these FCF slides and antibody signals of each spot were normalized accordingly. Before FCF-normalization, signal intensities were background corrected using the method described in detail in @reference. Each sample was printed as technical triplicate on the slide.

label: Alexa Fluor® 680

molecule: protein

label_protocol: Alexa Fluor® 680

extract_protocol: Trastuzumab (10 ng/μL), pertuzumab (10 ng/μL), and erlotinib (1 μM) (Roche Diagnostics GmbH, Penzberg, Germany) was added to cells starved for 24 h in DMEM medium lacking FBS but supplemented with 1x NEAA (GIBCO, Darmstadt, Germany) either alone or in combination. After 1 h preincubation with inhibitors, 5 nM epidermal growth factor (Sigma, Munich, Germany) was added. Each experiment was carried out as three biological replicates. Cell lysates were prepared after 0, 5, 20, 60, 70, 80, 120, and 180 min. EGF was added at the 60 min time point to plates representing the time points >60 min. Incubations were stopped by transferring 6-well plates on ice. Before lysis, medium was replaced with ice-cold PBS, and cells were harvested manually by scraping in M-PER lysis buffer (Pierce, Bonn, Germany) containing protease inhibitor Complete Mini and phosphatase inhibitor PhosSTOP (Roche, Mannheim, Germany). Cells were lysed for 20 min on an end-over-end shaker and lysates were cleared by centrifugation at 16,000 x g. Total protein concentration was determined by bicinchoninic acid assay (Thermo Scientific, Rockford, IL, USA) and adjusted to 1.8 μg/μl. Prior to spotting, lysates were mixed with 4x SDS sample buffer (10% Glycerol, 4% SDS, 10 mM DTT, 125 mM Tris-HCl, pH 6.8) and boiled for 5 min at 95°C.

tag: target protein

value: SRC family

tag: phospho site

tag: antibody id

tag: antibody manufacturer

value: Cell Signaling Technology


title: BreastSys_RPPA_pp90RSK_S380

description:
Anti-rabbit IgG
Corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 2


title: BreastSys_RPPA_pcRAF_S259

description:
Anti-rabbit IgG
Corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 3


title: BreastSys_RPPA_pcRAF_S338

description:
Anti-rabbit IgG
Corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 4


title: BreastSys_RPPA_pPKCa_bII_T638_T641

value: PRKCA/PRKCB


title: 26B_3T3


title: BreastSys_RPPA_pmTOR_S2448

value: MTOR


title: BreastSys_RPPA_cRAF


title: BreastSys_RPPA_pRPS6_S235_S236


title: BreastSys_RPPA_pMEK_T286


title: 26A_3T3


title: BreastSys_RPPA_pMEK_S298


title: BreastSys_RPPA_pcRAF_S289_S296_S301


title: BreastSys_RPPA_pMEK_S217_S221

value: Sigma-Aldrich Corporation


title: BreastSys_RPPA_pERBB3_Y1289


title: BreastSys_RPPA_pERBB3_Y1222


title: 012-001

description:
hepatocacellular carcinoma (HCC)
55

tag: individual

value: patient 012

tag: disease state


title: BreastSys_RPPA_MEK

description:
Anti-mouse IgG
Corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 3

value: BD


title: BreastSys_RPPA_pEGFR_Y1173

value: EGFR


title: BreastSys_RPPA_pERBB3_Y1197


title: BreastSys_RPPA_pERBB2_Y1139

value: Abcam


title: BreastSys_RPPA_ERBB3

value: Neomarkers


title: BreastSys_RPPA_pEGFR_Y845


title: BreastSys_RPPA_pEGFR_Y1086


title: BreastSys_RPPA_pERK1_pERK2_T202_Y204


title: BreastSys_RPPA_pERBB2_Y1112

description:
Anti-mouse IgG
Corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 2

value: Millipore


title: BreastSys_RPPA_pERBB2_Y877


title: BreastSys_RPPA_EGFR


title: BreastSys_RPPA_pERBB2_Y1221_Y1222


title: BreastSys_RPPA_pAKT_S473


title: BreastSys_RPPA_pERBB2_Y1248


title: BreastSys_RPPA_ERBB2

description:
Anti-mouse IgG
Corresponding array used for normalization of target specific signal intensities to total protein amount: FCF 1


title: GGS124_Atmospheric_pCO2

city: Tokyo

first: Shinya

last: Watanabe

address: 1-21-1 Toyama

department: Department of Infectious Diseases

institute: National Center for Global Health and Medicine

description: Gene expression of 30 min incubation under atmospheric pCO2

hyb_protocol: 0.6 ug of Cy3-labeled cDNA was used for hybridization. Hybridization and wash processes were carried out using Gene Expression Hybridization Kit (Agilent) and Gene Expression Wash Pack (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Streptococcus dysgalactiae subsp. equisimilis GGS_124

source_name: SDSE GGS_124, Atmospheric pCO2

label_protocol: 5 ug total RNA was labeled with FairPlay III Microarray Labeling Kit (Agilent).

growth_protocol: SDSE strains were incubated in BHI in a 5% CO2 incubator at 37C.

extract_protocol: The bacterial cells were stabilized by RNAprotect Bacteria Reagent (Qiagen). The cell-wall of collected cells was lysed by 3000 units of Mutanolysin (Sigma) in TE buffer at 37oC for 1hr. After cell lysis, RNA was extracted by RNeasy mini kit (Qiagen) and RNase-Free DNase set (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Overnight culture of GGS_124 in BHI were adjusted to 1×10^8 CFU/ml. 100 ul of the suspended cells was added into a 50 ml tube containing 10 ml of BHI broth. It was incubated at 37oC in a 5% CO2 incubator until OD600=0.6 and was exposed to following stress conditions. To exposure antibacterial agents, 100 ul of eight antibacterial agents (penicillin G, erythromycin, levofloxacin, hydrogen peroxide, sodium nitrite, potassium cyanide, CCCP and mitomycin) was added into the mid-log phase culture to adjust final concentration as ×1 MIC. The bacteria were incubated for additional 30 min in a CO2 incubator. To culture SDSE under nutrient starvation condition, the mid-log phase culture was centrifuged and cells were suspended in same volume of PBS, and then the bacteria were incubated for additional 30 min in a 5% CO2 incubator. UV exposure: the mid-log phase culture was transferred into a 9 cm dish. 25 mJ UV was exposed by UV Stratalinker 2400 (Stratagene). The cells were retransferred into a 50 ml tube and were incubated for additional 30 min in a 5% CO2 incubator. Atmospheric pCO2: the mid-log phase culture was transferred to an incubator without CO2 supply and was incubated at 37oC with shaking at 200 rpm for 30 min. For analyzing stationary phase culture, after 100 ul of the 1×10^8 CFU/ml cell suspension was inoculated into a fresh 10 ml BHI broth, the culture was incubated at 37oC in a 5% CO2 incubator for 20 h. To analyze anaerobic condition, 100 ul of the 1×10^8 CFU/ml SDSE cells were inoculated into a fresh 10 ml BHI and were transferred into a chamber of Anaeropack Kenki (Mitsubishi Gus Chemical Company, Tokyo Japan), which generates about 16% CO2 and simultaneously reduces oxygen concentration at less than 0.1% inside chamber within 2 h. After 2 h 30 min, the culture reached mid-log phase (OD600=0.6) when the sample was harvested.


title: BreastSys_RPPA_pPRAS40_T246


title: GGS124_25mJ_UV

description: Gene expression of 25 mJ UV exposure

source_name: SDSE GGS_124, 25mJ UV


title: GGS124_62.5nM_Mitomycin

description: Gene expression of 30 min treatmeant with 62.5 nM Mitomycin

source_name: SDSE GGS_124, 62.5 nM Mitomycin


title: GGS124_24uM_CCCP

description: Gene expression of 30 min treatmeant with 24 uM CCCP

source_name: SDSE GGS_124, 24 uM CCCP


title: BreastSys_RPPA_pAKT_T308


title: H_PMN_A23187_60_2

city: New Delhi

first: Meraj

middle: Alam

last: Khan

state: Delhi

address: Room No.2029

department: Physiology

institute: All India Institute of Medical Sciences

description: Human transcriptome array2 gene expression data from neurtophils tearetd with A23187 (4 uM) for 60 mins time point

hyb_protocol: Hybridization was performed by using HTA2 gene chip. All the experimental procedure was followed by manufacturer's guidelines at the Center for Applied Genomics (TCAG) facility, The Hospital for Sick Children Research Institute, Toronto, Canada.

scan_protocol: After completing the hybridization, gene chips were washed and scanned  in the Affymetrix station at TCAG and raw data was retrieved in .CEL files.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. For further normalization and down streamanalysis Transcriptomics Array Console 3.0 (TAC3), Parteck Genomics Suit and GeneSpring GX13 softwares were used to the gain the transcript expression change and affecting biology.

label: biotin

source_name: Human neutrophils treated with A23187 (4 uM) for 60 mins

label_protocol: For In vitro transcription (IVT)  >200 ng good quality total RNA (RIN >7.5) have been used to label with dUTP. All the experimental procedure was followed by manufacturer's guidelines at the Center for Applied Genomics (TCAG) facility, The Hospital for Sick Children Research Institute, Toronto, Canada.

growth_protocol: Purified neutrophils from healthy male donors were immedeatly used for the experiments.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and purified RNA preserved in RNAlater (sigma) in -80 freezer for further use.

treatment_protocol: Purified neutrophils were treated with DMOS (-ve control), PMA(25 nM) and A23187 (4 uM) in a separate tubes (2 million cells in each conditions) and incubated for 30 and 60 min time points. After these time points the incubated cell suspensions (each condition) were further subjected to RNA isolation for microarray experiments.

tag: tissue

value: Peripheral Blood neutrophils

tag: gender

value: male

tag: diagnosis

value: Healthy donor

tag: age

value: Adult (20-40 years)


title: GGS124_1mM_H2O2

description: Gene expression of 30 min treatmeant with 1 mM Hydrogen Peroxide

source_name: SDSE GGS_124, 1 mM Hydrogen Peroxide


title: H_PMN_A23187_60_1


title: H_PMN_A23187_30_2

description: Human transcriptome array2 gene expression data from neurtophils tearetd with A23187 (4 uM) for 30 mins time point

source_name: Human neutrophils treated with A23187 (4 uM) for 30 mins


title: H_PMN_A23187_60_3


title: H_PMN_A23187_30_1


title: H_PMN_A23187_30_3


title: H_PMN_P_60_1

description: Human transcriptome array2 gene expression data from neurtophils tearetd with PMA (25 nM) for 60 mins time point

source_name: Human neutrophils treated with PMA (25 nM) for 60 mins


title: GGS124_Stationary_phase

description: Gene expression during stationary phase

source_name: SDSE GGS_124, Stationary phase


title: GGS124_512mM_NaNO2

description: Gene expression of 30 min treatmeant with 512 mM Sodium Nitirte

source_name: SDSE GGS_124, 512 mM Sodium Nitrite


title: GGS124_Anaeropack_Kenki

description: Gene expression during mid-log phase under anaerobic condtion

source_name: SDSE GGS_124, Anaeropack Kenki


title: GGS124_1mM_Levofloxacin

description: Gene expression of 30 min treatmeant with 1 mM levofloxacin

source_name: SDSE GGS_124, 1 mM Levofloxacin


title: GGS124_256mM_KCN

description: Gene expression of 30 min treatmeant with 256 mM Potacium Cyanide

source_name: SDSE GGS_124, 256 mM  Potacium Cyanide


title: GGS124_125nM_Erythromycin

description: Gene expression of 30 min treatmeant with 125 nM Erythromycin

source_name: SDSE GGS_124, 125 nM Erythromycin


title: H_PMN_P_60_2


title: H_PMN_P_30_3

description: Human transcriptome array2 gene expression data from neurtophils tearetd with PMA (25 nM) for 30 mins time point

source_name: Human neutrophils treated with PMA (25 nM) for 30 mins


title: GGS124_46.9nM_PenicillinG

description: Gene expression of 30 min treatmeant with 46.9 nM Penicillin G

source_name: SDSE GGS_124, 46.9 nM Penicillin G


title: GGS124_PBS

description: Gene expression of 30 min incubation in PBS

source_name: SDSE GGS_124, PBS 30 min


title: H_PMN_C_30_3

description: Human transcriptome array2 gene expression data from neurtophils tearetd with DMSO (-ve control) for 30 mins time point

source_name: Human neutrophils treated with DMSO (-ve control) for 30 mins


title: H_PMN_C_60_3

description: Human transcriptome array2 gene expression data from neurtophils tearetd with DMSO (-ve control) for 60 mins time point

source_name: Human neutrophils treated with DMSO (-ve control) for 60 mins


title: H_PMN_P_60_3


title: H_PMN_P_30_2


title: H_PMN_C_30_1


title: H_PMN_C_60_2


title: H_PMN_P_30_1


title: TUSC3 Knock-out replicate 3

city: Austin

first: Bum-Kyu

state: TX

address: 2506 Speedway Stop A5000

country: USA

institute: University of Texas at Austin

description: TUSC3 KO cells

hyb_protocol: A hybridization mixture including the fragmented DNA and probe array controls were prepared, and then hybridized to the probe array   during a 16-hour incubation

scan_protocol: GeneChips were scanned by Scanner 3000, Affymetrix

data_processing: Robust multi-array (RMA) normalization method was applied to calculate averaged expression values from replicates

source_name: lung carcinoma cells

label_protocol: cDNAs were generated using qScript (Qunta) and then labeled with Cy3

growth_protocol: A549 control and TUSC3 knockout cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS)

extract_protocol: Total RNAs were extracted using RNeasy plus mini kit (Qiagen)

treatment_protocol: A549 and A549-TUSC3 knockout cells were exposed to DMSO or Tunicamycin (3ug/ml, 16 hours).


title: TUSC3 Knock-out replicate 1

description: TUSC3 KO cells


title: H_PMN_C_60_1


title: TUSC3 Knock-out replicate 2

description: TUSC3 KO cells


title: H_PMN_C_30_2


title: Adenosarcoma patient 13

type: genomic

city: Taipei

first: Tzu-Pin

last: Lu

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

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

description: Hybridized to Oncoscan FFPE Assay Kit

hyb_protocol: Affymetrix standard protocol

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G. Raw data were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2.

data_processing: The raw CEL files were imported into the Affymetrix Oncoscan Console Ver1.1 software using its default settings to generate the corresponding copy number values. Copy number analysis was performed by using the Nexus Express for Oncoscan 3 software provided by the Affymetrix company.

label: Biotin

molecule: genomic DNA

source_name: Adenosarcoma patient 13

label_protocol: Affymetrix standard protocol

extract_protocol: QIAamp DNA FFPE Tissue Kit according to the manufacturer’s instructions

tag: disease

value: Adenosarcoma

value: Female

tag: site

value: Uterus

tag: Stage

value: IB

tag: group


title: ES stress TUSC3 Knock-out replicate 1

description: Tunicamycin treatment onto TUSC3 KO cells


title: ES stress TUSC3 Knock-out replicate 3


title: Adenosarcoma patient 15

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 15

value: Famale


title: ES stress TUSC3 Knock-out replicate 2


title: Adenosarcoma patient 14

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 14


title: Adenosarcoma patient 12

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 12

value: IA


title: Adenosarcoma patient 16

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 16


title: ER stress control replicate 2

description: Tunicamycin treatment onto wild-type cell


title: ER stress control replicate 3


title: Adenosarcoma patient 9

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 9


title: Adenosarcoma patient 11

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 11

value: IIB


title: 3333.3 - replicate 1, 2 & 3

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

hyb_protocol: The SDA slides were pre-hybridized for 45 min at 42°C in a pre-warmed solution containing 5X standard saline citrate (SSC), 0.1% sodium dodecyl sulphate (SDS), 1% bovine serum albumin (BSA) and 25% formamide. The slides were rinsed twice with sterile MilliQ water and immediately dried with an air gun.     The biotin-labelled targets (dried to 16 μL) were added to 17.5 μL of fresh 2X Hybridization buffer (250 μL of formamide, 250 μL of 10X SSC, 10 μL of 10% SDS), 0.5 μL of 5 μg/μL Human Cot1 DNA (Sigma-Aldrich, St Louis, MO), 0.5 μL of 10 mg/mL Poly A (Sigma-Aldrich) and 0.5 μL of 10 mg/mL salmon sperm DNA (Sigma-Aldrich). The mixture was denatured at 100°C for 2 min and immediately applied onto the array under a 22 × 25-mm lifter slip (Grale Scientific, Victoria, Australia). The slides were then placed in waterproof, humidified hybridization chambers (Corning Incorporated Life Sciences) and incubated overnight in a 42°C water bath. Following hybridization, the slides were washed twice for 5 min in 500 mL Wash buffer 1 (1X SSC with 0.1% SDS), once for 5 min in 500 mL Wash buffer 3 (0.1X SSC with 0.1% SDS), and once for 5 min in 500 mL Wash buffer 4 (0.1X SSC). Subsequently the slides were transferred to 500 mL of 6X SSPE-T buffer (0.9 M NaCl, 0.06 M NaH2PO4.H2O, 0.006 M EDTA, 0.005% Triton X-100, pH 7.4) without allowing them to dry.     The biotinylated DNA targets bound on the array were then labelled with fluorescent FluoroLink™ streptavidin-labelled Cy3 dye (Amersham Pharmacia, UK) using a biotin–streptavidin system. Briefly, 200 μL of a Detection solution (0.5 µL of 0.8 µg/µL streptavidin-labelled Cy3, 0.8 µl of 25 µg/µL BSA, made to 200 µL with 6X SSPE-T) was applied directly onto the array surface and a 22 × 25-mm lifter slip was placed over it to evenly distribute the solution on the array. The slides were placed in hybridization chambers, wrapped in aluminum foil and incubated at 37oC for 1 h in the dark. Finally, the slides were washed thrice in 6X SSPE-T for 5 min and rinsed with sterile MilliQ water before being dried with an air gun. All hybridizations were performed with six technical replicates (corresponding to six sub-arrays) and two biological replicates, resulting in 12 data points for each array feature.

scan_protocol: Slides were scanned with a ScanArray Gx (PerkinElmer Life and Analytical Sciences, Downers Grove, IL) microarray scanner in conjunction with the supplied software. The slides were scanned at 10 μm resolutions at 532 nm (Cy3, green laser) and 50% photomultiplicator (PMT) gain to keep background noise low. The quantitation of scanned array was performed using PerkinElmer ScanArray Express software v 2.0. The designed grid which was provided with the program was fully adjusted to match and fit all the printed spots on the array image, and the signal intensities were quantified using the adaptive circle and LOWESS functions.

data_processing: The scanning software flagged Probes which did not hybridize automatically and labelled as ‘bad’ while some other abnormal spots were flagged manually. ‘Good’ probes were accepted as having a mean ‘signal to noise ratio’ (SNR) value of a minimum 5, all the quantified data was then exported to Microsoft Excel Sheet.     Data analysis included subtracting the background from median signal intensity for each feature, log2 transformation and combining technical replicates by taking average.

label: Biotin/Steptavidin

organism: Streptococcus uberis

source_name: milk

label_protocol: The pooled tester and driver (Target DNA) as well as the 29 S. uberis strains were digested with Rsa 1 and subsequently purification on a column using QIAquick PCR Purification Kit. Approximately 200 ng of restriction digested gDNA fragments were then labeled with Biotin-11-dUTP using the Biotin DecaLabelTM DNA Labeling Kit in accordance with manufacturer’s instructions. However, the reaction was incubated at 37oC for 20 h, and stopped with 1 µL of 0.5M EDTA, pH 8.0 and no further purification was performed.

growth_protocol: Milk samples were cultured immediately on arrival at the laboratory by spreading 50 μl on the surface of SBA plates and Edward’s agar plates followed by incubation at 37°C for 48 hrs. Bacterial colonies resembling Streptococcus spp. were subcultured onto BHI agar and incubated at 37°C for 24 hrs. If multiple morphologically different colonies grew on a primary culture plate, each of these was subcultured to BHI agar.

extract_protocol: Genomic DNA was extracted from the different S. uberis strains using a Wizard® Genomic DNA Purification Kit in accordance with the manufacturer’s instructions.

tag: family

value: Uberis

tag: order

value: Low cell count


title: Adenosarcoma patient 7

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 7

value: Ovary

value: IIA


title: 3217.3 - replicate 1, 2 & 3


title: Adenosarcoma patient 8

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 8


title: Control replicate 3

description: wild-type cell

tag: cell line


title: ER stress control replicate 1


title: Adenosarcoma patient 6

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 6


title: Control replicate 1

description: wild-type cell


title: 3217.1 - replicate 1, 2 & 3


title: HCT116 colorectal adenocarcinoma cell line, array 2

city: Catania

first: Daniele

middle: F

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

hyb_protocol: Fragmented and labeled target (Sense Strand-cDNA  5.2-5.5 µg) was used for hybridization to the “GeneChip Human Transcriptome Array 2.0” according to the protocol supplied by the manufacturer was used for  hybridization step. The hybridization has been performed in an hybridization oven at 45°C for 16 hours with rotation at 60 rpm.

scan_protocol: Scanning was performed using the  Affymetrix Scanner GCS3000 7G.

data_processing: Data analysis was performed using Affymetrix® Expression Console™ software (v.1.4). Expression level analysis was obtained using the normalization method based on the processing algorithm Robust Multi-array Average (RMA).

source_name: colorectal carcinoma cell line

label_protocol: Biotinylated fragmented sense strand cDNA were prepared according to the protocol supplied by the Affymetrix for Human Transcriptome Array 2.0 (HTA).

growth_protocol: Caco-2 and HT29 cell lines have been cultured in D-MEM medium (Dulbecco's Modified Eagle Medium 1X; GIBCO, COD:31965-023 containing 4.5g/L of  D-glucose), supplemented with 10% FBS (Fetal Bovine Serum) and 100 U/ml of antibiotics (Penicillin-Streptomycin). HCT116 cell line was cultured in McCoy 5A+ (McCoy’s 5A Medium 1X GIBCO, COD: 36600021 containing 3 g/L of D-glucose) supplemented with 10%FBS (Fetal Bovine Serum), 1.5 mM L-glutamine and 2200 mg/L of sodium bicarbonate. Cell lines were incubated at 37 °C in humidified atmosphere with 5% of CO2  and 95% of air. The culture medium was changed twice a week, then RNA was extracted using RNeasy Mini Kit- (Qiagen, Milan-Italy).

extract_protocol: Total RNA (100 ng) was extracted from frozen tissue and cell cultures using RNeasy Mini Kit (Qiagen, Milan - Italy) according to the manufacturer’s instructions. The concentration and the quality of  RNA were determined using a ND-1000 spectrophotometer (NanoDrop, Thermo Scientific, USA).

value: colorectal carcinoma cell line

tag: tissue preparation

value: confluent cell cultures

tag: anatomical site

value: colon

tag: patient age

value: adult

tag: tumor stage

value: colorectal adenocarcinoma cell line


title: HCT116 colorectal adenocarcinoma cell line, array 1

value: male


title: Adenosarcoma patient 5

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 5

value: Adenosarcoma

value: IIIA


title: HT29 colorectal adenocarcinoma cell line, array 2

source_name: colorectal adenocarcinoma cell line

value: female


title: Adenosarcoma patient 1

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 1

value: Female

value: Uterus

value: IVB


title: Adenosarcoma patient 4

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 4

value: IIIC


title: 3147.1 - replicate 1, 2 & 3

value: Uberis


title: 3133.3 - replicate 1, 2 & 3

value: Low cell count


title: 3068.2 - replicate 1, 2 & 3


title: 2945.3- replicate 1, 2 & 3


title: 2917.2 - replicate 1, 2 & 3


title: 7218(1) - replicate 1, 2 & 3

value: Clinical


title: 4707(2) - replicate 1, 2 & 3


title: Adenosarcoma patient 3

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 3

value: IA


title: 3147.5 - replicate 1, 2 & 3


title: 3885(1) - replicate 1, 2 & 3


title: 3599(1) - replicate 1, 2 & 3


title: 3571(1) - replicate 1, 2 & 3


title: 2905(1) - replicate 1, 2 & 3


title: 3531(1) - replicate 1, 2 & 3


title: 6104 - replicate 1, 2 & 3


title: 6093 - replicate 1, 2 & 3


title: Adenosarcoma patient 2

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 2


title: 5838.3 - replicate 1, 2 & 3


title: Adenosarcoma patient 10

description: Hybridized to Oncoscan FFPE Assay Kit

source_name: Adenosarcoma patient 10

value: IIB


title: 3064.1 - replicate 1, 2 & 3


title: Control replicate 2

description: wild-type cell

source_name: lung carcinoma cells


title: HT29 colorectal adenocarcinoma cell line, array 1

value: confluent cell cultures


title: patient 97, normal sample, array 2

source_name: normal colonic mucosa

value: normal colonic mucosa

value: frozen sample

value: sigmoid colon


title: Caco-2 colorectal adenocarcinoma cell line, array 1

value: colorectal adenocarcinoma cell line

value: colon

value: male


title: patient 77, normal sample, single array

value: right colon


title: patient 93, normal sample, array 2

value: rectum

value: female


title: patient 93, normal sample, array 1


title: patient 75, normal sample, array 1


title: patient 75, normal sample, array 2


title: patient 71, normal sample,  single array


title: patient 79, normal sample,  single array


title: patient 65,normal colonic mucosa, array 2


title: patient 97, normal sample, array 1


title: patient 63, normal colonic mucosa, array 2


title: Caco-2 colorectal adenocarcinoma cell line, array 2


title: patient 73, normal sample, array 2


title: patient 91, normal sample,  single array


title: patient 65, normal colonic mucosa, array 1


title: patient 63, normal colonic mucosa, array 1


title: patient 73, normal sample, array 1


title: 2874.4 - replicate 1, 2 & 3


title: 2730.5 - replicate 1, 2 & 3


title: 6232(1) - replicate 1, 2 & 3


title: 2565.2 - replicate 1, 2 & 3


title: 2530.2 - replicate 1, 2 & 3


title: 2988.1 - replicate 1, 2 & 3


title: 2285.1 - replicate 1, 2 & 3


title: 883.4 - replicate 1, 2 & 3


title: Tester - replicate 1, 2 & 3


title: 2169.2 - replicate 1, 2 & 3


title: Driver - replicate 1, 2 & 3


title: NNL-35

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

institute: National Taiwan University

description: Approximately 0.1 μg of total RNAs were extracted from from formalin-fixed paraffin-embedded tissue blocks.

hyb_protocol: The miRtagged mature miRNAs were hybridized to fluorescent reporter probes and to capture probes

scan_protocol: The samples were immobilized to a solid-phase cartridge, and a CCD digital analyzer was used for data acquisition.

data_processing: CCD digital analyzer was used for data acquisition, and the data were normalized to the internal positive controls using nSolver Analysis Software at http://www.nanostring.com.

source_name: nasal NK-cell lymphoma

label_protocol: Mature miRNAs were ligated to sequence-specific miRtags

extract_protocol:
Total RNA sample was extracted by TRIzol® reagent (Invitrogen )
Approximately 0.1 ug of total RNAs were extracted from from formalin-fixed paraffin-embedded tissue blocks.

value: nasal NK-cell lymphoma


title: NNL-36


title: patient 59, normal colonic mucosa, array 2


title: NNL-33


title: NNL-34


title: patient 49, normal colonic mucosa, array 2

value: left colon


title: NNL-32


title: patient 59, normal colonic mucosa, array 1


title: patient 43, normal colonic mucosa,  single array


title: NNL-30


title: NNL-31


title: patient 47, normal colonic mucosa, array 2


title: patient 37, normal colonic mucosa, array 2


title: patient 37, normal colonic mucosa, array 1


title: NNL-29


title: patient 47, normal colonic mucosa, array 1


title: patient 13, normal colonic mucosa, array 1

value: transverse colon


title: patient 19, normal colonic mucosa, array 1


title: patient 31, normal colonic mucosa,  single array


title: patient 19, normal colonic mucosa, array 2


title: NNL-28


title: NNL-27


title: patient 97, tumoral sample2, array 1

source_name: colon adenocarcinoma

value: colon adenocarcinoma

value: tumor stage 2


title: patient AA1, normal colonic mucosa,  single array


title: NNL-26


title: patient 97, tumoral sample2, array 2


title: NNL-24


title: NNL-25


title: NNL-23


title: patient 93, tumoral sample2, single array

source_name: rectal adenocarcinoma

value: rectal adenocarcinoma

value: tumor stage 3


title: patient 13, normal colonic mucosa, array 2


title: patient 49, normal colonic mucosa, array 1


title: NNL-22


title: patient 93, tumoral sample1,  single array


title: NNL-21


title: NNL-20


title: patient 91, tumoral sample1, single array


title: patient 85, tumoral sample2, array 2


title: patient 85, tumoral sample1, array 2


title: patient 85, tumoral sample1, array 1


title: NNL-19


title: patient 85, tumoral sample2, array 1


title: NNL-17


title: NNL-18


title: NNL-14


title: NNL-16


title: NNL-15


title: NNL-13


title: NNL-12


title: NNL-11


title: patient 77, tumoral sample1,  single array


title: patient 79, tumoral sample2,  single array


title: NNL-10


title: patient 75, tumoral sample2, array 2


title: patient 77, tumoral sample2,  single array


title: NNL-9


title: patient 79, tumoral sample1,  single array


title: patient 75, tumoral sample1, array 1


title: NNL-8


title: patient 75, tumoral sample1, array 2


title: patient 73, tumoral sample1,  single array


title: patient 65, tumoral sample2, array 2


title: patient 69, tumoral sample1,  single array 1


title: NNL-7


title: patient 65, tumoral sample2, array 1


title: patient 75, tumoral sample2, array 1


title: patient 71, tumoral sample2,  single array


title: patient 71, tumoral sample1,  single array


title: patient 69, tumoral sample2,  single array 2


title: patient 65, tumoral sample1, array 2


title: NNL-5


title: NNL-6


title: NNL-3


title: patient 65, tumoral sample1, array 1


title: NNL-1


title: NNL-2


title: NNL-4


title: patient 59, tumoral sample2, array 1


title: patient 59, tumoral sample2, array 2


title: patient 43, tumoral sample1,  single array

value: tumor stage 4


title: patient 47, tumoral sample1, array 2


title: patient 63, tumoral sample1, array 2


title: patient 37, tumoral sample3, array 2


title: patient 37, tumoral sample1, single array


title: patient 41, tumoral sample1, array 1


title: patient 63, tumoral sample1, array 1


title: patient 49, tumoral sample1, array 1


title: patient 41, tumoral sample1, array 2


title: patient 29, tumoral sample1, array 2


title: patient 23, tumoral sample1, array 1


title: patient 23, tumoral sample1, array 2


title: patient 15, tumoral sample1, array 1


title: patient 47, tumoral sample1, array 1


title: patient 31, tumoral sample1,  single array


title: patient 49, tumoral sample1, array 2


title: patient 13, tumoral sample1, array 1


title: patient 37, tumoral sample2, array 1


title: patient 17, tumoral sample1, single array


title: patient 37, tumoral sample2, array 2


title: patient 29, tumoral sample1, array 1


title: patient 13, tumoral sample1, array 2