title: in vivo vs. in vitro stationary phase, rep2

status: Public on Sep 30 2012

type: RNA

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

hyb_protocol: The labelled samples were mixed and competitively hybridised using an Agilent Gene Expression Hybridisation Kit (part number: 5188-524_12) in an Agilent hybridization oven (G254_15A) at 65°C for 24_1 hours.

scan_protocol: In vivo vs. in vitro arrays: Microarray slides were scanned using a GenePix 4_100B Scanner (Axon Instruments, USA) and the GenePix Pro 6.0 software. The slides were scanned at 5 μm and a photomultiplier tube (PMT) setting of 780 for the red channel (635 nm laser measuring the Cy5 labelled nucleic acid) and 510 for the green channel (532 nm laser measuring the Cy3 labelled nucleic acid). The GenePix array list (GAL) file was used for extraction of the microarray results. Control hybridisation: Microarrays were scanned using the Agilent Microarray Scanner System (G2505B) and Agilent scan control software version 7.0 at a resolution of 5 micrometres.

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5.3.1) which performs a lowess normalization. Microarray data was processed as described by García de la Nava et al. 2003 and van Hijum et al. 2005. Differential gene expression was determined by Cyber-T test (Long 2001).

molecule: total RNA

organism: Limosilactobacillus reuteri subsp. rodentium

source_name: Lactobacillus reuteri 100-23 grown in MRS to stationary phase

label_protocol: Five hundred nanograms of total RNA was used as a template for RNA amplification using the MessageAmp II Bacteria kit (Ambion, USA) according to the manufacturer's protocol. During the in vitro transcription step of the RNA amplification protocol to synthesize amplified RNA (aRNA), the modified nucleotide, 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion, USA), was incorporated into the aRNA in equal proportion to unmodified UTP. Ten micrograms of purified aRNA was labelled with either Cy3 or Cy5 Post-labelling Reactive Dyes (Amersham biosciences, USA). The labelled aRNA was purified using the RNeasy Kit (Qiagen) following the RNA cleanup protocol, and the dye incorporation rate was determined by a NanoDrop ND-1000 UV-Vis spectrophotometer.

growth_protocol:
In vitro: Lactobacillus reuteri 100-23 was cultured in Lactobacilli MRS medium (Difco, Becton Dickinson Co., Sparks, MD, USA) incubated anaerobically at 37oC.  Liquid media were filter-sterilised, and agar media were autoclaved.
In vivo: Groups of six to eight female Lactobacillus-free BALB/C mice were anaesthetised using 250 mg/kg body weight avertin injected intraperitoneally prior to inoculation with 100 µl of L. reuteri 100-23C suspended in 0.9% (w/v) NaCl by intragastric gavage (109 cells per ml).  After two weeks, the animals were sacrificed by cervical dislocation and the stomach contents and scrapings of the stomach surface used for RNA extraction. For the control hybridisation, Lactobacillus-free BALB/C mice were sacrificed by cervical dislocation and the stomach contents and scrapings of the stomach surface used for RNA extraction.

extract_protocol:
Total RNA was extracted from cultures of strain 100-23 grown in Lactobacilli MRS medium for four hours and eight hours and from cells harvested from the stomachs of mice colonised for 14_1 days with L. reuteri 100-23.
From bacterial culture (in vitro): Bacterial cells were harvested by brief centrifugation at 12,000 x g and washed with 750 µl of RNAprotect reagent (Qiagen). The bacterial cells were disrupted by bead beating (5000 rpm, 2 x 4_10 seconds) in TRIzol reagent (Invitrogen) and extracted with chloroform. RNA was precipitated with isopropanol and dried after removal of isopropanol. The dried RNA was then dissolved in nuclease-free water. The RNA was further purified using the RNeasy Mini Kit (Qiagen) and DNase treated using a DNA-free kit (Ambion).
From the mouse stomach (in vivo): Stomach contents and scrapings from the forestomach surface of mice were washed once with RNAprotect Bacteria Reagent. Samples were centrifuged at 150 x g for 5 min at 5°C, and the supernatant was further centrifuged at 300 x g for 5 min at 5°C to remove debris. Cells were recovered by centrifugation at 5000 x g for 5 min at 5°C. Cell pellets from 6-8 mice were pooled in 1 ml of TRIzol Reagent and cells were disrupted by bead beating (5000 rpm, 2 x 4_10 seconds) and extracted with chloroform. RNA was precipitated with isopropanol and dried after removal of isopropanol. The dried RNA was then dissolved in nuclease-free water. The RNA was further purified using the RNeasy Mini Kit (Qiagen) and DNase treated using a DNA-free kit (Ambion).  Contaminating mouse RNA from the stomach-derived samples of L. reuteri 100-23 RNA was removed with the MICROBEnrich Kit (Ambion, USA).

tag: growth type

value: in vitro

tag: growth phase

value: stationary

source_name: Lactobacillus reuteri 100-23 harvested from the mouse stomach, two weeks after intragastric inoculation of reconstituted-Lactobacillus free mice

value: in vivo

tag: growth source

value: stomach of inoculated mouse


title: Uninoculated mouse gut sample vs. log phase L. reuteri 100-23, rep2

source_name: Lactobacillus reuteri 100-23 grown in MRS to log phase

value: log

source_name: Uninoculated mouse stomach contents and stomach lining scrapings

value: stomach of uninoculated mouse


title: in vivo vs. in vitro stationary phase, rep1


title: Uninoculated mouse gut sample vs. log phase L. reuteri 100-23, rep1


title: U87MG EGFRvA Cy3 vs. U87MG EGFR Cy5

city: Shanghai

first: Min

last: Zhou

address: No.25/Ln2200, XieTu Road

country: China

institute: Medical School of Shanghai Jiao Tong University

hyb_protocol: Resuspend the Cy3- or Cy5-labeled samples in the desired volume of hybridization buffer; Microarray hybridization was performed at 42°C overnight; After hybridization, slides were washed sequential.

scan_protocol: Scanned on a LuxSan 10K-A Microarray Scanner. Images were quantified using Microarray Image Analysis Software (LuxScan  3.0).

data_processing: Data obtained from spots were subtracted background and lowess normalized.

organism: Homo sapiens

source_name: Human primary glioblastoma cells U87MG with stable expression of EGFRvA

label_protocol: The first strand cDNA synthesis (T7 Oligo (dT) primer, CbcScript); The second strand cDNA synthesis (DNA polymerase); Double strand cDNA purification; cRNA synthesis (T7 Enzyme mix); cDNA synthesis (Random Primer, CbcScript Ⅱ); Cy3 or Cy5 labeling of cDNA samples; Purification of Cy3- or Cy5-labeled cDNA.

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and incubated in a humidified 37°C, 5% CO2 incubator.

extract_protocol: Total RNA was extracted with Trizol following manufacturer's instructions and purified using NucleoSpin® RNA clean-up.

tag: cell line

value: U87MG EGFRvA

value: U87MG EGFR


title: in vivo vs. in vitro log phase, rep2


title: U87MG EGFRvA Cy5 vs. U87MG EGFR Cy3

source_name: Human primary glioblastoma cells U87MG with stable expression of EGFR


title: in vivo vs. in vitro log phase, rep1


title: 14486.fa/NA18507

type: genomic

city: Seattle

first: Megan

middle: Y

last: Dennis

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

country: USA

institute: University of Washington

hyb_protocol: The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) with 10 ug of labelled test sample and 10 ug of labelled reference sample

scan_protocol: The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

data_processing: The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf)

molecule: genomic DNA

source_name: whole blood DNA

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.

extract_protocol: unsonicated genomic DNA

tag: group

tag: gender

value: male

tag: family status

value: father

tag: ndar guid

tag: tissue

value: whole blood

source_name: lymphoblast cell line DNA


title: 14491.mo/NA12878

value: female

value: mother


title: 14491.p1/NA18507

value: proband


title: 14486.mo/NA12878


title: 14491.fa/NA18507


title: 14483.p1/NA18507


title: 14486.p1/NA18507


title: 14555.p1/NA12878


title: 14489.p1/NA18507


title: 14487.p1/NA18507


title: 14490.p1/NA18507


title: 14484.p1/NA18507


title: 14477.p1/NA18507


title: 14492.p1/NA18507


title: 14478.p1/NA18507


title: 14484.fa/NA18507


title: 14479.p1/NA18507


title: 14484.mo/NA12878


title: 14482.p1/NA18507


title: 14471.p1/NA18507


title: 14481.p1/NA18507


title: 14475.p1/NA18507


title: 14496.p1/NA18507


title: 14469.p1/NA18507


title: 14468.p1/NA18507


title: 14472.p1/NA18507


title: 14463.p1/NA18507


title: 14473.p1/NA18507


title: 14474.p1/NA18507


title: 14458.p1/NA18507


title: 14438.p1/NA12878


title: 14450.p1/NA18507


title: 14452.p1/NA18507


title: 14459.p1/NA18507


title: 14449.p1/NA12878


title: 14454.p1/NA18507


title: 14445.p1/NA18507


title: 14442.p1/NA18507


title: 14427.p1/NA18507


title: 14433.p1/NA18507


title: 14446.p1/NA18507


title: 14432.p1/NA18507


title: 14442.mo/NA12878


title: 14435.p1/NA18507


title: 14424.p1/NA18507


title: 14440.p1/NA18507


title: 14429.p1/NA18507


title: 14425.p1/NA18507


title: 14461.p1/NA18507


title: 14436.p1/NA18507


title: 14437.p1/NA18507


title: 14442.fa/NA18507


title: 14443.p1/NA18507


title: 14439.p1/NA18507


title: 14417.p1/NA18507


title: 14418.p1/NA18507


title: 14455.p1/NA12878


title: 14413.p1/NA18507


title: 14411.p1/NA18507


title: 14414.p1/NA18507


title: 14410.p1/NA18507


title: 14408.p1/NA18507


title: 14409.p1/NA18507


title: 14420.p1/NA18507


title: 14387.p1/NA18507


title: 14401.p1/NA18507


title: 14395.p1/NA12878


title: 14376.p1/NA18507


title: 14381.p1/NA18507


title: 14447.p1/NA18507


title: 14376.mo/NA12878


title: 14370.p1/NA18507


title: 14397.p1/NA18507


title: 14376.fa/NA18507


title: 14396.p1/NA18507


title: 14416.p1/NA18507


title: 14364.p1/NA18507


title: 14371.p1/NA18507


title: 14404.p1/NA18507


title: 14390.p1/NA18507


title: 14362.p1/NA18507


title: 14369.p1/NA18507


title: 14354.p1/NA18507


title: 14366.p1/NA18507


title: 14359.p1/NA18507


title: 14354.mo/NA12878


title: 14348.fa/NA18507


title: 14354.fa/NA18507


title: 14363.p1/NA18507


title: 14343.p1/NA18507


title: 14349.p1/NA12878


title: 14345.p1/NA18507


title: 14343.mo/NA12878


title: 14348.p1/NA18507


title: 14344.p1/NA18507


title: 14342.p1/NA18507


title: 14331.p1/NA18507


title: 14338.p1/NA18507


title: 14339.p1/NA18507


title: 14391.p1/NA18507


title: 14343.fa/NA18507


title: 14335.p1/NA18507


title: 14328.p1/NA18507


title: 14334.p1/NA18507


title: 14316.p1/NA18507


title: 14327.p1/NA18507


title: 14326.p1/NA18507


title: 14313.p1/NA18507


title: 14365.p1/NA18507


title: 14322.p1/NA12878


title: 14314.p1/NA18507


title: 14306.p1/NA18507


title: 14311.p1/NA18507


title: 14329.p1/NA18507


title: 14323.p1/NA18507


title: 14299.p1/NA18507


title: 14348.mo/NA12878


title: 14319.p1/NA18507


title: 14305.p1/NA18507


title: 14297.mo/NA12878


title: 14297.p1/NA18507


title: 14298.p1/NA18507


title: 14415.p1/NA18507


title: 14295.p1/NA18507


title: 14296.p1/NA18507


title: 14297.fa/NA18507


title: 14394.p1/NA18507


title: 14291.p1/NA18507


title: 14292.mo/NA12878


title: 14290.p1/NA18507


title: 14292.p1/NA18507


title: 14287.p1/NA18507


title: 14292.fa/NA18507


title: 14288.p1/NA18507


title: 14290.p2/NA18507


title: 14284.mo/NA12878


title: 14284.p1/NA18507


title: 14285.p1/NA18507


title: 14280.p1/NA18507


title: 14356.p1/NA18507


title: 14309.p1/NA18507


title: 14284.fa/NA18507


title: 14282.p1/NA12878


title: 14284.p2/NA18507


title: 14279.p1/NA18507


title: 14281.p1/NA12878


title: 14278.p1/NA18507


title: 14275.p1/NA18507


title: 14346.p1/NA12878


title: 14273.p1/NA18507


title: 14276.p1/NA18507


title: 14269.p1/NA18507


title: 14271.p1/NA18507


title: 14268.p1/NA18507


title: 14272.p1/NA18507


title: 14266.p1/NA18507


title: 14267.p1/NA18507


title: 14286.p1/NA18507


title: 14259.p1/NA18507


title: 14293.p1/NA18507


title: 14274.p1/NA12878


title: 14263.p1/NA18507


title: 14260.p1/NA18507


title: 14265.fa/NA18507


title: 14266.fa/NA18507


title: 14265.mo/NA12878


title: 14264.p1/NA18507


title: 14265.p1/NA18507


title: 14257.p1/NA18507


title: 14310.p1/NA18507


title: 14257.mo/NA12878


title: 14258.p1/NA18507


title: 14262.p1/NA18507


title: 14266.mo/NA12878


title: 14277.p1/NA18507


title: 14270.p1/NA12878


title: 14308.p1/NA18507


title: 14320.p1/NA12878


title: 14255.p1/NA18507


title: 14253.p1/NA18507


title: 14254.p1/NA18507


title: 14254.mo/NA12878


title: 14256.p1/NA18507


title: 14254.fa/NA18507


title: 14257.fa/NA18507


title: 14239.p1/NA18507


title: 14249.p1/NA18507


title: 14252.p1/NA18507


title: 14247.p1/NA18507


title: 14236.p1/NA18507


title: 14243.p1/NA18507


title: 14240.p1/NA18507


title: 14245.p1/NA12878


title: 14246.p1/NA18507


title: 14238.p1/NA18507


title: 14244.p1/NA18507


title: 14234.p1/NA18507


title: 14237.p1/NA18507


title: 14242.p1/NA18507


title: 14235.p1/NA18507


title: 14233.p1/NA18507


title: 14225.p1/NA18507


title: 14231.p1/NA18507


title: 14241.p1/NA12878


title: 14230.p1/NA18507


title: 14232.p1/NA12878


title: 14224.p1/NA18507


title: 14228.p1/NA18507


title: 14223.p1/NA18507


title: 14250.p1/NA18507


title: 14229.p1/NA12878


title: 14221.p1/NA12878


title: 14227.p1/NA18507


title: 14226.p1/NA18507


title: 14215.p1/NA12878


title: 14214.p1/NA18507


title: 14208.p1/NA18507


title: 14208.mo/NA12878


title: 14209.mo/NA12878


title: 14205.p1/NA18507


title: 14198.mo/NA12878


title: 14201.mo/NA12878


title: 14202.p1/NA18507


title: 14210.p1/NA18507


title: 14209.p1/NA18507


title: 14201.p1/NA18507


title: 14201.fa/NA18507


title: 14207.p1/NA12878


title: 14219.p1/NA18507


title: 14212.p1/NA18507


title: 14209.fa/NA18507


title: 14206.p1/NA12878


title: 14200.p1/NA12878


title: 14216.p1/NA18507


title: 14208.fa/NA18507


title: 14204.p1/NA12878


title: 14213.p1/NA18507


title: 14220.p1/NA18507


title: 14198.p1/NA18507


title: 14198.fa/NA18507


title: 14196.p1/NA18507


title: 14197.p1/NA18507


title: 14195.p1/NA18507


title: 14193.p1/NA18507


title: 14194.p1/NA18507


title: 14188.p1/NA18507


title: 14191.p1/NA18507


title: 14187.p1/NA18507


title: 14174.mo/NA12878


title: 14184.p1/NA18507


title: 14177.p1/NA18507


title: 14174.p1/NA18507


title: 14179.p1/NA18507


title: 14176.p1/NA18507


title: 14186.p1/NA18507


title: 14174.fa/NA18507


title: 14185.p1/NA18507


title: 14169.p1/NA18507


title: 14183.p1/NA18507


title: 14168.p1/NA18507


title: 14175.p1/NA18507


title: 14178.p1/NA18507


title: 14180.p1/NA18507


title: 14170.p1/NA18507


title: 14166.p1/NA18507


title: 14172.p1/NA18507


title: 14167.p1/NA18507


title: 14162.p1/NA18507


title: 14181.p1/NA18507


title: 14163.p1/NA18507


title: 14165.p1/NA18507


title: 14166.fa/NA18507


title: 14166.mo/NA12878


title: 14159.p1/NA18507


title: 14161.p1/NA18507


title: 14147.p1/NA18507


title: 14146.p1/NA18507


title: 14160.p1/NA18507


title: 14152.p1/NA18507


title: 14154.p1/NA18507


title: 14151.p1/NA18507


title: 14144.p1/NA12878


title: 14155.p1/NA18507


title: 14153.p1/NA12878


title: 14139.p1/NA18507


title: 14158.p1/NA12878


title: 14152.fa/NA18507


title: 14142.p1/NA18507


title: 14152.mo/NA12878


title: 14122.p1/NA18507


title: 14136.p1/NA18507


title: 14127.p1/NA12878


title: 14149.p1/NA18507


title: 14128.p1/NA12878


title: 14133.p1/NA12878


title: 14125.p1/NA18507


title: 14123.p1/NA18507


title: 14135.p1/NA18507


title: 14130.p1/NA18507


title: 14126.p1/NA18507


title: 14137.p1/NA18507


title: 14132.p1/NA18507


title: 14119.p1/NA18507


title: 14116.p1/NA18507


title: 14115.p1/NA18507


title: 14114.p1/NA18507


title: 14112.p1/NA12878


title: 14141.p1/NA18507


title: 14101.p1/NA12878


title: 14103.p1/NA18507


title: 14107.p1/NA12878


title: 14113.p1/NA18507


title: 14100.p1/NA18507


title: 14098.p1/NA12878


title: 14088.p1/NA18507


title: 14104.p1/NA18507


title: 14096.p1/NA18507


title: 14120.p1/NA18507


title: 14105.p1/NA12878


title: 14108.p1/NA18507


title: 14093.p1/NA18507


title: 14089.p1/NA12878


title: 14088.mo/NA12878


title: 14094.p1/NA12878


title: 14095.p1/NA18507


title: 14097.p1/NA18507


title: 14088.fa/NA18507


title: 14090.p1/NA18507


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title: 14084.p1/NA18507


title: 14082.p1/NA18507


title: 14084.fa/NA18507


title: 14081.p1/NA18507


title: 14070.p1/NA18507


title: 14079.fa/NA18507


title: 14079.p1/NA18507


title: 14079.mo/NA12878


title: 14076.p1/NA18507


title: 14080.p1/NA18507


title: 14111.p1/NA12878


title: 14070.mo/NA12878


title: 14071.p1/NA12878


title: 14074.p1/NA12878


title: 14068.p1/NA18507


title: 14118.p1/NA18507


title: 14072.p1/NA18507


title: 14071.p2/NA12878


title: 14061.p1/NA18507


title: 14077.p1/NA18507


title: 14063.p1/NA18507


title: 14065.p1/NA18507


title: 14060.p1/NA18507


title: 14059.p1/NA18507


title: 14078.p1/NA18507


title: 14075.p1/NA18507


title: 14058.p1/NA18507


title: 14059.fa/NA18507


title: 14084.mo/NA12878


title: 14109.p1/NA18507


title: 14070.fa/NA18507


title: 14056.p1/NA18507


title: 14054.p1/NA18507


title: 14049.p1/NA18507


title: 14050.p1/NA18507


title: 14055.p1/NA18507


title: 14055.mo/NA12878


title: 14057.p1/NA18507


title: 14055.fa/NA18507


title: 14053.fa/NA18507


title: 14045.p1/NA18507


title: 14059.mo/NA12878


title: 14051.p1/NA18507


title: 14046.mo/NA12878


title: 14066.p1/NA18507


title: 14053.mo/NA12878


title: 14046.fa/NA18507


title: 14048.p1/NA18507


title: 14047.p1/NA18507


title: 14043.p1/NA18507


title: 14045.fa/NA18507


title: 14073.p1/NA18507


title: 14046.p1/NA18507


title: 14042.p1/NA12878


title: 14044.p1/NA18507


title: 14039.p1/NA18507


title: 14045.mo/NA12878


title: 14038.p1/NA18507


title: 14037.p1/NA18507


title: 14034.p1/NA18507


title: 14053.p1/NA18507


title: 14036.p1/NA18507


title: 14030.p1/NA18507


title: 14035.p1/NA12878


title: 14032.mo/NA12878


title: 14031.mo/NA12878


title: 14032.p1/NA18507


title: 14033.p1/NA18507


title: 14032.fa/NA18507


title: 14031.p1/NA18507


title: 14025.p1/NA12878


title: 14029.p1/NA18507


title: 14019.p1/NA12878


title: 14021.p1/NA18507


title: 14019.mo/NA12878


title: 14018.p1/NA18507


title: 14028.p1/NA18507


title: 14022.p1/NA18507


title: 14027.p1/NA12878


title: 14017.p1/NA18507


title: 14031.fa/NA18507


title: 14026.p1/NA18507


title: 14018.mo/NA12878


title: 14018.fa/NA18507


title: 14019.fa/NA18507


title: 14011.p1/NA12878


title: 14013.mo/NA12878


title: 14016.p1/NA18507


title: 14015.p1/NA18507


title: 14023.p1/NA18507


title: 14016.fa/NA18507


title: 14009.p1/NA12878


title: 14011.mo/NA12878


title: 14016.mo/NA12878


title: 14012.p1/NA18507


title: 14010.p1/NA18507


title: 14013.p1/NA18507


title: 14011.fa/NA18507


title: 14007.p1/NA18507


title: 14006.p1/NA12878


title: 14006.mo/NA12878


title: 14004.fa/NA18507


title: 14004.mo/NA12878


title: 13999.p1/NA18507


title: 14013.fa/NA18507


title: 14008.p1/NA18507


title: 14003.p1/NA18507


title: 13995.mo/NA12878


title: 14002.p1/NA18507


title: 13995.fa/NA18507


title: 13998.p1/NA18507


title: 13997.p1/NA18507


title: 13993.p1/NA18507


title: 13990.fa/NA18507


title: 13988.fa/NA18507


title: 13990.mo/NA12878


title: 13987.p1/NA18507


title: 13992.p1/NA12878


title: 13988.p1/NA18507


title: 14004.p1/NA18507


title: 13990.p1/NA18507


title: 13996.p1/NA18507


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title: 12630.mo/NA12878


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title: 12628.p1/NA18507


title: 12637.p1/NA18507


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title: 12604.p1/NA18507


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title: 12555.mo/NA12878


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title: 12521.p1/NA12878


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title: 12484.p1/NA18507


title: 12467.p1/NA18507


title: 12510.p1/NA18507


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title: 12449.p1/NA18507


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title: 12441.p1/NA18507


title: 12435.p1/NA18507


title: 12444.p1/NA12878


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title: 12430.p1/NA12878


title: 12432.p1/NA18507


title: 12437.mo/NA12878


title: 12432.mo/NA12878


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title: 12439.p1/NA18507


title: 12445.p1/NA18507


title: 12430.mo/NA12878


title: 12430.fa/NA18507


title: 12432.fa/NA18507


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title: 12426.p1/NA18507


title: 12420.p1/NA18507


title: 12418.p1/NA18507


title: 12424.p1/NA18507


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title: 12396.p1/NA18507


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title: 12395.p1/NA18507


title: 12388.p1/NA12878


title: 12381.mo/NA12878


title: 12399.p1/NA12878


title: 12384.p1/NA12878

value: unknown


title: 12381.p1/NA12878


title: 12383.p1/NA12878


title: 12390.fa/NA18507


title: 12382.p1/NA12878


title: 12379.p1/NA18507


title: 12385.p1/NA12878


title: 12378.fa/NA18507


title: 12378.p1/NA12878


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title: 12375.p1/NA18507


title: 12376.p1/NA12878


title: 12366.p1/NA12878


title: 12378.mo/NA12878


title: 12376.fa/NA18507


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title: 12370.p1/NA12878


title: 12359.p1/NA12878


title: 12362.p1/NA18507


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title: 12373.mo/NA12878


title: 12370.mo/NA12878


title: 12370.fa/NA18507


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title: 12361.p1/NA12878


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title: 12358.mo/NA12878


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title: 12317.p1/NA18507


title: 12310.p2/NA18507


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title: 12315.p1/NA18507


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title: 12302.p1/NA12878


title: 12304.mo/NA12878


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title: 12300.mo/NA12878


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title: 12301.p1/NA18507


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title: 12295.p1/NA12878


title: 12297.p1/NA12878


title: 12296.mo/NA12878


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title: 12296.fa/NA18507


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title: 12284.p1/NA18507


title: 12285.fa/NA18507


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title: 12287.p1/NA18507


title: 12260.p1/NA18507


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title: 12285.p1/NA12878


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title: 12246.p1/NA12878


title: 12238.mo/NA12878


title: 12239.p1/NA12878


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title: 12228.p1/NA12878


title: 12245.p1/NA12878


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title: 12233.fa/NA18507


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title: 12161.mo/NA12878


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title: 12153.mo/NA12878


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title: 12160.p1/NA18507


title: 12161.p1/NA12878


title: 12153.p1/NA12878


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title: 12032.mo/NA12878


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title: 12028.p1/NA18507


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title: 11981.p1/NA12878


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title: 11925.p1/NA18507


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title: 11913.p1/NA12878


title: 11913.fa/NA18507


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title: 11919.p1/NA12878


title: 11913.mo/NA12878


title: 11910.p1/NA18507


title: 11916.p1/NA12878


title: 11928.p1/NA12878


title: 11888.p1/NA12878


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title: 11893.p1/NA12878


title: 11881.p1/NA12878


title: 11895.p1/NA12878


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title: 11905.p1/NA12878


title: 11879.p1/NA12878


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title: 11872.p1/NA12878


title: 11883.p1/NA12878


title: 11860.p1/NA12878


title: 11872.mo/NA12878


title: 11872.fa/NA18507


title: 11857.p1/NA12878


title: 11868.p1/NA18507


title: 11869.p1/NA12878


title: 11863.p1/NA12878


title: 11863.mo/NA12878


title: 11855.p1/NA12878


title: 11863.fa/NA18507


title: 11895.fa/NA18507


title: 11859.p1/NA18507


title: 11851.p1/NA18507


title: 11846.p1/NA18507


title: 11839.p1/NA12878


title: 11842.p1/NA18507


title: 11845.p1/NA12878


title: 11838.mo/NA12878


title: 11843.fa/NA18507


title: 11843.p1/NA12878


title: 11843.mo/NA12878


title: 11835.p1/NA12878


title: 11838.fa/NA18507


title: 11834.mo/NA12878


title: 11828.p1/NA12878


title: 11811.p1/NA18507


title: 11818.p1/NA18507


title: 11834.p1/NA18507


title: 11834.fa/NA18507


title: 11824.p1/NA12878


title: 11808.p1/NA12878


title: 11827.mo/NA12878


title: 11831.p1/NA18507


title: 11827.fa/NA18507


title: 11804.p1/NA12878


title: 11827.p1/NA12878


title: 11806.p1/NA18507


title: 11829.p1/NA18507


title: 11800.p1/NA12878


title: 11810.p1/NA12878


title: 11838.p1/NA18507


title: 11809.p1/NA12878


title: 11825.p1/NA18507


title: 11794.p1/NA18507


title: 11788.p1/NA12878


title: 11788.mo/NA12878


title: 11781.p1/NA18507


title: 11782.p1/NA12878


title: 11797.p1/NA12878


title: 11792.p1/NA12878


title: 11788.fa/NA18507


title: 11783.p1/NA18507


title: 11776.p1/NA18507


title: 11793.p1/NA12878


title: 11768.mo/NA12878


title: 11768.fa/NA18507


title: 11773.p1/NA12878


title: 11773.fa/NA18507


title: 11753.fa/NA18507


title: 11756.mo/NA12878


title: 11780.p1/NA18507


title: 11740.p1/NA18507


title: 11753.p1/NA12878


title: 11756.p1/NA12878


title: 11765.p1/NA12878


title: 11734.p1/NA12878


title: 11766.p1/NA12878


title: 11772.p1/NA18507


title: 11733.p1/NA12878


title: 11768.p1/NA18507


title: 11753.mo/NA12878


title: 11756.fa/NA18507


title: 11773.mo/NA12878


title: 11734.fa/NA18507


title: 11723.p1/NA12878


title: 11729.p1/NA12878


title: 11736.p1/NA12878


title: 11731.p1/NA12878


title: 11722.mo/NA12878


title: 11724.p1/NA12878


title: 11734.mo/NA12878


title: 11726.p1/NA18507


title: 11722.p1/NA18507


title: 11721.p1/NA12878


title: 11722.fa/NA18507


title: 11720.p1/NA12878


title: 11715.mo/NA12878


title: 11718.p1/NA12878


title: 11710.mo/NA12878


title: 11710.fa/NA18507


title: 11710.p1/NA18507


title: 11707.mo/NA12878


title: 11714.p1/NA12878


title: 11716.p1/NA18507


title: 11715.fa/NA18507


title: 11700.p1/NA12878


title: 11715.p1/NA12878


title: 11709.p1/NA12878


title: 11707.p1/NA12878


title: 11712.p1/NA12878


title: 11711.fa/NA18507


title: 11711.mo/NA12878


title: 11691.fa/NA18507


title: 11707.fa/NA18507


title: 11696.mo/NA12878


title: 11704.p1/NA18507


title: 11696.fa/NA18507


title: 11679.p1/NA12878


title: 11711.p1/NA18507


title: 11685.p1/NA12878


title: 11681.p1/NA18507


title: 11691.p1/NA12878


title: 11696.p1/NA12878


title: 11676.p1/NA12878


title: 11693.p1/NA18507


title: 11689.p1/NA18507


title: 11673.p1/NA12878


title: 11677.p1/NA18507


title: 11665.p1/NA12878


title: 11666.p1/NA12878


title: 11660.p1/NA12878


title: 11664.p2/NA18507


title: 11671.p1/NA12878


title: 11657.p1/NA12878


title: 11691.mo/NA12878


title: 11659.mo/NA12878


title: 11654.p1/NA12878


title: 11660.fa/NA18507


title: 11653.p1/NA18507


title: 11667.p1/NA12878


title: 11659.p1/NA12878


title: 11651.fa/NA18507


title: 11659.fa/NA18507


title: 11642.p1/NA12878


title: 11638.mo/NA12878


title: 11651.mo/NA12878


title: 11641.p1/NA12878


title: 11653.fa/NA18507


title: 11653.mo/NA12878


title: 11638.fa/NA18507


title: 11645.p1/NA12878


title: 11651.p1/NA18507


title: 11644.p1/NA12878


title: 11630.p1/NA12878


title: 11629.p1/NA18507


title: 11634.fa/NA18507


title: 11634.mo/NA12878


title: 11660.mo/NA12878


title: 11638.p1/NA18507


title: 11627.p1/NA12878


title: 11619.p1/NA18507


title: 11621.p1/NA18507


title: 11622.p1/NA12878


title: 11616.p1/NA12878


title: 11620.p1/NA12878


title: 11610.p1/NA12878


title: 11634.p1/NA12878


title: 11629.mo/NA12878


title: 11610.mo/NA12878


title: 11625.p1/NA12878


title: 11608.p1/NA18507


title: 11601.p1/NA18507


title: 11609.p1/NA18507


title: 11600.p1/NA12878


title: 11601.fa/NA18507


title: 11604.p1/NA12878


title: 11615.p1/NA18507


title: 11629.fa/NA18507


title: 11612.p1/NA18507


title: 11599.p1/NA18507


title: 11601.mo/NA12878


title: 11599.mo/NA12878


title: 11610.fa/NA18507


title: 11599.fa/NA18507


title: 11611.p1/NA12878


title: 11587.mo/NA12878


title: 11592.p1/NA12878


title: 11575.p1/NA12878


title: 11584.p1/NA18507


title: 11581.p1/NA12878


title: 11590.p1/NA18507


title: 11577.p1/NA18507


title: 11587.p1/NA18507


title: 11571.fa/NA18507


title: 11566.p1/NA18507


title: 11571.mo/NA12878


title: 11571.p1/NA12878


title: 11580.p1/NA12878


title: 11569.mo/NA12878


title: 11569.fa/NA18507


title: 11587.fa/NA18507


title: 11569.p1/NA12878


title: 11565.p1/NA18507


title: 11572.p1/NA12878


title: 11597.p1/NA12878


title: 11561.p1/NA12878


title: 11573.p1/NA12878


title: 11567.p1/NA12878


title: 11563.p1/NA12878


title: 11558.mo/NA12878


title: 11568.p1/NA12878


title: 11578.p1/NA12878


title: 11556.fa/NA18507


title: 11558.p1/NA12878


title: 11558.fa/NA18507


title: 11550.p1/NA18507


title: 11556.mo/NA12878


title: 11556.p1/NA12878


title: 11549.p1/NA12878


title: 11551.p1/NA12878


title: 11545.mo/NA12878


title: 11544.p1/NA12878


title: 11552.p1/NA18507


title: 11555.p1/NA12878


title: 11549.mo/NA12878


title: 11557.p1/NA12878


title: 11549.fa/NA18507


title: 11546.p1/NA12878


title: 11545.p1/NA12878


title: 11543.fa/NA18507


title: 11540.p1/NA12878


title: 11540.mo/NA12878


title: 11543.p1/NA12878


title: 11542.p1/NA12878


title: 11545.fa/NA18507


title: 11538.p1/NA18507


title: 11540.fa/NA18507


title: 11543.mo/NA12878


title: 11535.p1/NA12878


title: 11529.p1/NA12878


title: 11526.p1/NA18507


title: 11530.p1/NA12878


title: 11526.fa/NA18507


title: 11532.p1/NA12878


title: 11524.p1/NA12878


title: 11526.mo/NA12878


title: 11537.p1/NA12878


title: 11523.fa/NA18507


title: 11521.p1/NA12878


title: 11520.p1/NA12878


title: 11523.mo/NA12878


title: 11518.mo/NA12878


title: 11519.p1/NA12878


title: 11518.p1/NA18507


title: 11536.p1/NA12878


title: 11508.p1/NA12878


title: 11518.fa/NA18507


title: 11522.p1/NA12878


title: 11506.fa/NA18507


title: 11510.p1/NA12878


title: 11516.p1/NA18507


title: 11510.fa/NA18507


title: 11512.p1/NA12878


title: 11523.p1/NA12878


title: 11554.p1/NA12878


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title: 11505.p1/NA12878


title: 11510.mo/NA12878


title: 11506.mo/NA12878


title: 11504.mo/NA12878


title: 11511.p1/NA12878


title: 11501.p1/NA18507


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title: 11499.p1/NA12878


title: 11498.p1/NA12878


title: 11506.p1/NA12878


title: 11504.fa/NA18507


title: 11498.fa/NA18507


title: 11502.p1/NA12878


title: 11494.p1/NA12878


title: 11490.p1/NA12878


title: 11498.mo/NA12878


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title: 11491.mo/NA12878


title: 11484.p1/NA18507


title: 11479.mo/NA12878


title: 11480.mo/NA12878


title: 11485.p1/NA18507


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title: 11483.p1/NA18507


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title: 11497.p1/NA12878


title: 11475.p1/NA12878


title: 11480.fa/NA18507


title: 11480.p1/NA12878


title: 11474.p1/NA12878


title: 11471.mo/NA12878


title: 11488.p1/NA12878


title: 11471.fa/NA18507


title: 11471.p1/NA18507


title: 11473.p1/NA12878


title: 11470.p1/NA12878


title: 11496.p1/NA12878


title: 11476.p1/NA12878


title: 11472.mo/NA12878


title: H. pylori pH 7.4 rep11

city: Los Angeles

first: David

last: Scott

state: CA

address: 11301 Wilshire Blvd

institute: UCLA/VA GLAHS

description: Gene expression after 4  hrs incubation in pH 7.4 media

hyb_protocol: To prepare the cRNA for hybridization the Agilent Fragmentation mix was used according to the Quick Amp Protocol. After a 30 minute incubation period at 60º C, 55uL of 2x GE Hybridization Buffer HI-RPM was added to each reaction tube. Samples were then vortexed and briefly spun for 1 minute at 13,000 RPM to collect the sample at the bottom of the tube. Samples were then loaded onto the microarray slides and incubated in a hybridization chamber for 17 hours at 65 º C. The preparation was then washed with Agilent’s Gene Expression Wash Buffer 1 and 2 (with Triton X) according to the protocol and scanned using the DNA Microarray Scanner11.0.2.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20101102) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were filtered by expression (20-100%) using GeneSpring GX Software 11.5.1. All data with at least a two- fold change compared to control were subjected to a T-test. Only those genes whose expression was altered by at least 2 fold with a P-value less than 0.05 were considered to represent significantly regulated genes.
Normalized signal intensity of genes filtered by expression (20%-100%) with a fold-change greater than 2.0 and were significant after subjected to a T-test.

organism: Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093

source_name: H. pylori ATCC 53504, pH 7.4, 4 hours

label_protocol: All total RNA samples were serially diluted to a concentration of 1000ng in 5.3uL for use with the Quick Amp Labeling kit (Agilent, Santa Clara). In preparation for the microarray, the Agilent One-Color Spike-In Kit was used as a positive control. As per the manufacturer's protocol, known synthetic RNAs were added to the sample RNA isolated from cells exposed to pH 3.0 or 7.4 and amplified and labeled using the Quick Amp Labeling kit protocol.

growth_protocol: H. pylori strain ATCC 43504 was used. Bacteria were grown under microaerobic conditions (5% O2, 10% CO2, 85% N2) either on Trypticase Soy Agar (TSA) plates supplemented with 5% sheep blood (Gibco) or in brain heart infusion (BHI) medium (Difco) supplemented with 7% horse serum (Gibco), 0.25% yeast extract (Difco) and Dent selective supplement (Oxoid).

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, California) combined with RNeasy columns (Qiagen, Valencia, California) .

treatment_protocol: Bacteria harvested from TSA plates (1 x 108) were suspended in 3mL of BHI and injected into a sterile Slide-A-Lyzer® Dialysis Chamber (Pierce), then placed in 1,500mL of BHI containing 7% horse serum, 0.25% yeast extract and 5mM urea with pH adjusted to 3.0 or 7.4 and incubated for 4 hours.

tag: ph


title: 11479.fa/NA18507


title: 11469.mo/NA12878


title: 11472.p1/NA12878


title: 11469.p1/NA12878


title: 11472.fa/NA18507


title: H. pylori pH 7.4 rep9


title: H. pylori pH 7.4 rep10


title: 11466.p1/NA12878


title: H. pylori pH 7.4 rep6


title: H. pylori pH 7.4 rep8


title: H. pylori pH 7.4 rep7


title: H. pylori pH 7.4 rep4


title: 11468.p1/NA18507


title: H. pylori pH 7.4 rep3


title: H. pylori pH 7.4 rep5


title: H. pylori pH 7.4 rep2


title: Patient_#65_IgG

type: other

city: Budapest

first: Krisztian

last: Papp

address: 1/C Pazmany P.

country: Hungary

institute: MTA-ELTE Immunology Research Group

hyb_protocol: Probe: APC-conjugated F(ab')2 fragment goat anti-human IgG

scan_protocol: Arrays were scanned on Typhoon Trio+ imager (Amersham Bioscience) (Excitation:633nm ; Emission: 670BP, PMT:420 Mode:Fluorescence, Sensitivity:Normal, FocalPlane=+3 mm). Data were analyzed with GenePix Pro 6 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
Local background of spot was substracted from the value of signal. The value of signal is set to zero if it is lower than 2*SD of local backgrounds on the given chip. For interassay comparison, data were normalized to the mean of 5 times diluted human IgG control material (ID_REF: #388, #389, #390).
Normalization procedure was carried out with Microsoft Office Exel software

label: APC

molecule: other

source_name: serum

label_protocol: Antigens were spotted onto nitrocellulose-covered FAST slides  (GE Healthcare) using BioOdyssey Calligrapher miniarrayer (BioRad). Features were printed in triplicates of 1:5 serial dilutions then stored at 4°C in sealed bags. Dried arrays were rinsed in PBS for 15 minutes before use, then incubated with diluted serum at 37°C for 1 hour, providing suitable conditions for complement activation. For each patient 5- times diluted serum was used in two different arrays for the detection of bound C3-IgM and IgG-C4. Sera were diluted in 5% BSA, 0.05% Tween 20, Ca and Mg supplemented Veronal buffer. Serum treated slides were washed with 0.05% Tween 20 containing PBS, then incubated in the mixture of 1:5000 diluted Alexa647-conjugated  F(ab')2 fragment goat anti-human C3 antibody (Cappel) and 1:5000 diluted Cy3-conjugated F(ab')2 fragment goat anti-human IgM (mu chain speific) (Jackson ImmunoResearch) or 1:2500 diluted FITC-conjugated goat anti-human C4 (Cappel) and 1:2500 diluted APC-conjugated F(ab')2 fragment goat anti-human IgG (gamma chain specific) (Jackson ImmunoResearch).Labeling with fluorescent antibodies was carried out at room temperature for 30 min in 5% BSA and 0.05% Tween 20 containing PBS. Following washing in 0.05% Tween 20 containing PBS, arrays were dried and scanned.

extract_protocol: Serum sample was centrifuged for 6min at 15000g for removing particles

treatment_protocol: Serum samples were stored at -70C

tag: Sex

value: Female

tag: sle (yes/no)

value: Yes


title: H. pylori pH 7.4 rep1


title: Patient_#63_IgG


title: Patient_#62_IgG


title: 11462.p1/NA12878


title: 11463.p1/NA12878


title: H. pylori pH 3.0 rep10

description: Gene expression after 4  hrs incubation in pH 3.0 media

source_name: H. pylori ATCC 53504, pH 3.0, 4 hours


title: 11464.p1/NA18507


title: H. pylori pH 3.0 rep11


title: 11452.p1/NA12878


title: 11469.fa/NA18507


title: Patient_#61_IgG


title: Patient_#60_IgG


title: 11459.mo/NA12878


title: Patient_#59_IgG


title: Patient_#66_IgG


title: H. pylori pH 3.0 rep8


title: 11459.fa/NA18507


title: 11453.p1/NA12878


title: Patient_#58_IgG


title: 11452.fa/NA18507


title: Patient_#57_IgG


title: 11456.p1/NA12878


title: H. pylori pH 3.0 rep6


title: H. pylori pH 3.0 rep5


title: Patient_#56_IgG


title: 11452.mo/NA12878


title: Patient_#64_IgG


title: Patient_#54_IgG


title: Patient_#53_IgG

value: Male


title: 11458.p1/NA12878


title: H. pylori pH 3.0 rep7


title: 11459.p1/NA18507


title: H. pylori pH 3.0 rep4


title: Patient_#52_IgG


title: H. pylori pH 3.0 rep3


title: Patient_#50_IgG


title: Patient_#51_IgG


title: Patient_#49_IgG


title: Patient_#44_IgG


title: Patient_#45_IgG


title: Patient_#46_IgG


title: Patient_#47_IgG


title: Patient_#48_IgG


title: Patient_#55_IgG


title: H. pylori pH 3.0 rep2


title: Patient_#41_IgG


title: Patient_#42_IgG


title: Patient_#43_IgG


title: Patient_#19_IgG


title: Patient_#21_IgG


title: Patient_#20_IgG


title: H. pylori pH 3.0 rep9


title: Patient_#16_IgG


title: Patient_#18_IgG


title: Patient_#17_IgG


title: 11455.p1/NA12878


title: H. pylori pH 3.0 rep1


title: 11450.p1/NA18507


title: Patient_#15_IgG


title: Patient_#13_IgG


title: Patient_#14_IgG


title: Patient_#11_IgG


title: Patient_#10_IgG


title: Patient_#9_IgG


title: Patient_#8_IgG


title: Patient_#7_IgG


title: 11446.p1/NA18507


title: Patient_#12_IgG


title: Patient_#6_IgG


title: 11440.p1/NA12878


title: 11433.p1/NA12878


title: Patient_#5_IgG


title: 11431.p1/NA18507


title: Patient_#4_IgG


title: 11432.p1/NA12878


title: 11444.p1/NA12878


title: 11441.p1/NA12878


title: 11447.p1/NA12878


title: 11447.fa/NA18507


title: Patient_#3_IgG


title: 11436.p1/NA12878


title: 11433.mo/NA12878


title: Patient_#2_IgG


title: 11433.fa/NA18507


title: 11429.p1/NA12878


title: 11435.p1/NA18507


title: 11437.p1/NA12878


title: 11445.p1/NA18507


title: 11425.mo/NA12878


title: Patient_#230_C4

hyb_protocol: Probe: FITC-conjugated goat anti-human C4

scan_protocol: Arrays were scanned on Typhoon Trio+ imager (Amersham Bioscience) (Excitation:488nm ; Emission: 526SP, PMT:420 Mode:Fluorescence, Sensitivity:Normal, FocalPlane=+3 mm). Data were analyzed with GenePix Pro 6 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
Local background of spot was substracted from the value of signal. The value of signal is set to zero if it is lower than 2*SD of local backgrounds on the given chip. For interassay comparison, data were normalized to the mean of 5 times diluted Protein G control material (ID_REF: #52, #53, #54).
Normalization procedure was carried out with Microsoft Office Exel software

label: FITC

value: No


title: Patient_#229_C4


title: 11425.fa/NA18507


title: Patient_#1_IgG


title: Patient_#227_C4


title: Patient_#228_C4


title: Patient_#226_C4


title: Patient_#225_C4


title: Patient_#222_C4


title: Patient_#221_C4


title: 11421.p1/NA18507


title: 11417.p1/NA18507


title: 11422.p1/NA18507


title: 11425.p1/NA12878


title: Patient_#224_C4


title: Patient_#220_C4


title: 11447.mo/NA12878


title: Patient_#219_C4


title: Patient_#218_C4


title: 11414.fa/NA18507


title: Patient_#217_C4


title: 11422.fa/NA18507


title: Patient_#216_C4


title: 11422.mo/NA12878


title: Patient_#215_C4


title: Patient_#214_C4


title: 11412.p1/NA12878


title: 11424.p1/NA12878


title: Patient_#213_C4


title: Patient_#212_C4


title: Patient_#223_C4


title: 11413.p1/NA12878


title: Patient_#211_C4


title: 11414.mo/NA12878


title: Patient_#210_C4


title: Patient_#209_C4


title: Patient_#208_C4


title: Patient_#207_C4


title: 11415.p1/NA18507


title: Patient_#206_C4


title: 11414.p1/NA12878


title: 11411.p1/NA12878


title: 11400.p1/NA12878


title: 11404.p1/NA12878


title: 11401.p1/NA12878


title: Patient_#205_C4


title: 11406.mo/NA12878


title: 11407.p1/NA12878


title: 11398.fa/NA18507


title: Patient_#204_C4


title: 11398.mo/NA12878


title: Patient_#203_C4


title: 11406.fa/NA18507


title: Patient_#202_C4


title: 11397.p1/NA12878


title: Patient_#201_C4


title: 11409.p1/NA18507


title: Patient_#200_C4


title: Patient_#80_C4


title: 11396.fa/NA18507


title: 11396.mo/NA12878


title: 11406.p1/NA12878


title: 11398.p1/NA18507


title: 11396.p1/NA18507


title: 11394.p1/NA18507


title: Patient_#79_C4


title: 11395.p1/NA18507


title: Patient_#77_C4


title: 11390.p1/NA12878


title: 11393.p1/NA12878


title: Patient_#76_C4


title: 11410.p1/NA12878


title: Patient_#74_C4


title: Patient_#73_C4


title: Patient_#75_C4


title: Patient_#72_C4


title: Patient_#71_C4


title: 11391.p1/NA18507


title: 11390.mo/NA12878


title: Patient_#78_C4


title: 11390.fa/NA18507


title: Patient_#69_C4


title: Patient_#70_C4


title: 11388.p1/NA18507


title: Patient_#67_C4


title: Patient_#65_C4


title: 11387.p1/NA18507


title: Patient_#64_C4


title: 11386.p1/NA12878


title: 11388.mo/NA12878


title: Patient_#68_C4


title: 11383.p1/NA12878


title: 11381.p1/NA12878


title: Patient_#66_C4


title: Patient_#62_C4


title: 11380.p1/NA18507


title: Patient_#61_C4


title: Patient_#63_C4


title: 11388.fa/NA18507


title: 11378.p1/NA12878


title: 11383.mo/NA12878


title: Patient_#60_C4


title: 11382.p1/NA18507


title: 11376.p1/NA18507


title: 11375.p1/NA18507


title: Patient_#59_C4


title: 11375.mo/NA12878


title: Patient_#58_C4


title: Patient_#54_C4


title: Patient_#57_C4


title: 11375.fa/NA18507


title: 11374.p1/NA12878


title: Patient_#56_C4


title: 11372.p1/NA12878


title: Patient_#55_C4


title: 11379.p1/NA12878


title: 11371.p1/NA18507


title: Patient_#52_C4


title: 11368.p1/NA12878


title: Patient_#53_C4


title: Patient_#50_C4


title: Patient_#51_C4


title: Patient_#49_C4


title: Patient_#47_C4


title: 11370.p2/NA18507


title: Patient_#48_C4


title: Patient_#46_C4


title: 11365.p1/NA12878


title: 11364.fa/NA18507


title: 11366.p1/NA12878


title: 11370.p1/NA18507


title: Patient_#45_C4


title: 11367.p1/NA12878


title: Patient_#43_C4


title: Patient_#41_C4


title: Patient_#21_C4


title: Patient_#42_C4


title: Patient_#20_C4


title: 11364.mo/NA12878


title: 11360.p1/NA12878


title: 11356.p1/NA12878


title: 11364.p1/NA18507


title: 11363.p1/NA12878


title: Patient_#18_C4


title: 11357.p1/NA12878


title: Patient_#17_C4


title: 11359.p1/NA12878


title: Patient_#16_C4


title: 11355.p1/NA12878


title: Patient_#15_C4


title: 11352.p1/NA18507


title: Patient_#19_C4


title: Patient_#14_C4


title: 11349.p1/NA12878


title: 11353.p1/NA12878


title: Patient_#13_C4


title: 11347.p1/NA12878


title: Patient_#44_C4


title: 11345.p1/NA12878


title: Patient_#8_C4


title: 11348.p1/NA12878


title: Patient_#12_C4


title: Patient_#11_C4


title: 11346.mo/NA12878


title: Patient_#9_C4


title: Patient_#7_C4


title: 11336.p1/NA12878


title: 11350.p1/NA12878


title: 11339.p1/NA12878


title: Patient_#5_C4


title: Patient_#4_C4


title: 11334.p1/NA12878


title: 11330.p1/NA12878


title: 11346.p1/NA18507


title: 11333.p1/NA18507


title: 11329.p1/NA12878


title: 11328.p1/NA12878


title: 11341.p1/NA12878


title: 11346.fa/NA18507


title: Patient_#2_C4


title: 11324.fa/NA18507


title: Patient_#1_C4


title: 11327.p1/NA18507


title: Patient_#228_IgM

hyb_protocol: Probe: Cy3-conjugated F(ab')2 fragment goat anti-human IgM

scan_protocol: Arrays were scanned on Typhoon Trio+ imager (Amersham Bioscience) (Excitation:532nm ; Emission: 580BP, PMT:420 Mode:Fluorescence, Sensitivity:Normal, FocalPlane=+3 mm). Data were analyzed with GenePix Pro 6 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
Local background of spot was substracted from the value of signal. The value of signal is set to zero if it is lower than 2*SD of local backgrounds on the given chip. For interassay comparison, data were normalized to the mean of 5 times diluted F(ab)2 Goat anti-human IgM  control material (ID_REF: #373, #374, #375).
Normalization procedure was carried out with Microsoft Office Exel software


title: 11324.p2/NA12878


title: Patient_#227_IgM


title: Patient_#226_IgM


title: Patient_#225_IgM


title: Patient_#10_C4


title: 11324.p1/NA12878


title: Patient_#230_IgM


title: 11318.p1/NA12878


title: Patient_#224_IgM


title: Patient_#223_IgM


title: 11325.p1/NA18507


title: 11316.p1/NA12878


title: Patient_#222_IgM


title: Patient_#221_IgM


title: 11324.mo/NA12878


title: 11321.p1/NA12878


title: 11322.p1/NA18507


title: 11310.p1/NA18507


title: 11323.p1/NA12878


title: Patient_#219_IgM


title: Patient_#218_IgM


title: 11309.p1/NA18507


title: Patient_#229_IgM


title: Patient_#3_C4


title: 11307.p1/NA12878


title: 11303.p1/NA12878


title: Patient_#217_IgM


title: 11306.p1/NA12878


title: Patient_#6_C4


title: Patient_#214_IgM


title: Patient_#211_IgM


title: Patient_#213_IgM


title: Patient_#216_IgM


title: Patient_#215_IgM


title: 11304.p1/NA12878


title: Patient_#212_IgM


title: 11298.p1/NA12878


title: 11312.p1/NA12878


title: Patient_#210_IgM


title: 11308.p1/NA18507


title: 11303.mo/NA12878


title: Patient_#209_IgM


title: 11299.p1/NA12878


title: Patient_#220_IgM


title: Patient_#208_IgM


title: Patient_#206_IgM


title: Patient_#205_IgM


title: Patient_#207_IgM


title: Patient_#204_IgM


title: Patient_#201_IgM


title: Patient_#203_IgM


title: Patient_#80_IgM


title: Patient_#79_IgM


title: Patient_#200_IgM


title: Patient_#202_IgM


title: 11301.p1/NA12878


title: 11300.p1/NA18507


title: Patient_#78_IgM


title: 11303.fa/NA18507


title: 11305.p1/NA18507


title: Patient_#76_IgM


title: 11291.p1/NA12878


title: Patient_#75_IgM


title: 11297.p1/NA18507


title: 11291.mo/NA12878


title: 11296.p1/NA12878


title: Patient_#74_IgM


title: Patient_#73_IgM


title: 11291.fa/NA18507


title: 11282.mo/NA12878


title: 11282.p1/NA12878


title: 11285.p1/NA12878


title: 11277.p1/NA12878


title: Patient_#77_IgM


title: 11289.p1/NA18507


title: 11290.p1/NA12878


title: Patient_#70_IgM


title: Patient_#71_IgM


title: 11263.p1/NA12878


title: 11284.p1/NA12878


title: 11267.p1/NA12878


title: 11270.p1/NA12878


title: Patient_#72_IgM


title: 11276.p1/NA12878


title: 11266.p1/NA12878


title: 11262.mo/NA12878


title: 11274.p1/NA12878


title: 11282.fa/NA18507


title: 11280.p1/NA12878


title: Patient_#68_IgM


title: 11294.p1/NA18507


title: Patient_#66_IgM


title: 11258.p1/NA12878


title: 11262.p1/NA12878


title: Patient_#67_IgM


title: Patient_#69_IgM


title: Patient_#64_IgM


title: Patient_#62_IgM


title: Patient_#60_IgM


title: Patient_#58_IgM


title: Patient_#61_IgM


title: Patient_#57_IgM


title: Patient_#65_IgM


title: Patient_#56_IgM


title: Patient_#55_IgM


title: Patient_#54_IgM


title: Patient_#53_IgM


title: Patient_#59_IgM


title: Patient_#52_IgM


title: Patient_#63_IgM


title: Patient_#51_IgM


title: 11265.p1/NA12878


title: 11257.p1/NA12878


title: 11262.fa/NA18507


title: Patient_#49_IgM


title: Patient_#50_IgM


title: 11257.fa/NA18507


title: Patient_#48_IgM


title: 11256.p1/NA12878


title: Patient_#46_IgM


title: 11257.mo/NA12878


title: 11255.p1/NA18507


title: 11254.p1/NA12878


title: Patient_#45_IgM


title: Patient_#44_IgM


title: 11250.p1/NA18507


title: Patient_#47_IgM


title: Patient_#43_IgM


title: 11251.p1/NA12878


title: Patient_#42_IgM


title: 11234.fa/NA18507


title: 11252.p1/NA12878


title: 11233.fa/NA18507


title: 11233.p1/NA12878


title: 11235.p1/NA12878


title: 11234.p1/NA18507


title: 11246.mo/NA12878


title: Patient_#41_IgM


title: 11246.p1/NA12878


title: 11232.p1/NA12878


title: 11236.p1/NA12878


title: 11242.p1/NA12878


title: Patient_#21_IgM


title: 11246.fa/NA18507


title: Patient_#20_IgM


title: 11245.p1/NA18507


title: 11249.p1/NA18507


title: 11241.p1/NA12878


title: 11247.p1/NA12878


title: 11239.p1/NA12878


title: Patient_#19_IgM


title: 11234.mo/NA12878


title: Patient_#18_IgM


title: 11229.mo/NA12878


title: Patient_#17_IgM


title: Patient_#15_IgM


title: 11233.mo/NA12878


title: Patient_#16_IgM


title: Patient_#14_IgM


title: Patient_#11_IgM


title: Patient_#12_IgM


title: 11229.p1/NA12878


title: 11229.fa/NA18507


title: Patient_#8_IgM


title: Patient_#7_IgM


title: Patient_#6_IgM


title: Patient_#9_IgM


title: Patient_#13_IgM


title: Patient 12

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University Graduate School of Medicine

hyb_protocol: Ten mg of labelled cRNA was hybridized to each pre-hybed microarray at 55℃ for 16 hours.

scan_protocol: After Chemiluminescence detection using Applied Biosystems Chemiluminescence Detection Kit, images were collected by the AB1700 Chemiluminescent Microarray Aanalyzer.

data_processing: The robust multichip average (RMA) method was used background correction and normalization.

label: digoxigenin

source_name: primary oral squamous cell carcinoma

label_protocol: Digoxigenin-UTP-labelled cRNA was generated and amplified from 1 mg of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labelling Kit.

extract_protocol: After fresh tissues were homogenized by TissueLyser, total RNA was extracted by ISOGEN.

tag: cell type

value: primary oral squamous cell carcinoma


title: Patient 13


title: Patient_#5_IgM


title: 11224.mo/NA12878


title: Patient_#10_IgM


title: Patient 8


title: 11224.fa/NA18507


title: Patient_#4_IgM


title: 11223.p1/NA18507


title: 11220.p1/NA12878


title: Patient 7


title: 11224.p1/NA12878


title: Patient 10


title: Patient 9


title: Patient 6


title: Patient_#3_IgM


title: 11225.p1/NA12878


title: Patient_#2_IgM


title: 11206.p1/NA12878


title: 11218.mo/NA12878


title: 11218.fa/NA18507


title: 11219.p1/NA12878


title: 11216.p1/NA12878


title: 11207.p1/NA12878


title: Patient 5


title: 11205.mo/NA12878


title: 11218.p1/NA18507


title: Patient 1


title: 11230.p1/NA12878


title: Patient 4


title: 11215.p1/NA12878


title: Patient 3

source_name: normal oral mucosa

value: normal oral mucosa


title: Cell line 11

description: SAS

source_name: oral squamous cell carcinoma cell lines

value: SAS

value: oral squamous cell carcinoma


title: Patient_#230_C3

hyb_protocol: Probe: Alexa647-conjugated  F(ab')2 fragment goat anti-human C3 antibody


title: Patient_#1_IgM


title: Patient_#229_C3


title: 11212.p1/NA12878


title: 11205.fa/NA18507


title: Patient_#228_C3


title: Cell line 9


title: 11203.p1/NA12878


title: Patient_#227_C3